[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
> 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
>>
>> ------------------------------------------------------------------------
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe:phenixbb-leave at phenix-online.org
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20201203/cee8a45a/attachment.htm>
More information about the phenixbb
mailing list