[phenixbb] Alternative conformation of ligand with near zero occupancy

Singh, Bishal b.singh at dkfz-heidelberg.de
Wed Nov 26 08:28:26 PST 2014

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 

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