[phenixbb] "H" atom refining occupancy with previous altconf residue in sequence

Nathaniel Echols nechols at lbl.gov
Fri Oct 26 13:20:41 PDT 2012

On Fri, Oct 26, 2012 at 1:06 PM, Alexander Scouras <scouras at berkeley.edu> wrote:
> 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.


More information about the phenixbb mailing list