[phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density

Igor Petrik petrik1 at illinois.edu
Thu Dec 3 08:42:25 PST 2020

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> 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 <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?
>> Thanks,
>> - Igor Petrik, PhD
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