Re: [ccp4bb] rmsd calculation

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

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

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From: "Bryan W {- dot -} Lepore" bryanlepore {- at -} MAIL {- dot -} UTEXAS {- dot -} EDU
Date: 2007-05-11

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

I would highly recommend Doug Theobald's program Theseus for this -
the pictures at www.theseus3d.org say it all. Theseus does maximum
likely hood superimpositions of multiple structures (i.e. NOT
pairwise against a "master" copy), and the real beauty of it is that
you don't have to pick which residues you want to superimpose.
Places where the whole set of structures show divergence are
effectively down-weighted and don't contribute much to the final
solution vs. least squares where every atom position has equal weight
and the "bad" parts screw up the alignment of the "good" parts. For
this, I would do a Theseus superposition of all the structures and
then analyze the set of superimposed structures by whatever method
you want (e.g. rmsd of variances in important sections of the
structures).

- Olve

-------------------------------------------------------
Olve Peersen
Associate Professor
Dept. of Biochemistry & Molecular Biology
1870 Campus Delivery
Colorado State University
Ft. Collins, CO 80523-1870
-------------------------------------------------------
970.491-0433 Office (MRB 279)
970.491-0271 Lab (MRB 149)
970.491-0494 Fax
Olve.Peersen@ColoState.edu
-------------------------------------------------------

On May 11, 2007, at 11:15 AM, Donnie Berkholz wrote:

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

Next message:
Subject: Laue for heavy atoms, etc.
From: "Bryan W {- dot -} Lepore" bryanlepore {- at -} MAIL {- dot -} UTEXAS {- dot -} EDU
Date: 2007-05-11