Recently my (Ubuntu 11.10 64bit) machine stopped playing nice with PyMOL and whenever I tried to render or move an object I was facing a >40 second render time, while both of my CPU cores jumped to >90%

When I paid close attention to the startup messages in the PyMOL command window I could see:

Detected OpenGL version 2.0 or greater.  Shaders available.

 PyMOLShader_NewFromFile-Error: Unable to open file '/usr/lib/pymodules/python2.7/pymol/data/shaders/default.vs' PYMOL_PATH='/usr/lib/pymodules/python2.7/pymol'

 PyMOLShader_NewFromFile-Warning: default shader files not found, loading from memory.

 PyMOLShader_NewFromFile-Error: Unable to open file '/usr/lib/pymodules/python2.7/pymol/data/shaders/volume.vs' PYMOL_PATH='/usr/lib/pymodules/python2.7/pymol'

 PyMOLShader_NewFromFile-Warning: volume shader files not found, loading from memory.

In short, the current version of PyMOL supported by Ubuntu (1.4.1-1) was having troubles playing nicely with the new version of Python (2.7).

Going through the Debian bug pages you can find that there's a similar problem for all Debian OSs, which is apparently solved in PyMOL 1.5.

 

So all we need to do is download the new PyMOL and install it.

The x64 version is available here and can be installed with pointing a terminal window at your Downloads folder

cd ~/Downloads

sudo dpkg -i pymol_1.5.0.1-1_amd64.deb

However, the installation fails because our OpenGL drivers aren't modern enough and we need at least version 1.7 of the libglew library, Ubuntu currently supports v1.5.

So download libglew v1.7 from Debian and install

sudo dpkg -i libglew1.7_1.7.0-3_amd64.deb

Now PyMOL will install correctly with

sudo dpkg -i pymol_1.5.0.1-1_amd64.deb

Load up PyMOL and you'll find that it responds now as it should.

 

About Morgan Bye

Scientist, programmer and all around techie

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