PyMOL

# CentOS
gcc gcc-c++ kernel-devel python-devel tkinter python-pmw glew-devel \
  freeglut-devel libpng-devel freetype-devel libxml2-devel glm-devel

[root@c ~]# yum --enablerepo=epel install msgpack-devel

[root@c ~]# yum install PyQt4-devel PyQt4-webkit-devel

[root@c ~]# cd /Appl/src/
[root@c src]# git clone https://github.com/schrodinger/pymol-open-source
[root@c src]# cd pymol-open-source/
[root@c pymol-open-source]# python -V
Python 2.7.5
[root@c pymol-open-source]#
[root@c pymol-open-source]# python setup.py --help
usage: setup.py [-h] [--no-glut] [--glut] [--no-osx-frameworks]
                [--osx-frameworks] [--jobs JOBS] [--no-libxml]
                [--use-msgpackc {c++11,c,guess,no}] [--help-distutils]
                [--testing]
 
optional arguments:
  -h, --help            show this help message and exit
  --no-glut
  --glut                link with GLUT (legacy GUI)
  --no-osx-frameworks
  --osx-frameworks      on MacOS use OpenGL and GLUT frameworks instead of
                        shared libraries from XQuartz. Note that the GLUT
                        framework has no mouse wheel support, so this option
                        is generally not desired.
  --jobs JOBS, -j JOBS  for parallel builds (defaults to number of processors)
  --no-libxml           skip libxml2 dependency, disables COLLADA export
  --use-msgpackc {c++11,c,guess,no}
                        c++11: use msgpack-c header-only library; c: link
                        against shared library; no: disable fast MMTF load
                        support
  --help-distutils      show help for distutils options and exit
  --testing             Build C-level tests
[root@c pymol-open-source]# python setup.py build
 :
[root@c pymol-open-source]# python setup.py install --prefix=/Appl/pymol
running install
running build
running build_py
running build_ext
running install_lib
creating /Appl/pymol
creating /Appl/pymol/lib64
creating /Appl/pymol/lib64/python2.7
creating /Appl/pymol/lib64/python2.7/site-packages
 :
 :
 :
running install_egg_info
Writing /Appl/pymol/lib64/python2.7/site-packages/pymol-2.4.0a0-py2.7.egg-info
creating /Appl/pymol/lib64/python2.7/site-packages/pymol/pymol_path
copying LICENSE -> /Appl/pymol/lib64/python2.7/site-packages/pymol/pymol_path
copying data -> /Appl/pymol/lib64/python2.7/site-packages/pymol/pymol_path/data
copying test -> /Appl/pymol/lib64/python2.7/site-packages/pymol/pymol_path/test
copying scripts -> /Appl/pymol/lib64/python2.7/site-packages/pymol/pymol_path/scripts
copying examples -> /Appl/pymol/lib64/python2.7/site-packages/pymol/pymol_path/examples
creating /Appl/pymol/bin
 
[root@c pymol-open-source]#

[root@c ~]# cat /Appl/pymol/bin/pymol
#!/bin/sh
export PYMOL_PATH="/Appl/pymol/lib64/python2.7/site-packages/pymol/pymol_path"
"/bin/python" "/Appl/pymol/lib64/python2.7/site-packages/pymol/__init__.py" "$@"
[root@c ~]#

[saber@c ~]$ /Appl/pymol/bin/pymol
 PyMOL(TM) Molecular Graphics System, Version 2.4.0a0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.
 
    Created by Warren L. DeLano, Ph.D.
 
    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.
 
    If PyMOL is helpful in your work or study, then please volunteer
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.
 
    More information can be found at "http://www.pymol.org".
 
    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.
 
 Hit ESC anytime to toggle between text and graphics.
 
 Detected OpenGL version 1.4. Shaders and volumes unavailable.
 OpenGL graphics engine:
  GL_VENDOR:   Intel
  GL_RENDERER: Mobile Intel(R) 4 Series Express Chipset Family
  GL_VERSION:  1.4 (2.1.0 - Build 8.15.10.2302)
 Disabling shaders for Intel Express graphics
 Detected 4 CPU cores.  Enabled multithreaded rendering.

export LIBGL_ALWAYS_INDIRECT=1

[root@c ~]# cd /Appl/src/pymol-open-source/
 
[root@c pymol-open-source]# git branch
* master
 
[root@c pymol-open-source]# git pull
[root@c pymol-open-source]# git branch -a
* master
  remotes/origin/HEAD -> origin/master
  remotes/origin/master
 
[root@c pymol-open-source]# git tag
v2.2.0
v2.3.0
 
[root@c pymol-open-source]# git checkout -b v2.3 refs/tags/v2.3.0
Switched to a new branch 'v2.3'
 
[root@c pymol-open-source]# git branch
  master
* v2.3
 
[root@c pymol-open-source]# python2.7 setup.py install --prefix=/Appl/pymol

yum install glew-devel glm-devel netcdf-devel python3-pyqt5-sip python3-tkinter
pip3 install pmw
python3 setup.py build  install --glut --prefix=/apps/pymol