Both REFMAC and COOT have an option to regularise (coot) or idealise (refmac) a structure. These options will correct bad gemetry if possible, but pay no attention to the fit to density.
In general i think it is sensible to inspect the map for regions where there are serious errors high lighted. However if the resolution is low, or the region of the protein is poorly ordered, it may be difficult to see what needs fixing. Eleanor On Sat, 9 Mar 2019 at 21:23, Raymond Brown <ray-br...@att.net> wrote: > Hi folks, > > The WHATIF server found the following issue in evaluating a protein > structure. > > Structure Z-scores, positive is better than average: > > chi-1 / chi-2 rotamer normality : -7.278 (bad ( > -3.8, 1.6) ) > > > RMS Z-scores, should be close to 1.0: > > Improper dihedral distribution : 2.025 (loose) > > > Does anyone have a suggestion of what can be done for example > in Coot or Refmac5 to improve or fix these results? > > > Many thanks > Ray Brown > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
