[phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density
pafonine at lbl.gov
Thu Dec 3 09:22:24 PST 2020
thanks for the info! Yes, there was a bug at some point that we fixed
right after we discovered it. So it's best to use the latest version
from nightly builds.
On 12/3/20 09:19, Boniecki, Michal wrote:
> I had similar case with Tyr side chain, but after installing latest
> upgrades worked fine
> On 12/3/20 11:16 AM, Pavel Afonine wrote:
>> CAUTION: External to USask. Verify sender and use caution with links
>> and attachments. Forward suspicious emails to phishing at usask.ca
>> Hi Igor,
>> 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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