Hi I do this now as well. I have progressed from not modelling, to modelling them in now at lower resolutions as “riding", especially since Clashscores and Molprobity take them into account as well.
For me to use them during refinement even as riding, but deleting them before deposition also poses some issues in representing the assumptions used during the refinement process. For me at the of the day, are we depositing the best structure we think we are modelling or add another criteria based on others usage patterns. It is also simple for an end user to delete/hide hydrogens or trim side chains themselves. But I think as you said, it’s all just a matter of preference nowadays. On 15.07.2026, 16:09, "CCP4 bulletin board" <[email protected]> wrote: Hi Flavio, This is always a very interesting topic. Personally, I don't like to model hydrogens atoms at resolutions where they cannot be seen. However, a while ago I had a very interesting discussion with Pavel Afonine about it, once the overall geometry of the molecule improves and this probably represents better what happens in vivo. I wouldn't leave the hydrogens in my final model, once this can be misleading to non structural biologists.However, many people don't trim the side chains or even the alpha carbon chain if there is no electron density for a few residues, At the end of the day I believe that many times this becomes more a personal preference. 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 Flavio Di Pisa <[email protected]> Enviado: quarta-feira, 15 de julho de 2026 14:47 Para: [email protected] <[email protected]> Assunto: [ccp4bb] Hydrogen atoms at 3.3 ang 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 ######################################################################## 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/
