Thanks for the advice Pavel! I don't want to celebrate prematurely, but I just re-ran the same refinement in both the stable and in nightly 4070, and it _seems_ to be corrected in the nightly. Will let you know if it pops up again.
- Igor Petrik, PhD On Thu, Dec 3, 2020 at 9:16 AM Pavel Afonine <[email protected]> wrote: > Hi Igor, > > please make sure to try the same refinement using the latest Phenix > version from nightly builds first: > > http://phenix-online.org/download/nightly_builds.cgi > > The latest I see here is 1.19rc7-4070. > > Chances are the version you used had a bug that we fixed by now. > > If the problem persists please go ahead and send me inputs and indicate > residues that are bad and I will investigate right away! > > Pavel > > On 12/3/20 08:42, Igor Petrik wrote: > > 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 <[email protected]> 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 <[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 >>> >> > _______________________________________________ > phenixbb mailing > [email protected]http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: [email protected] > > > ######################################################################## 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/
