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

[Pavel Afonine]

Hi Michal,

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.

Pavel

On 12/3/20 09:19, Boniecki, Michal wrote:
>
> I had similar case with Tyr side chain, but after installing latest 
> upgrades worked fine
>
> Michal
>
>
> 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:
>>
>> 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 <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
>>>
>>>     Folmer
>>>
>>>
>>>
>>>     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?
>>>
>>>         Thanks,
>>>         - Igor Petrik, PhD
>>>
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