Have you ever tried to represent your protein as a “sausage”-style cartoon, with the tube diameter scaled by values in the B-factor column ? We present an array of useful PyMOL scripts links to solve your problem.
PyMOL is, as defined on its home page: “.. a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation”. Indeed it is one of the most popular molecular viewers out there. One of the main strengths of PyMOL is its inherent scripting abilities. I’m sure that many of you knew that, but have never really taken the time to write such scripts, and why would you ? others have done the job for you!
We present to you a pile of PyMOL scripts, some are extremely useful, others can color your protein salmon pink.
- The PyMOL wiki is a great PyMOL resource by itself, but its scripts library is the real gem.
- cool script: a Wizard to draw planes between three picked points.
- Dr. Robert L. Campbell, shares with us his own little directory of useful PyMOL scripts.
- cool script: Extract data produced by other programs and alter the B-factor or occupancy of a molecule within PyMOL.
- As Does Dr. Gareth Stockwell, from the EBI.
- cool script: Draws pretty h-bonds, with arrows.
- On Cam’s PyMOL page you’ll find lots of examples for specific tasks and amongst them the highly coveted…
- cool script: “sausage”-style cartoon representation, with the tube diameter scaled by values in the B-factor column.
- Update: as indicated in the comments “cartoon putty” will do the trick since v0.98
- Extending beyond the reach of scripts, at the sourceforge PyMOL plugins page you can find some PyMOL plugins for useful tasks such as visualizing electrostatic potentials, identifying and visualizing access routes to protein cavities, download a PDB file straight into PyMOL, loading of multiple pdb files, dihedral restraints checks, NOE restraints checks, and superposition routines.
- cool plugin: visualizing surfaces and voids using the CASTp algorithm.
What’s your favorite Pymol script ? share with us in the comments.
By Nir London.
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