Re: [ccp4bb] RMSD value is different from O and superpose

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

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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

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Subject: Re: RMSD value is different from O and superpose
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-07-05

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

Peter,

Depending on the method implemented in one software or another - I wouldn't
be surprised if some of them fall into local minima during gradient
optimization for best fit. Depending on how you define the region of
interest, there may also be ambiguity with respect to pair definition - this
may not be relevant if you are looking at exactly same regions of exactly
the same sequence.

I recommend LSQMAN from the Uppsala software package, as final verification.

Regarding plots of RMSD versus number of atoms - LSQMAN can be scripted
(externally, via e.g. Perl) to do that. I wouldn't be surprised if Coot can
also be scripted to do the exact same thing via Python.

Artem

"Nothing is built on stone; all is built on sand, but we must build as if
the sand were stone"

Jorge Luis Borges

_____

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of peter
hudson
Sent: Sunday, July 05, 2009 2:33 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] RMSD value is different from O and superpose

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

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

Previous message:
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

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Subject: Re: RMSD value is different from O and superpose
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-07-05