Another idea is to use qfit: http://smb.slac.stanford.edu/qFitServer/qFit.jsp On Mon, Feb 13, 2012 at 3:58 PM, Nathaniel Echols wrote:

On Mon, Feb 13, 2012 at 11:53 AM, Subhani Bandara wrote:

...

I have a protein where three consecutive amino acids have alternative conformations. I edited the PDB file to have those altloc and made total occupancy of A and B to 1.00. But after refinement both A and B are overlapping and I could see the positive density for one conformation away from that (may be b'se I didn't change coordinates of B conformation). How can I move the B altloc in to the positive density. Do I have to edit the coordinates on PDB and if so how can Ido that?

phenix.refine won't automatically move the alternate conformations for you - you need to do this with Coot. An alternative is to try simulated annealing to try to "shake" them into the correct place, but rebuilding in Coot is probably going to be faster and more accurate.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb