Freitag, 13. Januar 2012

PyMOL 005: Partial structure optimization

PyMOL is amazing. Say you have a structure where, eg., water molecules are too close to your protein atoms. Maybe you want to optimize the water molecules (only the water molecules) by some crude approach before submitting to more sophisticated theory.
Here's how you can do it at the PyMOL prompt. You loaded the structure as "enz". The waters in "enz" all have the same id 500. So typing

select wat, enz/PROT/A/500/

should select your waters. "PROT" is some sort of segment and "A" is the chain of the structure, these depend and maybe need some adjustment in your system. Alternatively, try

select wat, enz///500/

Having selected the waters (if nothing else then manually), enter the following commands

cmd.protect('(not wat)')
cmd.sculpt_iterate('enz', cycles=5000)

The number of cycles can be adjusted. Also, it is possible to optimize locally only a side chain of one residue in the protein. Then you would enter

cmd.protect('(not enz///105/) or name C+CA+O+N+OXT')
[same commands like above]

Dont forget the trailing forward slash in the selection commands.

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