Hi, 1) Occupancy refinement and alternative conformations - explained here (in great detail, I hope): http://phenix-online.org/documentation/refinement.htm#anch20 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: http://www.rcsb.org/pdb/files/1EJG.pdb You can even have a mixture of two or more residues sharing the space. http://cci.lbl.gov/~afonine/for_ccp4/PavelAfonine_PHENIX.pdf 3) Have a look at occupancy refinement page here: http://cci.lbl.gov/~afonine/for_ccp4/PavelAfonine_PHENIX.pdf 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. Pavel. On 3/21/11 6:35 AM, [email protected] 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