[phenixbb] table 1 no CC values, selenomethionine occupancy refinement

Pavel Afonine pafonine at lbl.gov
Thu Apr 4 19:39:09 PDT 2013

Hi Georg,

> 2. I see some negative density around the seleniums in my 
> selenomethionine labeled protein. I guess this is due to radiation 
> damage. Is the accepted standard to do occupancy refinement for just 
> the sidechain, or just parts of the sidechain, the whole residue  or 
> just leave it like it is.

if there is a chance that seleniums in MSE are partially occupied then 
refining their occupancy is a good idea. This would do it

refinement.refine.occupancies {
   individual = element SE

Make sure "occupancies" included into refinement strategy (it's on by 


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