On May 5, 2009, at 3:16 PM, CK wrote:
Hi all,
I am refining a structure that contains RNA. I've added hydrogens
in the riding positions to help with maintaining proper geometry
during refinement. However, when I go to adjust the model between
refinements in coot using Real Space Refine (or even Regularize for
that matter) the RNA "explodes" with atoms going every which way.
This didn't happen before I had added in hydrogens (with Molprobity
via Reduce). Also, when I Real Space Refine residues from the
protein portion, the heavy atoms (C, O, N) behave normally while
about half of the riding hydrogens go wandering off. Any particular
reason why this might be happening?
Hydrogen can be quite explosive. Have you tried helium?
But seriously, if the program you used to hydrogenate uses a
nomenclature that coot/refmac doesn't expect, this could happen. Also
the zero occupancy might be the culprit.
However you mentioned that without hydrogens it was hard to maintain
proper geometry. This might be a cause for concern, or re-examination
of the structure and its density.
