Re: [ccp4bb] RMSD of pairs of atoms?

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

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Subject: Re: MTZ to Shel-X?
From: S {- dot -} E {- dot -} KOLSTOE {- at -} SOTON {- dot -} AC {- dot -} UK
Date: 2007-03-01

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Subject: Re: RMSD of pairs of atoms?
From: gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2007-03-01

> Risking a potentially trivial question:
>
> Is there a program that will calculate the RMS of distances
> between specified (listed) atoms in two different structures?
>
> As far as I could see, LSQMAN will only compute same with same?

lsqman does in fact calculate rmsd valus between arbitrary sets of atoms.
however, it turns out that there was a buglet that caused the alpha version of
lsqman to crash rather unelegantly (but not the sgi, osx or linux versions).
it did not affect the rmsd calculation (only more exotic statistics such as
the TM-score and the Crippen rho) so should have been quite harmless

fixed versions of lsqman are available from the ftp server
(ftp://xray.bmc.uu.se/pub/gerard/dejavu/)

--dvd

******************************************************************
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
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CCP4bb navigation

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

Previous message:
Subject: Re: MTZ to Shel-X?
From: S {- dot -} E {- dot -} KOLSTOE {- at -} SOTON {- dot -} AC {- dot -} UK
Date: 2007-03-01

Next message:
Subject: Re: Extraction of test set from CNS reflection file
From: Olve {- dot -} Peersen {- at -} COLOSTATE {- dot -} EDU
Date: 2007-03-01