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I've split this off from the too many clashes thread as it's not directly related. I was under the impression that the default in refmac was to add riding hydrogens but some investigation suggests this may be only appear to be the case. If the default option in the CCP4i GUI for refmac with regards to hydrogens - "use if present in file" (which corresponds to MAKE HYDR YES) - is selected then if there are no hydrogens present in the input pdb the log file contains no mention of riding hydrogens but the output pdb contains "REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS" A bit of trawling through the CCP4bb archive shows that this has been mentioned before in 2007: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0711&L=CCP4BB&F=&S=&P=56491 but there is no answer to the question can the line "REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS" appear in the output pdb when this is not (?) the case. Can anyone explain this please? Thanks, Huw