Skip to content

bieniekmateusz/pymol-mdanalysis

mdanalysis
Switch branches/tags
Code
This branch is 105 commits ahead, 94 commits behind schrodinger:master.
Contribute

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

PyMOL-MDAnalysis exploratory project

This is an exploratory project started as a PyMOL Fellowship in 2019 which combines PyMOL and MDAnalysis together.

If you need any help, feel free to create an issue.

Installation

This fork uses a dumbed-down version of the installation file setup.py which might be lacking in various ways.

If you have a problem with missing dependencies, check the official instructions: please see INSTALL and the upstream github page.

CONDA

It is easiest to use conda to install some necessary dependencies.

conda install -c conda-forge glew glm libpng freetype libxml2 netcdf4

Download the repository, e.g. with git: git clone git@github.com:bieniekmateusz/pymol-mdanalysis.git then go to the pymol-mdanalysis directory and enter:

pip install .

In this case pip should refer to conda's pip, which you can check with the command where pip.

From now on, whenever your conda environment is active, type pymol to start the application.

Linux Ubuntu example

An example on ubuntu:

apt-get install build-essential python3-dev libglew-dev \
  libpng-dev libfreetype6-dev libxml2-dev \
  libmsgpack-dev python3-pyqt5.qtopengl libglm-dev libnetcdf-dev

Then download the directory and use pip install .

Test the installation with python -c "import pymol ; pymol.start_pymol()"

For other operating systems and their dependancies, please see https://pymolwiki.org/index.php/Linux_Install

Errors / Debugging

You might use python setup.py build and check the errors in the output.

In a conda environment, gcc version 10 works fine. However, gcc 11.2 led to the following error:

ImportError: ... _cmd.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZSt28__throw_bad_array_new_lengthv

You can switch to an older compiler in that case by configuirng CC and CXX:

export CC=gcc-10
export CXX=g++-10

Remember to empty the build directory before reattempting the installation.

Citations

If you find this useful, please cite the SI of Mateusz Bieniek's thesis: https://librarysearch.kcl.ac.uk/permalink/f/1fdleu2/TN_proquest2475221287

Direct Thesis Download via KCLPure: https://kclpure.kcl.ac.uk/portal/en/theses/fibronectin-iii910-adsorption-to-selfassembled-monolayers-and-interdomain-orientation-in-the-context-of-materialdriven-fibrillogenesis-studied-with-molecular-dynamics-simulations(11b1d705-79f0-4d0a-8c53-b68bc2c3338e).html

Official repo info

Contributing

See DEVELOPERS.

License

Copyright (c) Schrodinger, LLC

Published under a BSD-like license, see LICENSE.

About

Exploratory PyMOL-MDAnalysis molecular visualization system.

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Languages

  • C 61.8%
  • C++ 26.0%
  • Python 10.1%
  • JavaScript 1.5%
  • HTML 0.5%
  • GLSL 0.1%