[phenixbb] refinement for ligands with alternative conformation

Pavel Afonine pafonine at lbl.gov
Mon Mar 21 08:41:08 PDT 2011


1) Occupancy refinement and alternative conformations - explained here 
(in great detail, I hope):

2) If your input PDB file contains alternative conformations (two or 
more entries corresponding to each alternative location) then everything 
will be done automatically - you don't need to do anything. For example, 
something like this would be handled automatically:
You can even have a mixture of two or more residues sharing the space.

3) Have a look at occupancy refinement page here:
there is a page with a list of examples there.

If you still having problems with this then please send me the data and 
model files, and I will send you back a working refinement example.


On 3/21/11 6:35 AM, zhengyi at msu.edu wrote:
> Hello,
> I am working on the refinement of a structure about 2.8A, which the 
> substrate ligand has an odd conformation. A blob of negative 
> difference density about 4.8 sigma between the one portion of the 
> ligand and the other. If I break down the ligand into two parts, the 
> negative density disappears, however, one part of the ligands does not 
> fit well. We suspect a mixture of conformations.
> Any suggestions would be appreciated on how to setup refinement for 
> ligands with alternative conformation.
> Many thanks,
> Yi Zheng
> Department of Biochemistry
> Michigan State University

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