[phenixbb] Modifications for Ca-binding site

[Keller, Jacob]

How does one change the ideal bond length/sigma in Phenix?

JPK

From: Nigel Moriarty [mailto:nwmoriarty at lbl.gov]
Sent: Tuesday, December 29, 2015 10:12 AM
To: Keller, Jacob
Cc: Boaz Shaanan; phenixbb at phenix-online.org
Subject: Re: [phenixbb] Modifications for Ca-binding site

Jacob

Boaz has some sage advice. I recommend not excluding the Ca-O coordination but changing the ideal to better reflect the distances in your files.

PS I'd also like the PDB files, directly, so as not to put noise on the list.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov<mailto:NWMoriarty at LBL.gov>
Fax   : 510-486-5909       Web  : CCI.LBL.gov<http://CCI.LBL.gov>

On Tue, Dec 29, 2015 at 5:49 AM, Keller, Jacob <kellerj at janelia.hhmi.org<mailto:kellerj at janelia.hhmi.org>> wrote:
Well, I think it's more of a data-vs-geometry battle, with the geometry dragging in the side chains towards the calciums, and the data pulling them out. When I real-space refine them in Coot, some of the Ca-O distances are pretty different from the "ideal" values. Maybe I could just exclude them from xyz refinement in Phenix after making sure they're correct in Coot? I'll give that a shot.

Kol tuv,

Jacob




-----Original Message-----
From: Boaz Shaanan [mailto:bshaanan at bgu.ac.il<mailto:bshaanan at bgu.ac.il>]
Sent: Tuesday, December 29, 2015 7:52 AM
To: Keller, Jacob; phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Subject: RE: Modifications for Ca-binding site

Hi Jacob,

Sucking-up neighboring residues into the  Calcium (or other heavier atoms) density is a known issue. Turning-off the Ca-O or other distance restraints around the Calcium is the last thing you want to do, in my experience. You'd better check those distance restraints and verify that they're compatible with the distances in other (preferably high resolution, of course) structures with calcium binding sites similar to yours and then make sure they're given the appropriate weight during refinement. That's my view but Pavel will give you more advices I'm sure.

  Cheers,

            Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan at bgu.ac.il<mailto:bshaanan at bgu.ac.il>
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





________________________________________
From: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> [phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>] on behalf of Keller, Jacob [kellerj at janelia.hhmi.org<mailto:kellerj at janelia.hhmi.org>]
Sent: Tuesday, December 29, 2015 4:44 AM
To: phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Subject: [phenixbb] Modifications for Ca-binding site

I am getting a lot of problems with my calcium binding sites--there is clear density for the calciums and the protein side chains, but Phenix keeps sucking the side chains out of their density towards the calciums and also the calciums show some positive difference density, perhaps due to too-high b-factors (or potentially partial occupancy by Na?). I think what might work best is to turn off the Ca-O bond length restraints somehow, but don't see where/how to do that. I tried releasing them from geometrical restraints, but that made things worse, since things went haywire in the sidechains themselves.

Is it possible to make Phenix ignore the Ca-O bond distance restraints?

JPK

*******************************************
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kellerj at janelia.hhmi.org<mailto:kellerj at janelia.hhmi.org>
*******************************************



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