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[ccp4bb]: Summary: validation of protein crystal structures
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The question was:
> I have refined a high resolution crystal structure using various program
> packages (cns, refmac, shelx). For the comparison and validation of the
> models I would like to get some statistics such as rmsd of chiral
> volume, bond length, bond angles, torsion angles, contacts between non
> bonded atoms etc. (the refmac output includes these information).
> I am not searching for a program which produces plots (procheck) or
> individual rmsd. I would like to have overall values.
> Is there a program able to do this and is such an analyse reasonable to
> compare the models?
Manfred Weiss wrote:
This analysis only makes sense if the used restraints for all programs
would be comparable. Example: XPLOR/CNS defines chiral volumes as
improper dehydrals.
Roberto Steiner wrote:
Annotation: CNS has no implementation to refine anisotropic temerature
factor refinement.
He wrote his own jiffies to calculate characteristic parameters from
SHELXL outputs.
Eleanor Dodson:
The easiest way to compare results is take all the models and run each
of them through REFMAC for 1 cycle only;
The Initial statistics will give you a direct comparison..
Whether or not any of these statistics tell you that one model is
better or worse than another is of course another matter!
Flip Hoedemaeker and Gali Prag:
Some useful web sites are
RCSB validation server
http://pdb.rutgers.edu/validate/
Biotech Validation Suite for Protein Structures (WHAT_CHECK, PROCHECK,
PROVE):
http://biotech.embl-heidelberg.de:8400/
or
WHAT_CHECK (WHAT_IF) (the program is free for academic users)
http://www.sander.embl-heidelberg.de/whatcheck
(better to have also DSSP to utilize all options !)
Thanks again!
Joerg
--
Joerg Mueller Department of Biochemistry
Phone +49-221-4706443 University of Cologne
6455 Zuelpicher Strasse 47
Fax +49-221-4705092 50674 Koeln, Germany
http://www.uni-koeln.de/math-nat-fak/biochemie/ds/dsak_e.htm