[phenixbb] refinement for ligands with alternative conformation
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:
> 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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