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
<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
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