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' hydroxyl of the RNA wanders during Real Space
Refinement. As it is only a single hydrogen per RNA residue and I can
manually place it where it needs to go after doing RSR, it is a
problem I can live with.
Thanks,
Chris
On May 6, 2009, at 6:06 AM, Paul Emsley wrote:
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 molprobity server to take a closer look at
geometry and clashes.
OK, so that's the issue, right there. Molprobity is a modern
program - using PDB v3 atom names. Coot uses the Refmac dictionary,
i.e. version 2.3 names. Coot does not recognise the new atom names
e.g. C1' (in Ar) or HB3 (in ARG) and so pushes them out with non-
bonded contact restraints.
If you want to use the output of molprobity with coot/Refmac
dictionary, then you will need to downgrade the molprobity output
file.
Yes, this needs to be fixed - upgrading and validating the new
dictionary is a substantial task.
For the record, Coot ignores the occupancy of the atoms when
refining. Adding hydrogens to a model should do reasonable (if not
good) things no matter the resolution of the data.
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.
Yes, it should.
Paul.
