[phenixbb] Modifications for Ca-binding site

Nigel Moriarty nwmoriarty at lbl.gov
Wed Dec 30 07:11:57 PST 2015


Jacob

Once again Boaz is leading you in the correct direction. You did send me a
*.metals.edits file. You just need to change the ideal distances in this
file.

On another point, I ran a refinement with your inputs and the values don't
seem a long way off. However, I'd wait for Pavel to take a look because the
density around the Calcium ion itself seems unusual.

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
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Wed, Dec 30, 2015 at 6:27 AM, Boaz Shaanan <bshaanan at bgu.ac.il> wrote:

> Hi Jacob,
>
> My guess is that answer (or hint) is here (taken from this link :
> https://www.phenix-online.org/documentation/faqs/refine.html#targets-and-restraints):
>
>
> *I have ions very close to water molecules/protein atoms, and
> phenix.refine keeps tring to move them apart. How can I prevent this?*
>
> Use phenix.ready_set or *phenix.metal_coordination* to generate custom
> bond (and optionally, bond angle) restraints, which will be output to a
> parameter file ending in ".edits". If you are using the PHENIX GUI, there
> is a toolbar button for ReadySet in the phenix.refine interface, which will
> automatically load the output files for use in phenix.refine.
>
> I have not used it myself but I assume that the sigmas for the restraints
> would be in the *.edits files that you'll generate.
>
> Hope this helps.
>
>             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 <bshaanan at bgu.ac.il> Phone: 972-8-647-2220  Skype:
> boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710    *
>
>
>
>
>
> ------------------------------
> *From:* Keller, Jacob [kellerj at janelia.hhmi.org]
> *Sent:* Wednesday, December 30, 2015 4:09 PM
> *To:* Nigel Moriarty
> *Cc:* בעז שאנן; phenixbb at phenix-online.org
> *Subject:* RE: [phenixbb] Modifications for Ca-binding site
>
> 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
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
>
>
> On Tue, Dec 29, 2015 at 5:49 AM, Keller, Jacob <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]
> Sent: Tuesday, December 29, 2015 7:52 AM
> To: Keller, Jacob; 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
> 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 [
> phenixbb-bounces at phenix-online.org] on behalf of Keller, Jacob [
> kellerj at janelia.hhmi.org]
> Sent: Tuesday, December 29, 2015 4:44 AM
> To: 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
> *******************************************
>
>
>
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