├── .gitignore ├── IntroEasyPyMOL.png ├── LICENSE ├── ProteinScience.png ├── README.md ├── exam2.py ├── exam2Windows.py ├── quat.py ├── quatWindows.py ├── roundview.py ├── roundviewWindows.py ├── site31labels.pml ├── site31labelsWindows.pml ├── startupAliases.py ├── startupAliasesWindows.py ├── wtT4L.py └── wtT4LWindows.py /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | 5 | # C extensions 6 | *.so 7 | 8 | # Distribution / packaging 9 | .Python 10 | env/ 11 | build/ 12 | develop-eggs/ 13 | dist/ 14 | downloads/ 15 | eggs/ 16 | .eggs/ 17 | lib/ 18 | lib64/ 19 | parts/ 20 | sdist/ 21 | var/ 22 | *.egg-info/ 23 | .installed.cfg 24 | *.egg 25 | 26 | # PyInstaller 27 | # Usually these files are written by a python script from a template 28 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 29 | *.manifest 30 | *.spec 31 | 32 | # Installer logs 33 | pip-log.txt 34 | pip-delete-this-directory.txt 35 | 36 | # Unit test / coverage reports 37 | htmlcov/ 38 | .tox/ 39 | .coverage 40 | .coverage.* 41 | .cache 42 | nosetests.xml 43 | coverage.xml 44 | *,cover 45 | 46 | # Translations 47 | *.mo 48 | *.pot 49 | 50 | # Django stuff: 51 | *.log 52 | 53 | # Sphinx documentation 54 | docs/_build/ 55 | 56 | # PyBuilder 57 | target/ 58 | -------------------------------------------------------------------------------- /IntroEasyPyMOL.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MooersLab/EasyPyMOL/098426f55712bf4eb737c9da75f8f6f032ccbf69/IntroEasyPyMOL.png -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. {http://fsf.org/} 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see {http://www.gnu.org/licenses/}. 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | pymol Copyright (C) 2013 Javier Otegui 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | {http://www.gnu.org/licenses/}. 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | {http://www.gnu.org/philosophy/why-not-lgpl.html}. 675 | -------------------------------------------------------------------------------- /ProteinScience.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MooersLab/EasyPyMOL/098426f55712bf4eb737c9da75f8f6f032ccbf69/ProteinScience.png -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ![Version](https://img.shields.io/static/v1?label=EasyPyMO&message=0.2&color=brightcolor) 2 | [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT) 3 | 4 | 5 | # PyMOL made easier with horizontal scripting 6 | *Script to facilitate the making of horizontal scripts* 7 | 8 | [![DOI](https://zenodo.org/badge/20847/MooersLab/EasyPyMOL.svg)](https://zenodo.org/badge/latestdoi/20847/MooersLab/EasyPyMOL) 9 | 10 | Welcome to the `EasyPyMOL` repository, which implements horizontal scripting with PyMOL described in the manuscript: 11 | "[Simplifying and enhancing the use of PyMOL with horizontal scripts](http://onlinelibrary.wiley.com/doi/10.1002/pro.2996/abstract;jsessionid=3BFE5B68AD44844F55AAE6E273D88375.f02t03)" published in the September 2016 issue of Protein Science. 12 | 13 | See this 4-minute introductory video. 14 | Scroll down to find tutorial videos about downloading the scripts from GitHub and installing them on Windows, Linux, mac PyMOLX11 and Mac PyMOL: 15 | 16 | ### Click on the image immediately below to start the video (4:17 min). 17 | 18 | [![ScreenShot](http://i3.ytimg.com/vi/XRsAaKq4afs/hqdefault.jpg)](https://www.youtube.com/watch?v=XRsAaKq4afs) 19 | 20 | 21 | Video Highlights for Protein Science methods paper: Simplifying and enhancing the use of PyMOL with horizontal scripts. 22 | ### Click on the image immediately below to start the video (5:43 min). 23 | [![ScreenShot](http://i3.ytimg.com/vi/96lSGbrcnyw/hqdefault.jpg)](http://www.youtube.com/watch?v=96lSGbrcnyw) 24 | 25 | 26 | #### Ambient occlusion image of phage T4 lysozyme made with the alias "AO" 27 | The 17 commands that are on 17 lines in a traditional vertical script were placed on one line as a horizontal script. 28 | 29 | 30 | 31 | 32 | #### Ribbon diagram of the above molecule made with the alias "T4L" 33 | Another image is made with a horizontal script. 34 | 35 | 36 | 37 | ### Problem: 38 | the viewport settings returned on seven lines with line continuation symbols from the command [`get_view()`](http://pymolwiki.org/index.php/Get_View) in [PyMOL](https://www.pymol.org/) are too hard to copy and paste onto the command line because the line breaks have to be removed. These settings are often changed many times while editing a new scene. 39 | 40 | ```python 41 | PyMOL>get_view 42 | 43 | ### cut below here and paste into script ### 44 | set_view(\ 45 | -0.832868993, 0.398498207, 0.383896619,\ 46 | -0.260102808, -0.894237876, 0.363985002,\ 47 | 0.488390923, 0.203309149, 0.848513067,\ 48 | 0.000000000, 0.000000000, -61.396984100,\ 49 | -46.246913910, -4.663769245, 42.401920319,\ 50 | 56.260883331, 66.533096313, -20.000000000 ) 51 | ### cut above here and paste into script ### 52 | ``` 53 | 54 | ### Solution: 55 | The function `roundview()` in the script [`roundview.py`](.\roundview.py), which is available from this website. 56 | 57 | ``` 58 | PyMOL>roundview 59 | set_view(-0.83,0.4,0.38,-0.26,-0.89,0.36,0.49,0.2,0.85,0.0,0.0,-61.4,-46.25,-4.66,42.4,56.26,66.53,-20.0); 60 | ``` 61 | 62 | Paste the above reformatted [`set_view()`](http://pymolwiki.org/index.php/Set_View) command onto the PyMOL [command line](http://pymolwiki.org/index.php/Command_Line_Options) in the external gui or into a [script](http://www.pymolwiki.org/index.php/Running_Scripts) in a plain text editor. 63 | 64 | ### What is the `roundview()` function? 65 | 66 | The Python script roundview.py includes the function `roundview()` that reformats the viewing port settings from seven rows to one row. The more compact format from `roundview()` is easy to copy and paste onto the command line. Other commands that are separated by semicolons can be added to the command line along with the settings. This defines a horizontal script. The script can include comments that are isolated by semicolons. The horizontal script can be edited and tested repeatedly within PyMOL for many cycles without using an external text editor. This saves time during the development of a new molecular scene. The cursor can be moved around quickly on the command line with the readline commands: 67 | 68 | * **cntrl-a** moves the cursor to the beginning of the line 69 | * **cntrl-e** moves the cursor to the end of the line 70 | * **shift-cntrl-a** selects everything to from the cursor to the beginning of the line 71 | * **shift-cntrl-e** selects everything to from the cursor to the end of the line 72 | * **command-f** move forward by one word 73 | * **commend-b** move backward by one word 74 | 75 | ### Requirements 76 | 77 | Requires a molecular object loaded into an interactive session of PyMOL. Does not require any modules other than two in PyMOL. Should work on all versions of PyMOL. 78 | Tested on: 79 | * Ubuntu 14.04 64 bit with PyMOL 1.7.2.2. 80 | * Windows 8 32 bit running PyMOL 1.7.6.2 and PyMOL 1.7.6.6. 81 | * Mac OSX 10.10.5 64 bit running PyMOL 1.5.0.5, 1.7.6.6 (via MacPorts), 1.8.0.5, and 1.8.2.0. 82 | 83 | We tried to make the code backward compatible with PyMOL 1.5. However, we do not guarantee that this code works with earlier versions of PyMOL or that it will not fail in future versions. Several changes in PyMOL version 1.6 reduced the backward compatibility. We also do not guarantee that the code will work if you install it in a location other than that described below. 84 | 85 | ### Instructions 86 | 87 | #### Quick start instructions for beginning users of Github 88 | 89 | Click on the image immediately below to watch 1-minute video or read on. 90 | 91 | [![ScreenShot](http://i3.ytimg.com/vi/GnRtEhGvPBQ/hqdefault.jpg)](https://www.youtube.com/watch?v=XRsAaKq4afs) 92 | 93 | 94 | Copy the script from [this link](https://github.com/MooersLab/EasyPyMOL/blob/master/roundview.py) after clicking on "RAW" in the upper right corner and paste it into a plain text file (NOT a doc, docx, or rtf file). Name the script [`roundview.py`](./roundview.py). Save the file to your home directory (e.g., /Users/username or /home/username or C:\Users\username). Start PyMOL. Check that PyMOL's current directory is the home directory by entering `pwd` on the command line in PyMOL. Check for the presence of roundview.py by entering `ls *.py` on the command line in PyMOL. 95 | 96 | Note that the scripts were developed on a Mac, and most have UTF-8 encoding instead of ASCII encoding, as expected on Windows. A second set of script files was opened in Sublime Text and saved with Western encoding for Windows, with the filename modified with Windows appended. 97 | The line below in the scripts for Mac and Linux instructs the Python interpreter to read the file with utf-8 encoding. 98 | #-*- coding: utf-8 -*- 99 | 100 | ```shell 101 | ls *.py 102 | ``` 103 | Paste the following horizontal script on the command line just below the command history window in the top or external gui: 104 | ```shell 105 | fetch 1lw9, async=0; run roundview.py; roundview 0,1 106 | ``` 107 | You should see the following in the command history window of the top gui: 108 | ```shell 109 | set_view (1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,-155.2,35.1,11.5,9.7,122.3,188.0,-20.0); 110 | ``` 111 | 112 | Type the following to see the default format from get_view. 113 | ```shell 114 | get_view 115 | ``` 116 | 117 | Which output looks easier to copy from the command history window and paste onto the command line in PyMOL? 118 | 119 | #### More advanced ways to install roundview.py 120 | 121 | Get the script. Either download the folder from [this link](https://github.com/MooersLab/EasyPyMOL/archive/master.zip) or type the following command in a terminal window in your home directory or the directory where you store your PyMOL Python scripts 122 | 123 | ```shell 124 | git clone https://github.com/MooersLab/EasyPyMOL.git 125 | ``` 126 | 127 | You need the program [Git](https://git-scm.com/) installed on your computer. Git is available via MacPorts or otherwise [see these instructions for installing git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git). 128 | 129 | 130 | There are at least four different ways of loading the script into PyMOL: 131 | 132 | 1. move [`roundview.py`](./roundview.py) to the working directory. Then in PyMOL, type 133 | 134 | ```py 135 | run roundview.py 136 | ``` 137 | Please note that the `run` command just loads the script into PyMOL. It does not execute it. Now the "roundview()" command is available by typing `roundview` and the on-line documentation is available by typing "help roundview". 138 | 139 | 2. load [`roundview.py`](./roundview.py) with the plugin manager (see plugin pulldown) in PyMOL 140 | 141 | 3. copy [`roundview.py`](./roundview.py) to a safe folder that will not be deleted when you delete PyMOL. I use `~/Scripts/PyMOLScripts/`. Then load `roundview()` into PyMOL using method 1 or 2. 142 | 143 | 4. create or edit the hidden text file `.pymolrc` (named `pymolrc.pml` and not hidden on Windows) in the home directory so that it includes the following lines so that `roundview.py` is always loaded upon startup. This option also works without the first two lines. 144 | ```py 145 | import sys 146 | sys.path.append('/Path/To/roundview') 147 | run /Path/To/roundview.py 148 | ``` 149 | For example: 150 | ```py 151 | import sys 152 | sys.path.append('/Users/blaine-mooers/Scripts/PyMOLScripts/') 153 | run /Users/blaine-mooers/Scripts/Scripts_PyMOL/roundview.py 154 | ``` 155 | Restart PyMOL. You should see something like the following in the command history window if your path to the script is correct. 156 | ```py 157 | PyMOL>import sys 158 | PyMOL>sys.path.append('/Users/blaine-mooers/Scripts/PyMOLScripts/') 159 | PyMOL>run /Users/blaine-mooers/Scripts/Scripts_PyMOL/roundview.py 160 | ``` 161 | 162 | Type `roundview` on either command line. You should get back the following in the command history window if no molecule is loaded: 163 | ```py 164 | set_view (1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,-50.0,0.0,0.0,0.0,40.0,100.0,-20.0); 165 | ``` 166 | 167 | 168 | ## roundview.py installation video for PyMOL on Windows (4:20 minutes): 169 | 170 | ### Click on the image immediately below to start video. 171 | 172 | 173 | [![ScreenShot](http://i3.ytimg.com/vi/C0NWphiTEYE/hqdefault.jpg)](https://www.youtube.com/watch?v=C0NWphiTEYE) 174 | 175 | 176 | Note that the scripts were developed on a Mac and most have utf-8 encoding instead of ascii encoding as expected on Windows. A second set of script files were opened in Sublime Text and saved with Western encoding for Windows and with the filename modified with Windows appended. 177 | The line below in the scripts for Mac and Linux instructs the Python interpreter to read the file with utf-8 encoding. 178 | #-*- coding: utf-8 -*- 179 | 180 | 181 | ## roundview.py installation video for PyMOL on Linux and PyMOLX11Hybrid on Mac (3:24 minutes): 182 | 183 | ### Click on the image immediately below to start video. 184 | 185 | [![ScreenShot](http://i3.ytimg.com/vi/XQWQzq48DeA/hqdefault.jpg)](https://www.youtube.com/watch?v=XQWQzq48DeA) 186 | 187 | 188 | 189 | ## Link to roundview.py installation video for MacPyMOL (5:50 minutes): 190 | 191 | ### Click on the image immediately below to start video. 192 | 193 | [![ScreenShot](http://i3.ytimg.com/vi/XTwwWgwj4z0/hqdefault.jpg)](https://www.youtube.com/watch?v=XTwwWgwj4z0) 194 | 195 | 196 | #### How to run 197 | --------------- 198 | 199 | After loading a pdb file and setting up the molecular scene, type on a command line in PyMOL: 200 | 201 | ``` 202 | PyMOL>roundview 203 | ``` 204 | 205 | ##### How to get help 206 | 207 | Type the following on a command line in PyMOL 208 | 209 | ``` 210 | PyMOL> help roundview 211 | ``` 212 | 213 | Something like the following should be printed to the command history window: 214 | 215 | Usage: `roundview [view, decimal places, outname]` 216 | * The values in the [ ] are optional. 217 | * The default view is "0". 218 | * The default number of `decimal places` is 2. 219 | * The `outname` is the name of a plain text file to which the output of `roundveiw()` is written. 220 | 221 | Quick test with wildtype bacteriophage T4 lysozyme, 3fa0 222 | -------------------------------------------------------------------------------- 223 | 224 | Start PyMOL. Copy and paste the entire line below onto the command line in the external gui (the on above the GL viewing port). This is an example of a horizontal script. By hitting the up arrow key, you can recall this command for editing on the command line. This code block is more agile to edit than opening, editing, saving, and loading an external script file. 225 | 226 | ``` 227 | fetch 3fa0,async=0;orient;turn z,-90;turn y,-5;turn x,10; hide everything; bg_color white; show cartoon;color red, ss H;color yellow, ss S;color green, ss L+'';roundview 228 | ``` 229 | 230 | To apply the canonical view similar to that in [Gassner et al. 2003](http://www.ncbi.nlm.nih.gov/pubmed/12646375), copy and paste the following onto the command line: 231 | 232 | ``` 233 | set_view (-0.18,-0.69,-0.7,0.98,-0.17,-0.09,-0.06,-0.7,0.71,0.0,0.0,-154.87,34.77,11.27,9.52,121.27,188.47,-20.0); ray 1500,1600; png canonical.png 234 | ``` 235 | 236 | You should get back an image that looks like the following: 237 | 238 | 239 | 240 | To test some other argument values, copy and paste the following command into PyMOL. 241 | 242 | ``` 243 | PyMOL>roundview 0,1,firstscene.txt 244 | ``` 245 | 246 | Do a `ls *.txt` to list the files in the working directory. The file "firstscene.txt" should be listed. The default filename is "roundedview.txt". This file is appended with each execution of the roundview command. You may find it easier to copy the set_view line from this text file than from the command history window in PyMOL. 247 | 248 | ## Scripts that use aliases to horizontal scripts. Some aliases contain compact scene settings from `roundview()`. 249 | 250 | ### Exam2function.py 251 | 252 | Defines aliases `q1-q8` for questions 1-8 from exam 2 of the OUHSC Macromolecular Systems [course](https://apps.ouhsc.edu/studentinfo/Courses.aspx?College=GRAD). Each alias is mapped to a number of commands. 253 | 254 | 1. Create `~/Scripts/PyMOLScripts` and store the script in this subfolder. 255 | 256 | 1. Enter on the command line in PyMOL the following command: 257 | 258 | ``` 259 | run ~/Scripts/PyMOLScripts/exam2function.py 260 | ``` 261 | 262 | 1. Type `q1` to execute the alias associated with exam question 1. 263 | 264 | 1. Type `help q1` to print the documentation to the PyMOL command history window. 265 | The bottom of the documentation includes the corresponding horizontal script. 266 | All or parts of the horizontal script can be copied from the command history 267 | window for reuse of the code in another horizontal script or a traditional 268 | vertical script. 269 | 270 | Tested on PyMOL versions 1.5.0.5, 1.7.7.2 (from macports), and 1.8.0.5. 271 | 272 | 273 | ### StartupAliases.py 274 | 275 | 1. Copy to ~/Scripts/PyMOLScripts/. 276 | 277 | 1. Add this command on one line in your .pymolrc file (pymolrc.pml on Windows): 278 | 279 | ```shell 280 | run ~/Scripts/PyMOLScripts/StartUpAliases.py 281 | ``` 282 | 283 | Now these aliases will be available whenever you startup PyMOL. 284 | 285 | 1. Type the `alias ` to execute it. 286 | 287 | 1. Type `help alias name` to see the documentation, which includes a vertical list of the commands mapped to the alias to ease the copying of isolated commands from the command history window during code reuse. The corresponding horizontal script without line breaks is also printed. It can be selected in the command history window and pasted onto the command line. 288 | 289 | Format of list below: 290 | 291 | Alias name, description: PDB code, where applicable. 292 | 293 | #### Molecules in standard orientations: 294 | 295 | * **T4L**, WT T4 lysozyme (1.09 ang) as a ribbon diagram: 3fa0. 296 | * **U8**, 16-mer dsRNA with 8 contiguous Us. U-helix RaNA (1.37 ang): 3nd3. 297 | * **WC8**, 16-mer RNA with all Watson-Crick base pairs (1.67 ang): 3nd4. 298 | * **N9**, neuraminidase as cartoon, biological unit (1.55 ang): 4dgr. 299 | * **GGT**, gamma glutamyl transpeptidase as cartoon (1.67 ang): 4gdx. 300 | * **GU**, 10-mer RNA with eight GU base pairs (1.32 ang): 4pco. 301 | 302 | 303 | #### Complex figures to serve as templates: 304 | 305 | * **BST**, Base-stacking figure, (1.32 ang): 4pco. 306 | * **LG**, Electron density map of nine sugar glycan,(1.55 ang):, 4dgr. 307 | * **NA**, Sodium cation in major groove of 16-mer RNA: 3nd4. 308 | 309 | 310 | #### Complex representations applied to any visible molecular object: 311 | 312 | * **AO**, Make ambient occlusion image. Requires global view of protein. 313 | * **BU**, Display biological unit. 314 | * **CB**, Define color blind compatible coloring scheme. 315 | * **BW**, Make black and white ribbon cartoon on white background. 316 | * **CSS**, Color ribbon and cartoons by secondary structure: red, green and yellow. 317 | * **CBSS**, Color ribbon and cartoons with colorblind friendly colors. 318 | * **CR**, Commands to make colored filled-ring cartoon of nucleic acids.. 319 | * **FR**, Commands to make filled-ring cartoon of nucleic acids. 320 | 321 | #### Demo 1: 322 | 323 | Type `T4L` on the command line. Now type "AO". You should get an image like the following: 324 | 325 | 326 | 327 | 328 | Type `help AO` on the command line to see the documentation for the `AO` alias. It is mapped to 17 commands. 329 | 330 | PyMOL>help AO 331 | 332 | DESCRIPTION 333 | 334 | Commands to make ambient occlusion image like those in Qutemole. 335 | 336 | 337 | USAGE 338 | Type 'AO' to execute. Type 'help AO' to see this documentation 339 | printed to the command history window. Select from the command 340 | history individual lines of code to build a new script. Select the 341 | horizontal script at the bottom if retaining most of the commands 342 | in your new script. Copy and paste onto the command line below. 343 | Works only with the command line immediately under the command 344 | history window in the top (external) gui. 345 | 346 | The commands with linebreaks: 347 | 348 | set_color oxygen, [1.0,0.4,0.4]; 349 | set_color nitrogen, [0.5,0.5,1.0]; 350 | remove solvent; 351 | as spheres; 352 | util.cbaw; 353 | bg white; 354 | set light_count,10; 355 | set spec_count,1; 356 | set shininess, 10; 357 | set specular,0.25; 358 | set ambient,0; 359 | set direct,0; 360 | set reflect,1.5; 361 | set ray_shadow_decay_factor, 0.1; 362 | set ray_shadow_decay_range, 2; 363 | unset depth_cue; 364 | ray 365 | 366 | The commands without linebreaks: 367 | 368 | set_color oxygen, [1.0,0.4,0.4];set_color nitrogen, [0.5,0.5,1.0];remove solvent;as spheres;util.cbaw;bg white;set light_count,10;set spec_count,1;set shininess, 10;set specular,0.25;set ambient,0;set direct,0;set reflect,1.5;set ray_shadow_decay_factor, 0.1;set ray_shadow_decay_range, 2;unset depth_cue;ray 369 | 370 | #### Demo 2: 371 | 372 | Type `T4L` on the command line. Now type `BW`. You should get a black and white image like the following. These black and white figures are useful when color figures are not needed: 373 | 374 | 375 | 376 | 377 | #### Demo 3: 378 | 379 | Type `U8` on the command line. Convert the cartoon to a black-and-white image with `BW`. 380 | 381 | 382 | 383 | #### Demo 4: 384 | 385 | Type 'help NA' to see a very long script mapped to two a letter command. 386 | 387 | DESCRIPTION 388 | 389 | Hydrated sodium cation bound in major groove of a 390 | 16-mer RNA of Watson-Crick base pairs. 391 | The sodium is bound to the N7 nitrogen atom of 392 | Adenine 3 at 1.55 Angstrom resolution, PDB code 3nd4. 393 | 57 commands were used to make this figure. 394 | 395 | More than one label in a horizontal script is not 396 | allowed. This one label has to be at the end of the line. 397 | Labels can be imported from a Labels.pml file. 398 | Store the label commands one per row in this file. 399 | Import the file with the @Labels.pml command. 400 | Include the path to the file if the labels file is not 401 | in the current working directory of PyMOL. 402 | 403 | 404 | USAGE 405 | 406 | Type `NA` to activate. Type `help NA` to see this documentation 407 | printed to the command history window. Select from the command 408 | history individual lines of code to build a new script. Select the 409 | horizontal script at the bottom if retaining most of the commands 410 | in your new script. Copy and paste onto the command line below. 411 | Works only with the command line immediately under the command 412 | history window at the top of the gui. 413 | 414 | delete all; 415 | viewport 900,600; 416 | fetch 3nd4, type=pdb, async=0; 417 | run ~/Scripts/PyMOLScripts/quat.py; 418 | quat 3nd4; 419 | show sticks; 420 | set stick_radius=0.125; 421 | hide everything, name H*; 422 | bg_color white; 423 | create coorCov, (3nd4_1 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7))); 424 | bond (coorCov//A/NA`19/NA),(coorCov//A/A`3/N7); 425 | bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`119/O); 426 | bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`219/O); 427 | bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`319/O); 428 | bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`419/O); 429 | bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`519/O); 430 | distance (3nd4_1 and chain A,and resi 19 and name NA), (3nd4_1 and chain A and resi 519); 431 | distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 419); 432 | distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 119); 433 | distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 319); 434 | distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 219); 435 | show nb_spheres; 436 | set nb_spheres_size, .35; 437 | distance hbond1,/3nd4_1/1/A/HOH`119/O, /3nd4_1/1/A/A`3/OP2; 438 | distance hbond2,/3nd4_1/1/A/HOH`319/O, /3nd4_1/1/A/A`3/OP2; 439 | distance hbond3,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/HOH`119/O; 440 | distance hbond4,/3nd4_1/1/A/G`4/N7,/3nd4_1/1/A/HOH`91/O; 441 | distance hbond5,/3nd4_1/1/A/G`4/O6, /3nd4_1/1/A/HOH`419/O; 442 | distance hbond6,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2; 443 | distance hbond7,/3nd4_1/1/A/HOH`319/O,/3nd4_1/1/A/G`2/OP2; 444 | distance hbond9,/3nd4_1/1/A/HOH`419/O,/3nd4_2/2/A/HOH`74/O; 445 | distance hbond10,/3nd4_2/2/A/C`15/O2,/3nd4_1/1/A/G`2/N2; 446 | distance hbond11, /3nd4_2/2/A/C`15/N3,/3nd4_1/1/A/G`2/N1; 447 | distance hbond12,/3nd4_2/2/A/C`15/N4,/3nd4_1/1/A/G`2/O6; 448 | distance hbond13, /3nd4_2/2/A/U`14/N3,/3nd4_1/1/A/A`3/N1; 449 | distance hbond14,3nd4_2/2/A/U`14/O4,/3nd4_1/1/A/A`3/N6; 450 | distance hbond15, /3nd4_2/2/A/C`13/N4,/3nd4_1/1/A/G`4/O6; 451 | distance hbond16,/3nd4_2/2/A/C`13/N3, /3nd4_1/1/A/G`4/N1; 452 | distance hbond17, /3nd4_1/1/A/G`4/N2,/3nd4_2/2/A/C`13/O2; 453 | distance hbond18,/3nd4_1/1/A/G`2/N2,/3nd4_2/2/A/C`15/O2; 454 | distance hbond19,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2; 455 | set depth_cue=0; 456 | set ray_trace_fog=0; 457 | set dash_color, black; 458 | set label_font_id, 5; 459 | set label_size, 36; 460 | set label_position, (0.5, 1.0, 2.0); 461 | set label_color, black;set dash_gap, 0.2; 462 | set dash_width, 2.0;set dash_length, 0.2; 463 | set label_color, black;set dash_gap, 0.2; 464 | set dash_width, 2.0;set dash_length, 0.2; 465 | select carbon, element C; 466 | color yellow, carbon; 467 | disable carbon; 468 | set_view (-0.9,0.34,-0.26,0.33,0.18,-0.93,-0.27,-0.92,-0.28,-0.07,-0.23,-27.83,8.63,19.85,13.2,16.0,31.63,-20.0) 469 | 470 | Commands without linebreaks for easy selecting, copying, and pasting onto the command line for code reuse: 471 | delete all;viewport 900,600;fetch 3nd4, type=pdb,async=0;run ~/Scripts/PyMOLScripts/quat.py;quat 3nd4; show sticks;set stick_radius=0.125;hide everything, name H*;bg_color white;create coorCov, (3nd4_1 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)));bond (coorCov//A/NA`19/NA),(coorCov//A/A`3/N7); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`119/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`219/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`319/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`419/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`519/O);distance (3nd4_1 and chain Aand resi 19 and name NA), (3nd4_1 and chain A and resi 519);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 419);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 119);distance (3nd4_1 and chain A and resi 19 and name NA),(3nd4_1 and chain A and resi 319);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 219);show nb_spheres; set nb_spheres_size, .35;distance hbond1,/3nd4_1/1/A/HOH`119/O, /3nd4_1/1/A/A`3/OP2;distance hbond2,/3nd4_1/1/A/HOH`319/O, /3nd4_1/1/A/A`3/OP2;distance hbond3,/3nd4_1/1/A/HOH`91/O, /3nd4_1/1/A/HOH`119/O;distance hbond4,/3nd4_1/1/A/G`4/N7,/3nd4_1/1/A/HOH`91/O;distance hbond5,/3nd4_1/1/A/G`4/O6, /3nd4_1/1/A/HOH`419/O;distance hbond6,/3nd4_1/1/A/HOH`91/O, /3nd4_1/1/A/G`4/OP2;distance hbond7,/3nd4_1/1/A/HOH`319/O, /3nd4_1/1/A/G`2/OP2;distance hbond9,/3nd4_1/1/A/HOH`419/O,/3nd4_2/2/A/HOH`74/O;distance hbond10,/3nd4_2/2/A/C`15/O2,/3nd4_1/1/A/G`2/N2;distance hbond11, /3nd4_2/2/A/C`15/N3,/3nd4_1/1/A/G`2/N1;distance hbond12,/3nd4_2/2/A/C`15/N4,/3nd4_1/1/A/G`2/O6;distance hbond13, /3nd4_2/2/A/U`14/N3,/3nd4_1/1/A/A`3/N1;distance hbond14,3nd4_2/2/A/U`14/O4,/3nd4_1/1/A/A`3/N6;distance hbond15, /3nd4_2/2/A/C`13/N4,/3nd4_1/1/A/G`4/O6;distance hbond16,/3nd4_2/2/A/C`13/N3, /3nd4_1/1/A/G`4/N1;distance hbond17, /3nd4_1/1/A/G`4/N2,/3nd4_2/2/A/C`13/O2;distance hbond18,/3nd4_1/1/A/G`2/N2,/3nd4_2/2/A/C`15/O2;distance hbond19,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2;set depth_cue=0;set ray_trace_fog=0;set dash_color, black;set label_font_id, 5;set label_size, 36;set label_position, (0.5, 1.0, 2.0);set label_color, black;set dash_gap, 0.2;set dash_width, 2.0;set dash_length, 0.2;set label_color, black;set dash_gap, 0.2;set dash_width, 2.0;set dash_length, 0.2;select carbon, element C; color yellow, carbon;disable carbon;set_view (-0.9,0.34,-0.26,0.33,0.18,-0.93,-0.27,-0.92,-0.28,-0.07,-0.23,-27.83,8.63,19.85,13.2,16.0,31.63,-20.0); 472 | 473 | 474 | Type `NA` to get the resulting image of a sodium cation bound with inner sphere coordination to the N7 nitrogen of an adenine and to five waters. The sodium is in the major groove of a double-stranded RNA molecule (PDB-ID 3nd4). The dashed lines represent hydrogen bonds. The numbers are distances in angstroms. 475 | 476 | ![naadenine](https://cloud.githubusercontent.com/assets/15176203/13609887/853536a4-e520-11e5-9978-9ea1da4f0884.png) 477 | 478 | 479 | Reference, License, Copyright, and Date of last update 480 | -------------------------------------------------------------------------------- 481 | 482 | * Mooers, B. H. (2016). Simplifying and enhancing the use of PyMOL with horizontal scripts. *Protein Science*, 25(10), 1873-1882. 483 | * GNU General Public License ([GPL-3](http://www.gnu.org/licenses/gpl-3.0.en.html)) 484 | * (C) [Blaine Mooers](https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd), Ph.D., [University of Oklahoma Health Sciences Center](http://www.ouhsc.edu/), 2015-2017 485 | * This work was supported by NIH grants RO1 AI088011 (PI: Mooers) from the National Institute of Allergy and Infectious Diseases and ROP20 GM103640 (PI: Ann West), an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health. 486 | * Updated 25 September 2022 487 | 488 | 489 | Bibtex entry 490 | ------------ 491 | 492 | ```bibtex 493 | @article{mooers2016simplifying, 494 | title={Simplifying and enhancing the use of PyMOL with horizontal scripts}, 495 | author={Mooers, Blaine HM}, 496 | journal={Protein Science}, 497 | volume={25}, 498 | number={10}, 499 | pages={1873--1882}, 500 | year={2016}, 501 | publisher={Wiley Online Library} 502 | } 503 | ``` 504 | 505 | Related Repos 506 | ------------- 507 | 508 | - [pymolshortcuts](https://github.com/MooersLab/pymolshortcuts) 509 | - [pymolsnips](https://github.com/MooersLab/pymolsnips) 510 | - [orgpymolpysnips](https://github.com/MooersLab/orgpymolpysnips) 511 | - [rstudiopymolpysnips](https://github.com/MooersLab/rstudiopymolpysnips) 512 | - [taggedpymolpysnips](https://github.com/MooersLab/taggedpymolpysnips) 513 | - [jupyterlabpymolpysnips](https://github.com/MooersLab/jupyterlabpymolpysnips) 514 | - [colabOpenSourcePyMOLpySnips](https://github.com/MooersLab/colabOpenSourcePyMOLpySnips) 515 | - [colabPyMOLpySnips](https://github.com/MooersLab/colabPyMOLpySnips) 516 | - [PyMOLwallhangings](https://github.com/MooersLab/PyMOLwallhangings) 517 | 518 | ## Update history 519 | 520 | |Version | Changes | Date | 521 | |:-----------:|:------------------------------------------------------------------------------------------------------------------------------------------:|:--------------------:| 522 | | Version 0.2 | Added badges, funding, and update table. | 2024 May 24 | 523 | 524 | -------------------------------------------------------------------------------- /exam2.py: -------------------------------------------------------------------------------- 1 | from __future__ import print_function 2 | # -*- coding: utf-8 -*- 3 | """ 4 | DESCRIPTION AND INSTALLATION 5 | 6 | Defines aliases for exam 2 of the OUHSC Macromolecular Systems course. 7 | The aliases have actually been recoded as python functions but they 8 | can be thought of as aliases. 9 | 10 | Create ~/Scripts/PyMOLScripts 11 | and store the script in this subfolder 12 | or store in some other folder of your choosing IF you know what you are doing. 13 | 14 | Enter on the command line in PyMOL the following command: 15 | 16 | run ~/Scripts/PyMOLScripts/S4_File.py 17 | 18 | Now the aliases q1,q2, ..., q8 are active. 19 | 20 | Tested on PyMOL versions 1.5.0.5, 1.8.0.5, 1.8.2.0. 21 | 22 | Copyright Notice 23 | ================ 24 | Copyright (C) 2016 Blaine Mooers 25 | 26 | This program is free software: you can redistribute it and/or modify 27 | it under the terms of the GNU General Public License as published by 28 | the Free Software Foundation, either version 3 of the License. 29 | 30 | This program is distributed in the hope that it will be useful, 31 | but WITHOUT ANY WARRANTY; without even the implied warranty of 32 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 33 | See the GNU General Public License for more details. 34 | 35 | You should have received a copy of the GNU General Public License 36 | along with this program. If not, see . 37 | 38 | The source code in this file is copyrighted, but you can 39 | freely use and copy it as long as you don't change or remove any of 40 | the copyright notices. 41 | 42 | Blaine Mooers , PhD 43 | blaine-mooers@ouhsc.edu 44 | 975 NE 10th St, BRC 466 45 | University of Oklahoma Health Sciences Center 46 | Oklahoma City, OK, USA 73104 47 | """ 48 | from pymol import cmd 49 | __author__ = "Blaine Mooers" 50 | __copyright__ = "Blaine Mooers, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104" 51 | __license__ = "GPL-3" 52 | __version__ = "1.0.3" 53 | __credits__ = ["William Beasley","Chiedza Kanyumbu"] 54 | # people who reported bug fixes, made suggestions, etc. 55 | __date__ = "24 July 2016" 56 | __maintainer__ = "Blaine Mooers" 57 | __email__ = "blaine-mooers@ouhsc.edu" 58 | __status__ = "Production" 59 | 60 | print("2015 OUHSC MSI-Lecture 17 and 18 takehome exam") 61 | print("on nucleic acid structure.") 62 | print(" ") 63 | print("Enter 'q1' for question 1, 'q2' for question 2, ...,") 64 | print("'q8' for question 8.") 65 | print(" ") 66 | print("Questions (1-4). HIV reverse transcriptase bound to DNA") 67 | print("with AZT incorporated (PDB-ID 3V6D).") 68 | print(" ") 69 | print("Questions (5-8). The full-length hammerhead") 70 | print("ribozyme (PDB-ID 3zp8).") 71 | print(" ") 72 | print("Enter 'help exam2' to learn how to use this script.") 73 | print("Enter 'help q1' to see quesiton 1 and the corresponding horizontal script.") 74 | print(" ") 75 | print("All or part of the horizontal script can be copied from the command history window for reuse.") 76 | print(" ") 77 | print("Positon cursor on command line with left mouse button.") 78 | print("Readline commands move the cursor to left or right:") 79 | print(" control-a will move the cursor to the beginning of the command line.") 80 | print(" control-e will move the cursor to the end of the line.") 81 | print(" command-f will move the cursor to the end of the current word.") 82 | print(" command-b will move the cursor to the begining of the current word.") 83 | print(" control-f will move the cursor to the right one character.") 84 | print(" control-b will move the cursor to the left by one character.") 85 | print(" ") 86 | print("Enter 'help rline' to see these commands again in the command history window.") 87 | print(" ") 88 | print("Up arrow key recalls last line of commands for editing.") 89 | 90 | 91 | 92 | def exam2(): 93 | """ 94 | USAGE: 95 | 96 | Enter 'run exam2.py' without including the quotation marks. 97 | 98 | Enter 'q1' to make the molecular scene for question 1. 99 | (Need active internet connection). 100 | 101 | Enter 'help q1' to see question 1 and the commands used to 102 | make the molecular scene. 103 | 104 | When you are ready for question 2, 105 | enter 'q2' for question 2, and so on. 106 | 107 | Enter 'help rline' to see the commands to move cursor on command line. 108 | 109 | DESCRIPTION 110 | 111 | Defines the molecular scenes for MSI-Lecture 17 and 112 | 18 takehome exam. 113 | 114 | Each question with a molecular scene has the scene 115 | defined by a specific function qX(), where X is the 116 | number of the question. 117 | 118 | Each function defines a series of PyMOL commands. Each 119 | function also has its own documentation that explains 120 | the molecular scene and that is printed to the 121 | command history window when you type 'help q1' or 122 | 'help q2' and so on. 123 | 124 | Each row of commands starts with 'reinitialize' to 125 | remove old molecules and settings. Each 126 | function prints to the command history window 127 | an alias to the commands in the function. 128 | 129 | LIMITATIONS 130 | 131 | An active internet connection is required because 132 | each alias uses the fetch command. 133 | 134 | Replace the fetch command with the load command to 135 | load atomic coordinates from your harddrive. 136 | 137 | Enter "rock" to stop the rocking motion. 138 | 139 | REQUIREMENTS 140 | 141 | When developing a variant of this program., run the 142 | program roundview.py to obtained a shorter version 143 | of the viewport settings. 144 | 145 | NOTES 146 | 147 | Use gray scroll bar to the right side of the command 148 | history window to see all of this documentation. or hit 149 | escape after moving the cursor to the viewing port 150 | (the GUI with the molecule). 151 | 152 | Copyright Notice 153 | ================ 154 | 155 | The PyMOL function source code in this file is copyrighted, but you can 156 | freely use and copy it as long as you don't change or remove any of 157 | the copyright notices. 158 | 159 | """ 160 | print("The function exam2() stores this docstring.") 161 | cmd.extend( "exam2",exam2) 162 | 163 | 164 | def rline(): 165 | ''' 166 | DESCRIPTION 167 | 168 | These commands are sufficient for most editing tasks: 169 | To edit code, positon cursor on command line with left mouse button. 170 | Control-e moves the cursor to the end of the line, even when it is out of view. 171 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 172 | Up arrow key recalls last line of commands for editing. 173 | 174 | These commands may not be available on all systems: 175 | Shift-control-a selects everything from the right of the cursor to the end of the line. 176 | Shift-control-e selects everything to the left of the cursor to the end of the line. 177 | Command-f moves the cursor to the end of the current word. 178 | Command-b moves the cursor to the begining of the current word. 179 | Control-f moves the cursor to the right by one character. 180 | Control-b moves the cursor to the left by one character. 181 | ''' 182 | cmd.extend("rline",rline) 183 | 184 | 185 | def q1(): 186 | ''' 187 | DESCRIPTION 188 | 189 | Question 1: Explain how AZT terminates extension of the DNA chain. 190 | 191 | The following commands created the scene for "q1": 192 | 193 | delete all; fetch 3v6d, HIVrt, async=0; rock;preset.ball_and_stick("c. P and i. 822");set_view (-0.99,-0.1,0.06,0.09,-0.39,0.92,-0.07,0.92,0.39,0.0,0.0,-29.2,-10.56,24.72,39.27,23.02,35.38,-20.0); 194 | 195 | To reuse of parts or all of the above commands, copy and paste the commands 196 | onto the command line or into a plain text file. 197 | 198 | These commands are sufficient for most editing tasks: 199 | To edit code, positon cursor on command line with left mouse button. 200 | Control-e moves the cursor to the end of the line, even when it is out of view. 201 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 202 | Up arrow key recalls last line of commands for editing. 203 | 204 | These commands may not be available on all systems: 205 | Shift-control-a selects everything from the right of the cursor to the end of the line. 206 | Shift-control-e selects everything to the left of the cursor to the end of the line. 207 | Command-f moves the cursor to the end of the current word. 208 | Command-b moves the cursor to the begining of the current word. 209 | Control-f moves the cursor to the right by one character. 210 | Control-b moves the cursor to the left by one character. 211 | ''' 212 | cmd.reinitialize() 213 | cmd.fetch('3v6d', type='pdb', name='HIVrt',async='0') 214 | cmd.rock() 215 | preset.ball_and_stick('c. P and i. 822') 216 | cmd.set_view('(-0.99,-0.1,0.06,0.09,-0.39,0.92,-0.07,\ 217 | 0.92,0.39,0.0,0.0,-29.2,-10.56,24.72,39.27,\ 218 | 23.02,35.38,-20.0)') 219 | print('Enter "q1" to set scene for question 1.') 220 | print('Enter "help q1" for more information.') 221 | cmd.extend( 'q1',q1) 222 | 223 | 224 | 225 | def q2(): 226 | ''' 227 | DESCRIPTION 228 | 229 | Question 2: Look along the helical axis of the DNA. 230 | Is the DNA helix bent? 231 | 232 | The following commands created the scene for "q2": 233 | 234 | delete all; fetch 3v6d, HIVrt, async=0; rock;show cartoon, c. P or c. T;set_view (0.61,0.29,-0.73,0.78,-0.37,0.51,-0.12,-0.88,-0.45,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0); 235 | 236 | To reuse of parts or all of the above commands, copy and paste the commands 237 | onto the command line or into a plain text file. 238 | 239 | These commands are sufficient for most editing tasks: 240 | To edit code, positon cursor on command line with left mouse button. 241 | Control-e moves the cursor to the end of the line, even when it is out of view. 242 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 243 | Up arrow key recalls last line of commands for editing. 244 | 245 | These commands may not be available on all systems: 246 | Shift-control-a selects everything from the right of the cursor to the end of the line. 247 | Shift-control-e selects everything to the left of the cursor to the end of the line. 248 | Command-f moves the cursor to the end of the current word. 249 | Command-b moves the cursor to the begining of the current word. 250 | Control-f moves the cursor to the right by one character. 251 | Control-b moves the cursor to the left by one character. 252 | 253 | ''' 254 | cmd.reinitialize() 255 | cmd.fetch('3v6d',type='pdb',name='HIVrt',async='0') 256 | cmd.rock() 257 | cmd.show_as("cartoon","chain P or chain T") 258 | cmd.set_view('(0.61,0.29,-0.73,0.78,-0.37,0.51,-0.12,-0.88,-0.45,-0.0, 0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);') 259 | print('Enter "q2" to make the scene for question 2.') 260 | print('Enter "help q2" to see question 2 and the commands to make the scene.') 261 | cmd.extend( 'q2',q2) 262 | 263 | 264 | def q3(): 265 | ''' 266 | DESCRIPTION 267 | 268 | Question 3: In which groove of the DNA 269 | is the protein making the most contacts? 270 | Is this unusual? 271 | 272 | The following commands created the scene for "q3": 273 | 274 | delete all; fetch 3v6d, HIVrt, async=0; show cartoon, c. A or c. B;hide lines, c. A or c. B;set_view (0.53,-0.06,-0.84,0.82,-0.21,0.53,-0.21,-0.98,-0.07,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);rock; 275 | 276 | To reuse of parts or all of the above commands, copy and paste the commands 277 | onto the command line or into a plain text file. 278 | 279 | These commands are sufficient for most editing tasks: 280 | To edit code, positon cursor on command line with left mouse button. 281 | Control-e moves the cursor to the end of the line, even when it is out of view. 282 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 283 | Up arrow key recalls last line of commands for editing. 284 | 285 | These commands may not be available on all systems: 286 | Shift-control-a selects everything from the right of the cursor to the end of the line. 287 | Shift-control-e selects everything to the left of the cursor to the end of the line. 288 | Command-f moves the cursor to the end of the current word. 289 | Command-b moves the cursor to the begining of the current word. 290 | Control-f moves the cursor to the right by one character. 291 | Control-b moves the cursor to the left by one character. 292 | ''' 293 | cmd.reinitialize() 294 | cmd.fetch('3v6d', type='pdb', name= 'HIVrt', async='0') 295 | cmd.show_as("cartoon","c. A or c. B") 296 | cmd.hide("lines","c. A or c. B") 297 | cmd.rock() 298 | cmd.set_view('(0.53,-0.06,-0.84,0.82,-0.21,0.53,-0.21,-0.98,-0.07,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);') 299 | print('Enter "q3" to make the scene for question 3.') 300 | print('Enter "help q3" to see question 3 and the commands to make the scene.') 301 | cmd.extend( 'q3',q3) 302 | 303 | 304 | 305 | def q4(): 306 | ''' 307 | DESCRIPTION 308 | 309 | Question 4: What the dihedral angle about the disulfide 310 | bond between MRG81 of chain F and Cys258 of chain C? 311 | This is a cross link between the protein and the DNA. Is 312 | this a cis or trans conformation of the bonds about the 313 | S--S bond? Is this conformation energetically favorable 314 | or unfavorable? 315 | 316 | The following commands created the scene for "q4": 317 | 318 | delete all; fetch 3v6d, HIVrt, async=0;preset.ball_and_stick("(c. C and i. 258) or (c. F and i. 817 )");set_view (0.21,-0.91,0.34,-0.84,0.01,0.54,-0.5,-0.4,-0.77,0.0,-0.0,-38.82,-39.67,-55.1,10.96,36.31,41.34,-20.0); 319 | 320 | To reuse of parts or all of the above commands, copy and paste the commands 321 | onto the command line or into a plain text file. 322 | 323 | These commands are sufficient for most editing tasks: 324 | To edit code, positon cursor on command line with left mouse button. 325 | Control-e moves the cursor to the end of the line, even when it is out of view. 326 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 327 | Up arrow key recalls last line of commands for editing. 328 | 329 | These commands may not be available on all systems: 330 | Shift-control-a selects everything from the right of the cursor to the end of the line. 331 | Shift-control-e selects everything to the left of the cursor to the end of the line. 332 | Command-f moves the cursor to the end of the current word. 333 | Command-b moves the cursor to the begining of the current word. 334 | Control-f moves the cursor to the right by one character. 335 | Control-b moves the cursor to the left by one character. 336 | ''' 337 | cmd.reinitialize() 338 | cmd.fetch('3v6d',type='pdb',name='HIVrt',async='0') 339 | cmd.do("preset.ball_and_stick(selection='(chain C and resi 258) or (chain F and resi 817 )')") 340 | cmd.set_view('(0.21,-0.91,0.34,-0.84,0.01,0.54,-0.5,-0.4,-0.77,0.0,-0.0,-38.82,-39.67,-55.1,10.96,36.31,41.34,-20.0);') 341 | cmd.rock() 342 | print('Enter "q4" to make the scene for question 4.') 343 | print('Enter "help q4" to see question 4 and the commands to make the scene.') 344 | cmd.extend('q4',q4) 345 | 346 | 347 | 348 | def q5(): 349 | ''' 350 | DESCRIPTION 351 | 352 | Question 5: How many axial stacks of helices does 353 | the ribozyme have? 354 | 355 | The following commands created the scene for "q5": 356 | 357 | delete all;fetch 3zp8, hammer, async=0;show cartoon, hammer;set_view (-0.5,0.18,-0.85,-0.17,-0.98,-0.11,-0.85,0.09,0.52,0.0,0.0,-167.2,-18.45,10.92,-12.11,126.37,208.02,-20.0);rock; 358 | 359 | To reuse of parts or all of the above commands, copy and paste the commands 360 | onto the command line or into a plain text file. 361 | 362 | These commands are sufficient for most editing tasks: 363 | To edit code, positon cursor on command line with left mouse button. 364 | Control-e moves the cursor to the end of the line, even when it is out of view. 365 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 366 | Up arrow key recalls last line of commands for editing. 367 | 368 | These commands may not be available on all systems: 369 | Shift-control-a selects everything from the right of the cursor to the end of the line. 370 | Shift-control-e selects everything to the left of the cursor to the end of the line. 371 | Command-f moves the cursor to the end of the current word. 372 | Command-b moves the cursor to the begining of the current word. 373 | Control-f moves the cursor to the right by one character. 374 | Control-b moves the cursor to the left by one character. 375 | ''' 376 | cmd.reinitialize() 377 | cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0') 378 | cmd.show_as('cartoon','hammer') 379 | cmd.rock() 380 | cmd.set_view('(-0.5,0.18,-0.85,-0.17,-0.98,-0.11,-0.85,0.09,0.52,0.0,0.0,-167.2,-18.45,10.92,-12.11,126.37,208.02,-20.0);') 381 | print('Enter "q5" to make the scene for question 5.') 382 | print('Enter "help q5" to see question 5 and the commands to make the scene.') 383 | cmd.extend('q5',q5) 384 | 385 | 386 | def q6(): 387 | ''' 388 | DESCRIPTION 389 | 390 | Question 6: What is the average distance of the Na1044 391 | ligand bonds? Give the residue numbers of the RNA 392 | nucleotides and the sodium to identify them. How many 393 | ligands are from RNA? 394 | 395 | The following commands created the scene for "q6": 396 | 397 | delete all;fetch 3zp8, hammer, async=0; rock;preset.ball_and_stick("all");distance ligand1, i. 1044, c. A and i. 22 and n. N7;distance ligand2, i. 1044, c. A and i. 21 and n. OP2;distance ligand3, i. 1044, i. 2121;distance ligand4, i. 1044, i. 2120;distance ligand5, i. 1044, i. 2122;distance ligand6, i. 1044, i. 2130;set_view (-0.87,0.18,-0.46,-0.39,-0.81,0.44,-0.29,0.56,0.78,-0.0,0.0,-20.47,-18.05,14.02,-18.89,17.47,23.47,-20.0); 398 | 399 | To reuse of parts or all of the above commands, copy and paste the commands 400 | onto the command line or into a plain text file. 401 | 402 | These commands are sufficient for most editing tasks: 403 | To edit code, positon cursor on command line with left mouse button. 404 | Control-e moves the cursor to the end of the line, even when it is out of view. 405 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 406 | Up arrow key recalls last line of commands for editing. 407 | 408 | These commands may not be available on all systems: 409 | Shift-control-a selects everything from the right of the cursor to the end of the line. 410 | Shift-control-e selects everything to the left of the cursor to the end of the line. 411 | Command-f moves the cursor to the end of the current word. 412 | Command-b moves the cursor to the begining of the current word. 413 | Control-f moves the cursor to the right by one character. 414 | Control-b moves the cursor to the left by one character. 415 | ''' 416 | cmd.reinitialize() 417 | cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0') 418 | cmd.rock() 419 | cmd.do('preset.ball_and_stick("all")') 420 | cmd.distance('Sodiumligand1',' resi 1044', 'chain A and i. 22 and n. N7') 421 | cmd.distance('Sodiumligand2', 'resi 1044', 'chain A and i. 21 and n. OP2') 422 | cmd.distance('Sodiumligand3', 'resi 1044', 'resi 2121') 423 | cmd.distance('Sodiumligand4', 'resi 1044', 'resi 2120') 424 | cmd.distance('Sodiumligand5', 'resi 1044', 'resi 2122') 425 | cmd.distance('Sodiumligand6', 'resi 1044', 'resi 2130') 426 | cmd.do('set label_size, -0.4') 427 | cmd.set_view('(-0.87,0.18,-0.46,-0.39,-0.81,0.44,-0.29,0.56,0.78,-0.0,0.0,-20.47,-18.05,14.02,-18.89,17.47,23.47,-20.0);') 428 | print('Enter "q6" to make the scene for question 6.') 429 | print('Enter "help q6" to see question 6 and the commands to make the scene.') 430 | cmd.extend('q6',q6) 431 | 432 | 433 | def q7(): 434 | ''' 435 | DESCRIPTION 436 | 437 | Question 7: Measure the longest dimension and the 438 | shortest dimension of the ribozyme. Enter "rock" to 439 | stop the rocking motion. What is the ratio of 440 | the longest dimension to the shortest dimension? Is it 441 | globular like a protein? 442 | 443 | The following commands created the scene for "q7": 444 | 445 | delete all;fetch 3zp8, hammer, async=0;show ribbon, hammer;set_view (0.62,0.14,0.78,0.13,-0.99,0.07,0.78,0.05,-0.63,-0.0,-0.0,-169.8,-16.43,9.44,-9.63,143.54,196.05,-20.0); rock; 446 | 447 | To reuse of parts or all of the above commands, copy and paste the commands 448 | onto the command line or into a plain text file. 449 | 450 | These commands are sufficient for most editing tasks: 451 | To edit code, positon cursor on command line with left mouse button. 452 | Control-e moves the cursor to the end of the line, even when it is out of view. 453 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 454 | Up arrow key recalls last line of commands for editing. 455 | 456 | These commands may not be available on all systems: 457 | Shift-control-a selects everything from the right of the cursor to the end of the line. 458 | Shift-control-e selects everything to the left of the cursor to the end of the line. 459 | Command-f moves the cursor to the end of the current word. 460 | Command-b moves the cursor to the begining of the current word. 461 | Control-f moves the cursor to the right by one character. 462 | Control-b moves the cursor to the left by one character. 463 | ''' 464 | cmd.reinitialize() 465 | cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0') 466 | cmd.show_as('ribbon', 'hammer') 467 | cmd.rock() 468 | cmd.set_view('(0.62,0.14,0.78,0.13,-0.99,0.07,0.78,0.05,-0.63,-0.0,-0.0,-169.8,-16.43,9.44,-9.63,143.54,196.05,-20.0);') 469 | print('Enter "q7" to make the scene for question 7.') 470 | print('Enter "help q7" to see question 7 and the commands to make the scene.') 471 | cmd.extend('q7',q7) 472 | 473 | 474 | def q8(): 475 | ''' 476 | DESCRIPTION 477 | 478 | Question 8: Find the unusual base pair between A21 and 479 | G36. What is the length of the H-bonds between the bases 480 | (ignore the H atoms in the distance measurement)? List 481 | the distance with the residue name, residue number, and 482 | atom name. What additional H-bond occurs between a base 483 | in this base pair and a ribose ring of one of the two 484 | nucleotides in this base pair? 485 | 486 | The following commands created the scene for "q8": 487 | 488 | fetch 3zp8, hammer, async=0;hide everything;show ribbon;show sticks, resi 21 or resi 36;set_view (-0.9,-0.19,0.39,0.39,-0.74,0.55,0.19,0.65,0.74,0.0,0.0,-37.58,-21.66,15.71,-23.32,35.42,39.74,-20.0);rock; 489 | 490 | To reuse of parts or all of the above commands, copy and paste the commands 491 | onto the command line or into a plain text file. 492 | 493 | These commands are sufficient for most editing tasks: 494 | To edit code, positon cursor on command line with left mouse button. 495 | Control-e moves the cursor to the end of the line, even when it is out of view. 496 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 497 | Up arrow key recalls last line of commands for editing. 498 | 499 | These commands may not be available on all systems: 500 | Shift-control-a selects everything from the right of the cursor to the end of the line. 501 | Shift-control-e selects everything to the left of the cursor to the end of the line. 502 | Command-f moves the cursor to the end of the current word. 503 | Command-b moves the cursor to the begining of the current word. 504 | Control-f moves the cursor to the right by one character. 505 | Control-b moves the cursor to the left by one character. 506 | ''' 507 | cmd.reinitialize() 508 | cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0') 509 | cmd.show_as('ribbon', 'hammer') 510 | cmd.rock() 511 | cmd.hide('everything') 512 | cmd.show_as( 'ribbon','all') 513 | cmd.show_as('sticks', 'resi 21 or resi 36') 514 | cmd.set_view('(-0.9,-0.19,0.39,0.39,-0.74,0.55,0.19,0.65,0.74,0.0,0.0,-37.58,-21.66,15.71,-23.32,35.42,39.74,-20.0);') 515 | print('Enter "q8" to make the scene for question 8.') 516 | print('Enter "help q8" to see question 8 and the commands to make the scene.') 517 | cmd.extend('q8',q8) 518 | 519 | -------------------------------------------------------------------------------- /exam2Windows.py: -------------------------------------------------------------------------------- 1 | from __future__ import print_function 2 | # -*- coding: utf-8 -*- 3 | """ 4 | DESCRIPTION AND INSTALLATION 5 | 6 | Defines aliases for exam 2 of the OUHSC Macromolecular Systems course. 7 | The aliases have actually been recoded as python functions but they 8 | can be thought of as aliases. 9 | 10 | Create ~/Scripts/PyMOLScripts 11 | and store the script in this subfolder 12 | or store in some other folder of your choosing IF you know what you are doing. 13 | 14 | Enter on the command line in PyMOL the following command: 15 | 16 | run ~/Scripts/PyMOLScripts/S4_File.py 17 | 18 | Now the aliases q1,q2, ..., q8 are active. 19 | 20 | Tested on PyMOL versions 1.5.0.5, 1.8.0.5, 1.8.2.0. 21 | 22 | Copyright Notice 23 | ================ 24 | Copyright (C) 2016 Blaine Mooers 25 | 26 | This program is free software: you can redistribute it and/or modify 27 | it under the terms of the GNU General Public License as published by 28 | the Free Software Foundation, either version 3 of the License. 29 | 30 | This program is distributed in the hope that it will be useful, 31 | but WITHOUT ANY WARRANTY; without even the implied warranty of 32 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 33 | See the GNU General Public License for more details. 34 | 35 | You should have received a copy of the GNU General Public License 36 | along with this program. If not, see . 37 | 38 | The source code in this file is copyrighted, but you can 39 | freely use and copy it as long as you don't change or remove any of 40 | the copyright notices. 41 | 42 | Blaine Mooers , PhD 43 | blaine-mooers@ouhsc.edu 44 | 975 NE 10th St, BRC 466 45 | University of Oklahoma Health Sciences Center 46 | Oklahoma City, OK, USA 73104 47 | """ 48 | from pymol import cmd 49 | __author__ = "Blaine Mooers" 50 | __copyright__ = "Blaine Mooers, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104" 51 | __license__ = "GPL-3" 52 | __version__ = "1.0.3" 53 | __credits__ = ["William Beasley","Chiedza Kanyumbu"] 54 | # people who reported bug fixes, made suggestions, etc. 55 | __date__ = "24 July 2016" 56 | __maintainer__ = "Blaine Mooers" 57 | __email__ = "blaine-mooers@ouhsc.edu" 58 | __status__ = "Production" 59 | 60 | print("2015 OUHSC MSI-Lecture 17 and 18 takehome exam") 61 | print("on nucleic acid structure.") 62 | print(" ") 63 | print("Enter 'q1' for question 1, 'q2' for question 2, ...,") 64 | print("'q8' for question 8.") 65 | print(" ") 66 | print("Questions (1-4). HIV reverse transcriptase bound to DNA") 67 | print("with AZT incorporated (PDB-ID 3V6D).") 68 | print(" ") 69 | print("Questions (5-8). The full-length hammerhead") 70 | print("ribozyme (PDB-ID 3zp8).") 71 | print(" ") 72 | print("Enter 'help exam2' to learn how to use this script.") 73 | print("Enter 'help q1' to see quesiton 1 and the corresponding horizontal script.") 74 | print(" ") 75 | print("All or part of the horizontal script can be copied from the command history window for reuse.") 76 | print(" ") 77 | print("Positon cursor on command line with left mouse button.") 78 | print("Readline commands move the cursor to left or right:") 79 | print(" control-a will move the cursor to the beginning of the command line.") 80 | print(" control-e will move the cursor to the end of the line.") 81 | print(" command-f will move the cursor to the end of the current word.") 82 | print(" command-b will move the cursor to the begining of the current word.") 83 | print(" control-f will move the cursor to the right one character.") 84 | print(" control-b will move the cursor to the left by one character.") 85 | print(" ") 86 | print("Enter 'help rline' to see these commands again in the command history window.") 87 | print(" ") 88 | print("Up arrow key recalls last line of commands for editing.") 89 | 90 | 91 | 92 | def exam2(): 93 | """ 94 | USAGE: 95 | 96 | Enter 'run exam2.py' without including the quotation marks. 97 | 98 | Enter 'q1' to make the molecular scene for question 1. 99 | (Need active internet connection). 100 | 101 | Enter 'help q1' to see question 1 and the commands used to 102 | make the molecular scene. 103 | 104 | When you are ready for question 2, 105 | enter 'q2' for question 2, and so on. 106 | 107 | Enter 'help rline' to see the commands to move cursor on command line. 108 | 109 | DESCRIPTION 110 | 111 | Defines the molecular scenes for MSI-Lecture 17 and 112 | 18 takehome exam. 113 | 114 | Each question with a molecular scene has the scene 115 | defined by a specific function qX(), where X is the 116 | number of the question. 117 | 118 | Each function defines a series of PyMOL commands. Each 119 | function also has its own documentation that explains 120 | the molecular scene and that is printed to the 121 | command history window when you type 'help q1' or 122 | 'help q2' and so on. 123 | 124 | Each row of commands starts with 'reinitialize' to 125 | remove old molecules and settings. Each 126 | function prints to the command history window 127 | an alias to the commands in the function. 128 | 129 | LIMITATIONS 130 | 131 | An active internet connection is required because 132 | each alias uses the fetch command. 133 | 134 | Replace the fetch command with the load command to 135 | load atomic coordinates from your harddrive. 136 | 137 | Enter "rock" to stop the rocking motion. 138 | 139 | REQUIREMENTS 140 | 141 | When developing a variant of this program., run the 142 | program roundview.py to obtained a shorter version 143 | of the viewport settings. 144 | 145 | NOTES 146 | 147 | Use gray scroll bar to the right side of the command 148 | history window to see all of this documentation. or hit 149 | escape after moving the cursor to the viewing port 150 | (the GUI with the molecule). 151 | 152 | Copyright Notice 153 | ================ 154 | 155 | The PyMOL function source code in this file is copyrighted, but you can 156 | freely use and copy it as long as you don't change or remove any of 157 | the copyright notices. 158 | 159 | """ 160 | print("The function exam2() stores this docstring.") 161 | cmd.extend( "exam2",exam2) 162 | 163 | 164 | def rline(): 165 | ''' 166 | DESCRIPTION 167 | 168 | These commands are sufficient for most editing tasks: 169 | To edit code, positon cursor on command line with left mouse button. 170 | Control-e moves the cursor to the end of the line, even when it is out of view. 171 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 172 | Up arrow key recalls last line of commands for editing. 173 | 174 | These commands may not be available on all systems: 175 | Shift-control-a selects everything from the right of the cursor to the end of the line. 176 | Shift-control-e selects everything to the left of the cursor to the end of the line. 177 | Command-f moves the cursor to the end of the current word. 178 | Command-b moves the cursor to the begining of the current word. 179 | Control-f moves the cursor to the right by one character. 180 | Control-b moves the cursor to the left by one character. 181 | ''' 182 | cmd.extend("rline",rline) 183 | 184 | 185 | def q1(): 186 | ''' 187 | DESCRIPTION 188 | 189 | Question 1: Explain how AZT terminates extension of the DNA chain. 190 | 191 | The following commands created the scene for "q1": 192 | 193 | delete all; fetch 3v6d, HIVrt, async=0; rock;preset.ball_and_stick("c. P and i. 822");set_view (-0.99,-0.1,0.06,0.09,-0.39,0.92,-0.07,0.92,0.39,0.0,0.0,-29.2,-10.56,24.72,39.27,23.02,35.38,-20.0); 194 | 195 | To reuse of parts or all of the above commands, copy and paste the commands 196 | onto the command line or into a plain text file. 197 | 198 | These commands are sufficient for most editing tasks: 199 | To edit code, positon cursor on command line with left mouse button. 200 | Control-e moves the cursor to the end of the line, even when it is out of view. 201 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 202 | Up arrow key recalls last line of commands for editing. 203 | 204 | These commands may not be available on all systems: 205 | Shift-control-a selects everything from the right of the cursor to the end of the line. 206 | Shift-control-e selects everything to the left of the cursor to the end of the line. 207 | Command-f moves the cursor to the end of the current word. 208 | Command-b moves the cursor to the begining of the current word. 209 | Control-f moves the cursor to the right by one character. 210 | Control-b moves the cursor to the left by one character. 211 | ''' 212 | cmd.reinitialize() 213 | cmd.fetch('3v6d', type='pdb', name='HIVrt',async='0') 214 | cmd.rock() 215 | preset.ball_and_stick('c. P and i. 822') 216 | cmd.set_view('(-0.99,-0.1,0.06,0.09,-0.39,0.92,-0.07,\ 217 | 0.92,0.39,0.0,0.0,-29.2,-10.56,24.72,39.27,\ 218 | 23.02,35.38,-20.0)') 219 | print('Enter "q1" to set scene for question 1.') 220 | print('Enter "help q1" for more information.') 221 | cmd.extend( 'q1',q1) 222 | 223 | 224 | 225 | def q2(): 226 | ''' 227 | DESCRIPTION 228 | 229 | Question 2: Look along the helical axis of the DNA. 230 | Is the DNA helix bent? 231 | 232 | The following commands created the scene for "q2": 233 | 234 | delete all; fetch 3v6d, HIVrt, async=0; rock;show cartoon, c. P or c. T;set_view (0.61,0.29,-0.73,0.78,-0.37,0.51,-0.12,-0.88,-0.45,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0); 235 | 236 | To reuse of parts or all of the above commands, copy and paste the commands 237 | onto the command line or into a plain text file. 238 | 239 | These commands are sufficient for most editing tasks: 240 | To edit code, positon cursor on command line with left mouse button. 241 | Control-e moves the cursor to the end of the line, even when it is out of view. 242 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 243 | Up arrow key recalls last line of commands for editing. 244 | 245 | These commands may not be available on all systems: 246 | Shift-control-a selects everything from the right of the cursor to the end of the line. 247 | Shift-control-e selects everything to the left of the cursor to the end of the line. 248 | Command-f moves the cursor to the end of the current word. 249 | Command-b moves the cursor to the begining of the current word. 250 | Control-f moves the cursor to the right by one character. 251 | Control-b moves the cursor to the left by one character. 252 | 253 | ''' 254 | cmd.reinitialize() 255 | cmd.fetch('3v6d',type='pdb',name='HIVrt',async='0') 256 | cmd.rock() 257 | cmd.show_as("cartoon","chain P or chain T") 258 | cmd.set_view('(0.61,0.29,-0.73,0.78,-0.37,0.51,-0.12,-0.88,-0.45,-0.0, 0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);') 259 | print('Enter "q2" to make the scene for question 2.') 260 | print('Enter "help q2" to see question 2 and the commands to make the scene.') 261 | cmd.extend( 'q2',q2) 262 | 263 | 264 | def q3(): 265 | ''' 266 | DESCRIPTION 267 | 268 | Question 3: In which groove of the DNA 269 | is the protein making the most contacts? 270 | Is this unusual? 271 | 272 | The following commands created the scene for "q3": 273 | 274 | delete all; fetch 3v6d, HIVrt, async=0; show cartoon, c. A or c. B;hide lines, c. A or c. B;set_view (0.53,-0.06,-0.84,0.82,-0.21,0.53,-0.21,-0.98,-0.07,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);rock; 275 | 276 | To reuse of parts or all of the above commands, copy and paste the commands 277 | onto the command line or into a plain text file. 278 | 279 | These commands are sufficient for most editing tasks: 280 | To edit code, positon cursor on command line with left mouse button. 281 | Control-e moves the cursor to the end of the line, even when it is out of view. 282 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 283 | Up arrow key recalls last line of commands for editing. 284 | 285 | These commands may not be available on all systems: 286 | Shift-control-a selects everything from the right of the cursor to the end of the line. 287 | Shift-control-e selects everything to the left of the cursor to the end of the line. 288 | Command-f moves the cursor to the end of the current word. 289 | Command-b moves the cursor to the begining of the current word. 290 | Control-f moves the cursor to the right by one character. 291 | Control-b moves the cursor to the left by one character. 292 | ''' 293 | cmd.reinitialize() 294 | cmd.fetch('3v6d', type='pdb', name= 'HIVrt', async='0') 295 | cmd.show_as("cartoon","c. A or c. B") 296 | cmd.hide("lines","c. A or c. B") 297 | cmd.rock() 298 | cmd.set_view('(0.53,-0.06,-0.84,0.82,-0.21,0.53,-0.21,-0.98,-0.07,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);') 299 | print('Enter "q3" to make the scene for question 3.') 300 | print('Enter "help q3" to see question 3 and the commands to make the scene.') 301 | cmd.extend( 'q3',q3) 302 | 303 | 304 | 305 | def q4(): 306 | ''' 307 | DESCRIPTION 308 | 309 | Question 4: What the dihedral angle about the disulfide 310 | bond between MRG81 of chain F and Cys258 of chain C? 311 | This is a cross link between the protein and the DNA. Is 312 | this a cis or trans conformation of the bonds about the 313 | S--S bond? Is this conformation energetically favorable 314 | or unfavorable? 315 | 316 | The following commands created the scene for "q4": 317 | 318 | delete all; fetch 3v6d, HIVrt, async=0;preset.ball_and_stick("(c. C and i. 258) or (c. F and i. 817 )");set_view (0.21,-0.91,0.34,-0.84,0.01,0.54,-0.5,-0.4,-0.77,0.0,-0.0,-38.82,-39.67,-55.1,10.96,36.31,41.34,-20.0); 319 | 320 | To reuse of parts or all of the above commands, copy and paste the commands 321 | onto the command line or into a plain text file. 322 | 323 | These commands are sufficient for most editing tasks: 324 | To edit code, positon cursor on command line with left mouse button. 325 | Control-e moves the cursor to the end of the line, even when it is out of view. 326 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 327 | Up arrow key recalls last line of commands for editing. 328 | 329 | These commands may not be available on all systems: 330 | Shift-control-a selects everything from the right of the cursor to the end of the line. 331 | Shift-control-e selects everything to the left of the cursor to the end of the line. 332 | Command-f moves the cursor to the end of the current word. 333 | Command-b moves the cursor to the begining of the current word. 334 | Control-f moves the cursor to the right by one character. 335 | Control-b moves the cursor to the left by one character. 336 | ''' 337 | cmd.reinitialize() 338 | cmd.fetch('3v6d',type='pdb',name='HIVrt',async='0') 339 | cmd.do("preset.ball_and_stick(selection='(chain C and resi 258) or (chain F and resi 817 )')") 340 | cmd.set_view('(0.21,-0.91,0.34,-0.84,0.01,0.54,-0.5,-0.4,-0.77,0.0,-0.0,-38.82,-39.67,-55.1,10.96,36.31,41.34,-20.0);') 341 | cmd.rock() 342 | print('Enter "q4" to make the scene for question 4.') 343 | print('Enter "help q4" to see question 4 and the commands to make the scene.') 344 | cmd.extend('q4',q4) 345 | 346 | 347 | 348 | def q5(): 349 | ''' 350 | DESCRIPTION 351 | 352 | Question 5: How many axial stacks of helices does 353 | the ribozyme have? 354 | 355 | The following commands created the scene for "q5": 356 | 357 | delete all;fetch 3zp8, hammer, async=0;show cartoon, hammer;set_view (-0.5,0.18,-0.85,-0.17,-0.98,-0.11,-0.85,0.09,0.52,0.0,0.0,-167.2,-18.45,10.92,-12.11,126.37,208.02,-20.0);rock; 358 | 359 | To reuse of parts or all of the above commands, copy and paste the commands 360 | onto the command line or into a plain text file. 361 | 362 | These commands are sufficient for most editing tasks: 363 | To edit code, positon cursor on command line with left mouse button. 364 | Control-e moves the cursor to the end of the line, even when it is out of view. 365 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 366 | Up arrow key recalls last line of commands for editing. 367 | 368 | These commands may not be available on all systems: 369 | Shift-control-a selects everything from the right of the cursor to the end of the line. 370 | Shift-control-e selects everything to the left of the cursor to the end of the line. 371 | Command-f moves the cursor to the end of the current word. 372 | Command-b moves the cursor to the begining of the current word. 373 | Control-f moves the cursor to the right by one character. 374 | Control-b moves the cursor to the left by one character. 375 | ''' 376 | cmd.reinitialize() 377 | cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0') 378 | cmd.show_as('cartoon','hammer') 379 | cmd.rock() 380 | cmd.set_view('(-0.5,0.18,-0.85,-0.17,-0.98,-0.11,-0.85,0.09,0.52,0.0,0.0,-167.2,-18.45,10.92,-12.11,126.37,208.02,-20.0);') 381 | print('Enter "q5" to make the scene for question 5.') 382 | print('Enter "help q5" to see question 5 and the commands to make the scene.') 383 | cmd.extend('q5',q5) 384 | 385 | 386 | def q6(): 387 | ''' 388 | DESCRIPTION 389 | 390 | Question 6: What is the average distance of the Na1044 391 | ligand bonds? Give the residue numbers of the RNA 392 | nucleotides and the sodium to identify them. How many 393 | ligands are from RNA? 394 | 395 | The following commands created the scene for "q6": 396 | 397 | delete all;fetch 3zp8, hammer, async=0; rock;preset.ball_and_stick("all");distance ligand1, i. 1044, c. A and i. 22 and n. N7;distance ligand2, i. 1044, c. A and i. 21 and n. OP2;distance ligand3, i. 1044, i. 2121;distance ligand4, i. 1044, i. 2120;distance ligand5, i. 1044, i. 2122;distance ligand6, i. 1044, i. 2130;set_view (-0.87,0.18,-0.46,-0.39,-0.81,0.44,-0.29,0.56,0.78,-0.0,0.0,-20.47,-18.05,14.02,-18.89,17.47,23.47,-20.0); 398 | 399 | To reuse of parts or all of the above commands, copy and paste the commands 400 | onto the command line or into a plain text file. 401 | 402 | These commands are sufficient for most editing tasks: 403 | To edit code, positon cursor on command line with left mouse button. 404 | Control-e moves the cursor to the end of the line, even when it is out of view. 405 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 406 | Up arrow key recalls last line of commands for editing. 407 | 408 | These commands may not be available on all systems: 409 | Shift-control-a selects everything from the right of the cursor to the end of the line. 410 | Shift-control-e selects everything to the left of the cursor to the end of the line. 411 | Command-f moves the cursor to the end of the current word. 412 | Command-b moves the cursor to the begining of the current word. 413 | Control-f moves the cursor to the right by one character. 414 | Control-b moves the cursor to the left by one character. 415 | ''' 416 | cmd.reinitialize() 417 | cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0') 418 | cmd.rock() 419 | cmd.do('preset.ball_and_stick("all")') 420 | cmd.distance('Sodiumligand1',' resi 1044', 'chain A and i. 22 and n. N7') 421 | cmd.distance('Sodiumligand2', 'resi 1044', 'chain A and i. 21 and n. OP2') 422 | cmd.distance('Sodiumligand3', 'resi 1044', 'resi 2121') 423 | cmd.distance('Sodiumligand4', 'resi 1044', 'resi 2120') 424 | cmd.distance('Sodiumligand5', 'resi 1044', 'resi 2122') 425 | cmd.distance('Sodiumligand6', 'resi 1044', 'resi 2130') 426 | cmd.do('set label_size, -0.4') 427 | cmd.set_view('(-0.87,0.18,-0.46,-0.39,-0.81,0.44,-0.29,0.56,0.78,-0.0,0.0,-20.47,-18.05,14.02,-18.89,17.47,23.47,-20.0);') 428 | print('Enter "q6" to make the scene for question 6.') 429 | print('Enter "help q6" to see question 6 and the commands to make the scene.') 430 | cmd.extend('q6',q6) 431 | 432 | 433 | def q7(): 434 | ''' 435 | DESCRIPTION 436 | 437 | Question 7: Measure the longest dimension and the 438 | shortest dimension of the ribozyme. Enter "rock" to 439 | stop the rocking motion. What is the ratio of 440 | the longest dimension to the shortest dimension? Is it 441 | globular like a protein? 442 | 443 | The following commands created the scene for "q7": 444 | 445 | delete all;fetch 3zp8, hammer, async=0;show ribbon, hammer;set_view (0.62,0.14,0.78,0.13,-0.99,0.07,0.78,0.05,-0.63,-0.0,-0.0,-169.8,-16.43,9.44,-9.63,143.54,196.05,-20.0); rock; 446 | 447 | To reuse of parts or all of the above commands, copy and paste the commands 448 | onto the command line or into a plain text file. 449 | 450 | These commands are sufficient for most editing tasks: 451 | To edit code, positon cursor on command line with left mouse button. 452 | Control-e moves the cursor to the end of the line, even when it is out of view. 453 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 454 | Up arrow key recalls last line of commands for editing. 455 | 456 | These commands may not be available on all systems: 457 | Shift-control-a selects everything from the right of the cursor to the end of the line. 458 | Shift-control-e selects everything to the left of the cursor to the end of the line. 459 | Command-f moves the cursor to the end of the current word. 460 | Command-b moves the cursor to the begining of the current word. 461 | Control-f moves the cursor to the right by one character. 462 | Control-b moves the cursor to the left by one character. 463 | ''' 464 | cmd.reinitialize() 465 | cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0') 466 | cmd.show_as('ribbon', 'hammer') 467 | cmd.rock() 468 | cmd.set_view('(0.62,0.14,0.78,0.13,-0.99,0.07,0.78,0.05,-0.63,-0.0,-0.0,-169.8,-16.43,9.44,-9.63,143.54,196.05,-20.0);') 469 | print('Enter "q7" to make the scene for question 7.') 470 | print('Enter "help q7" to see question 7 and the commands to make the scene.') 471 | cmd.extend('q7',q7) 472 | 473 | 474 | def q8(): 475 | ''' 476 | DESCRIPTION 477 | 478 | Question 8: Find the unusual base pair between A21 and 479 | G36. What is the length of the H-bonds between the bases 480 | (ignore the H atoms in the distance measurement)? List 481 | the distance with the residue name, residue number, and 482 | atom name. What additional H-bond occurs between a base 483 | in this base pair and a ribose ring of one of the two 484 | nucleotides in this base pair? 485 | 486 | The following commands created the scene for "q8": 487 | 488 | fetch 3zp8, hammer, async=0;hide everything;show ribbon;show sticks, resi 21 or resi 36;set_view (-0.9,-0.19,0.39,0.39,-0.74,0.55,0.19,0.65,0.74,0.0,0.0,-37.58,-21.66,15.71,-23.32,35.42,39.74,-20.0);rock; 489 | 490 | To reuse of parts or all of the above commands, copy and paste the commands 491 | onto the command line or into a plain text file. 492 | 493 | These commands are sufficient for most editing tasks: 494 | To edit code, positon cursor on command line with left mouse button. 495 | Control-e moves the cursor to the end of the line, even when it is out of view. 496 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 497 | Up arrow key recalls last line of commands for editing. 498 | 499 | These commands may not be available on all systems: 500 | Shift-control-a selects everything from the right of the cursor to the end of the line. 501 | Shift-control-e selects everything to the left of the cursor to the end of the line. 502 | Command-f moves the cursor to the end of the current word. 503 | Command-b moves the cursor to the begining of the current word. 504 | Control-f moves the cursor to the right by one character. 505 | Control-b moves the cursor to the left by one character. 506 | ''' 507 | cmd.reinitialize() 508 | cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0') 509 | cmd.show_as('ribbon', 'hammer') 510 | cmd.rock() 511 | cmd.hide('everything') 512 | cmd.show_as( 'ribbon','all') 513 | cmd.show_as('sticks', 'resi 21 or resi 36') 514 | cmd.set_view('(-0.9,-0.19,0.39,0.39,-0.74,0.55,0.19,0.65,0.74,0.0,0.0,-37.58,-21.66,15.71,-23.32,35.42,39.74,-20.0);') 515 | print('Enter "q8" to make the scene for question 8.') 516 | print('Enter "help q8" to see question 8 and the commands to make the scene.') 517 | cmd.extend('q8',q8) 518 | 519 | -------------------------------------------------------------------------------- /quat.py: -------------------------------------------------------------------------------- 1 | ''' 2 | (c) 2010-2011 Thomas Holder, MPI for Developmental Biology 3 | 4 | Module for reading REMARK records from PDB files and in particular 5 | generate quaterny structure from REMARK 350. 6 | ''' 7 | 8 | import sys, os 9 | from pymol import cmd, stored 10 | 11 | local_mirror_divided = '/mnt/bio/db/pdb.divided' 12 | 13 | def pdbremarks(filename): 14 | ''' 15 | Read REMARK lines from PDB file. Return dictionary with remarkNum as key 16 | and list of lines as value. 17 | ''' 18 | remarks = dict() 19 | if not isinstance(filename, basestring): 20 | f = filename 21 | elif filename[-3:] == '.gz': 22 | import gzip 23 | f = gzip.open(filename) 24 | else: 25 | f = open(filename) 26 | for line in f: 27 | recname = line[0:6] 28 | if recname == 'REMARK': 29 | num = int(line[7:10]) 30 | lstring = line[11:] 31 | remarks.setdefault(num, []).append(lstring) 32 | return remarks 33 | 34 | def quat350(rem350): 35 | ''' 36 | Get transformation matrices for biomolecule 1 from REMARK 350. 37 | ''' 38 | biomt = dict() 39 | chains = tuple() 40 | seenbiomolecule = False 41 | for line in rem350: 42 | if line.startswith('BIOMOLECULE:'): 43 | if seenbiomolecule: 44 | break 45 | seenbiomolecule = True 46 | elif line.startswith('APPLY THE FOLLOWING TO CHAINS:'): 47 | chains = tuple(chain.strip() for chain in line[30:].split(',')) 48 | elif line.startswith(' AND CHAINS:'): 49 | chains += tuple(chain.strip() for chain in line[30:].split(',')) 50 | elif line.startswith(' BIOMT'): 51 | row = int(line[7]) 52 | num = int(line[8:12]) 53 | vec = line[12:].split() 54 | vec = map(float, vec) 55 | biomt.setdefault(chains, dict()).setdefault(num, []).extend(vec) 56 | return biomt 57 | 58 | def quat(name=None, filename=None, prefix=None, quiet=0): 59 | ''' 60 | DESCRIPTION 61 | 62 | Read REMARK 350 from `filename` and create biological unit 63 | (quaternary structure) 64 | 65 | USAGE 66 | 67 | quat [name [, filename [, prefix]]] 68 | 69 | ARGUMENTS 70 | 71 | name = string: name of object and basename of PDB file, if 72 | filename is not given {default: first loaded object} 73 | 74 | filename = string: file path {default: .pdb} 75 | 76 | prefix = string: prefix for new objects {default: } 77 | 78 | EXAMPLE 79 | 80 | fetch 1rmv 81 | quat 1rmv 82 | ''' 83 | quiet = int(quiet) 84 | if name is None: 85 | name = cmd.get_object_list()[0] 86 | if prefix is None: 87 | prefix = name 88 | if filename is None: 89 | candidates = [ 90 | '%s.pdb' % (name), 91 | '%s/%s.pdb' % (cmd.get('fetch_path'), name), 92 | '%s/%s/pdb%s.ent.gz' % (local_mirror_divided, name[1:3], name), 93 | ] 94 | for filename in candidates: 95 | if os.path.exists(filename): 96 | break 97 | else: 98 | print 'please provide filename' 99 | return 100 | if not quiet: 101 | print 'loading from %s' % (filename) 102 | remarks = pdbremarks(filename) 103 | if 350 not in remarks: 104 | print 'There is no REMARK 350 in', filename 105 | return 106 | quat = quat350(remarks[350]) 107 | for chains in quat: 108 | matrices = quat[chains] 109 | for num in matrices: 110 | mat = matrices[num][0:12] 111 | mat.extend([0,0,0,1]) 112 | copy = '%s_%d' % (prefix, num) 113 | if not quiet: 114 | print 'creating %s' % (copy) 115 | cmd.create(copy, '/%s//%s' % (name, '+'.join(chains))) 116 | cmd.alter(copy, 'segi="%d"' % (num)) 117 | cmd.transform_object(copy, mat) 118 | cmd.disable(name) 119 | cmd.group('%s_quat' % (prefix), '%s_*' % (prefix)) 120 | 121 | cmd.extend('quat', quat) 122 | 123 | # vi:expandtab:smarttab 124 | -------------------------------------------------------------------------------- /quatWindows.py: -------------------------------------------------------------------------------- 1 | ''' 2 | (c) 2010-2011 Thomas Holder, MPI for Developmental Biology 3 | 4 | Module for reading REMARK records from PDB files and in particular 5 | generate quaterny structure from REMARK 350. 6 | ''' 7 | 8 | import sys, os 9 | from pymol import cmd, stored 10 | 11 | local_mirror_divided = '/mnt/bio/db/pdb.divided' 12 | 13 | def pdbremarks(filename): 14 | ''' 15 | Read REMARK lines from PDB file. Return dictionary with remarkNum as key 16 | and list of lines as value. 17 | ''' 18 | remarks = dict() 19 | if not isinstance(filename, basestring): 20 | f = filename 21 | elif filename[-3:] == '.gz': 22 | import gzip 23 | f = gzip.open(filename) 24 | else: 25 | f = open(filename) 26 | for line in f: 27 | recname = line[0:6] 28 | if recname == 'REMARK': 29 | num = int(line[7:10]) 30 | lstring = line[11:] 31 | remarks.setdefault(num, []).append(lstring) 32 | return remarks 33 | 34 | def quat350(rem350): 35 | ''' 36 | Get transformation matrices for biomolecule 1 from REMARK 350. 37 | ''' 38 | biomt = dict() 39 | chains = tuple() 40 | seenbiomolecule = False 41 | for line in rem350: 42 | if line.startswith('BIOMOLECULE:'): 43 | if seenbiomolecule: 44 | break 45 | seenbiomolecule = True 46 | elif line.startswith('APPLY THE FOLLOWING TO CHAINS:'): 47 | chains = tuple(chain.strip() for chain in line[30:].split(',')) 48 | elif line.startswith(' AND CHAINS:'): 49 | chains += tuple(chain.strip() for chain in line[30:].split(',')) 50 | elif line.startswith(' BIOMT'): 51 | row = int(line[7]) 52 | num = int(line[8:12]) 53 | vec = line[12:].split() 54 | vec = map(float, vec) 55 | biomt.setdefault(chains, dict()).setdefault(num, []).extend(vec) 56 | return biomt 57 | 58 | def quat(name=None, filename=None, prefix=None, quiet=0): 59 | ''' 60 | DESCRIPTION 61 | 62 | Read REMARK 350 from `filename` and create biological unit 63 | (quaternary structure) 64 | 65 | USAGE 66 | 67 | quat [name [, filename [, prefix]]] 68 | 69 | ARGUMENTS 70 | 71 | name = string: name of object and basename of PDB file, if 72 | filename is not given {default: first loaded object} 73 | 74 | filename = string: file path {default: .pdb} 75 | 76 | prefix = string: prefix for new objects {default: } 77 | 78 | EXAMPLE 79 | 80 | fetch 1rmv 81 | quat 1rmv 82 | ''' 83 | quiet = int(quiet) 84 | if name is None: 85 | name = cmd.get_object_list()[0] 86 | if prefix is None: 87 | prefix = name 88 | if filename is None: 89 | candidates = [ 90 | '%s.pdb' % (name), 91 | '%s/%s.pdb' % (cmd.get('fetch_path'), name), 92 | '%s/%s/pdb%s.ent.gz' % (local_mirror_divided, name[1:3], name), 93 | ] 94 | for filename in candidates: 95 | if os.path.exists(filename): 96 | break 97 | else: 98 | print 'please provide filename' 99 | return 100 | if not quiet: 101 | print 'loading from %s' % (filename) 102 | remarks = pdbremarks(filename) 103 | if 350 not in remarks: 104 | print 'There is no REMARK 350 in', filename 105 | return 106 | quat = quat350(remarks[350]) 107 | for chains in quat: 108 | matrices = quat[chains] 109 | for num in matrices: 110 | mat = matrices[num][0:12] 111 | mat.extend([0,0,0,1]) 112 | copy = '%s_%d' % (prefix, num) 113 | if not quiet: 114 | print 'creating %s' % (copy) 115 | cmd.create(copy, '/%s//%s' % (name, '+'.join(chains))) 116 | cmd.alter(copy, 'segi="%d"' % (num)) 117 | cmd.transform_object(copy, mat) 118 | cmd.disable(name) 119 | cmd.group('%s_quat' % (prefix), '%s_*' % (prefix)) 120 | 121 | cmd.extend('quat', quat) 122 | 123 | # vi:expandtab:smarttab 124 | -------------------------------------------------------------------------------- /roundview.py: -------------------------------------------------------------------------------- 1 | from __future__ import division 2 | from __future__ import print_function 3 | # -*- coding: utf-8 -*- 4 | 5 | """ 6 | 7 | version 1.0 26 October 2015 8 | Posted in github for first time. 9 | 10 | version 1.1 23 November 2015 11 | Corrected description of the rounding off the matrix elements. 12 | Corrected hard wrapped text the broke the script. 13 | Added example of running program as a horizontal script. 14 | Made code pep8 compliant (changed use of blank lines, 15 | removed whitespaces in defualt arguments assignments, 16 | inserted whitespaces after commas in lists, 17 | removed whitespaces at the ends of lines). 18 | Added version number. 19 | 20 | version 1.2 23 May 2016 21 | Edited copyright notice. 22 | Corrected typos 23 | 24 | version 1.3 23 July 2016 25 | Added missing parenthesis at end of file. 26 | 27 | 28 | Copyright Notice 29 | ================ 30 | 31 | Copyright (C) 2016 Blaine Mooers 32 | 33 | This program is free software: you can redistribute it and/or modify 34 | it under the terms of the GNU General Public License as published by 35 | the Free Software Foundation, either version 3 of the License. 36 | 37 | This program is distributed in the hope that it will be useful, 38 | but WITHOUT ANY WARRANTY; without even the implied warranty of 39 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 40 | See the GNU General Public License for more details: 41 | http://www.gnu.org/licenses/. 42 | 43 | The source code in this file is copyrighted, but you can 44 | freely use and copy it as long as you don't change or remove any of 45 | the copyright notices. 46 | 47 | Blaine Mooers, PhD 48 | blaine-mooers@ouhsc.edu 49 | 975 NE 10th St, BRC 466 50 | University of Oklahoma Health Sciences Center, 51 | Oklahoma City, OK, USA 73104 52 | 53 | """ 54 | from pymol import stored, cmd 55 | __author__ = "Blaine Mooers" 56 | __copyright__ = "Blaine Mooers, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104" 57 | __license__ = "GPL-3" 58 | __version__ = "1.0.2" 59 | __credits__ = ["William Beasley","Chiedza Kanyumbu"] 60 | # people who reported bug fixes, made suggestions, etc. 61 | __date__ = "30 May 2016" 62 | __maintainer__ = "Blaine Mooers" 63 | __email__ = "blaine-mooers@ouhsc.edu" 64 | __status__ = "Production" 65 | 66 | 67 | def roundview(StoredView=0, decimal_places=2, outname="roundedview.txt"): 68 | 69 | """ 70 | DESCRIPTION 71 | 72 | Adds the command "roundview" that gets a view (default is 0, 73 | the current view; you can get a stored view assigned to some 74 | other digit with the view command) and rounds to two decimal 75 | places (two digits to the right of the decimal point) the 76 | viewpoint matrix elements and rewrites the matrix elements 77 | on a single line with no whitespaces and a semicolon at the 78 | end. The saved space eases the making of a single line of 79 | PyMOL commands separated by semicolons. This enables rapid 80 | and interactive editing of chunks of PyMOL commands. The 81 | viewpoints are appended to the bottom of a text file in the 82 | present working directory called "roundedview.txt". The line 83 | could be easier to copy from this file than from the command 84 | history window in the external gui. A semicolon with nothing 85 | to the right of it at the end of a line of grouped commands 86 | is harmless. 87 | 88 | 89 | USAGE 90 | 91 | roundview [view, decimal_places, outname] 92 | 93 | Note that the values in the [] are optional. 94 | 95 | The default values for the arguments of the function 96 | are "0,2, roundedview.txt". 97 | 98 | Simple one-line example with roundview.py script in current working 99 | directory--check by typing 'pwd' and 'ls *.py' on the command line. PyMOL 100 | should return 'roundview.py' in the lisf of files in the external (top) gui. 101 | Next, paste the following command on the external (top) commandline, hit 102 | return, and wait 5-10 seconds: 103 | 104 | fetch 1lw9, async=0; run roundview.py; roundview 0,1 105 | 106 | 107 | The following view setting will be returned without the blackslash. 108 | 109 | set_view (1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,-155.2,35.1,11.5,9.7,122.3,188.0,-20.0); 110 | 111 | Advanced option: 112 | 113 | Copy roundview.py to the folder ~/.pymol/startup and then 114 | the command will always be accessible. You may have to 115 | create these directories. 116 | 117 | 118 | 18 elements of the view matrix (0-17) 119 | 120 | 0 - 8 = column-major 3x3 matrix that rotates the model axes 121 | to camera axes 122 | 123 | 9 - 11 = origin of rotation relative to the camera 124 | in camera space 125 | 126 | 12 - 14 = origin of rotation in model space 127 | 128 | 15 = front plane distance from the camera 129 | 130 | 16 = rear plane distance from the camera 131 | 132 | 17 = orthoscopic flag 133 | (not implemented in older versions) 134 | 135 | """ 136 | 137 | #convert the commandline arguments from strings to integers 138 | 139 | StoredView = int(StoredView) 140 | decimal_places = int(decimal_places) 141 | 142 | 143 | #call the get_view function 144 | 145 | m = cmd.get_view(StoredView) 146 | 147 | 148 | #Make a list of the elements in the orientation matrix. 149 | 150 | myList = [m[0], m[1], m[2], m[3], m[4], m[5], m[6], 151 | m[7], m[8], m[9], m[10], m[11], m[12], m[13], m[14], 152 | m[15], m[16], m[17]] 153 | 154 | 155 | #Round off the matrix elements to two decimal places (two fractional places) 156 | #This rounding approach solved the problem of unwanted 157 | #whitespaces when I tried using a string format statement 158 | 159 | myRoundedList = [ round(elem, decimal_places) for elem in myList] 160 | 161 | 162 | #x is the format of the output. The whitespace is required 163 | #between the "set_view" and "(". 164 | 165 | x = 'set_view ({0},{1},{2},{3},{4},{5},{6},{7},\ 166 | {8},{9},{10},{11},{12},{13},{14},{15},{16},{17});' 167 | 168 | 169 | #print to the external gui. 170 | 171 | print x.format(*myRoundedList) 172 | 173 | 174 | #Write to a text file. 175 | 176 | myFile = open("roundedview.txt", "a") 177 | myFile.write(x.format(*myRoundedList) + "\n") 178 | myFile.close() 179 | return 180 | 181 | 182 | #The extend command makes roundview into a PyMOL command. 183 | 184 | cmd.extend("roundview", roundview) 185 | -------------------------------------------------------------------------------- /roundviewWindows.py: -------------------------------------------------------------------------------- 1 | from __future__ import division 2 | from __future__ import print_function 3 | 4 | """ 5 | 6 | version 1.0 26 October 2015 7 | Posted in github for first time. 8 | 9 | version 1.1 23 November 2015 10 | Corrected description of the rounding off the matrix elements. 11 | Corrected hard wrapped text the broke the script. 12 | Added example of running program as a horizontal script. 13 | Made code pep8 compliant (changed use of blank lines, 14 | removed whitespaces in defualt arguments assignments, 15 | inserted whitespaces after commas in lists, 16 | removed whitespaces at the ends of lines). 17 | Added version number. 18 | 19 | version 1.2 23 May 2016 20 | Edited copyright notice. 21 | Corrected typos 22 | 23 | version 1.3 23 July 2016 24 | Added missing parenthesis at end of file. 25 | 26 | 27 | Copyright Notice 28 | ================ 29 | 30 | Copyright (C) 2016 Blaine Mooers 31 | 32 | This program is free software: you can redistribute it and/or modify 33 | it under the terms of the GNU General Public License as published by 34 | the Free Software Foundation, either version 3 of the License. 35 | 36 | This program is distributed in the hope that it will be useful, 37 | but WITHOUT ANY WARRANTY; without even the implied warranty of 38 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 39 | See the GNU General Public License for more details: 40 | http://www.gnu.org/licenses/. 41 | 42 | The source code in this file is copyrighted, but you can 43 | freely use and copy it as long as you don't change or remove any of 44 | the copyright notices. 45 | 46 | Blaine Mooers, PhD 47 | blaine-mooers@ouhsc.edu 48 | 975 NE 10th St, BRC 466 49 | University of Oklahoma Health Sciences Center, 50 | Oklahoma City, OK, USA 73104 51 | 52 | """ 53 | from pymol import stored, cmd 54 | __author__ = "Blaine Mooers" 55 | __copyright__ = "Blaine Mooers, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104" 56 | __license__ = "GPL-3" 57 | __version__ = "1.0.2" 58 | __credits__ = ["William Beasley","Chiedza Kanyumbu"] 59 | # people who reported bug fixes, made suggestions, etc. 60 | __date__ = "30 May 2016" 61 | __maintainer__ = "Blaine Mooers" 62 | __email__ = "blaine-mooers@ouhsc.edu" 63 | __status__ = "Production" 64 | 65 | 66 | def roundview(StoredView=0, decimal_places=2, outname="roundedview.txt"): 67 | 68 | """ 69 | DESCRIPTION 70 | 71 | Adds the command "roundview" that gets a view (default is 0, 72 | the current view; you can get a stored view assigned to some 73 | other digit with the view command) and rounds to two decimal 74 | places (two digits to the right of the decimal point) the 75 | viewpoint matrix elements and rewrites the matrix elements 76 | on a single line with no whitespaces and a semicolon at the 77 | end. The saved space eases the making of a single line of 78 | PyMOL commands separated by semicolons. This enables rapid 79 | and interactive editing of chunks of PyMOL commands. The 80 | viewpoints are appended to the bottom of a text file in the 81 | present working directory called "roundedview.txt". The line 82 | could be easier to copy from this file than from the command 83 | history window in the external gui. A semicolon with nothing 84 | to the right of it at the end of a line of grouped commands 85 | is harmless. 86 | 87 | 88 | USAGE 89 | 90 | roundview [view, decimal_places, outname] 91 | 92 | Note that the values in the [] are optional. 93 | 94 | The default values for the arguments of the function 95 | are "0,2, roundedview.txt". 96 | 97 | Simple one-line example with roundview.py script in current working 98 | directory--check by typing 'pwd' and 'ls *.py' on the command line. PyMOL 99 | should return 'roundview.py' in the lisf of files in the external (top) gui. 100 | Next, paste the following command on the external (top) commandline, hit 101 | return, and wait 5-10 seconds: 102 | 103 | fetch 1lw9, async=0; run roundview.py; roundview 0,1 104 | 105 | 106 | The following view setting will be returned without the blackslash. 107 | 108 | set_view (1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,-155.2,35.1,11.5,9.7,122.3,188.0,-20.0); 109 | 110 | Advanced option: 111 | 112 | Copy roundview.py to the folder ~/.pymol/startup and then 113 | the command will always be accessible. You may have to 114 | create these directories. 115 | 116 | 117 | 18 elements of the view matrix (0-17) 118 | 119 | 0 - 8 = column-major 3x3 matrix that rotates the model axes 120 | to camera axes 121 | 122 | 9 - 11 = origin of rotation relative to the camera 123 | in camera space 124 | 125 | 12 - 14 = origin of rotation in model space 126 | 127 | 15 = front plane distance from the camera 128 | 129 | 16 = rear plane distance from the camera 130 | 131 | 17 = orthoscopic flag 132 | (not implemented in older versions) 133 | 134 | """ 135 | 136 | #convert the commandline arguments from strings to integers 137 | 138 | StoredView = int(StoredView) 139 | decimal_places = int(decimal_places) 140 | 141 | 142 | #call the get_view function 143 | 144 | m = cmd.get_view(StoredView) 145 | 146 | 147 | #Make a list of the elements in the orientation matrix. 148 | 149 | myList = [m[0], m[1], m[2], m[3], m[4], m[5], m[6], 150 | m[7], m[8], m[9], m[10], m[11], m[12], m[13], m[14], 151 | m[15], m[16], m[17]] 152 | 153 | 154 | #Round off the matrix elements to two decimal places (two fractional places) 155 | #This rounding approach solved the problem of unwanted 156 | #whitespaces when I tried using a string format statement 157 | 158 | myRoundedList = [ round(elem, decimal_places) for elem in myList] 159 | 160 | 161 | #x is the format of the output. The whitespace is required 162 | #between the "set_view" and "(". 163 | 164 | x = 'set_view ({0},{1},{2},{3},{4},{5},{6},{7},\ 165 | {8},{9},{10},{11},{12},{13},{14},{15},{16},{17});' 166 | 167 | 168 | #print to the external gui. 169 | 170 | print x.format(*myRoundedList) 171 | 172 | 173 | #Write to a text file. 174 | 175 | myFile = open("roundedview.txt", "a") 176 | myFile.write(x.format(*myRoundedList) + "\n") 177 | myFile.close() 178 | return 179 | 180 | 181 | #The extend command makes roundview into a PyMOL command. 182 | 183 | cmd.extend("roundview", roundview) 184 | -------------------------------------------------------------------------------- /site31labels.pml: -------------------------------------------------------------------------------- 1 | label n. CG and i. 70, "%s %s" % (resn,resi) 2 | label n. ND1 and i. 31, "%s %s" % (resn, resi) 3 | -------------------------------------------------------------------------------- /site31labelsWindows.pml: -------------------------------------------------------------------------------- 1 | label n. CG and i. 70, "%s %s" % (resn,resi) 2 | label n. ND1 and i. 31, "%s %s" % (resn, resi) 3 | -------------------------------------------------------------------------------- /startupAliasesWindows.py: -------------------------------------------------------------------------------- 1 | from __future__ import print_function 2 | """ 3 | DESCRIPTION 4 | 5 | On the startup of PyMOL, this script defines a number of aliases. 6 | The aliases are listed here instead of in the pymolrc file 7 | to avoid clutter of the command history window. Source this 8 | file from your .pymolrc file on the mac or linux or 9 | from your pymolrc.pml file on Windows by adding the command: 10 | 11 | run ~/Scripts/PyMOLScripts/startupAliases.py 12 | 13 | Requires quat.py from the PyMOL Wiki 14 | (http://www.pymolwiki.org/index.php/BiologicalUnit/Quat) 15 | 16 | Store quat.py in ~/Scripts/PyMOLScripts/. 17 | 18 | Tested on PyMOL versions 1.5.0.5, 1.8.0.5, 1.8.1.0 and 1.8.2.0 19 | 20 | No guarantee is given that this script will work with older 21 | or newer versions of PyMOL. 22 | 23 | 24 | Copyright Notice 25 | ================ 26 | 27 | Copyright (C) 2016 Blaine Mooers 28 | 29 | This program is free software: you can redistribute it and/or modify 30 | it under the terms of the GNU General Public License as published by 31 | the Free Software Foundation, either version 3 of the License. 32 | 33 | This program is distributed in the hope that it will be useful, 34 | but WITHOUT ANY WARRANTY; without even the implied warranty of 35 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 36 | See the GNU General Public License for more details: 37 | http://www.gnu.org/licenses/. 38 | 39 | The source code in this file is copyrighted, but you can 40 | freely use and copy it as long as you don't change or remove any of 41 | the copyright notices. 42 | 43 | Blaine Mooers , PhD 44 | blaine-mooers@ouhsc.edu 45 | 975 NE 10th St, BRC 466 46 | University of Oklahoma Health Sciences Center, 47 | Oklahoma City, OK, USA 73104 48 | 49 | """ 50 | from pymol import cmd 51 | __author__ = "Blaine Mooers" 52 | __copyright__ = "Blaine Mooers, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104" 53 | __license__ = "GPL-3" 54 | __version__ = "1.0.3" 55 | __credits__ = ["William Beasley","Chiedza Kanyumbu"] 56 | # people who reported bug fixes, made suggestions, etc. 57 | __date__ = "24 July 2016" 58 | __maintainer__ = "Blaine Mooers" 59 | __email__ = "blaine-mooers@ouhsc.edu" 60 | __status__ = "Production" 61 | 62 | def SA(): 63 | ''' 64 | DESCRIPTION 65 | 66 | startupAliases.py Copyright (C) 2016 Blaine Mooers. 67 | This script comes with ABSOLUTELY NO WARRANTY; for details, 68 | please see the license file. 69 | 70 | Copy to ~/Scripts/PyMOLScripts/. 71 | Add this command on one line in your .pymolrc file 72 | (pymolrc.pml on Windows): 73 | 74 | run ~/Scripts/PyMOLScripts/startupAliases.py 75 | 76 | Format of list below: 77 | alias name, description of alias: PDB code (where applicable). 78 | 79 | Molecules in standard orientations: 80 | 81 | T4L, WT T4 lysozyme (1.09 ang) as a ribbon diagram: 3fa0. 82 | U8, 16-mer dsRNA with 8 contiguous Us. U-helix RaNA (1.37 ang): 3nd3. 83 | WC8, 16-mer RNA with all Watson-Crick base pairs (1.52 ang): 3nd4. 84 | N9, neuraminidase as cartoon, biological unit (1.55 ang): 4dgr. 85 | GGT, gamma glutamyl transpeptidase as cartoon (1.67 ang): 4gdx. 86 | GU, 10-mer RNA with eight GU base pairs (1.32 ang): 4pco. 87 | 88 | 89 | Complex figures to serve as templates: 90 | 91 | BST, Base-stacking figure, (1.32 ang): 4pco. 92 | LG, Electron density map of nine sugar glycan (1.55 ang): 4dgr. 93 | NA, Sodium cation in major groove of 16-mer RNA (1.52 ang): 3nd4. 94 | 95 | 96 | Complex representations applied to any visible molecular object: 97 | 98 | AO, Make ambient occlusion image. Requires global view of protein. 99 | BU, Display biological unit. 100 | CB, Define color blind compatible coloring scheme. 101 | BW, Make black and white ribbon cartoon on white background. 102 | CSS, Color ribbon and cartoons by secondary structure: red, green and yellow. 103 | CBSS, Color ribbon and cartoons with colorblind friendly colors. 104 | CR, Make colored filled-ring cartoon of nucleic acids.. 105 | FR, Make filled-ring cartoon of nucleic acids. 106 | SE, Make SAXS envelope from a bead model. 107 | 108 | Type the alias name to execute the commands. The names are case sensitive. 109 | 110 | Type 'help ' (e.g., help T4L) for a description of the 111 | alias and for two sets of commands. The first set of commands has 112 | line breaks for easy selection single lines of commands. The second 113 | set of commands is one one line for easy copying and pasting of the 114 | entire horizontal script. The commands can be copied from the 115 | command history window and pasted onto the command line for code 116 | reuse. Some aliases require additional scripts. 117 | 118 | Type 'SA' to refresh the list of aliases. 119 | 120 | Type 'help rline' to see commands for moving cursor on the command line. 121 | 122 | ''' 123 | print(SA.__doc__) 124 | cmd.extend('SA',SA) 125 | 126 | 127 | def T4L(): 128 | ''' 129 | DESCRIPTION 130 | 131 | WT T4 lysozyme as ribbon diagram (1.08 Ang): 3FA0. 132 | 133 | USAGE 134 | 135 | Type 'T4L' to activate. Type 'help T4L' to see this documentation 136 | printed to the command history window. Select from the command 137 | history individual lines of code to build a new script. Select the 138 | hortizontal script at the bottom if retaining most of the commands 139 | in your new script. Copy and paste onto the command line below. 140 | Works only with the command line immediately under the command 141 | history window at the top of the gui. 142 | 143 | The commands with linebreaks: 144 | 145 | delete all; 146 | fetch 3fa0,type=pdb,async=0; 147 | orient; 148 | turn z,-90; 149 | turn y,-5; 150 | turn x,10; 151 | hide everything; 152 | bg_color white; 153 | show cartoon; 154 | color red, ss H; 155 | color yellow, ss S; 156 | color green, ss L+; 157 | set_view (-0.18,-0.69,-0.7,0.98,-0.17,-0.09,-0.06,-0.7,0.71,0.0,0.0,-165.67,34.77,11.27,9.52,132.07,199.27,-20.0); 158 | ray 1500,1600; 159 | 160 | The commands without linebreaks: 161 | 162 | delete all;fetch 3fa0,type=pdb,async=0;orient;turn z,-90;turn y,-5;turn x,10; hide everything; bg_color white;show cartoon;color red, ss H;color yellow, ss S;color green, ss L+;set_view (-0.18,-0.69,-0.7,0.98,-0.17,-0.09,-0.06,-0.7,0.71,0.0,0.0,-165.67,34.77,11.27,9.52,132.07,199.27,-20.0); ray 1500,1600; 163 | 164 | ''' 165 | cmd.reinitialize() 166 | cmd.fetch('3fa0', type='pdb', async='0') 167 | cmd.orient() 168 | cmd.turn('z', '-90') 169 | cmd.turn('y', '-5') 170 | cmd.turn('x', '10') 171 | cmd.hide('everything') 172 | cmd.bg_color('white') 173 | cmd.show('cartoon') 174 | cmd.color('red', 'ss H') 175 | cmd.color('yellow', 'ss S') 176 | cmd.color('green', 'ss L+') 177 | cmd.set_view('(-0.18,-0.69,-0.7,0.98,-0.17,-0.09,-0.06,-0.7,0.71,0.0,0.0,-165.67,34.77,11.27,9.52,132.07,199.27,-20.0)') 178 | cmd.ray('1500', '1600') 179 | cmd.extend('T4L',T4L) 180 | 181 | 182 | def U8(): 183 | ''' 184 | DESCRIPTION 185 | 186 | 16-mer dsRNA with 8 contiguous Us. U-helix RNA (1.37 Ang): 3nd3. 187 | Has one strand in the asymmetric unit. Uses quat.py to generate 188 | the second strand. Cartoon with filled rings and bases cartoon. 189 | 190 | USAGE 191 | 192 | Type 'U8' to activate. Type 'help U8' to see this documentation 193 | printed to the command history window. Select from the command 194 | history individual lines of code to build a new script. Select the 195 | hortizontal script at the bottom if retaining most of the commands 196 | in your new script. Copy and paste onto the command line below. 197 | Works only with the command line immediately under the command 198 | history window at the top of the gui. 199 | 200 | The commands with linebreaks: 201 | 202 | delete all; 203 | fetch 3nd3,type=pdb,async=0; 204 | run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py; 205 | quat 3nd3; 206 | hide everything; 207 | bg_color white; 208 | show sticks; 209 | set cartoon_ring_mode, 3; 210 | set cartoon_ring_finder, 1; 211 | set cartoon_ladder_mode, 1; 212 | set cartoon_nucleic_acid_mode, 4; 213 | set cartoon_ring_transparency, 0.5; 214 | as cartoon; 215 | set_view (-1.0,-0.03,0.06,-0.06,0.01,-1.0,0.04,-1.0,-0.01,-0.09,-0.02,-168.02,7.85,15.56,-0.21,137.38,199.33,-20.0);draw; 216 | 217 | The commands without linebreaks: 218 | 219 | delete all;fetch 3nd3,type=pdb,async=0;run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py;quat 3nd3;hide everything;bg_color white; show sticks;set cartoon_ring_mode, 3;set cartoon_ring_finder, 1;set cartoon_ladder_mode, 1;set cartoon_nucleic_acid_mode, 4;set cartoon_ring_transparency, 0.5;as cartoon;set_view (-1.0,-0.03,0.06,-0.06,0.01,-1.0,0.04,-1.0,-0.01,-0.09,-0.02,-168.02,7.85,15.56,-0.21,137.38,199.33,-20.0);draw; 220 | 221 | ''' 222 | 223 | cmd.reinitialize() 224 | cmd.fetch('3nd3', type='pdb', async='0') 225 | cmd.do('run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py') 226 | cmd.do('quat 3nd3') 227 | cmd.hide('everything') 228 | cmd.bg_color('white') 229 | cmd.show('sticks') 230 | cmd.set('cartoon_ring_mode', '3') 231 | cmd.set('cartoon_ring_finder', '1') 232 | cmd.set('cartoon_ladder_mode', '1') 233 | cmd.set('cartoon_nucleic_acid_mode', '4') 234 | cmd.set('cartoon_ring_transparency', '0.5') 235 | cmd.show_as('cartoon') 236 | cmd.set_view('(-1.0,-0.03,0.06,-0.06,0.01,-1.0,0.04,-1.0,-0.01,-0.09,-0.02,-168.02,7.85,15.56,-0.21,137.38,199.33,-20.0)') 237 | cmd.draw() 238 | cmd.extend('U8',U8) 239 | 240 | 241 | def WC8(): 242 | ''' 243 | DESCRIPTION 244 | 245 | 16-mer dsRNA, Watson-Crick helix RNA. 1.55 Angstrom 246 | resolution: 3nd4. Has one strand in the asymmetric unit. 247 | Needs quat.py to generate the second strand. Use the 248 | BU alias. Cartoon with filled rings and bases cartoon. 249 | 250 | 251 | USAGE 252 | 253 | Type 'WC8' to activate. Type 'help WC8' to see this documentation 254 | printed to the command history window. Select from the command 255 | history individual lines of code to build a new script. Select the 256 | hortizontal script at the bottom if retaining most of the commands 257 | in your new script. Copy and paste onto the command line below. 258 | Works only with the command line immediately under the command 259 | history window at the top of the gui. 260 | 261 | The commands with linebreaks: 262 | 263 | delete all; 264 | fetch 3nd4,type=pdb,async=0; 265 | hide everything; 266 | run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py; 267 | quat 3nd4; 268 | bg_color white; 269 | show sticks; 270 | set stick_radius, 0.12; 271 | set nb_spheres_size, 0.25; 272 | show nb_spheres; 273 | set stick_ball, on; 274 | set stick_ball_ratio, 1.8; 275 | set_view (-0.99,-0.03,0.17,-0.18,0.02,-0.98,0.03,-1.0,-0.03,0.0,0.0,-169.97,8.1,15.62,-1.69,139.24,200.7,-20.0); 276 | hide everything,name H*; 277 | rock 278 | 279 | The commands without linebreaks: 280 | 281 | delete all; fetch 3nd4,type=pdb,async=0;hide everything; run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py; quat 3nd4;bg_color white; show sticks; set stick_radius, 0.12; set nb_spheres_size, 0.25; show nb_spheres; set stick_ball, on; set stick_ball_ratio, 1.8;set_view (-0.99,-0.03,0.17,-0.18,0.02,-0.98,0.03,-1.0,-0.03,0.0,0.0,-169.97,8.1,15.62,-1.69,139.24,200.7,-20.0);hide everything, name H*;rock 282 | 283 | ''' 284 | cmd.reinitialize() 285 | cmd.fetch('3nd4', type='pdb', async='0') 286 | cmd.remove('name H*') 287 | cmd.hide('everything') 288 | cmd.do('run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py') 289 | cmd.do('quat 3nd4') 290 | cmd.bg_color('white') 291 | cmd.do('show stick') 292 | cmd.do('set stick_radius, 0.12') 293 | cmd.do('set nb_spheres_size, 0.25') 294 | cmd.do('show nb_spheres') 295 | cmd.do('set stick_ball, on') 296 | cmd.do('set stick_ball_ratio, 1.8') 297 | cmd.set_view('(-0.96,-0.03,0.3,-0.31,0.02,-0.95,0.03,-1.0,-0.03,0.0,0.0,-231.24,8.16,15.68,-1.66,200.47,262.01,-20.0)') 298 | cmd.rock() 299 | cmd.extend('WC8',WC8) 300 | 301 | 302 | def N9(): 303 | ''' 304 | DESCRIPTION 305 | 306 | Influenza N9 neuraminidase at 1.55 Angstrom resolution, PDB code 307 | 4dgr. The biological unit has four copies of the asymmetric unit. 308 | View is down the four-fold axis. Requires the quat.py script by 309 | Thomas Holder and available at the PyMOL Wiki page. Store quat.py 310 | in ~/Scripts/PyMOLScripts. 311 | 312 | USAGE 313 | 314 | Type 'N9' to activate. Type 'help N9' to see this documentation 315 | printed to the command history window. Select from the command 316 | history individual lines of code to build a new script. Select the 317 | hortizontal script at the bottom if retaining most of the commands 318 | in your new script. Copy and paste onto the command line below. 319 | Works only with the command line immediately under the command 320 | history window at the top of the gui. 321 | 322 | The commands with linebreaks: 323 | 324 | delete all; 325 | fetch 4dgr, type=pdb, async=0; 326 | run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py; 327 | quat 4dgr; 328 | as cartoon; 329 | bg_color white; 330 | color red, 4dgr_1 and ss H; 331 | color yellow,4dgr_1 and ss S; 332 | color green, 4dgr_1 and ss L+; 333 | color cyan, (not 4dgr_1 and ss H); 334 | color magenta, (not 4dgr_1 and ss S); 335 | color orange, (not 4dgr_1 and ss L+); 336 | set_view (0.98,-0.22,0.01,0.22,0.98,0.02,-0.01,-0.02,1.0,-0.0,0.0,-323.44,1.46,5.33,56.19,274.72,372.15,-20.0); 337 | draw 338 | 339 | The commands without linebreaks: 340 | 341 | delete all;fetch 4dgr, type=pdb, async=0;run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py; quat 4dgr;as cartoon; bg_color white;color red, 4dgr_1 and ss H;color yellow,4dgr_1 and ss S;color green, 4dgr_1 and ss L+;color cyan, (not 4dgr_1 and ss H);color magenta, (not 4dgr_1 and ss S);color orange, (not 4dgr_1 and ss L+);set_view (0.98,-0.22,0.01,0.22,0.98,0.02,-0.01,-0.02,1.0,-0.0,0.0,-323.44,1.46,5.33,56.19,274.72,372.15,-20.0); draw 342 | 343 | ''' 344 | cmd.reinitialize() 345 | cmd.fetch('4dgr', type='pdb', async='0') 346 | cmd.do('run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py') 347 | cmd.do('quat 4dgr') 348 | cmd.show_as('cartoon') 349 | cmd.bg_color('white') 350 | cmd.color('red', '4dgr_1 and ss H') 351 | cmd.color('yellow', '4dgr_1 and ss S') 352 | cmd.color('green', '4dgr_1 and ss L+') 353 | cmd.color('cyan', '(not 4dgr_1 and ss H)') 354 | cmd.color('magenta', '(not 4dgr_1 and ss S)') 355 | cmd.color('orange', '(not 4dgr_1 and ss L+)') 356 | cmd.set_view('(0.98,-0.22,0.01,0.22,0.98,0.02,-0.01,-0.02,1.0,-0.0,0.0,-323.44,1.46,5.33,56.19,274.72,372.15,-20.0)') 357 | cmd.draw() 358 | cmd.extend('N9',N9) 359 | 360 | 361 | def GGT(): 362 | ''' 363 | DESCRIPTION 364 | 365 | WT human gamma glutamyl transpeptidase at 1.67 Angstrom 366 | resolution as cartoon. PDB Code 4gdx. 367 | 368 | USAGE 369 | 370 | Type 'GGT' to activate. Type 'help GGT' to see this documentation 371 | printed to the command history window. Select from the command 372 | history individual lines of code to build a new script. Select the 373 | hortizontal script at the bottom if retaining most of the commands 374 | in your new script. Copy and paste onto the command line below. 375 | Works only with the command line immediately under the command 376 | history window at the top of the gui. 377 | 378 | The commands with linebreaks: 379 | 380 | delete all; 381 | fetch 4gdx, type=pdb, async=0; 382 | remove name H*; 383 | as cartoon; 384 | bg_color white; 385 | hide (name c+o+n); 386 | set cartoon_side_chain_helper, on;color red, 4gdx and ss H; 387 | color yellow,4gdx and ss S;color green,4gdx and ss L+; 388 | select ASNNAG, resn NAG or resi 95 or i. 120 or i. 230 or 389 | i. 266 or i. 344 or i. 511 or i. 381; 390 | color red, elem o and ASNNAG; 391 | color blue, elem n and ASNNAG; 392 | color yellow, elem c and ASNNAG; 393 | show sticks,ASNNAG; 394 | disable ASNNAG; 395 | set_view (0.55,-0.83,0.07,0.5,0.26,-0.82,0.66,0.49,0.56,0.0,0.0,-197.16,-22.42,-22.69,-12.01,155.44,238.88,-20.0); 396 | draw 397 | 398 | The commands without linebreaks: 399 | 400 | delete all;fetch 4gdx, type=pdb, async=0;remove name H*;as cartoon;bg_color white; hide (name c+o+n);set cartoon_side_chain_helper, on;color red, 4gdx and ss H; color yellow,4gdx and ss S;color green,4gdx and ss L+; select ASNNAG,resn NAG or resi 95 or i. 120 or i. 230 or i. 266 or i. 344 ori. 511 or i. 381; color red, elem o and ASNNAG; color blue, elem n and ASNNAG;color yellow, elem c and ASNNAG;show sticks,ASNNAG;disable ASNNAG; set_view(0.55,-0.83,0.07,0.5,0.26,-0.82,0.66,0.49,0.56,0.0,0.0,-197.16,-22.42,-22.69,-12.01,155.44,238.88,-20.0); draw 401 | 402 | ''' 403 | cmd.reinitialize() 404 | cmd.fetch('4gdx', type='pdb', async='0') 405 | cmd.remove('name H*') 406 | cmd.show_as('cartoon') 407 | cmd.bg_color('white') 408 | cmd.hide('(name c+o+n)') 409 | cmd.set('cartoon_side_chain_helper', 'on') 410 | cmd.color('red', '4gdx and ss H') 411 | cmd.color('yellow', '4gdx and ss S') 412 | cmd.color('green', '4gdx and ss L+') 413 | cmd.select('ASNNAG', 'resn NAG or resi 95 or i. 120 or i. 230 or i. 266 or i. 344 or i. 511 or i. 381') 414 | cmd.color('red', 'elem o and ASNNAG') 415 | cmd.color('blue', 'elem n and ASNNAG') 416 | cmd.color('yellow', 'elem c and ASNNAG') 417 | cmd.show('sticks', 'ASNNAG') 418 | cmd.disable('ASNNAG') 419 | cmd.set_view('(0.55,-0.83,0.07,0.5,0.26,-0.82,0.66,0.49,0.56,0.0,0.0,-197.16,-22.42,-22.69,-12.01,155.44,238.88,-20.0)') 420 | cmd.draw() 421 | cmd.extend('GGT',GGT) 422 | 423 | 424 | def GU(): 425 | ''' 426 | DESCRIPTION 427 | 428 | 10-mer dsRNA with 8 contiguous Us. U-helix RNA. 429 | 1.32 Angstrom resolution: 4PCO. Has five strands in 430 | the asymmetric unit. Deleted chain E and cobalt 431 | hexammine 102. Cartoon with filled rings and 432 | bases cartoon. 433 | 434 | 435 | USAGE 436 | 437 | Type 'GU' to activate. Type 'help GU' to see this documentation 438 | printed to the command history window. Select from the command 439 | history individual lines of code to build a new script. Select the 440 | hortizontal script at the bottom if retaining most of the commands 441 | in your new script. Copy and paste onto the command line below. 442 | Works only with the command line immediately under the command 443 | history window at the top of the gui. 444 | 445 | The commands with linebreaks: 446 | 447 | delete all; 448 | fetch 4PCO,type=pdb,async=0; 449 | hide everything; 450 | bg_color white; 451 | cartoon oval; 452 | set cartoon_ring_mode, 3; 453 | set cartoon_nucleic_acid_color, blue; 454 | select rna_A, resn A; 455 | select rna_C, resn C; 456 | select rna_G, resn G; 457 | select rna_U, resn U; 458 | color yellow, rna_A; 459 | color red, rna_C; 460 | color gray40, rna_G; 461 | color palecyan, rna_U; 462 | as cartoon; 463 | disable rna_U; 464 | set stick_radius, 0.12; 465 | set nb_spheres_size, 0.3; 466 | show nb_spheres; 467 | set stick_ball, on; 468 | set stick_ball_ratio, 1.8; 469 | show sticks, resn NCO; 470 | show spheres, name Cl; 471 | set_view (0.34,-0.81,0.48,0.89,0.11, 472 | -0.45,0.31,0.58,0.76,-0.0,0.0,-196.36,-9.82,6.76,15.84,159.01, 473 | 233.71,-20.0); 474 | draw 475 | 476 | The commands without linebreaks: 477 | 478 | delete all;fetch 4PCO,type=pdb,async=0;hide everything;bg_color white; cartoon oval;set cartoon_ring_mode, 3;set cartoon_nucleic_acid_color, blue;select rna_A, resn A;select rna_C,resn C;select rna_G, resn G;select rna_U, resn U;color yellow, rna_A; color red, rna_C;color gray40, rna_G; color palecyan, rna_U;as cartoon;disable rna_U; set stick_radius, 0.12;set nb_spheres_size, 0.3; show nb_spheres; set stick_ball, on;set stick_ball_ratio, 1.8; show sticks, resn NCO;show spheres, name Cl; set_view (0.34,-0.81,0.48,0.89,0.11,-0.45,0.31,0.58,0.76,-0.0,0.0,-196.36,-9.82,6.76,15.84,159.01,233.71,-20.0);draw 479 | 480 | ''' 481 | cmd.reinitialize(); 482 | cmd.fetch('4PCO', type='pdb', async='0') 483 | cmd.hide('everything') 484 | cmd.bg_color('white') 485 | cmd.cartoon('oval') 486 | cmd.set('cartoon_ring_mode', '3') 487 | cmd.set('cartoon_nucleic_acid_color', 'blue') 488 | cmd.select('rna_A', 'resn A') 489 | cmd.select('rna_C', 'resn C') 490 | cmd.select('rna_G', 'resn G') 491 | cmd.select('rna_U', 'resn U') 492 | cmd.color('yellow', 'rna_A') 493 | cmd.color('red', 'rna_C') 494 | cmd.color('gray40', 'rna_G') 495 | cmd.color('palecyan', 'rna_U') 496 | cmd.show_as('cartoon') 497 | cmd.disable('rna_U') 498 | cmd.set('stick_radius', '0.12') 499 | cmd.set('nb_spheres_size', '0.3') 500 | cmd.show('nb_spheres') 501 | cmd.set('stick_ball', 'on') 502 | cmd.set('stick_ball_ratio', '1.8') 503 | cmd.show('sticks', 'resn NCO') 504 | cmd.show('spheres', 'name Cl') 505 | cmd.set_view('(0.34,-0.81, 0.48,0.89,0.11,-0.45,0.31,0.58,0.76,-0.0,0.0,-196.36,-9.82,6.76,15.84,159.01,233.71,-20.0)') 506 | cmd.draw() 507 | cmd.extend('GU',GU) 508 | 509 | 510 | #######Commands to display complex scenes. ############# 511 | 512 | def BST(): 513 | ''' 514 | DESCRIPTION 515 | 516 | G2G3/U9U8 base step , PDB code 4PCO. 517 | From the 1.32 Angstrom resolution structure 518 | of the RNA decamer with 8 GU base pairs. 519 | 520 | USAGE 521 | 522 | Type 'BST' to execute. Type 'help BST' to see this documentation 523 | printed to the command history window. Select from the command 524 | history individual lines of code to build a new script. Select the 525 | hortizontal script at the bottom if retaining most of the commands 526 | in your new script. Copy and paste onto the command line below. 527 | Works only with the command line immediately under the command 528 | history window at the top of the gui. 529 | 530 | The commands with linebreaks: 531 | 532 | delete all; 533 | fetch 4PCO, type=pdb, async=0; 534 | select G2G3, ( ((resi 2 or resi 3) and chain A) or ((resi 8 or resi 9) and chain B)); 535 | remove not G2G3; 536 | bg_color white; 537 | show sticks; 538 | set stick_radius=0.14; 539 | set stick_ball, on; 540 | set stick_ball_ratio,1.9; 541 | set_view 542 | (-0.75,0.09,0.66,-0.2,0.92,-0.35,-0.64,-0.39,-0.67,-0.0,-0.0,-43.7,7.24,9.55,11.78,29.46,57.91,-20.0); 543 | remove name H*; 544 | select carbon1, element C and (resi 3 or resi 8) 545 | # select lower base pair; 546 | select carbon2, element C and (resi 2 or resi 9) 547 | #select upper base pair; 548 | color gray70, carbon1; 549 | color gray10, carbon2; 550 | show sticks; 551 | space cmyk; 552 | distance hbond1, /4PCO//B/U`9/N3,/4PCO//A/G`2/O6; 553 | distance hbond2, /4PCO//B/U`9/O2,/4PCO//A/G`2/N1; 554 | distance hbond3, /4PCO//A/U`3/N3,/4PCO//B/G`8/O6; 555 | distance hbond4, /4PCO//A/U`3/O2,/4PCO//B/G`8/N1; 556 | color black, hbond1; 557 | color black, hbond2; 558 | color gray70, hbond3; 559 | color gray70, hbond4; 560 | show nb_spheres; 561 | set nb_spheres_size, 0.35; 562 | hide labels; 563 | ray 1600,1000; 564 | png 4PCO.png 565 | 566 | Commands without linebreaks: 567 | 568 | delete all;fetch 4PCO, type=pdb, async=0;select G2G3, ( ((resi 2 or resi 3) and chain A) or ((resi 8 or resi 9) and chain B));remove not G2G3;bg_color white;show sticks;set stick_radius=0.14;set stick_ball, on;set stick_ball_ratio,1.9;set_view (-0.75,0.09,0.66,-0.2,0.92,-0.35,-0.64,-0.39,-0.67,-0.0,-0.0,-43.7,7. 24,9.55,11.78,29.46,57.91,-20.0);remove name H*;select carbon1, element C and (resi 3 or resi 8);select carbon2, element C and (resi 2 or resi 9);color gray70, carbon1;color gray10, carbon2;show sticks;space cmyk;distance hbond1, /4PCO//B/U`9/N3,/4PCO//A/G`2/O6;distance hbond2, /4PCO//B/U`9/O2,/4PCO//A/G`2/N1;distance hbond3, /4PCO//A/U`3/N3,/4PCO//B/G`8/O6;distance hbond4, /4PCO//A/U`3/O2,/4PCO//B/G`8/N1;color black, hbond1;color black, hbond2;color gray70, hbond3;color gray70, hbond4;show nb_spheres;set nb_spheres_size, 0.35;hide labels;ray 1600,1000;png 4PCO.png 569 | 570 | ''' 571 | cmd.reinitialize() 572 | cmd.fetch('4PCO', type='pdb', async='0') 573 | cmd.select('G2G3', '( ((resi 2 or resi 3) and chain A)or ((resi 8 or resi 9) and chain B) )') 574 | cmd.remove('not G2G3') 575 | cmd.bg_color('white') 576 | cmd.set('stick_radius', '0.14') 577 | cmd.set('stick_ball', 'on') 578 | cmd.set('stick_ball_ratio', '1.9') 579 | cmd.set_view('(-0.75,0.09,0.66,-0.2,0.92,-0.35,-0.64,-0.39,-0.67,-0.0,-0.0,-43.7,7.24,9.55,11.78,29.46,57.91,-20.0)') 580 | cmd.remove('name H*') 581 | cmd.select('carbon1', 'element C and (resi 3 or resi 8)') 582 | cmd.select('carbon2', 'element C and (resi 2 or resi 9)') 583 | cmd.color('gray70', 'carbon1') 584 | cmd.color('gray10', 'carbon2') 585 | cmd.show('sticks') 586 | cmd.space('cmyk') 587 | cmd.distance('hbond1', '/4PCO//B/U`9/N3', '/4PCO//A/G`2/O6') 588 | cmd.distance('hbond2', '/4PCO//B/U`9/O2', '/4PCO//A/G`2/N1') 589 | cmd.distance('hbond3', '/4PCO//A/U`3/N3', '/4PCO//B/G`8/O6') 590 | cmd.distance('hbond4', '/4PCO//A/U`3/O2', '/4PCO//B/G`8/N1') 591 | cmd.color('black', 'hbond1') 592 | cmd.color('black', 'hbond2') 593 | cmd.color('gray70', 'hbond3') 594 | cmd.color('gray70', 'hbond4') 595 | cmd.show('nb_spheres') 596 | cmd.set('nb_spheres_size', '0.35') 597 | cmd.hide('labels') 598 | cmd.ray('1600', '1000') 599 | cmd.png('4PCO.png') 600 | cmd.extend('BST',BST) 601 | 602 | 603 | def LG(): 604 | ''' 605 | DESCRIPTION 606 | 607 | Nine sugar glycan in influenza N9 neuraminidase at 608 | 1.55 Angstrom resolution, PDB code 4dgr. 609 | The electron density map is contoured at 1.0 sigma. 610 | 39 commands were used to make this figure. 611 | 612 | USAGE 613 | 614 | Type 'LG' to execute. Type 'help LG' to see this documentation 615 | printed to the command history window. Select from the command 616 | history individual lines of code to build a new script. Select the 617 | hortizontal script at the bottom if retaining most of the commands 618 | in your new script. Copy and paste onto the command line below. 619 | Works only with the command line immediately under the command 620 | history window at the top of the gui. 621 | 622 | The commands with linebreaks: 623 | 624 | delete all; 625 | fetch 4dgr, async=0; 626 | fetch 4dgr, type=2fofc,async=0; 627 | select LongGlycan, resi 469:477; 628 | orient LongGlycan; 629 | remove not LongGlycan; 630 | remove name H*; 631 | isomesh 2fofcmap, 4dgr_2fofc, 1, LongGlycan, carve = 1.8; 632 | color density, 2fofcmap; 633 | show sticks; 634 | show spheres; 635 | set stick_radius, .07; 636 | set sphere_scale, .19; 637 | set sphere_scale, .13, elem H; 638 | set bg_rgb=[1, 1, 1]; 639 | set stick_quality, 50; 640 | set sphere_quality, 4; 641 | color gray85, elem C; 642 | color red, elem O; 643 | color slate, elem N; 644 | color gray98, elem H; 645 | set stick_color, gray50; 646 | set ray_trace_mode, 1; 647 | set ray_texture, 2; 648 | set antialias, 3; 649 | set ambient, 0.5; 650 | set spec_count, 5; 651 | set shininess, 50; 652 | set specular, 1; 653 | set reflect, .1; 654 | set dash_gap, 0; 655 | set dash_color, black; 656 | set dash_gap, .15; 657 | set dash_length, .05; 658 | set dash_round_ends, 0; 659 | set dash_radius, .05; 660 | set_view (0.34,-0.72,0.61,0.8,0.56,0.22,-0.51,0.4,0.77,0.0,0.0,-81.31,44.64,-9.02,58.62,65.34,97.28,-20.0); 661 | preset.ball_and_stick("all",mode=1); 662 | draw 663 | 664 | Commands without linebreaks: 665 | 666 | delete all;fetch 4dgr, async=0;fetch 4dgr, type=2fofc, async=0;select LongGlycan, resi 469:477;orient LongGlycan;remove not LongGlycan;remove name H*;isomesh 2fofcmap, 4dgr_2fofc, 1, LongGlycan, carve = 1.8;color density, 2fofcmap; show sticks;show spheres;set stick_radius, .07;set sphere_scale, .19;set sphere_scale, .13, elem H;set bg_rgb=[1, 1, 1];set stick_quality, 50;set sphere_quality, 4;color gray85, elem C;color red, elem O;color slate, elem N;color gray98, elem H;set stick_color, gray50;set ray_trace_mode, 1;set ray_texture, 2;set antialias, 3;set ambient, 0.5;set spec_count, 5;set shininess, 50;set specular, 1;set reflect, .1;set dash_gap, 0;set dash_color, black;set dash_gap, .15;set dash_length, .05;set dash_round_ends, 0;set dash_radius, .05;set_view (0.34,-0.72,0.61,0.8,0.56,0.22,-0.51,0.4,0.77,0.0,0.0,-81.31,44.64,-9.02,58.62,65.34,97.28,-20.0);preset.ball_and_stick("all",mode=1);draw 667 | 668 | ''' 669 | cmd.reinitialize() 670 | cmd.fetch('4dgr', async='0') 671 | cmd.fetch('4dgr', type='2fofc', async='0') 672 | cmd.select('LongGlycan', 'resi 469:477') 673 | cmd.orient('LongGlycan') 674 | cmd.remove('not LongGlycan') 675 | cmd.remove('name H*') 676 | cmd.isomesh('2fofcmap', '4dgr_2fofc', '1', 'LongGlycan', carve ='1.8') 677 | cmd.color('density', '2fofcmap') 678 | cmd.show('sticks') 679 | cmd.show('spheres') 680 | cmd.set('stick_radius', '.07') 681 | cmd.set('sphere_scale', '.19') 682 | cmd.set('sphere_scale', '.13', 'elem H') 683 | cmd.set('bg_rgb', '[1, 1, 1]') 684 | cmd.set('stick_quality', '50') 685 | cmd.set('sphere_quality', '4') 686 | cmd.color('gray85', 'elem C') 687 | cmd.color('red', 'elem O') 688 | cmd.color('slate', 'elem N') 689 | cmd.color('gray98', 'elem H') 690 | cmd.set('stick_color', 'gray50') 691 | cmd.set('ray_trace_mode', '1') 692 | cmd.set('ray_texture', '2') 693 | cmd.set('antialias', '3') 694 | cmd.set('ambient', '0.5') 695 | cmd.set('spec_count', '5') 696 | cmd.set('shininess', '50') 697 | cmd.set('specular', '1') 698 | cmd.set('reflect', '.1') 699 | cmd.set('dash_gap', '0') 700 | cmd.set('dash_color', 'black') 701 | cmd.set('dash_gap', '.15') 702 | cmd.set('dash_length', '.05') 703 | cmd.set('dash_round_ends', '0') 704 | cmd.set('dash_radius', '.05') 705 | cmd.set_view('(0.34,-0.72,0.61,0.8,0.56,0.22,-0.51,0.4,0.77,0.0,0.0,-81.31,44.64,-9.02,58.62,65.34,97.28,-20.0)') 706 | preset.ball_and_stick("all",mode=1); 707 | cmd.draw() 708 | cmd.extend('LG',LG) 709 | 710 | 711 | def NA(): 712 | ''' 713 | DESCRIPTION 714 | 715 | Hydrated sodium cation bound in major groove of a 716 | 16-mer RNA of Watson-Crick base pairs. 717 | The sodium is bound to the N7 nitrogen atom of 718 | Adenine 3 at 1.55 Angstrom resolution, PDB code 3nd4. 719 | 57 commands were used to make this figure. 720 | 721 | More than one label in a horizontal script is not 722 | allowed. This one label has to be at the end of the line. 723 | Labels can be imported from a Labels.pml file. 724 | Store the label commands one per row in this file. 725 | Import the file with the @Labels.pml command. 726 | Include the path to the file if the labels file is not 727 | in the current working directory of PyMOL. 728 | 729 | USAGE 730 | 731 | Type 'NA' to execute. Type 'help NA' to see this documentation 732 | printed to the command history window. Select from the command 733 | history individual lines of code to build a new script. Select the 734 | hortizontal script at the bottom if retaining most of the commands 735 | in your new script. Copy and paste onto the command line below. 736 | Works only with the command line immediately under the command 737 | history window at the top of the gui. 738 | 739 | The commands with linebreaks: 740 | 741 | delete all; 742 | viewport 900,600; 743 | fetch 3nd4, type=pdb, async=0; 744 | run ~/Scripts/PyMOLScripts/quat.py; 745 | quat 3nd4; 746 | show sticks; 747 | set stick_radius=0.125; 748 | hide everything, name H*; 749 | bg_color white; 750 | create coorCov, (3nd4_1 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7))); 751 | bond (coorCov//A/NA`19/NA),(coorCov//A/A`3/N7); 752 | bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`119/O); 753 | bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`219/O); 754 | bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`319/O); 755 | bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`419/O); 756 | bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`519/O); 757 | distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 519); 758 | distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 419); 759 | distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 119); 760 | distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 319); 761 | distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 219); 762 | show nb_spheres; 763 | set nb_spheres_size, .35; 764 | distance hbond1,/3nd4_1/1/A/HOH`119/O, /3nd4_1/1/A/A`3/OP2; 765 | distance hbond2,/3nd4_1/1/A/HOH`319/O,/3nd4_1/1/A/A`3/OP2; 766 | distance hbond3,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/HOH`119/O; 767 | distance hbond4,/3nd4_1/1/A/G`4/N7,/3nd4_1/1/A/HOH`91/O; 768 | distance hbond5,/3nd4_1/1/A/G`4/O6, /3nd4_1/1/A/HOH`419/O; 769 | distance hbond6,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2; 770 | distance hbond7,/3nd4_1/1/A/HOH`319/O,/3nd4_1/1/A/G`2/OP2; 771 | distance hbond9,/3nd4_1/1/A/HOH`419/O,/3nd4_2/2/A/HOH`74/O; 772 | distance hbond10,/3nd4_2/2/A/C`15/O2,/3nd4_1/1/A/G`2/N2; 773 | distance hbond11, /3nd4_2/2/A/C`15/N3,/3nd4_1/1/A/G`2/N1; 774 | distance hbond12,/3nd4_2/2/A/C`15/N4,/3nd4_1/1/A/G`2/O6; 775 | distance hbond13, /3nd4_2/2/A/U`14/N3,/3nd4_1/1/A/A`3/N1; 776 | distance hbond14,3nd4_2/2/A/U`14/O4,/3nd4_1/1/A/A`3/N6; 777 | distance hbond15, /3nd4_2/2/A/C`13/N4,/3nd4_1/1/A/G`4/O6; 778 | distance hbond16,/3nd4_2/2/A/C`13/N3, /3nd4_1/1/A/G`4/N1; 779 | distance hbond17, /3nd4_1/1/A/G`4/N2,/3nd4_2/2/A/C`13/O2; 780 | distance hbond18,/3nd4_1/1/A/G`2/N2,/3nd4_2/2/A/C`15/O2; 781 | distance hbond19,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2; 782 | set depth_cue=0; 783 | set ray_trace_fog=0; 784 | set dash_color, black; 785 | set label_font_id, 5; 786 | set label_size, 36; 787 | set label_position, (0.5, 1.0, 2.0); 788 | set label_color, black; 789 | set dash_gap, 0.2; 790 | set dash_width, 2.0; 791 | set dash_length, 0.2; 792 | set label_color, black; 793 | set dash_gap, 0.2; 794 | set dash_width, 2.0; 795 | set dash_length, 0.2; 796 | select carbon, element C; 797 | color yellow, carbon; 798 | disable carbon; 799 | set_view (-0.9,0.34,-0.26,0.33,0.18,-0.93,-0.27,-0.92,-0.28,-0.07,-0.23,-27.83,8.63,19.85,13.2,16.0,31.63,-20.0) 800 | 801 | The commands without linebreaks: 802 | 803 | delete all;viewport 900,600;fetch 3nd4, type=pdb,async=0;run ~/Scripts/PyMOLScripts/quat.py;quat 3nd4; show sticks;set stick_radius=0.125;hide everything, name H*;bg_color white;create coorCov, (3nd4_1 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)));bond (coorCov//A/NA`19/NA),(coorCov//A/A`3/N7); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`119/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`219/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`319/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`419/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`519/O);distance (3nd4_1 and chain Aand resi 19 and name NA), (3nd4_1 and chain A and resi 519);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 419);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 119);distance (3nd4_1 and chain A and resi 19 and name NA),(3nd4_1 and chain A and resi 319);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 219);show nb_spheres; set nb_spheres_size, .35;distance hbond1,/3nd4_1/1/A/HOH`119/O, /3nd4_1/1/A/A`3/OP2;distance hbond2,/3nd4_1/1/A/HOH`319/O, /3nd4_1/1/A/A`3/OP2;distance hbond3,/3nd4_1/1/A/HOH`91/O, /3nd4_1/1/A/HOH`119/O;distance hbond4,/3nd4_1/1/A/G`4/N7,/3nd4_1/1/A/HOH`91/O;distance hbond5,/3nd4_1/1/A/G`4/O6, /3nd4_1/1/A/HOH`419/O;distance hbond6,/3nd4_1/1/A/HOH`91/O, /3nd4_1/1/A/G`4/OP2;distance hbond7,/3nd4_1/1/A/HOH`319/O, /3nd4_1/1/A/G`2/OP2;distance hbond9,/3nd4_1/1/A/HOH`419/O,/3nd4_2/2/A/HOH`74/O;distance hbond10,/3nd4_2/2/A/C`15/O2,/3nd4_1/1/A/G`2/N2;distance hbond11, /3nd4_2/2/A/C`15/N3,/3nd4_1/1/A/G`2/N1;distance hbond12,/3nd4_2/2/A/C`15/N4,/3nd4_1/1/A/G`2/O6;distance hbond13, /3nd4_2/2/A/U`14/N3,/3nd4_1/1/A/A`3/N1;distance hbond14,3nd4_2/2/A/U`14/O4,/3nd4_1/1/A/A`3/N6;distance hbond15, /3nd4_2/2/A/C`13/N4,/3nd4_1/1/A/G`4/O6;distance hbond16,/3nd4_2/2/A/C`13/N3, /3nd4_1/1/A/G`4/N1;distance hbond17, /3nd4_1/1/A/G`4/N2,/3nd4_2/2/A/C`13/O2;distance hbond18,/3nd4_1/1/A/G`2/N2,/3nd4_2/2/A/C`15/O2;distance hbond19,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2;set depth_cue=0;set ray_trace_fog=0;set dash_color, black;set label_font_id, 5;set label_size, 36;set label_position, (0.5, 1.0, 2.0);set label_color, black;set dash_gap, 0.2;set dash_width, 2.0;set dash_length, 0.2;set label_color, black;set dash_gap, 0.2;set dash_width, 2.0;set dash_length, 0.2;select carbon, element C; color yellow, carbon;disable carbon;set_view (-0.9,0.34,-0.26,0.33,0.18,-0.93,-0.27,-0.92,-0.28,-0.07,-0.23,-27.83,8.63,19.85,13.2,16.0,31.63,-20.0); 804 | 805 | ''' 806 | cmd.reinitialize(); 807 | cmd.viewport('900','600'); 808 | cmd.fetch('3nd4', type='pdb', async='0'); 809 | cmd.do('run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py') 810 | cmd.do('quat 3nd4'); 811 | cmd.show('sticks'); 812 | cmd.set('stick_radius', '0.125'); 813 | cmd.hide('everything', 'name H*'); 814 | cmd.bg_color('white'); 815 | cmd.create('coorCov', '(3nd4_1 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)))'); 816 | cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/A`3/N7)'); 817 | cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/HOH`119/O)'); 818 | cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/HOH`219/O)'); 819 | cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/HOH`319/O)'); 820 | cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/HOH`419/O)'); 821 | cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/HOH`519/O)'); 822 | cmd.distance('(3nd4_1 and chain A and resi 19 and name NA)','(3nd4_1 and chain A and resi 519)'); 823 | cmd.distance('(3nd4_1 and chain A and resi 19 and name NA)','(3nd4_1 and chain A and resi 419)'); 824 | cmd.distance('(3nd4_1 and chain A and resi 19 and name NA)','(3nd4_1 and chain A and resi 119)'); 825 | cmd.distance('(3nd4_1 and chain A and resi 19 and name NA)','(3nd4_1 and chain A and resi 319)'); 826 | cmd.distance('(3nd4_1 and chain A and resi 19 and name NA)','(3nd4_1 and chain A and resi 219)'); 827 | cmd.show('nb_spheres'); 828 | cmd.set('nb_spheres_size', '.35'); 829 | cmd.distance('hbond1', '/3nd4_1/1/A/HOH`119/O', '/3nd4_1/1/A/A`3/OP2'); 830 | cmd.distance('hbond2', '/3nd4_1/1/A/HOH`319/O', '/3nd4_1/1/A/A`3/OP2'); 831 | cmd.distance('hbond3', '/3nd4_1/1/A/HOH`91/O', '/3nd4_1/1/A/HOH`119/O'); 832 | cmd.distance('hbond4', '/3nd4_1/1/A/G`4/N7', '/3nd4_1/1/A/HOH`91/O'); 833 | cmd.distance('hbond5', '/3nd4_1/1/A/G`4/O6', '/3nd4_1/1/A/HOH`419/O'); 834 | cmd.distance('hbond6', '/3nd4_1/1/A/HOH`91/O', '/3nd4_1/1/A/G`4/OP2'); 835 | cmd.distance('hbond7', '/3nd4_1/1/A/HOH`319/O', '/3nd4_1/1/A/G`2/OP2'); 836 | cmd.distance('hbond9', '/3nd4_1/1/A/HOH`419/O', '/3nd4_2/2/A/HOH`74/O'); 837 | cmd.distance('hbond10', '/3nd4_2/2/A/C`15/O2', '/3nd4_1/1/A/G`2/N2'); 838 | cmd.distance('hbond11', '/3nd4_2/2/A/C`15/N3', '/3nd4_1/1/A/G`2/N1'); 839 | cmd.distance('hbond12', '/3nd4_2/2/A/C`15/N4', '/3nd4_1/1/A/G`2/O6'); 840 | cmd.distance('hbond13', '/3nd4_2/2/A/U`14/N3', '/3nd4_1/1/A/A`3/N1'); 841 | cmd.distance('hbond14', '/3nd4_2/2/A/U`14/O4', '/3nd4_1/1/A/A`3/N6'); 842 | cmd.distance('hbond15', '/3nd4_2/2/A/C`13/N4', '/3nd4_1/1/A/G`4/O6'); 843 | cmd.distance('hbond16', '/3nd4_2/2/A/C`13/N3', '/3nd4_1/1/A/G`4/N1'); 844 | cmd.distance('hbond17', '/3nd4_1/1/A/G`4/N2', '/3nd4_2/2/A/C`13/O2'); 845 | cmd.distance('hbond18', '/3nd4_1/1/A/G`2/N2', '/3nd4_2/2/A/C`15/O2'); 846 | cmd.distance('hbond19', '/3nd4_1/1/A/HOH`91/O', '/3nd4_1/1/A/G`4/OP2'); 847 | cmd.set('depth_cue', '0'); 848 | cmd.set('ray_trace_fog', '0'); 849 | cmd.set('dash_color', 'black'); 850 | cmd.set('label_font_id', '5'); 851 | cmd.set('label_size', '36') 852 | cmd.set('label_position', '(0.5, 1.0,2.0)'); 853 | cmd.set('label_color', 'black'); 854 | cmd.set('dash_gap', '0.2'); 855 | cmd.set('dash_width', '2.0'); 856 | cmd.set('dash_length', '0.2'); 857 | cmd.set('label_color', 'black'); 858 | cmd.set('dash_gap', '0.2'); 859 | cmd.set('dash_width', '2.0'); 860 | cmd.set('dash_length', '0.2'); 861 | cmd.select('carbon', 'element C'); 862 | cmd.color('yellow', 'carbon'); 863 | cmd.disable('carbon'); 864 | cmd.set_view('-0.9,0.34,-0.26,0.33,0.18,-0.93,-0.27,-0.92,-0.28,-0.07,-0.23,-27.83,8.63,19.85,13.2,16.0,31.63,-20.0'); 865 | cmd.extend('NA',NA) 866 | 867 | 868 | 869 | # ##### Commands applicable to displayed molecules. ########## 870 | def AO(): 871 | ''' 872 | DESCRIPTION 873 | 874 | Commands to make ambient occlusion image like those in Qutemole. 875 | 876 | 877 | USAGE 878 | 879 | Type 'AO' to execute. Type 'help AO' to see this documentation 880 | printed to the command history window. Select from the command 881 | history individual lines of code to build a new script. Select the 882 | hortizontal script at the bottom if retaining most of the commands 883 | in your new script. Copy and paste onto the comand line below. 884 | Works only with the command line immediately under the command 885 | history window at the top of the gui. 886 | 887 | The commands with linebreaks: 888 | 889 | set_color oxygen, [1.0,0.4,0.4]; 890 | set_color nitrogen, [0.5,0.5,1.0]; 891 | remove solvent; 892 | as spheres; 893 | util.cbaw; 894 | bg white; 895 | set light_count,10; 896 | set spec_count,1; 897 | set shininess, 10; 898 | set specular,0.25; 899 | set ambient,0; 900 | set direct,0; 901 | set reflect,1.5; 902 | set ray_shadow_decay_factor, 0.1; 903 | set ray_shadow_decay_range, 2; 904 | unset depth_cue; 905 | ray 906 | 907 | The commands without linebreaks: 908 | 909 | set_color oxygen, [1.0,0.4,0.4];set_color nitrogen, [0.5,0.5,1.0];remove solvent;as spheres;util.cbaw;bg white;set light_count,10;set spec_count,1;set shininess, 10;set specular,0.25;set ambient,0;set direct,0;set reflect,1.5;set ray_shadow_decay_factor, 0.1;set ray_shadow_decay_range, 2;unset depth_cue;ray 910 | 911 | ''' 912 | cmd.set_color('oxygen', '[1.0,0.4,0.4]') 913 | cmd.set_color('nitrogen', '[0.5,0.5,1.0]') 914 | cmd.remove('solvent') 915 | cmd.show_as('spheres') 916 | cmd.util.cbaw() 917 | cmd.bg_color('white') 918 | cmd.set('light_count', '10') 919 | cmd.set('spec_count', '1') 920 | cmd.set('shininess', '10') 921 | cmd.set('specular', '0.25') 922 | cmd.set('ambient', '0') 923 | cmd.set('direct', '0') 924 | cmd.set('reflect', '1.5') 925 | cmd.set('ray_shadow_decay_factor', '0.1') 926 | cmd.set('ray_shadow_decay_range', '2') 927 | cmd.unset('depth_cue') 928 | cmd.ray() 929 | cmd.extend('AO',AO) 930 | 931 | 932 | def BW(): 933 | ''' 934 | DESCRIPTION 935 | 936 | Commands to make black-and white-ribbon cartoon on a white background. 937 | Good for avoiding color figure charges. Requires a pdb file. Can cause PyMOL 938 | to crash if applied to a cartoon representation. Best applied while object is 939 | still shown as lines. 940 | 941 | 942 | USAGE 943 | 944 | Orient struture as desired. Then type 'BW' to execute the function. Type 945 | 'help BW' to see this documentation printed to the command history window. 946 | Select from the command history individual lines of code to build a new 947 | script. Select the hortizontal script at the bottom if retaining most of 948 | the commands in your new script. Copy and paste onto the command line below. 949 | Works only with the command line immediately under the command 950 | history window at the top of the gui. 951 | 952 | The commands with linebreaks: 953 | 954 | show cartoon; 955 | hide lines; 956 | hide nonbonded; 957 | # black and white cartoon; 958 | # note how the dcomment is on a separate line and not to the right of a command; 959 | set ray_trace_mode, 2; 960 | bg_color white; 961 | set antialias, 2; 962 | ray 1600,1600; 963 | png test.png 964 | 965 | Commands without linebreaks: 966 | 967 | show cartoon; hide lines; hide nonbonded; set ray_trace_mode, 2; # black and white cartoon; bg_color white; set antialias, 2; ray 1600,1600; png test.png 968 | 969 | ''' 970 | cmd.show_as("cartoon", "all"); 971 | cmd.hide('lines'); 972 | cmd.hide('nonbonded'); 973 | # black and white cartoon; 974 | cmd.set('ray_trace_mode', '2'); 975 | cmd.bg_color('white'); 976 | cmd.set('antialias', '2'); 977 | cmd.ray('600','600'); 978 | cmd.png('test.png') 979 | cmd.extend('BW',BW) 980 | 981 | 982 | def BU(): 983 | ''' 984 | DESCRIPTION 985 | 986 | Commands to make biological unit. Requires a pdb file. There are 987 | other ways of displaying the biological unit in PyMOL. Depends on 988 | the quat.py script by Thomas Holder. 989 | 990 | USAGE 991 | 992 | Type 'BU' to execute. Type 'help BU' to see this documentation 993 | printed to the command history window. Select from the command 994 | history individual lines of code to build a new script. Select the 995 | hortizontal script at the bottom if retaining most of the commands 996 | in your new script. Copy and paste onto the command line below. 997 | Works only with the command line immediately under the command 998 | history window at the top of the gui. 999 | 1000 | The commands with linebreaks: 1001 | 1002 | run ~/Scripts/PyMOLScripts/quat.py; 1003 | quat 1004 | 1005 | The commands without linebreaks: 1006 | 1007 | run ~/Scripts/PyMOLScripts/quat.py; quat 1008 | 1009 | ''' 1010 | # cmd.alias('aBU', 'run ~/Scripts/PyMOLScripts/quat.py; quat') 1011 | cmd.do('run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py') 1012 | # cmd.run('/Users/blaine-mooers/Scripts/PyMOLScripts/quat.py') 1013 | cmd.do('quat') 1014 | cmd.extend('BU',BU) 1015 | 1016 | def CB(): 1017 | ''' 1018 | DESCRIPTION 1019 | 1020 | Loads Jared Sampson's script "colorblindfriendly.py" from the 1021 | ~/Pymol-script-repo directory. The colorblind-friendly color 1022 | names are printed to the command history window and are available 1023 | for use like standard colors in PyMOL. 1024 | 1025 | Read the header of colorblindfriendly.py for more information. Although 1026 | this script is also in my PyMOL plugin collection, it is out of sight 1027 | and out of mind. The listing of the alias to this script is a 1028 | reminder to use it. 1029 | 1030 | USAGE 1031 | 1032 | Type 'CB' to execute. Type 'help CB' to see this documentation 1033 | printed to the command history window. 1034 | 1035 | Command: 1036 | 1037 | run ~/Pymol-script-repo/colorblindfriendly.py 1038 | 1039 | ''' 1040 | cmd.run('~/Pymol-script-repo/colorblindfriendly.py') 1041 | cmd.extend('CB',CB) 1042 | 1043 | 1044 | def CR(): 1045 | ''' 1046 | DESCRIPTION 1047 | 1048 | Commands to make colored filled-ring cartoon of nucleic acids. May 1049 | need to 'hide everything' first. If asymmetric unit has one strand 1050 | of a dsRNA or dsDNA, remember to apply the BU alias to display the 1051 | second strand. ddd 1052 | 1053 | Adapted from KP Wu's blog post: 1054 | https://kpwu.wordpress.com/2012/05/24/pymol-different-colors-of- 1055 | nucleic-acid-rings/ 1056 | 1057 | USAGE 1058 | 1059 | Type 'CR' to execute. Type 'help CR' to see this documentation 1060 | printed to the command history window. Select from the command 1061 | history individual lines of code to build a new 1062 | script. Select the hortizontal script at the bottom if retaining most of 1063 | the commands in your new script. Copy and paste onto the command line below. 1064 | Works only with the command line immediately under the command 1065 | history window at the top of the gui. 1066 | 1067 | The commands with linebreaks: 1068 | 1069 | hide everything; 1070 | bg_color white; 1071 | cartoon oval; 1072 | set cartoon_ring_mode,3; 1073 | set cartoon_nucleic_acid_color, blue; 1074 | select rna_A, resn A; 1075 | select rna_C, resn C; 1076 | select rna_G, resn G; 1077 | select rna_U, resn U; 1078 | color yellow, rna_A; 1079 | color red, rna_C; 1080 | color gray40, rna_G; 1081 | color palecyan, rna_U; 1082 | as cartoon 1083 | 1084 | The commands without linebreaks: 1085 | 1086 | hide everything;bg_color white;cartoon oval;set cartoon_ring_mode,3;set cartoon_nucleic_acid_color, blue;select rna_A, resn A;select rna_C, resn C;select rna_G, resn G;select rna_U, resn U;color yellow, rna_A;color red, rna_C;color gray40, rna_G;color palecyan, rna_U;as cartoon 1087 | 1088 | ''' 1089 | cmd.hide('everything') 1090 | cmd.bg_color('white') 1091 | cmd.cartoon('oval') 1092 | cmd.set('cartoon_ring_mode', '3') 1093 | cmd.set('cartoon_nucleic_acid_color', 'blue') 1094 | cmd.select('rna_A', 'resn A') 1095 | cmd.select('rna_C', 'resn C') 1096 | cmd.select('rna_G', 'resn G') 1097 | cmd.select('rna_U', 'resn U') 1098 | cmd.color('yellow', 'rna_A') 1099 | cmd.color('red', 'rna_C') 1100 | cmd.color('gray40', 'rna_G') 1101 | cmd.color('palecyan', 'rna_U') 1102 | cmd.show_as('cartoon') 1103 | cmd.disable('rna_U') 1104 | cmd.extend('CR',CR) 1105 | 1106 | 1107 | def CSS(): 1108 | ''' 1109 | DESCRIPTION 1110 | 1111 | Commands to color ribbon or cartoon representations of proteins by 1112 | secondary structures. 1113 | 1114 | USAGE 1115 | 1116 | Type 'CSS' to activateexecute. Type 'help CSS' to see this documentation 1117 | printed to the command history window. Select from the command 1118 | history individual lines of code to build a new 1119 | script. Select the hortizontal script at the bottom if retaining most of 1120 | the commands in your new script. Copy and paste onto the command line below. 1121 | Works only with the command line immediately under the command 1122 | history window at the top of the gui. 1123 | 1124 | The commands with linebreaks: 1125 | 1126 | as cartoon; 1127 | color red, ss H; 1128 | color yellow,ss S; 1129 | color green, ss L+; 1130 | 1131 | The commands without linebreaks: 1132 | 1133 | as cartoon; color red, ss H; color yellow,ss S; color green, ss L+; 1134 | 1135 | ''' 1136 | cmd.show_as('cartoon') 1137 | cmd.color('red', 'ss H') 1138 | cmd.color('yellow', 'ss S') 1139 | cmd.color('green', 'ss L+') 1140 | cmd.extend('CSS',CSS) 1141 | 1142 | 1143 | def CBSS(): 1144 | ''' 1145 | DESCRIPTION 1146 | 1147 | Commands to do colorblind friendly coloring by secondary 1148 | structures of ribbon or cartoon representations of proteins. 1149 | Depends on colorblindfriendly.py. Script assumed to be stored in 1150 | the home directory in ~/Pymol-script-repo. 1151 | 1152 | USAGE 1153 | 1154 | Type 'CBSS' to execute. Type 'help CBSS' to see this 1155 | documentation printed to the command history window. Select from the command 1156 | history individual lines of code to build a new 1157 | script. Select the hortizontal script at the bottom if retaining most of 1158 | the commands in your new script. Copy and paste onto the command line below. 1159 | Works only with the command line immediately under the command 1160 | history window at the top of the gui. 1161 | 1162 | The commands with linebreaks: 1163 | 1164 | run ~/Pymol-script-repo/colorblindfriendly.py; 1165 | as cartoon; 1166 | color cb_red, ss H; 1167 | color cb_yellow,ss S; 1168 | color cb_green, ss L+; 1169 | 1170 | The commands without linebreaks: 1171 | 1172 | run ~/Pymol-script-repo/colorblindfriendly.py;as cartoon;color cb_red, ss H;color cb_yellow,ss S;color cb_green, ss L+; 1173 | 1174 | ''' 1175 | 1176 | cmd.run('~/Pymol-script-repo/colorblindfriendly.py') 1177 | cmd.show_as('cartoon') 1178 | cmd.color('cb_red', 'ss H') 1179 | cmd.color('cb_yellow', 'ss S') 1180 | cmd.color('cb_green', 'ss L+') 1181 | cmd.extend('CBSS',CBSS) 1182 | 1183 | 1184 | def DU(): 1185 | ''' 1186 | DESCRIPTION 1187 | 1188 | Commands to make dumbbell (ribbons with rolled edges) cartoon of 1189 | the main chains of nucleic acids and proteins. 50% transparent 1190 | cartoon so it can be combined with lines, sticks, and 1191 | ball-and-sticks (try BS alias). 1192 | 1193 | USAGE 1194 | 1195 | Type 'DU' to execute. Type 'help DU' to see this documentation 1196 | printed to the command history window. Select from the command 1197 | history individual lines of code to build a new script. Select the 1198 | hortizontal script at the bottom if retaining most of the commands 1199 | in your new script. Copy and paste onto the comand line below. 1200 | Works only with the command line immediately under the command 1201 | history window at the top of the gui. 1202 | 1203 | Commands with linebreaks: 1204 | 1205 | cartoon dumbbell; 1206 | set cartoon_dumbbell_width, 0.2; 1207 | set cartoon_dumbbell_radius, 0.4; 1208 | show cartoon; 1209 | 1210 | Commands without linebreaks: 1211 | 1212 | cartoon dumbbell;set cartoon_dumbbell_width, 0.2;set cartoon_dumbbell_radius, 0.4;show cartoon; 1213 | 1214 | ''' 1215 | cmd.cartoon('dumbbell') 1216 | cmd.set('cartoon_dumbbell_width', '0.2') 1217 | cmd.set('cartoon_dumbbell_radius', '0.4') 1218 | cmd.show('cartoon') 1219 | cmd.extend('DU',DU) 1220 | 1221 | 1222 | def FR(): 1223 | ''' 1224 | DESCRIPTION 1225 | 1226 | Commands to make filled-ring cartoon of nucleic acids. May need to 1227 | 'hide everything' first. Adapted from the script on 1228 | http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol. 1229 | 1230 | USAGE 1231 | 1232 | Type 'FR' to execute. Type 'help FR' to see this documentation 1233 | printed to the command history window. Select from the command 1234 | history individual lines of code to build a new script. Select the 1235 | hortizontal script at the bottom if retaining most of the commands 1236 | in your new script. Copy and paste onto the command line below. 1237 | Works only with the command line immediately under the command 1238 | history window at the top of the PyMOL gui. 1239 | 1240 | Commands with linebreaks: 1241 | 1242 | show sticks; 1243 | set cartoon_ring_mode, 3; 1244 | set cartoon_ring_finder, 1; 1245 | set cartoon_ladder_mode, 1; 1246 | set cartoon_nucleic_acid_mode, 4; 1247 | set cartoon_ring_transparency, 0.5; 1248 | as cartoon; 1249 | 1250 | Commands without linebreaks: 1251 | 1252 | show sticks;set cartoon_ring_mode, 3;set cartoon_ring_finder, 1;set cartoon_ladder_mode, 1;set cartoon_nucleic_acid_mode, 4;set cartoon_ring_transparency, 0.5;as cartoon; 1253 | 1254 | ''' 1255 | cmd.show('sticks') 1256 | cmd.set('cartoon_ring_mode', '3') 1257 | cmd.set('cartoon_ring_finder', '1') 1258 | cmd.set('cartoon_ladder_mode', '1') 1259 | cmd.set('cartoon_nucleic_acid_mode', '4') 1260 | cmd.set('cartoon_ring_transparency', '0.5') 1261 | cmd.show_as('cartoon') 1262 | cmd.extend('FR',FR) 1263 | 1264 | 1265 | def HH(): 1266 | ''' 1267 | DESCRIPTION 1268 | 1269 | Command to hide hydrogen atoms. 1270 | 1271 | USAGE 1272 | 1273 | Type 'HH' to execute. Type 'help HH' to see this documentation 1274 | printed to the command history window. 1275 | 1276 | The command: 1277 | 1278 | hide everything, name H* 1279 | 1280 | ''' 1281 | cmd.hide('everything', 'name H*') 1282 | cmd.extend('HH',HH) 1283 | 1284 | 1285 | def PU(): 1286 | ''' 1287 | DESCRIPTION 1288 | 1289 | Commands to make putty cartoon of main chain of nucleic acids and 1290 | proteins. The radius of the cartoon is inversely proportional to 1291 | the B-factors. 50% transparent cartoon so it can be combined with 1292 | lines, sticks, and ball-and-sticks (try BS alias). 1293 | 1294 | USAGE 1295 | 1296 | Type 'PU' to execute. Type 'help PU' to see this documentation 1297 | printed to the command history window. Select from the command 1298 | history individual lines of code to build a new script. Select the 1299 | hortizontal script at the bottom if retaining most of the commands 1300 | in your new script. Copy and paste onto the comand line below. 1301 | Works only with the command line immediately under the command 1302 | history window at the top of the gui. 1303 | 1304 | The commands with linebreaks: 1305 | 1306 | cartoon putty; 1307 | set cartoon_ladder_mode, 0; 1308 | set cartoon_transparency,0.5; 1309 | set cartoon_ring_finder, 0; 1310 | show cartoon 1311 | 1312 | The commands without linebreaks: 1313 | 1314 | cartoon putty;set cartoon_ladder_mode, 0;set cartoon_transparency,0.5;set cartoon_ring_finder, 0;show cartoon 1315 | 1316 | ''' 1317 | cmd.cartoon('putty') 1318 | cmd.set('cartoon_ladder_mode', '0') 1319 | cmd.set('cartoon_transparency', '0.5') 1320 | cmd.set('cartoon_ring_finder', '0') 1321 | cmd.show('cartoon') 1322 | cmd.extend('PU',PU) 1323 | 1324 | 1325 | def SE(): 1326 | ''' 1327 | DESCRIPTION 1328 | 1329 | Commands to make SAXS envelope from a bead model. 1330 | 1331 | USAGE 1332 | 1333 | Type 'SE' to execute. Type 'help SE' to see this documentation 1334 | printed to the command history window. Select from the command 1335 | history individual lines of code to build a new script. Select the 1336 | hortizontal script at the bottom if retaining most of the commands 1337 | in your new script. Copy and paste onto the comand line below. 1338 | Works only with the command line immediately under the command 1339 | history window at the top of the gui. 1340 | 1341 | Commands with linebreaks: 1342 | 1343 | alter all,vdw=4.5; 1344 | set solvent_radius, 4.3; 1345 | show surface; 1346 | 1347 | Commands without linebreaks: 1348 | alter all,vdw=4.5;set solvent_radius, 4.3;show surface; 1349 | 1350 | ''' 1351 | cmd.alter('all,vdw=4.5') 1352 | cmd.set('solvent_radius', '4.3') 1353 | cmd.show('surface') 1354 | cmd.extend('SE',SE) 1355 | 1356 | 1357 | def rline(): 1358 | ''' 1359 | DESCRIPTION 1360 | 1361 | Navigating the command line with readline commands. 1362 | 1363 | These commands are sufficient for most editing tasks: 1364 | To edit code, positon cursor on command line with left mouse button. 1365 | Control-e moves the cursor to the end of the line, even when it is out of view. 1366 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 1367 | Up arrow key recalls last line of commands for editing. 1368 | 1369 | These commands may not be available on all systems: 1370 | Shift-control-a selects everything from the right of the cursor to the end of the line. 1371 | Shift-control-e selects everything to the left of the cursor to the end of the line. 1372 | Command-f moves the cursor to the end of the current word. 1373 | Command-b moves the cursor to the begining of the current word. 1374 | Control-f moves the cursor to the right by one character. 1375 | Control-b moves the cursor to the left by one character. 1376 | ''' 1377 | cmd.extend("rline",rline) 1378 | 1379 | 1380 | """ Print the aliases on startup of PyMOL""" 1381 | print(SA.__doc__) 1382 | -------------------------------------------------------------------------------- /wtT4L.py: -------------------------------------------------------------------------------- 1 | from __future__ import print_function 2 | # -*- coding: utf-8 -*- 3 | """ 4 | 5 | Copyright Notice 6 | ================ 7 | 8 | Copyright (C) 2016 Blaine Mooers 9 | 10 | This program is free software: you can redistribute it and/or modify 11 | it under the terms of the GNU General Public License as published by 12 | the Free Software Foundation, either version 3 of the License. 13 | 14 | This program is distributed in the hope that it will be useful, 15 | but WITHOUT ANY WARRANTY; without even the implied warranty of 16 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 17 | See the GNU General Public License for more details: 18 | http://www.gnu.org/licenses/. 19 | 20 | The source code in this file is copyrighted, but you can 21 | freely use and copy it as long as you don't change or 22 | remove any of the copyright notices. 23 | 24 | Blaine Mooers, PhD 25 | blaine-mooers@ouhsc.edu 26 | 975 NE 10th St, BRC 466 27 | University of Oklahoma Health Sciences Center, 28 | Oklahoma City, OK, USA 73104 29 | """ 30 | from pymol import cmd 31 | __author__ = "Blaine Mooers" 32 | __copyright__ = "Blaine Mooers, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104" 33 | __license__ = "GPL-3" 34 | __version__ = "1.0.3" 35 | __credits__ = ["William Beasley","Chiedza Kanyumbu"] # people who reported bug fixes, made suggestions, etc. 36 | __date__ = "24 July 2016" 37 | __maintainer__ = "Blaine Mooers" 38 | __email__ = "blaine-mooers@ouhsc.edu" 39 | __status__ = "Production" 40 | 41 | print("Enter the name of the alias to the left of the semicolon.") 42 | print(" ") 43 | print("site11: the active side glutamate Glu11") 44 | print(" ") 45 | print("site31: the His31-Asp 70 salt bridge in which His31's pKa") 46 | print(" is shifted by 3 orders of magnitude") 47 | print(" ") 48 | print("site96: the site of the Arg96-->His mutation that has a large loss in stability") 49 | print(" that was hard to explain from the structure alone.") 50 | print(" ") 51 | print("site99: the Leu99-->Ala mutant protein has a large cavity") 52 | print(" that can accomodate benzene.") 53 | print(" ") 54 | print("site145: poor H-bond geometery between Arg-145 and ") 55 | print(" Glu-11 suggests that the pKa of Glu11 is shifted upwards ") 56 | print(" by the unfavroable interactions.") 57 | print(" ") 58 | print("Type 'help wtT4L' for more information. ") 59 | print(" ") 60 | 61 | def wtT4L(): 62 | """ 63 | DESCRIPTION 64 | 65 | Creates aliases to compound commands or horizontal scripts. The compound commands 66 | are executed in PyMOL by typing their name. The command 67 | wtT4L.py only needs to be run once in a PyMOL session to 68 | create the aliases. The aliases disappear upon ending 69 | the PyMOL session. The names of the aliases and a short description 70 | of each aliases is printed to the command history window. 71 | 72 | LIMITATIONS 73 | 74 | The site31 alias requires the additional script 'wtT4Llabels.pml' must 75 | be present in the same directory as the wtT4L.py. You may have to 76 | give the full path to site31labels.pml if it is not in the present 77 | working directory. 78 | 79 | After changing the molecule's orientation, run the program 80 | 'roundview.py' to obtained a short version of the viewport settings. 81 | 82 | USAGE 83 | 84 | run wtT4L.py 85 | 86 | Then enter the name of an alias from the list above, for example: 87 | 88 | site11 89 | 90 | To reuse of parts or all of the above commands, copy and paste the commands 91 | onto the command line or into a plain text file. 92 | 93 | These commands are sufficient for most editing tasks: 94 | To edit code, positon cursor on command line with left mouse button. 95 | Control-e moves the cursor to the end of the line, even when it is out of view. 96 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 97 | Up arrow key recalls last line of commands for editing. 98 | 99 | These commands may not be available on all systems: 100 | Shift-control-a selects everything from the right of the cursor to the end of the line. 101 | Shift-control-e selects everything to the left of the cursor to the end of the line. 102 | Command-f moves the cursor to the end of the current word. 103 | Command-b moves the cursor to the begining of the current word. 104 | Control-f moves the cursor to the right by one character. 105 | Control-b moves the cursor to the left by one character. 106 | """ 107 | cmd.extend('wtT4L',wtT4L) 108 | print(wtT4L.__doc__) 109 | cmd.bg_color("white") 110 | cmd.fetch(code="3fa0", name="wtT4L",state = 0,async='0') 111 | cmd.alias('site11', 'zoom resi 11; preset.technical("wtT4L")') 112 | cmd.alias('site31', 'preset.ball_and_stick("wtT4L");@S3_File.pml;set_view (0.31,-0.93,0.21,0.92,0.24,-0.29,0.22,0.28,0.93,-0.09,-0.05,-9.88,37.55,10.06,30.09,20.0,23.82,-20.0);') 113 | cmd.alias('site96', 'preset.technical("wtT4L");set_view (-0.75,-0.65,0.11,0.62,-0.75,-0.22,0.22,-0.1,0.97,0.0,-0.0,-32.32,29.16,-1.45,6.77,27.32,37.32,-20.0);') 114 | cmd.alias('site99', 'preset.ball_and_stick("wtT4L");color bluewhite, i. 99; set_view (-0.24,-0.95,-0.21,0.51,0.07,-0.85,0.83,-0.32,0.46,0.03,-0.5,-5.37,22.35,-18.6,18.83,29.89,37.68,-20.0);') 115 | cmd.alias('site145', 'preset.technical("wtT4L");set_view (0.02,-0.63,-0.78,0.37,0.73,-0.56,0.93,-0.27,0.24,0.19,-0.3,-0.0,24.28,2 .24,13.53,15.23,21.26,-20.0);') 116 | -------------------------------------------------------------------------------- /wtT4LWindows.py: -------------------------------------------------------------------------------- 1 | from __future__ import print_function 2 | """ 3 | 4 | Copyright Notice 5 | ================ 6 | 7 | Copyright (C) 2016 Blaine Mooers 8 | 9 | This program is free software: you can redistribute it and/or modify 10 | it under the terms of the GNU General Public License as published by 11 | the Free Software Foundation, either version 3 of the License. 12 | 13 | This program is distributed in the hope that it will be useful, 14 | but WITHOUT ANY WARRANTY; without even the implied warranty of 15 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 16 | See the GNU General Public License for more details: 17 | http://www.gnu.org/licenses/. 18 | 19 | The source code in this file is copyrighted, but you can 20 | freely use and copy it as long as you don't change or 21 | remove any of the copyright notices. 22 | 23 | Blaine Mooers, PhD 24 | blaine-mooers@ouhsc.edu 25 | 975 NE 10th St, BRC 466 26 | University of Oklahoma Health Sciences Center, 27 | Oklahoma City, OK, USA 73104 28 | """ 29 | from pymol import cmd 30 | __author__ = "Blaine Mooers" 31 | __copyright__ = "Blaine Mooers, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104" 32 | __license__ = "GPL-3" 33 | __version__ = "1.0.3" 34 | __credits__ = ["William Beasley","Chiedza Kanyumbu"] # people who reported bug fixes, made suggestions, etc. 35 | __date__ = "24 July 2016" 36 | __maintainer__ = "Blaine Mooers" 37 | __email__ = "blaine-mooers@ouhsc.edu" 38 | __status__ = "Production" 39 | 40 | print("Enter the name of the alias to the left of the semicolon.") 41 | print(" ") 42 | print("site11: the active side glutamate Glu11") 43 | print(" ") 44 | print("site31: the His31-Asp 70 salt bridge in which His31's pKa") 45 | print(" is shifted by 3 orders of magnitude") 46 | print(" ") 47 | print("site96: the site of the Arg96-->His mutation that has a large loss in stability") 48 | print(" that was hard to explain from the structure alone.") 49 | print(" ") 50 | print("site99: the Leu99-->Ala mutant protein has a large cavity") 51 | print(" that can accomodate benzene.") 52 | print(" ") 53 | print("site145: poor H-bond geometery between Arg-145 and ") 54 | print(" Glu-11 suggests that the pKa of Glu11 is shifted upwards ") 55 | print(" by the unfavroable interactions.") 56 | print(" ") 57 | print("Type 'help wtT4L' for more information. ") 58 | print(" ") 59 | 60 | def wtT4L(): 61 | """ 62 | DESCRIPTION 63 | 64 | Creates aliases to compound commands or horizontal scripts. The compound commands 65 | are executed in PyMOL by typing their name. The command 66 | wtT4L.py only needs to be run once in a PyMOL session to 67 | create the aliases. The aliases disappear upon ending 68 | the PyMOL session. The names of the aliases and a short description 69 | of each aliases is printed to the command history window. 70 | 71 | LIMITATIONS 72 | 73 | The site31 alias requires the additional script 'wtT4Llabels.pml' must 74 | be present in the same directory as the wtT4L.py. You may have to 75 | give the full path to site31labels.pml if it is not in the present 76 | working directory. 77 | 78 | After changing the molecule's orientation, run the program 79 | 'roundview.py' to obtained a short version of the viewport settings. 80 | 81 | USAGE 82 | 83 | run wtT4L.py 84 | 85 | Then enter the name of an alias from the list above, for example: 86 | 87 | site11 88 | 89 | To reuse of parts or all of the above commands, copy and paste the commands 90 | onto the command line or into a plain text file. 91 | 92 | These commands are sufficient for most editing tasks: 93 | To edit code, positon cursor on command line with left mouse button. 94 | Control-e moves the cursor to the end of the line, even when it is out of view. 95 | Control-a moves the cursor to the beginning of the line, even when it is out of view. 96 | Up arrow key recalls last line of commands for editing. 97 | 98 | These commands may not be available on all systems: 99 | Shift-control-a selects everything from the right of the cursor to the end of the line. 100 | Shift-control-e selects everything to the left of the cursor to the end of the line. 101 | Command-f moves the cursor to the end of the current word. 102 | Command-b moves the cursor to the begining of the current word. 103 | Control-f moves the cursor to the right by one character. 104 | Control-b moves the cursor to the left by one character. 105 | """ 106 | cmd.extend('wtT4L',wtT4L) 107 | print(wtT4L.__doc__) 108 | cmd.bg_color("white") 109 | cmd.fetch(code="3fa0", name="wtT4L",state = 0,async='0') 110 | cmd.alias('site11', 'zoom resi 11; preset.technical("wtT4L")') 111 | cmd.alias('site31', 'preset.ball_and_stick("wtT4L");@S3_File.pml;set_view (0.31,-0.93,0.21,0.92,0.24,-0.29,0.22,0.28,0.93,-0.09,-0.05,-9.88,37.55,10.06,30.09,20.0,23.82,-20.0);') 112 | cmd.alias('site96', 'preset.technical("wtT4L");set_view (-0.75,-0.65,0.11,0.62,-0.75,-0.22,0.22,-0.1,0.97,0.0,-0.0,-32.32,29.16,-1.45,6.77,27.32,37.32,-20.0);') 113 | cmd.alias('site99', 'preset.ball_and_stick("wtT4L");color bluewhite, i. 99; set_view (-0.24,-0.95,-0.21,0.51,0.07,-0.85,0.83,-0.32,0.46,0.03,-0.5,-5.37,22.35,-18.6,18.83,29.89,37.68,-20.0);') 114 | cmd.alias('site145', 'preset.technical("wtT4L");set_view (0.02,-0.63,-0.78,0.37,0.73,-0.56,0.93,-0.27,0.24,0.19,-0.3,-0.0,24.28,2 .24,13.53,15.23,21.26,-20.0);') 115 | --------------------------------------------------------------------------------