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.
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.
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 email@example.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
From now on, whenever your conda environment is active,
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.
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
Copyright (c) Schrodinger, LLC
Published under a BSD-like license, see LICENSE.