I think perhaps I should clarify what I've been doing. I've been
refining my structure using phenix.refine and had reached a fairly
satisfactory point with suitably low R-factors (21/25) and very
reasonable RMSDs for bonds and angles. At this point I ran my
structure through the molprobity server to take a closer look at
geometry and clashes. As going through the entire clash list by hand
can be very tedious I wanted to see if adding hydrogens in the riding
positions and refining again would help alleviate some of the clashes,
which it did.
Note, the refinements have been stable both before and after the
addition of the riding hydrogens. with no significant changes in R-
factors or geometry RMSDs. Also, the hydrogens are explicitly
excluded from Fcalc during refinement as the resolution of the data
would not warrant their inclusion.
So now at this point I'm simply trying to make some minor adjustments
to the model using RSR in coot and have happened upon the exploding
RNA residue / wandering hydrogen phenomenon. I have tried changing
the occupancy of the hydrogens to various values (0.01-1.0) using the
"Residue Info" menu option but it has no effect on RSR and is not
likely the culprit. I'll next try the changing the nomenclature to
see if that fixes the problem.
-Chris
On May 5, 2009, at 3:59 PM, William G. Scott wrote:
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.
