Re: [ccp4bb] rmsd calculation

Protein crystallography Programs for crystallography X-ray detectors
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CCP4bb <-- 2007 <-- May 2007 <-- 11 May 2007

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Subject: Bioinformatics 2007 conference, June 4 – 7, 2007, in Umeå, Sweden
From: Uwe Sauer uwe {- at -} UCMP {- dot -} UMU {- dot -} SE
Date: 2007-05-11

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Subject: Re: rmsd calculation
From: Olve Peersen Olve {- dot -} Peersen {- at -} COLOSTATE {- dot -} EDU
Date: 2007-05-11

Subject: Re: rmsd calculation
From: Donnie Berkholz dberkholz {- at -} GENTOO {- dot -} ORG
Date: 2007-05-11

Eleanor Dodson wrote:
> 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.

There's a nice (non-CCP4) program called ProFit that does a pretty nice
job of superimposing with a lot of flexibility.

Thanks,
Donnie

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CCP4bb <-- 2007 <-- May 2007 <-- 11 May 2007

Previous message:
Subject: Bioinformatics 2007 conference, June 4 – 7, 2007, in Umeå, Sweden
From: Uwe Sauer uwe {- at -} UCMP {- dot -} UMU {- dot -} SE
Date: 2007-05-11

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Subject: Re: rmsd calculation
From: Olve Peersen Olve {- dot -} Peersen {- at -} COLOSTATE {- dot -} EDU
Date: 2007-05-11