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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
Roberto Steiner wrote:
Annotation: CNS has no implementation to refine anisotropic temerature
He wrote his own jiffies to calculate characteristic parameters from
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
Biotech Validation Suite for Protein Structures (WHAT_CHECK, PROCHECK,
WHAT_CHECK (WHAT_IF) (the program is free for academic users)
(better to have also DSSP to utilize all options !)
Joerg Mueller Department of Biochemistry
Phone +49-221-4706443 University of Cologne
6455 Zuelpicher Strasse 47
Fax +49-221-4705092 50674 Koeln, Germany