Re: [ccp4bb]: Averaging structures using optimize_average.inp

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Tristan Fiedler wrote:
> 
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> 
> I am dealing with the same issue that was posted to the CCP4BB about a
> year ago :
> 
> > [ccp4bb]: How to average coordinates?
> >
> >
> >
> >      To: "ccp4bb@dl.ac.uk" <ccp4bb@dl.ac.uk>
> >      Subject: [ccp4bb]: How to average coordinates?
> >      From: diane h peapus <dp72@cornell.edu>
> >      Date: Thu, 22 Feb 2001 21:53:51 -0500
> >      Sender: owner-ccp4bb@dl.ac.uk
> >
> >
> >
> > ***  For details on how to be removed from this list visit the  ***
> > ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> >
> >
> > Hi All:
> >
> > I'm looking for a program that can average several .pdb files
> > to give the average structure.  I got these .pdb files from
> > several different anneal runs using CNS.  I then ran CNS's
> > optimize_average.inp, which says that it...
> > "Finds optimum combination of coordinate files which produce
> > minimum free R-value from averaged structure factors."
> >
> > This tells me which of my .pdb files to average to get the
> > best Rfree... but doesn't output a .pdb file with the
> > averaged structures.   hummm...
> >
> > So, can anyone tell me a program that I can average my
> > structures, now that I know which will give the best Rfree?
> 
> No follow-up answers were posted to the CCP4BB, nor does anything useful
> come from a web search.
> 
> In order to use the best 4 structures (out of 10) listed in the end of
> the (CNS) optimize_average.list  file to obtain an SA omit map, should a
> single composite PDB be constructed (as suggested in the above posting)
> or should the best 4 (in this case) structures be input to CNS
> composite_omit_map.inp ?
> 
> Thank you for any suggestions,
> 
> tristan
> 
> --
> Tristan J. Fiedler, Ph.D.
> Malhotra Laboratory
> Department of Biochemistry & Molecular Biology
> University of Miami Medical School
> 
> t.fiedler@umiami.edu
> tfiedler@newssun.med.miami.edu


 There is a program superpose in the CCP4 suite. I believe it does an
excellent job -  written by Bob Diamond..

 However you have to have the same NUMBER of atoms in each pdb - I guess
you do?

 And I am not sure what it does about B factors and if there is any
weighting..
Eleanor Dodson