[phenixbb] phenix distorts ligand

Nigel Moriarty nwmoriarty at lbl.gov
Tue May 18 11:44:50 PDT 2010


Mustafa

Can you send me, directly, the input PDB and the resulting CIF file
generated by eLBOW.

Nigel

On Tue, May 18, 2010 at 10:47 AM, Mustafa Koksal <mkoksal at sas.upenn.edu> wrote:
> Hi,
> I have a problem in phenix refinement at 2.25 A resolution, data is 80%
> complete. I have protein, water, and ions in the .PDB file, and a ligand
> molecule that is distorted during refinement.
>
> I generated the pdb (with H atoms) with ChemDraw3D, edited the atom names
> etc. I used phenix.elbow to generate the .CIF file.
>
> Here is the first problem:
> Ligand has trans double bonds, which are written out by phenix.elbow as
> single rotatable bonds although I had correct connect records and H atoms in
> the .PDB file.
> I ran phenix.refine, it distorted the ligand, making double bonds not planar
> and nearly cis.
>
> Here is what I have tried:
> I edited the .CIF file to change these torsion agles to be CONSTANT and 180
> or 0 deg.
>
> Here is the second problem:
> phenix.refine still distorted the ligand.
>
> Here is what I have tried:
> I used optimize_wxc/wxu in phenix.refine to optimize the weight, to see if I
> overweighed the data.
>
> Here is the third problem:
> phenix.refine still distorted the ligand.
>
> Is there a way to solve this problem? Is there a way to tighten the
> constraints for the ligand only? I still do not understand why it even
> cannot keep the double bonds planar (and trans). I do not want to move back
> to good old CNS...
>
> Thanks to all,
> Mustafa
>
> --
> Mustafa Koksal
> Postdoctoral Fellow
> University of Pennsylvania
> Department of Chemistry
> Roy and Diana Vagelos Laboratories
> Office: 2090 IAST
> Office Phone: (215) 898-2227
> Mobile Phone: (267) 319-6443
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> Mawlana Jalal-ad-Din Rumi
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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
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