Pymol on Morgan Bye

PyMOL visualising e2 rotamers

Wed, 05 Sep 2012 12:44:00 +0000

This morning whilst writing some reports I wanted to show some rotamer populations of my spin label attached to the protein. Whilst MMM provides visualisation, and having had discussions with Jeschke I understand just how difficult it is to do, I do not consider them to be of publication standard. For this reason I needed to come up with something.

So first up do all the calculations in MMM as per normal but make sure you save your statistics.

PyMOL visualising binding interfaces

Fri, 24 Feb 2012 17:31:00 +0000

Today I’ve been trying to come up with a nice way of visualising the binding interface between protein-protein or protein-DNA complexes. What follows is a quick little walk-through mostly for my own purposes so that I can remember what I’ve done in the future.

Download PDB file from pdb.org, here XXXX will be your PDB accession code.

Point a terminal window at the download directory

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cd ~/Downloads

Run CCP4:

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ncont XYZIN XXXX.pdb >> XXXX.ncont << eof

source A [or whatever your protein chain is]

target E,F [or whatever the DNA chains are]

eof

This will give us a file XXXX.ncont in the Downloads folder which contains all the information about the binding interface

PyMOL with Ubuntu 11.10 rendering problems

Sun, 29 Jan 2012 12:00:00 +0000

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:

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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).