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

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, Pavel