On Wed, 2010-09-15 at 07:57 -0700, Pavel Afonine wrote:
> if you refined your structure with H, then you should deposit it with
> H
sure. But the structure is not *refined with hydrogens* when they are
in predicted positions. Following the same logic one could suggest that
electron density should be deposited, since we can approximate it. I
think it's useful to limit the information presented in a pdb-file to
what was actually refined + specific instructions on how the refinement
was done.
> Any post-refinement manipulation on final refined model
> is bad since it tends to invalidate the reported statistics
...
> Indeed, let's not add more
> inconsistencies to the database because of a fear that insufficiently
> trained people may misinterpret it.
I wouldn't call it a post-refinement manipulation, as nothing was really
changed (afaiu, in most cases riding hydrogens are placed automatically
by the program and not manipulated by user). On a digressing point, you
might be underestimating the problem of "misinterpretation by
insufficiently trained people".
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
