[phenixbb] build two helix run in opposite direction and set half occupancy or each in Coot

Pavel Afonine pafonine at lbl.gov
Fri Apr 29 18:55:28 PDT 2016

> One thing I learned is that: beside setting half occupancy, I also 
> need to set altloc (alternative locations), so that the subsequent 
> refine program (either Refmac or Phenix) would not think two peptides 
> are too close and have repulsion to each other.

If these are alternative conformations then starting occupancy does not 
matter - phenix.refine does not use occupancy value to decided about how 
to refine occupancies of atoms in alternative conformations.

All the best,

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