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

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

Previous message:
Subject: Re: ctruncate problems
From: Justin Lecher j {- dot -} lecher {- at -} FZ-JUELICH {- dot -} DE
Date: 2009-07-08

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Subject: Re: Why NCS doesn't help?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-07-08

Subject: Re: RMSD value is different from O and superpose
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-07-08

Are the chains numbered differently?
the SUPERPOSE LSQ program requires you to specify which residues to
superpose.

And any RMS is wildly distorted by a few outliers..
Look at the list of > average differences to see if you have such a problem.

The SSM superposition excludes outliers automatically.
Eleanor

Pavel Afonine wrote:
> 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
>
>

CCP4bb navigation

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

Previous message:
Subject: Re: ctruncate problems
From: Justin Lecher j {- dot -} lecher {- at -} FZ-JUELICH {- dot -} DE
Date: 2009-07-08

Next message:
Subject: Re: Why NCS doesn't help?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-07-08