[phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density
Pavel Afonine
pafonine at lbl.gov
Thu Dec 3 09:22:24 PST 2020
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
>>>
>>> ------------------------------------------------------------------------
>>>
>>> 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
>
> _______________________________________________
> 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/ee42e853/attachment.htm>
More information about the phenixbb
mailing list