On Wed, 2010-09-15 at 10:50 -0700, Pavel Afonine wrote:
> I wouldn't dare calling a model manipulation that typically changes
> the
> R-factor by 0.5 ... ~2% as "nothing". Although, you are may be right
> -
> "who cares"?
It's not a manipulation because no parameters were manipulated in the
model. Don't you agree that using the riding model does not add
additional refinable parameters?
But your insistence has awakened my curiosity. So I looked at hydrogens
as produced by phenix.refine for a 1.8A structure I randomly picked.
Just as George has pointed out, the "covalent bonds" are too short. for
instance, when hydrogens are added, the average N-H distance is
1.00001(5), but upon refinement the value is down to 0.85998(4). I
won't even begin discussing the fact that some of these hydrogens added
to K,Y,S etc are placed in positions that are not justified by data (not
in definitely wrong positions either, it's just that there is no
evidence to support a particular torsion angle). And that it is
unlikely that every histidine in the structure is fully protonated.
Do you see the problem? I fully understand your desire to be able to
reproduce the R-factors (although I don't necessarily share it), but if
I decide to deposit this model with hydrogens, am I essentially stating
that N-H bond is magically shortened to ~0.86A? Sure, it is driver's
(PDB user's) responsibility to know the meaning of the red light (riding
hydrogens), but wouldn't depositing riding hydrogens be equivalent to
putting 70 mph sign at the ramp, just because all the cops know that
it's not the actual safe speed? And then tell the accident victim that
there was a fine print in the rule book? I think this situation is
particularly problematic given that these days some enter the field the
same way many people (at least so it seems here in Baltimore) get their
driver's licenses, i.e. without ever learning the rules?
Cheers,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
