pymol

[yang-guoli]

Hi, i want to install with conda, and i follow your steps in the readme, but when i use the command (python setup.py install --prefix=~/software/pymol-mdanalysis/install), it has the error: error: command '/opt/rh/devtoolset-9/root/usr/bin/g++' failed with exit code 1. can you help me to solve this problem?

my env=python_3.10.4

[bieniekmateusz]

Thanks for reaching out @yang-guoli , I've just followed the instructions on a new PC to triple check it and it is working fine here. Would you mind scrolling higher to see what is the error that you encounter? Usually the error is highlighted in red, and sometimes it is buried in the text.

Note that I used "pip install ." instead as desribed here:
https://github.com/bieniekmateusz/pymol-mdanalysis

[yang-guoli]

@bieniekmateusz Thanks for your reply, but when i tried to install with pip commend, the error as follow:
error: legacy-install-failure

Could this be the cause of my gcc installation path?

[bieniekmateusz]

It looks like you are missing the OpenGL headers. Is your glew installed in your conda? You might also also try it libglew-dev on ubuntu. Here the system g++ is being used and maybe it doesn't search through the conda's glew.

A nuclear fix is to install PyMOL from the official channel on conda, and then uninstall just the PyMOL but leave all the dependancies installed (conda uninstall --force pymol), which ensures you have everything in the environment that you need.

Best, Mat

[yang-guoli]

@bieniekmateusz thanks for your help, and my system is centos. I had tried your suggestion, but it stiil have the same error.

can you make it install success in the centos system?

[bieniekmateusz]

Heya, which suggestion did you follow?

Also, before trying anything new, ensure you have a clean setup by removing fully the generated "build" directory which is created when you try to compile any code.

Note that on centos, you will need these:
yum install gcc gcc-c++ kernel-devel python-devel tkinter python-pmw glew-devel freeglut-devel libpng-devel freetype-devel libxml2-devel glm-devel msgpack-devel netcdf-devel

As listed in https://pymolwiki.org/index.php/Linux_Install