Hello Singh, this sounds like occupancy group is not defined correctly. You can read more about this here: http://phenix-online.org/documentation/reference/refinement.html#occupancy-r... or you can send me PDB file before and after refinement and I will suggest a solution. Pavel On 11/26/14 8:28 AM, Singh, Bishal wrote:

Hello everybody, I thank you for clarifying my previous doubts. Your suggestions matter a lot to me. Here I have another doubt. I have structure of a protein in complex with triglycan (fucose-galactose-galactose). The terminal galactose of this triglycan possesses two conformations with occupancies 0.4 and 0.6. In order to satisfy the geometric parameters of this triglycan, I derived the alternative conformation of fucose and the central galactose as well. Then I performed occupancy refinement. The occupancy of alternative central galactose is 0.06 and that of alternative fucose is 0.00. Now the question is, should I delete this fucose of zero occupancy or keep it to maintain the geometric parameters of triglycan? I am looking forward for your opinion. If you like I can provide a snapshot of ligand with electron density.

With regards, Bishal Singh PhD student DKFZ, University of Heidelberg, Germany _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb