Re: [ccp4bb] force display of sheet in PYMOL

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: force display of sheet in PYMOL
From: Charlie Bond Charles {- dot -} Bond {- at -} UWA {- dot -} EDU {- dot -} AU
Date: 2009-10-01

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From: Adam Ralph aralph {- at -} MATHS {- dot -} NUIM {- dot -} IE
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Subject: Re: force display of sheet in PYMOL
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2009-10-02

On Oct 1, 2009, at 7:51 PM, Charlie Bond wrote:
> A note of caution: if a program doesn't show something as a beta
> strand that must mean that that part of the molecule doesn't have
> the attributes for strand. Rather than cosmetically fix it by
> changing it in pymol, it might be a good idea to look closely at the
> structure/density and see if the model can be improved.

This is good general advice, but in the specific case of pymol, the
manual says:

'It is recommended that you read in PDB files which already have
correct secondary structure assignments from a program like DSSP.
However, PyMOL does have a reasonably fast secondary structure
alignment algorithm called "dss". Please be aware that due to the
subjective nature of secondary structure assignment in borderline
cases, dss results will differ somewhat from DSSP.'

http://pymol.sourceforge.net/newman/user/S0260cartoons.html

This may help: http://structure.usc.edu/dssp2pdb/

James

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: force display of sheet in PYMOL
From: Charlie Bond Charles {- dot -} Bond {- at -} UWA {- dot -} EDU {- dot -} AU
Date: 2009-10-01

Next message:
Subject: Re: missing subroutines
From: Adam Ralph aralph {- at -} MATHS {- dot -} NUIM {- dot -} IE
Date: 2009-10-02