gmx_MMPBSA_ana pymol does not launch and solution does not work

[Felipe Montecinos]

Hello everyone,

I can't find a solution to this problem. My gmx_MMPBSA package 1.6.3 is installed in an conda environment and all runs decomposition analysis well except for Pymol which does not run.

Pymol is installed in my system

which pymol = /usr/bin/pymol

I tried editing this file as explained but it did not work (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/331). However, pymol does run if launched outside of conda.

Pymol is not installed in my conda gmxMMPBSA environment. So I tried installing it from repository  but it did not work either and also breaks the environment functionality and it still does not run. The error I get after this attempt at installing pymolfrom within the conda environment relates to missing PyQt5 packages (AttributeError: module 'PyQt5.QtGui'...), etc.

Anyone else having this issue?

For visualization of decomposition analysis residues I tried loading the files in chimera and vmd but I can't reproduce the modified pdb with marked residues...

Any help would be appreciated,

Thanks

[Mario Sergio Valdes]

Please add the terminal output for every problem you get to review the error context.

[Felipe Montecinos]

Thank you for your reply,

The problem I have is the window has no output at all. After I start gmx_MMPBSA_ana, the GUI launches normally and I can open all files and plots, etc. When I try clicking on the "display labeled residues in pymol" button a little wheel shows up and it stays there but nothing happens. The terminal window shows no output at all even after interacting with the GUI.

I tried starting pymol from within the conda environment (pymol is installed in my system and it works) and this is what I get in the terminal:

$ pymol
.../anaconda3/envs/gmxMMPBSA/bin/python3: Error while finding module specification for 'pymol.__init__' (ModuleNotFoundError: No module named 'pymol')

Could this be the problem?

[gmx_MMPBSA]

Please, show me the pymol script content. 

[Felipe Montecinos]

#!/bin/sh
# debian wrapper script for pymol

test -r ${HOME}/.pymol && . ${HOME}/.pymol

PYMOL_PATH=${PYMOL_PATH:=`/usr/bin/python3 -c "import importlib.util; print(importlib.util.find_spec('pymol').submodule_search_locations[0])"`}
PYMOL_DATA=${PYMOL_DATA:=/usr/share/pymol/data}
PYMOL_SCRIPTS=${PYMOL_SCRIPTS:=/usr/share/pymol/scripts}
CHEMPY_DATA=${CHEMPY_DATA:=/usr/share/pymol/data/chempy}

export PYMOL_PATH
export PYMOL_DATA
export PYMOL_SCRIPTS
export CHEMPY_DATA

python3 -m pymol.__init__ ${1+"$@"}

[Mario Sergio Valdes]

Please, change the last line (python3 -m pymol.__init__ ${1+"$@"}) by (/usr/bin/python3 -m pymol.__init__ ${1+"$@"}) and check if it work for you

[Felipe Montecinos]

Hi Mario,

It works now, thanks!