Hello Charles, where would I insert the “noe.setShowAllRestraints(True)” in the wrefine.py script?
best regards, Mark > On Mar 18, 2024, at 7:26 AM, Charles Schwieters <[email protected]> > wrote: > > !-------------------------------------------------------------------| > This Message Is From an Untrusted Sender > You have not previously corresponded with this sender. > |-------------------------------------------------------------------! > > > 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
