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()"
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.