Dear Wladek,
Doesn't the procedure you advocate lead to the deposition of
non-reproducible results? Hydrogens are useful at resolutions at which
they cannot be seen because they are involved in contact terms that
contribute to producing good geometry by avoiding the kind of clashes
that MolProbity hunts down in its quality assessment. If you get that
benefit by including hydrogens in HKL-3000 but then omit these in its
output file, these refinement results cannot be reproduced by other
refinement programs using the information provided by your procedure.
They would have to use their own means of reintroducing hydrogens - so
why not simply write out "your" hydrogens? It is generally understood
that they may not be "experimental" in the sense in which they are in
small molecule structures, but that they may have played a significant
role in achieving the quality of the final geometry (as judged by
MolProbity).
Best wishes,
Gerard
--
On Sun, Jul 19, 2026 at 02:31:54PM -0400, Wladek Minor wrote:
> Yes, hydrogens are always present, but as opposed to small
> molecules, we do not see them in the map.
>
> Refinement in HKL-3000 includes hydrogens, but the final file does
> not include them because they are not experimental. See the paper
> that describes state-of-the-art refinement
>
> Shabalin IG, Porebski PJ, Minor W (2018)
> *Refining the macromolecular model - achieving the best agreement
> with the data from X-ray diffraction experiment.*
> /Crystallogr Rev/24(4): 236-262.[DOI:10.1080/0889311X.2018.1521805]
> <https://doi.org/10.1080/0889311X.2018.1521805>[Pub Med ID:
> 30416256]
> <https://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pubmed&term=30416256>[Pub
> Med Central ID: PMC6219471]
> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219471/?tool=pmcentrez>
>
> Wladek
>
> On 7/17/2026 4:33 PM, Pius Padayatti wrote:
> >support overwhelmingly adding hydrogens in all refinements
> >why not it is there if one were to be ignore it hydrogens are
> >always present
> >no matter
> >Pius
> >_Pius Padayatti_
> >
> >
> >
> >
> >On Thu, Jul 16, 2026 at 9:09 AM Wladek Minor
> ><[email protected]> wrote:
> >
> > There is another paper about waterless structures.
> >
> > W.
> >
> > On 7/16/2026 3:24 AM, Jan Dohnalek wrote:
> >> I always have mixed feelings here.
> >> Yes, they contribute and "belong" to the model and refinement.
> >> On the other hand we (software) does not build all of them,
> >> especially on the groups with protonation "freedom".
> >> In this way, our refined structures with hydrogens are closer to
> >> the reality but they partially lie - as we do not have Hs built
> >> in some places where they obviously belong.
> >>
> >> I would prefer the PDB keeps both - the model with
> >> "crystallographic H-set" with all the pluses and minuses it has
> >> and then the stripped model - for the reasons above.
> >>
> >> Jan
> >>
> >>
> >> On Wed, Jul 15, 2026 at 7:57 PM Pavel Afonine
> >> <[email protected]> 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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> >>
> >>
> >>
> >> -- Jan Dohnalek, Ph.D
> >> Institute of Biotechnology
> >> Academy of Sciences of the Czech Republic
> >> Biocev
> >> Prumyslova 595
> >> 252 50 Vestec near Prague
> >> Czech Republic
> >>
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> >>
> > -- Dr. Wladek Minor
> > Harrison Distinguished Professor
> > University of Virginia
> > Department of Molecular Physiology and Biological Physics
> > Phone: 434-243-6865
> > Fax: 434-243-2981
> > https://minorlab.org
> > WIKI:https://en.wikipedia.org/wiki/Wladek_Minor
> >
> >
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> --
> Dr. Wladek Minor
> Harrison Distinguished Professor
> University of Virginia
> Department of Molecular Physiology and Biological Physics
> Phone: 434-243-6865
> Fax: 434-243-2981
> https://minorlab.org
> WIKI:https://en.wikipedia.org/wiki/Wladek_Minor
>
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