Thanks Nigel, I will put together the input and output file from my latest refinement and send them to you and Pavel later today.
- Igor Petrik, PhD On Wed, Dec 2, 2020 at 9:46 PM Folmer Fredslund <folm...@gmail.com> wrote: > 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 <petr...@illinois.edu>: > >> 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/