Hi Rob, Just to second what Robbie said—if you want to boost your confidence in the numbers you get from refinement, you can do something like what's shown in Figure 3 here:
https://www.nature.com/articles/s41467-018-06957-w Good luck! Pavel On Fri, May 30, 2025 at 7:52 AM Robert Oeffner <[email protected]> wrote: > Hi, > > I am wondering if Refmac version 5.8 is suitable for refining occupancies > of a ligand reliably in a ligand-protein complex. I have heard that in > older versions there used to be some instability if refining occupancies > and B-factors together. Is that still the case? If I try fixing B-factors > during refinement would the following shell script below do the job (chain > X is for the ligand)? After running the refinement occupancies for the > ligand come out refined. But unexpectedly, so do the B-factors as far as I > can tell. > > Many thanks, > > Robert > > > #!/bin/bash > # > > refmac5 HKLIN data.mtz XYZIN model.pdb LIBIN ligands.dict << eof > > make refi bfac none > occupancy group id 1 chain X > occupancy refine > > eof > > ######################################################################## > > 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/ > ######################################################################## 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/
