[ccp4bb] RMSD value is different from O and superpose

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

Previous message:
Subject: Re: CCP4 / Ubuntu 9.04 64-bit
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-07-04

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Subject: Re: RMSD value is different from O and superpose
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2009-07-05

Subject: RMSD value is different from O and superpose
From: peter hudson peter {- dot -} hudson {- dot -} peter {- at -} GMAIL {- dot -} COM
Date: 2009-07-05

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. In my opinion the
superposition by O seems much better, after looking at the structure.

Apart from the difference in the RMSD, I would like to plot the RMSD values
against the no. of ca atoms superposed. That i only know to do through
superpose. Is there is any way to plot the RMSD values i get from O against
the no. of ca atoms. I would appreciate the help.

Thanks in advance.
peter

CCP4bb navigation

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

Previous message:
Subject: Re: CCP4 / Ubuntu 9.04 64-bit
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-07-04

Next message:
Subject: Re: RMSD value is different from O and superpose
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2009-07-05