It seems to be taken for granted that radiolysis of water generates hydrogen gas. I was in a lecture 25 years ago when the speaker said that the gas bubbles which appear when a protein crystal that has been in the beam is warmed to room temperature is also hydrogen. Seems eminently sensible. However a year or two later someone told me that some effort was going into finding out what gas it was experimentally. Only gossip and hearsay from long ago and I never heard any more about it, sorry ...
Best wishes, Jon Cooper (Emeritus at UCL) [email protected] Erratum and other hopefully useful things: https://crxp.org.uk Sent from [Proton Mail](https://proton.me/mail/home) for Android. -------- Original Message -------- On Monday, 07/20/26 at 18:43 Pavel Afonine <[email protected]> wrote: > Hi Rafael, > > Indeed, hydrogen abstraction is an interesting topic. Could you please point > to studies that document this effect, and in particular quantitatively > measure its scale (e.g., the fraction of hydrogen being abstracted)? Are > there specific types of hydrogen (or particular H sites) that are more prone > to this effect, etc.? > > Thanks, > Pavel > > On Mon, Jul 20, 2026 at 5:03 AM Rafael Marques > <[email protected]> wrote: > >> I just would like to add my two cents (again) to the topic when it comes to >> the presence of hydrogens. Although we generally assume they are there and >> cannot be seen due to their scattering properties, this is not completely >> true. Direct radiation damage or induced by water radicals during the x-ray >> diffraction experiment may remove them. If one needs to see the hydrogens, >> neutron diffraction should be used instead of assuming they are there. At >> the end of the day what every structural biologist produces is a model and >> one should choose wisely if their model can support or not the hypothesis. >> >> Best wishes >> >> ______________________________________________________ >> >> Rafael Marques da Silva >> >> PhD Student – Structural Biology >> >> University of Leicester >> >> Mestre em Física Biomolecular >> Universidade de São Paulo >> >> Bacharel em Ciências Biológicas >> Universidade Federal de São Carlos >> >> phone: +44 07861 273773 >> >> "A sorte acompanha uma mente bem treinada" >> ________________________________________________ >> >> --------------------------------------------------------------- >> >> De: CCP4 bulletin board <[email protected]> em nome de Gerard Bricogne >> <[email protected]> >> Enviado: domingo, 19 de julho de 2026 22:48 >> Para: [email protected] <[email protected]> >> Assunto: Re: [ccp4bb] Hydrogen atoms at 3.3 ang >> >> 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. >>> >> >>> >> >>> >> ------------------------------------------------------------------------ >>> >> >>> >> 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/ >> >> ######################################################################## >> >> 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/ >> >> --------------------------------------------------------------- >> >> To unsubscribe from the CCP4BB list, click the following link: >> 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 ######################################################################## 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/
