[phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density
pafonine at lbl.gov
Thu Dec 3 09:16:16 PST 2020
please make sure to try the same refinement using the latest Phenix
version from nightly builds first:
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!
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 <folmerf at gmail.com
> <mailto:folmerf at 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
> tor. 3. dec. 2020 05.48 skrev Igor Petrik <petrik1 at illinois.edu
> <mailto:petrik1 at 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?
> - Igor Petrik, PhD
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