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

Boniecki, Michal mtb101 at usask.ca
Thu Dec 3 09:19:34 PST 2020


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 
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>
> 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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