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 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > 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 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/
