For anyone that is interested, it appears as if the Refmac monomer
library has the hydrogen on the 2' hydroxyl of RNA backbone named as
HO2*, different from pdb v2.3 nomenclature which has it listed as
2HO*. Simply editing my PDB to reflect the Refmac library name makes
the hydrogen behave
Fortunately, the molprobity server has an option for converting your
PDB file back to v2.3 and this seems to have fixed almost everything.
My RNA is no longer explosive and the hydrogens in the protein
portions don't go wandering off. The only remaining issue is that the
hydrogen on the 2
CK wrote:
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 mo
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 molprobit
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
Also, does the resolution of your data warrant including the hydrogens
in the model ? Can you actually see them ?
You can add them in their riding positions, which may help stablise
your refinement, but not write them out to the coordinate file (uncheck
"and output to coordinate file in the GU
Chris,
The hydrogens are at 0 occupancy so their positions are not
refined...the other atoms at non-zero occupancy do move leaving the Hs
behind..set the hydrogens to non-zero occupancy (eg. 0.01).
HTH,
Iain
CK wrote:
Hi all,
I am refining a structure that contains RNA. I've added hydr
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) t
