Here’s my 2 cents. If you use a riding hydrogen model (even at low resolution), it affects not only the geometry statistics (due to incorporating them for Van der Waals clashes), it also improves the agreement of the R-factors between F(obs) and F(calc) below about 8 Å. Besides, not including them implies that you don’t believe those hydrogen atoms exist in the protein, which we all know isn’t true.
In Phenix, you have the option to explicitly add these hydrogen atoms using the ReadySet command. If you use these hydrogens during your refinement cycles and for the final coordinates that you use to deposit in the PDB, then include them in the PDB deposition. This is no different than thinking you can just delete one or two nuisance water molecules in those final coordinates because the PDB flagged them as close contacts. The final deposited coordinates should be EXACTLY what you used to generate the final set of structure factors from the last cycle of refinement. I wouldn’t worry too much about whether users think that these hydrogen atoms are written in stone. Personally I think a lot could be cleared up if the output coordinates from such a refinement could say in the CIF file that the hydrogen atoms were included as riding atoms, but if someone doesn’t understand that you can’t uniquely identify hydrogen atoms at even relatively high resolutions in most protein structures, they’re not going to understand what it means to use a riding hydrogen model during refinement. Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 [email protected] (214) 645-6383 (phone) (214) 645-6353 (fax) On Jul 15, 2026, at 8:47 AM, Flavio Di Pisa <[email protected]> wrote: External Mail This email originated from outside of UT Southwestern. Please be cautious. <https://us-phishalarm-ewt.proofpoint.com/EWT/v1/MznTZTSvDXGV0Co!VXxNObbzC_qX45EOx7OYrVBpBBTV9H7qwXkceZNBi5ixrCkK5TkoEew1Fa3fLTkMG_lhwbl0SpRVi_nutjx-alzk5YhwZJPNUrYbhPAtO9v5Og$> Report Suspicious Dear community, While refining a crystallographic model at 3.3 Å resolution, I noticed an improvement in the geometry statistics after adding hydrogen atoms in riding positions. Would it be inappropriate to keep these hydrogen atoms in the final model to be deposited in the PDB, given the relatively low resolution? Or is it generally preferable to remove them before deposition? Thank you very much in advance for your advice. Best regards, Flavio. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!H2vba-GLN84biEwyhBQGPLxg01oHQrfu2XRhFeL4bfc0iurbqJJ9LMWXLGrYfdktThgcWTTtLZ03zjf5WTMdnV6dfIQYW0h1Km5JXLkCsjKC5jw$> ________________________________ UT Southwestern Medical Center The future of medicine, today. ######################################################################## 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/
