Hello Mark-- > > I am working on reporting statistics for a structure of a Zn-finger > protein. The journal that we would like to send the work to asks us > to report the statistics for bond length, bond angle and improper > violations as the mean and standard deviation, rather than the > RMSD. When I look in the .sa.viol viols files I see the identity and > magnitude of violations for ANGL, BOND and IMPR are listed above a > defined threshold. Is there an easy way to calculate or output the > mean and SD, or can I alter the threshold to output all violations > from ideal values in the .sa.viols files, or do this for a list of > the 20 lowest overall energy structures?
I'm not entirely certain what the journal is looking for: the average (and SD) amount of violation? The average of the absolute value of the zero-threshold violation amount? You can specify noe.setShowAllRestraints(True) to get info on all restraints in the .viols file. Then you can calculate whichever value required. best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
