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A script for averaging zillions NMR structures in a PDB file

Simon M. Brocklehurst smb at bioch.ox.ac.uk
Thu Aug 10 14:54:41 EST 1995

abonvin at LAPLACE.CSB.YALE.EDU ("Alexandre Bonvin") wrote:
>>  Does anybody out there have a script to generate an averaged structure out
>> of those 20-50 structures that are quite often deposited in one file in the
>> PDB ? There is an Xplor script to generate the averaged structure from the
>> various NMR models as long as they're in separate files, but that wouldn't
>> help with such a PDB file as it is. I would appreciate if one could send me
>> (and probably others) a script  that would save the manual hand editing
>> involved.
>PROCHECK_NMR should do the job. It can handle PDB files with several structures  
>and generates an average structure.  For info on PROCHECK check the PDB web  
>| Alexandre Bonvin PhD           | Phone: (203) 432-5066                 |
>| Mol. Biophys. & Biochemistry   | Fax:   (203) 432-3923                 |
>| Yale University                | Email: abonvin at laplace.csb.yale.edu   |
>| New Haven CT 06520-8114, USA   | http://xplor.csb.yale.edu             |

  Thought it might be worth pointing out that PROCHECK_NMR doesn't itself do
any "optimal" superposition of structures, but if the structures in this
"multiple model" file are superimposed in the way that you want them to be,
then PROCHECK_NMR is fine to use.  If the file is out of the PDB, they _should_
be superimposed in some way or another of course.
|  ,_ o     Simon M. Brocklehurst,
| /  //\,   Oxford Centre for Molecular Sciences, Department of Biochemistry,
|   \>> |   University of Oxford, Oxford, UK.
|    \\,    E-mail: smb at bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/

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