Dear Igor There's a phenix bulletin board for question like this, which is where you should post the question. ( I crosspost here)
I would choose to not do the real space refinement in phenix.refine during the last rounds of refinement of a model, when sidechain positions are essentially correct. I hope this helps Folmer tor. 3. dec. 2020 05.48 skrev Igor Petrik <[email protected]>: > I am refining a 1.71A X-ray structure with phenix refine. I have > everything modelled in - ~150 residues in the ASU and a heme - and my > R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out > that two of my sidechains have distorted geometries. One is a His, and > looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct > geometry, but the actual coordinates that phenix refine produce don't lie > in that density; there are significant difference map peaks showing that > the coordinates are in the wrong place. If I use real space refine in Coot > to put the coordinates back into the correct density and refine it again in > phenix, they get distorted again. > > What settings in phenix should I check to try to get it to properly refine > the coordinates? > > Thanks, > - Igor Petrik, PhD > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
