[phenixbb] Multiple conformation, two ligands

Mayer, Mark (NIH/NICHD) [E] mayerm at mail.nih.gov
Tue Dec 31 18:38:52 PST 2013

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 [yanghai at sas.upenn.edu]
Sent: Tuesday, December 31, 2013 9:03 PM
To: phenixbb at phenix-online.org
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.

Happy new year!

Yang Hai
Christianson Lab
University of Pennsylvania

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