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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

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 !)

Thanks again!

Joerg Mueller                 Department of Biochemistry
Phone +49-221-4706443         University of Cologne
                 6455         Zuelpicher Strasse 47
Fax   +49-221-4705092         50674 Koeln, Germany