Hello, just to clarify, I do not use H atoms for refinement, but as idealised riding H atoms. In the old-style GI of Refmac one could use riding hydrogens during refinement without adding them in the output coordinate file. I do not find this option in the new GI of the CCP4i2 window. As a result from a a REFMAC job, the ouput PDB file does not contain H atoms, while the mmcif output file does. At the end of the story, I ran pdbx/mmcif to convert the PDB in a mmcif file that does not contain H atoms anymore. It seems to work.
Best regards Luca Mazzei Luca Mazzei - PhD Laboratory of Bioinorganic Chemistry Department of Pharmacy and Biotechnology (FaBiT) Alma Mater Studiorum - University of Bologna Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy Tel: +39 0512096235 > Il giorno 16 mag 2022, alle ore 15:43, Luca Mazzei <luca.mazz...@unibo.it> ha > scritto: > > Dear CCP4 people, > > Refining a 1.7 Angstroem structure with REFMAC (CCP4i2) using hydrogens > during refinements by generating riding hydrogens I obtain a PDB file that > does not contain H atoms. However, the corresponding mmcif file that I should > use for deposition contains their coordinates and give them either full or > zero occupancy. Do you know how I can safely delete H atoms from the mmcif > file prior deposition? Would this affect Rwork and Rfree calculated upon > validation on the wwPDB? > > Thanks in advance, > > Luca Mazzei > > > Luca Mazzei - PhD > Laboratory of Bioinorganic Chemistry > Department of Pharmacy and Biotechnology (FaBiT) > Alma Mater Studiorum - University of Bologna > Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy > Tel: +39 0512096235 > > > > ######################################################################## 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/
