[phenixbb] multiple ligand conformations

Leonard Thomas lmthomas at ou.edu
Fri Nov 18 10:36:44 PST 2011

Hello All,

One of the groups here has run into a problem in the refinement of  
their structure or more specifically a ligand bound to the structure.   
Through a series of other experiments they know that a photo reaction  
occurs to the compound when exposed to high flux as found at your  
everyday synchrotron source.  The exposure changes the bonding such  
that there are two conformations with a bit in between obviously.    
They collected 360 degrees worth of data and if the data is split you  
can model the two conformations depending which half of the data you  
use.  They are trying to refine with all of the data and modeling of  
the ligand into the two conformations.   In refmac they can model this  
with no problem but in Phenix the ligand adopts a chemically wrong  
conformation, sort of a halfway point between the two chemically  
relevant conformations.  They have used Phenix to do similar  
refinements on other structures but it appears either the last release  
or the latest release is causing problems.  They have started out with  
everything from 50% occupancy to shifting it towards on one  
conformation or the other and the ligand always ends up in the  
chemically wrong position.  Data is in the 1.4-1.5 ang. range.


Thanks in advance.

Leonard Thomas Ph.D.
Macromolecular Crystallography Laboratory Manager
University of Oklahoma
Department of Chemistry and Biochemistry
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019-5251

lmthomas at ou.edu
Office: (405)325-1126
Lab: (405)325-7571

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