Re: [ccp4bb] Protein PDB in Crystal Environment

Protein crystallography Programs for crystallography X-ray detectors
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Protein Peptide

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Subject: Protein PDB in Crystal Environment
From: "Manfred S {- dot -} Weiss" msweiss {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-03-08

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Subject: Re: Protein PDB in Crystal Environment
From: Christopher Colbert Christopher {- dot -} Colbert {- at -} UTSOUTHWESTERN {- dot -} EDU
Date: 2007-03-08

Subject: Re: Protein PDB in Crystal Environment
From: Lieven Buts lieven {- dot -} buts {- at -} VUB {- dot -} AC {- dot -} BE
Date: 2007-03-08

On Thursday 08 March 2007 16:33, Manfred S. Weiss wrote:
> before I start with some scripting myself, does anybody have a
> utility, which takes a PDB and the cell and space group information
> and then writes out the original PDB together with all molecules
> contacting the first one in the crystal?

I have a small PyMOL script (attached) which is a bit
finicky about its input, but has worked well for me.
The idea is to load or create an object called "protein"
in PyMOL and invoke the script with "run SymGen.py" to
generate all symmetry mates and save all those with
atoms within a certain cutoff from the base object.

--
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel

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CCP4bb <-- 2007 <-- March 2007 <-- 08 March 2007

Previous message:
Subject: Protein PDB in Crystal Environment
From: "Manfred S {- dot -} Weiss" msweiss {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-03-08

Next message:
Subject: Re: Protein PDB in Crystal Environment
From: Christopher Colbert Christopher {- dot -} Colbert {- at -} UTSOUTHWESTERN {- dot -} EDU
Date: 2007-03-08