Re: [ccp4bb] rmsd calculation. .

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CCP4bb <-- 2007 <-- May 2007 <-- 11 May 2007

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From: Liz Potterton lizp {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-11

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Subject: Re: rmsd calculation. .
From: Miguel Ortiz Lombardia molatwork {- at -} YAHOO {- dot -} ES
Date: 2007-05-11

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Excellent!
Thank you Gerard,

Miguel

Gerard DVD Kleywegt escribió:
>> But my understanding is that Iain's procedure gives the rmsds of the
>> _aligned_ C-alphas, whereas Jenny actually seems to be more interested
>> in those that she excludes from the alignment. I may be wrong, but in
>> these cases, I use lsqman (from DVD) or lsqkab (from ccp4) to superpose
>> the proteins (using one as reference) according to a particular scheme
>> (Jenny's 1-40,60-100) and then write a script to calculate the rmsds for
>> the "interesting" 41-59 residues. There may be an easier way, which I'll
>> be interested to learn about.
>
> hola miguel,
>
> i would use the rmsd command in lsqman, like so:
>
> read m1 m1.pdb
> read m2 m2.pdb
> expl m1 "a1-40 a60-100" m2 "a1 a60"
> rmsd m1 a41-59 m2 a41
>
> --gerard
>
> ******************************************************************
> Gerard J. Kleywegt
> [Research Fellow of the Royal Swedish Academy of Sciences]
> Dept. of Cell & Molecular Biology University of Uppsala
> Biomedical Centre Box 596
> SE-751 24 Uppsala SWEDEN
>
> http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
>
>

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: molatwork@yahoo.es
www: http://www.pangea.org/mol/spip.php?rubrique2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie. (Raoul Vaneigem)
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CCP4bb <-- 2007 <-- May 2007 <-- 11 May 2007

Previous message:
Subject: Re: CCP4 GUI
From: Liz Potterton lizp {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-11

Next message:
Subject: CNS problem: anneal.inp segmentation fault
From: jean jean {- at -} SCIENCE {- dot -} UCT {- dot -} AC {- dot -} ZA
Date: 2007-05-11