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

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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

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

Hi Peter,

you can also try superposition option in phenix:

phenix.superpose_pdbs [pdb_file_fixed] [pdb_file_moving] [parameter_file]

where optionally you can provide atom selections for "fixed" and "moving".

Pavel.

On 7/5/09 12:33 AM, 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. 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: Re: RMSD value is different from O and superpose
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2009-07-05

Next 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