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.
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following
link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic
Tel. +420 325 873 758
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
--
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
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
--
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
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
