Yes you are absolutely right. I believe the problem is the difficulty of fitting valine, leucine and isoleucine rotomers and sidechains to what are essentially "blobs" of map density. Refinement has a hard time with this. I guess we have to stick with the experimental density.
Best Ray -------------------------------------------- On Sun, 3/10/19, Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: Subject: Re: [ccp4bb] Protein modeling issue To: CCP4BB@JISCMAIL.AC.UK Date: Sunday, March 10, 2019, 3:40 PM 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
