On Fri, Oct 26, 2012 at 1:06 PM, Alexander Scouras
I was wondering if something like that was the idea, though I guess I might have expected the main chain nitrogen to also get an alternate conformation. Hydrogens are just second class atoms I guess, and that dihedral would be more important than actually moving the N.
When running iterative refinement between Phenix and Coot, adding altconfs as they come up, should you regularly be running ready_set (or anything else) after? I always just save the coordinates and then load that pdb in the next round of phenix.refine.
I would continually run phenix.ready_set in this case - actually, if you're using the phenix.refine GUI I think you can just click "Automatically add hydrogens to model" and everything else will be done automatically. (If not, that's a bug too!) Unless you are performing neutron refinement or some very specialized high-resolution enzymology, it is unlikely that you will actually care about preserving the hydrogen positions from round to round anyway. -Nat