On Wed, 2010-09-15 at 09:14 -0700, Dale Tronrud wrote:
> I know that in my refinements I manually move the hydrogen
> from one nitrogen to the other in a couple Histidine side chains,
> and have created my own rules for hydrogen generation in co-factors.
>
Excellent point. And I believe in this case you are perfectly justified
to either place a comment about this in the header or indeed deposit
hydrogens. But I suspect that this is not what happens in most cases
with, say, 2A refinement using refmac. The program is simply used to
autogenerate the riding hydrogens, thus making the whole thing perfectly
reproducible (with caveats). It may be seen as misleading when one
deposits these hydrogens and they appear to have the same standing as
other atoms which were actually refined.
On a related issue, I believe it's long overdue policy change that all
the input files, e.g. command scripts/cif-files for ligands/.ins files
etc. should be attached to a PDB deposition.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
