[phenixbb] refining multiple conformations

Kendall Nettles knettles at scripps.edu
Mon Aug 6 07:52:50 PDT 2012

We have a structure with the ligand showing two overlapping conformers. When we refine it with both conformers separately, it is pretty clear that there are substantial differences in the protein as a result, for about a third of the protein chain. My question is, would it be better to try to define altloc for those specific regions, or would it be OK to refine with two entire alternate protein chains? There is also a second protein chain that shows only a single binding mode for the ligand.  It's a 2.0 angstrom structure with 4000 atoms and 27,000 reflections. The yellow map goes with the green model in the attached pic. Also, do we want to let each amino acid have its own occupancy? or should one ligand copy and one chain all have the same occupancy? I'm leaning towards the latter since the differences should be directly tied to the ligand binding mode.
Kendall Nettles

[cid:4B7930EE-1BBA-4082-A15C-AD5F120D60C5 at fl.ad.scripps.edu]
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