Re: [ccp4bb] RMSD

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CCP4bb <-- 2007 <-- March 2007 <-- 14 March 2007

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Subject: RMSD
From: john kryst protkryst {- at -} GMAIL {- dot -} COM
Date: 2007-03-14

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From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-03-14

Subject: Re: RMSD
From: Dirk Kostrewa dirk {- dot -} kostrewa {- at -} PSI {- dot -} CH
Date: 2007-03-14

Dear John,

I don't know how different the RMSD values are, and whether the
calculated estimates are with or without hydrogen atoms (this can make a
difference). In principle, both programs use the Engh & Huber
stereochemistry library, but I've observed in the past that different
programs used slightly different "implementations" of this library,
resulting in different RMSD values, although they should all be the same ...

Good luck,

Dirk.

john kryst wrote:
> Hi ccp4bb !!!
>
> Does the rmsd estimation (for eg. rmsd_bonds ) depends on the program we
> use
> ??
>
> Example : shifting from Refmac to CNS. There appears to be an increase in
> rmsd of bonds even without refining the structure in CNS. Is the estimation
> methods are different or am i doing something wrong !!
>
> Thanks for your valuable inputs.
>
> regards
> john
>

--

****************************************
Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: dirk.kostrewa@psi.ch
http://sb.web.psi.ch
****************************************

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CCP4bb <-- 2007 <-- March 2007 <-- 14 March 2007

Previous message:
Subject: RMSD
From: john kryst protkryst {- at -} GMAIL {- dot -} COM
Date: 2007-03-14

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Subject: Re: RMSD
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-03-14