On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote:
> So the riding hydrogen model is imperfect. At least with
> phenix.refine
> you can measure it, unlike the default behavior of REFMAC. (But you
> can
> tell it to write hydrogens out, I believe).
>
My impression is that default behavior of phenix.refine is the same - I
had to change parameters to include hydrogens in the output.
Without breaking any new ground, there is really no conflict here. Is
it a good idea to make a complete model description (including riding
hydrogens, input files, cif-files, special case restraints etc)
available for structures deposited in the PDB? Absolutely. But not in
this form, when model is implying that we know the protonation states of
all the atoms and has unreasonable geometry. For the example that I
provided, the rmsd_bonds for that particular group is 0.14A, certainly
unacceptable. Maybe one can use different record for these atoms, say
RIDING instead of ATOM. Thus "complete model" can be recovered and at
the same time the nature of these items is explicitly stated. In this
way riding hydrogens are clearly distinguished from those that are
actually refined at ultrahigh resolution.
Cheers,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
|