[phenixbb] radiation damaged residues occupancy refinement

[Mikalai Lapkouski]

Hello,

I have a 1.2A model with the signs of radiation damage, judged by the
negative peaks around the carboxyls (atoms CD, OE1 and OE2) of glutamates
probably due to decarboxylation. I wan to refine occupancy of those atoms
to account for negative density. What is the proper way of doing it?

I tried to set the occupancy for those atoms 0.8 and refine individually.
But obviously occupancies for those atoms are individually refined to
different values which I dont think is the right way. Is there a way of how
to refine occupancies for those atoms so that they remain identical after
refinement (say all have 0.6)?
Or is there another procedure of how to deal with refinement of radiation
damaged side-chains?

Any suggestions, please?

Thank you

Nick
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