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.
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