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Dear ZhiYi, do you have any double conformations that include backbone atoms? To my knowledge, WHATCHECK has problems with dual/alternate/double conformations. IMHO, WHATCHECK serves the average. Your structure shouldn't be too bad, but also not too good. I had my own WHATCHECK experience. After a long and tedious refinement of a 1 Angstrom resolution structure, the program basically told me to throw the structure into the bin. I took the liberty to disagree. cheers, Rob Meijers --- Gerard DVD Kleywegt <[EMAIL PROTECTED]> wrote: > *** For details on how to be removed from this list > visit the *** > *** CCP4 home page http://www.ccp4.ac.uk > *** > > > > Dear Gerard, > > I use one monomer (6 monomers per asu) to run > whatcheck again, and got a report: > > > > Structure Z-scores, positive is better than > average: > > 2nd generation packing quality : -0.126 > > Ramachandran plot appearance : 0.197 > > chi-1/chi-2 rotamer normality : 2.482 > > Backbone conformation : -7.432 (bad) > > very strange. if you leave out the other 5 monomers, > one might have expected a > slightly reduced packing score, but it doesn't > explain the unusual backbone > score (esp. given the fact that your protein is > all-helical). all other > statistics seem normal. i'm as puzzled as you are. > > --dvd > > ****************************************************************** > Gerard J. Kleywegt > [Research Fellow of the Royal Swedish Academy > of Sciences] > Dept. of Cell & Molecular Biology University of > Uppsala > Biomedical Centre Box 596 > SE-751 24 Uppsala SWEDEN > > http://xray.bmc.uu.se/gerard/ > mailto:[EMAIL PROTECTED] > ****************************************************************** > The opinions in this message are fictional. Any > similarity > to actual opinions, living or dead, is purely > coincidental. > ****************************************************************** > > __________________________________________ Yahoo! DSL Something to write home about. Just $16.99/mo. or less. dsl.yahoo.com
