Re: [ccp4bb] rmsd calculation

- Protein crystallography

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

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Subject: Re: CCP4 GUI
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-11

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Subject: Re: xsect.dat=cossec.lib?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-11

Subject: Re: rmsd calculation
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-11

It is a bit clunky - you can use siperpose molecules - fit residues to
fit a selected range (1-40; 60-100 say) and write out a complete fitted
pdb file. Then you could use a VERY old program
compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb)
and it will match all pairs with the same RESIDUE ID and give the RMSD
distance

There is documentation for it.
Eleanor

Jenny wrote:
> Hi, All,
>
> I have a question about rmsd calculation.
>
> I have some pdbs (100 residues ) and these pdbs differ pretty much
> only the loop region 40-60. Is there any easy way that I can
> superimpose the fixed region ( 1-40,60-100) and then calculate the
> rmsd for the loop?I need to calculate for each pair, so if there is
> any script or program available to do this quickly, that would be great.
>
> Thanks.
>
> Jenny

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

Previous message:
Subject: Re: CCP4 GUI
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-11

Next message:
Subject: Re: xsect.dat=cossec.lib?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-11