Multiple conformation, two ligands
Dear Phenix Community, I tried to model two ligands one of which has two conformations. In other words, the two scenarios are: 1) ligand X with conformation A (XA, 75% occupancy); 2) ligand X with conformation B (XB, 25% occupancy) plus another ligand Y. However, the problem is ligand Y will have steric clash with ligand XA. If I rename ligand X and Y to the same residue name then I do not know how to define the CIF file. I apologize if this question was asked before and I do not know how Phenix or other refinement can deal with multiple conformation a group of ligands. Thanks. Happy new year! Yang Hai Christianson Lab University of Pennsylvania
I recently had to do this: i.e refine two different ligands in same binding site. I did this keeping ligands in same chain with same resid, using altlocs for the different ligands, and this refined well. If you can get cif files for X and Y at full occupancy, then I think you should be able to use these when you refine occupancies with the altloc flags set. Good luck. ________________________________________ From: YANG HAI [[email protected]] Sent: Tuesday, December 31, 2013 9:03 PM To: [email protected] Subject: [phenixbb] Multiple conformation, two ligands Dear Phenix Community, I tried to model two ligands one of which has two conformations. In other words, the two scenarios are: 1) ligand X with conformation A (XA, 75% occupancy); 2) ligand X with conformation B (XB, 25% occupancy) plus another ligand Y. However, the problem is ligand Y will have steric clash with ligand XA. If I rename ligand X and Y to the same residue name then I do not know how to define the CIF file. I apologize if this question was asked before and I do not know how Phenix or other refinement can deal with multiple conformation a group of ligands. Thanks. Happy new year! Yang Hai Christianson Lab University of Pennsylvania
Hello, if following manual does not help: http://phenix-online.org/documentation/refinement.htm#anch111 please send me data and model files (to me directly!), indicate atoms in question and I will send you back working example. Pavel On 12/31/13, 6:03 PM, YANG HAI wrote:
Dear Phenix Community, I tried to model two ligands one of which has two conformations. In other words, the two scenarios are: 1) ligand X with conformation A (XA, 75% occupancy); 2) ligand X with conformation B (XB, 25% occupancy) plus another ligand Y. However, the problem is ligand Y will have steric clash with ligand XA. If I rename ligand X and Y to the same residue name then I do not know how to define the CIF file. I apologize if this question was asked before and I do not know how Phenix or other refinement can deal with multiple conformation a group of ligands. Thanks.
Happy new year!
Yang Hai Christianson Lab University of Pennsylvania
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participants (3)
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Mayer, Mark (NIH/NICHD) [E] -
Pavel Afonine -
YANG HAI