Quality of your results depend very much on the resolution of your data I find…
On Wed, 11 Jun 2025 at 01:40, Robert Oeffner <[email protected]> wrote: > Thanks Pavel. I'll look into that method. I suppose having anomalous data > for the potassium ions yields an extra signal for those atoms and > significantly helps stabilising the refined occupancy of those atoms. > > Rob > On 10/06/2025 23:12, Pavel Afonine wrote: > > 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/ >> > -- > Robert Oeffner15 Bayford Place > Cambridge, CB4 2UF > <https://www.google.com/maps/search/15+Bayford+Place%0D%0ACambridge,+CB4+2UF?entry=gmail&source=g> > Tel: +44 (0)7712 887 162 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
