Dear all,
Very sensible advice I think.
If a user of a PDB entry doesn't like the hydrogens deposited,
stripping them is trivially easy for them: a deposition should
represent the full result of the upstream work and not necessarily
self-censor/adjust based on some assumed downstream that we know very
little about.
Several things we have to be aware of though: placed hydrogens in the
model can come in two flavours
(1) e-cloud position, or
(2) nuclear position
based on two policies
(a) riding-hydrogen model throughout (from initial placement to
final model), or
(b) explicit refinement (like any other atom, but maybe with tighter
positional and B-factor restraints)
This is (usually) recorded in the deposition.
And geometric analysis (clashscore!) can handle incoming hydrogens in
2x2=4 ways as well:
- keep them or strip and re-add them
- use e-cloud or nuclear positions
I'm not sure what the "standard" PDB validation process is to compute
clashscores for models with incoming hydrogens: the DCC software
release available at [1] is from 2015 and most likely doesn't
represent the current state-of-the art or implementation used on wwPDB
validation servers or within OneDep (maybe someone from the wwPDB
sites can shed some light on this). So don't be surprised if your own
geometry analysis in whatever tool you're using comes up with
different assessment of clashscore, contacts etc ... as always: the
devil is in the detail ;-)
Cheers
Clemens
[1] https://sw-tools.rcsb.org/apps/DCC/index.html
On Wed, Jul 15, 2026 at 12:56:26PM -0500, Pavel Afonine wrote:
> Hi Flavio,
>
> First off, this topic has been discussed a lot on this and other mailing
> lists, so it might be worthwhile to check the archives. There is even an
> article on this very topic:
>
> https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2012_01.pdf#page=18
>
> From a chemistry and crystallographic software/methods standpoint, I can’t
> think of a reason why one would even consider not adding H to their models.
> Hydrogen atoms are present in actual structures; they contribute to the
> scattering in a measurable way, and they can help improve crystal structure
> models in many ways that have been discussed before.
>
> It’s not about adding or not adding H, it’s about when to add them. It may
> be helpful (for you and for algorithms) to not include H in the early
> stages of atomic model building/refinement, but once major errors are
> finalized, just add H and keep them. For you, because it’s easier to work
> with a less cluttered model. Same for algorithms: simpler models facilitate
> convergence and make it easier to overcome energy barriers.
>
> And yes, don’t make the terrible mistake of having H throughout the
> refinement and then stripping them off right before deposition—that will
> invalidate many of the statistics reported in your model file header.
>
> All the best!
> Pavel
>
> On Wed, Jul 15, 2026 at 6:48 AM Flavio Di Pisa <
> [email protected]> wrote:
>
> > Dear community,
> >
> > While refining a crystallographic model at 3.3 Å resolution, I noticed an
> > improvement in the geometry statistics after adding hydrogen atoms in
> > riding positions.
> >
> > Would it be inappropriate to keep these hydrogen atoms in the final model
> > to be deposited in the PDB, given the relatively low resolution? Or is it
> > generally preferable to remove them before deposition?
> >
> > Thank you very much in advance for your advice.
> >
> > Best regards,
> >
> > Flavio.
> >
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