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

Weiergräber, Oliver H. o.h.weiergraeber at fz-juelich.de
Thu Dec 3 09:52:09 PST 2020


Dear Pavel,

Could you briefly indicate which scenario makes this bug become virulent, so one can assess in which cases re-refinement with a newer version is necessary?
Obviously, distorted geometry is easy to spot, but side chains moving a bit out of density here and there are a gradual phenomenon which may occur for various reasons ...

Best,
Oliver


________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Pavel Afonine [pafonine at lbl.gov]
Sent: 03 December 2020 18:22
To: Boniecki, Michal; phenixbb at phenix-online.org
Subject: Re: [phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density

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<mailto: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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