Pymol under El Capitan
When El Capitan first came out I upgraded a machine with an existing installation of a variety of cheminformatics tools installed using Homebrew and PIP as described here. Under this situation Pymol worked without problem. However I have had a few readers email me saying they are having problems so I took a new machine running El Capitan and tried to instal the same cheminformatics tools including Pymol using Homebrew and PIP. All worked fine except Pymol which opened but crashed with the following error.
Username:~ prompt$ pymol PyMOL(TM) Molecular Graphics System, Version 220.127.116.11. 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 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: NVIDIA GeForce 8600M GT OpenGL Engine GL_VERSION: 2.1 NVIDIA-10.0.40 310.90.10.05b12 Detected 2 CPU cores. Enabled multithreaded rendering. libpng warning: Application built with libpng-1.6.19 but running with 1.5.23 /usr/local/bin/pymol: line 4: 3628 Segmentation fault: 11 "/usr/local/opt/python/bin/python2.7" "/usr/local/Cellar/pymol/18.104.22.168/libexec/lib/python2.7/site-packages/pymol/__init__.py" "$@“
The helpful on the Pymol user list pointed me to this message on the Homebrew-Science issues
First uninstall pymol and libpng
brew uninstall pymol brew uninstall libpng
then install pymol first.
brew install pymol brew install libpng
Now when you type pymol in a Terminal window you should see.