Hello,
a few points to balance the discussion:
- if you refined your structure without H then it's obviously ok to
deposit it without H;
- if you refined your structure with H, then you should deposit it with
H, as your refinement software outputs it (if your software uses H but
removes it automatically for you - then it least it's not your
responsibility). Any post-refinement manipulation on final refined model
is bad since it tends to invalidate the reported statistics (R-factors,
for instance), which is illustrated in this paper (section 3.1.5: J.
Appl. Cryst. (2010). 43, 669-676). Indeed, let's not add more
inconsistencies to the database because of a fear that insufficiently
trained people may misinterpret it.
- removing H, if really needed, is a matter of one trivial command, but
adding them back the exact same way they were originally is less
straightforward.
- I agree that the X-H distances used in refinement and in validation
are slightly different, although I'm not sure how much of difference
that would make for validation.
Pavel.
On 9/14/10 10:38 PM, Ed Pozharski wrote:
Mark,
On Tue, 2010-09-14 at 13:34 -0400, Dr. Mark Mayer wrote:
Where does the crystallographic community stand
on deposition of coordinates with riding
hydrogens?
Surely community is divided on this. There could be arguments made both
ways. Personally, I think that riding hydrogens can be calculated if
necessary using the same algorithms/parameters employed upon refinement.
It is true that different programs may use different parameter sets and
reproducing exactly the same set of riding hydrogens may be difficult
without exact knowledge of which version was used and ability to unearth
that old version of the software. This may preclude one from getting
exactly the same riding hydrogen positions (how large that difference
would be I honestly don't know). But really, who cares? What is the
benefit of knowing exactly where this or that riding hydrogen was?
Maybe there is some benefit of such comparison in method development,
but I would think its rather limited.
I wholeheartedly agree with Ethan (even though that is not strictly what
he said :) that some minor benefit here is completely negated by the
danger of perception that somehow models tell us where hydrogens are.
It is bad enough that, in my estimate, roughly 10% of atomic coordinates
in the PDB are unwarranted as they come from disordered residues with
exact spatial positions unsupported by electron density. Let's not add
more things that PDB users may over-interpret.
Cheers,
Ed.
