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.
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