[phenixbb] phenix distorts ligand
Mustafa Koksal
mkoksal at sas.upenn.edu
Tue May 18 10:47:40 PDT 2010
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
Mail Address: 231 S. 34th St, Philadelphia 19104, USA
--
"If you grant me a pen, I shall destroy swords and spears"
Mawlana Jalal-ad-Din Rumi
--
More information about the phenixbb
mailing list