Hi Subhani,
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?
I'm sure I fully understood your question. Once you correctly formatted the PDB file (assigned altloc identifiers to corresponding conformers) just run phenix.refine and then inspect the refined model in the map. You don't need to change manually the occupancy values, coordinates, etc. For details see: http://www.phenix-online.org/documentation/refinement.htm#anch22 Let me know if you have any questions or problems with this. Pavel