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.