[phenixbb] Alternative conformation of ligand with near zero occupancy

Pavel Afonine pafonine at lbl.gov
Wed Nov 26 08:34:47 PST 2014

Hello Singh,

this sounds like occupancy group is not defined correctly.
You can read more about this here:

or you can send me PDB file before and after refinement and I will 
suggest a solution.


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
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