Hi Edward,
if I correctly understood this, you should be able to do it in
phenix.refine using constrained occupancy groups:
http://www.phenix-online.org/documentation/nightlies/1.4-173/refinement.htm#anch20
Please let me know if you have questions. If you send me the PDB file
and indicate the coupled conformations, I might be able to send you back
an example.
Pavel.
On 9/24/09 8:34 AM, Edward Collins wrote:
> Dear All,
> I have a protein with a small molecule inhibitor that appears to adopt
> two conformations. Unfortunately, one of the conformations that it
> adopts is the same location as a flexible loop. So, it seems that
> part of the molecule and the loop shift in a coordinated manner.
> Is there any way to model those alternate conformations in a
> refinement program? The positions clearly clash if I leave the loop
> and small molecule in place and vise versa.
> thanks for the help,
> -ed collins
> University of North Carolina
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