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
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 -- _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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