pyMODE-TASK

update: 13Apr2023. Earlier version was only python2 compatible. Now it works with python3 only.

MODE-TASK plugin for PyMOL

Command line version is available here.

For installing the pyMODE-TASK - a pymol plugin.

Requirements:

python3
Tkinter
Pmw
numpy==1.13.1
cython==0.26
scikit-learn==0.19.0
scipy==0.19.1
sklearn==0.0
matplotlib==2.0.2
mdtraj==1.8.0

1. Download the project:

git clone https://github.com/RUBi-ZA/pyMODE-TASK.git

OR

Download zip from github page and extract to a directory.

2. Install dependencies:

Run the following command from within pyMODE-TASK directory

sudo pip install -r requirements.txt

pyMODE-TASK requires Tkinter and Pmw.1.3. Tkinter comes prepackaged with most standard python. Pmw could be installed by following the instruction from: http://pmw.sourceforge.net/doc/starting.html

3. Install pyMODE-TASK plugin in pymol:

3.1. Start pymol

3.2. Go to Plugin -> Plugin Manager, and clcik on install new plugin tab. Under install from local file click on 'choose file...' button. Browse the pyMODE-TASK.py and follow the on screen installation instructions.

3.3. If everything goes well, you can start the plugin from pymol plugin menu.

Usage

For more detailed documentation on installation and usage of the tool suite please see our ReadTheDocs site

Contributing to the project

Questions and issues can be posted to the issue tracker.

Pull requests are welcome and will be reviewed however a guarentee can not me made as to your request being accepted.

The documentation is hosted by ReadTheDocs and makes use of reStructuredText for markdown with Latex for mathematical equasions. See here for a more detailed guideline on creating documentation for ReadTheDocs.

Citation

MODE-TASK: Large-scale protein motion tools

Caroline Ross, Bilal Nizami, Michael Glenister, Olivier Sheik Amamuddy, Ali Rana Atilgan, Canan Atilgan, Özlem Tastan Bishop; Bioinformatics, Volume 34, Issue 21, 1 November 2018

TODO list:

• Fully functional and ready to install plugin.
• Resize/adjust NMA tab.
• Add progress bar.
• Update link in MODE-TASK documentation.
• Add better handling of exceptions in NMA tab.
• Add feature to identify the MD frame in the PCA projection plot.