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Re: [ccp4bb] RMSD value is different from O and superpose
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: CALL FOR ESRF SYNCHROTRON BEAM TIME WITH ONLINE,DEHUMIDIFIER AT BEAMLINE ID14-2
From: David FLOT david {- dot -} flot {- at -} ESRF {- dot -} FR
Date: 2009-07-05		Next message:
Subject: AsCA'09 - October 22-25, 2009, Beijing, China - DEADLINE EXTENDED
From: Mark Bartlam mark {- at -} XTAL {- dot -} TSINGHUA {- dot -} EDU {- dot -} CN
Date: 2009-07-06


Subject: Re: RMSD value is different from O and superpose
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-07-05

peter hudson wrote:
> Hello all
>
> I superposed the two different chain, which are two different subunits
> of the same structure which are different in conformation with two
> differen t programmes.
>
> 1) First is with O, with LSQ command, it gives the RMSD values for
> different chain is 1.5A for 108 ca atoms.
> 2) Second programme i used is Superpose from CCP4i inbuilt, which gives
> the RMSD values of 2.4A for almost same ca atoms.
>
> Why this two programmes output RMSD are very different.


The devil's in the detail. If you were using ccp4i, which superpose
option did you use?

(If you used "superpose using secondary structure matching" then that is
very different to LSQ/LSQKAB matching - and you would expect a different
rmsd).

Paul.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: CALL FOR ESRF SYNCHROTRON BEAM TIME WITH ONLINE,DEHUMIDIFIER AT BEAMLINE ID14-2
From: David FLOT david {- dot -} flot {- at -} ESRF {- dot -} FR
Date: 2009-07-05		Next message:
Subject: AsCA'09 - October 22-25, 2009, Beijing, China - DEADLINE EXTENDED
From: Mark Bartlam mark {- at -} XTAL {- dot -} TSINGHUA {- dot -} EDU {- dot -} CN
Date: 2009-07-06
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