https://doi.org/10.1073/pnas.0905481107 from the abstract By using a combination of single-crystal x-ray diffraction, small-angle scattering, and qualitative and quantitative radiolysis experiments, we show that hydrogen gas, formed inside the sample during irradiation, rather than intramolecular bond cleavage between non-hydrogen atoms, is mainly responsible for the loss of high-resolution information and contrast in diffraction experiments and microscopy.
On Mon, Jul 20, 2026 at 4:14 PM Jon Cooper < [email protected]> wrote: > 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 > ######################################################################## 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/
