Hi Steve,

I believe this falls into one of 13 occupancy refinement options that you can do in phenix.refine:

https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12

specifically, see Figure 6 which I think represents your case. No need to use nay parameters, just format your PDB as shown and all should work.

Let me know if you need help setting this up!

Pavel

Dear phenix bb,

I am trying to refine a ligand in the active site of my protein where the ligand occupancy is ~50%.  The empty active site contains two chloride ions and the residual density from these ions is very prominent when the model is refined with the ligand alone.  I would like to refine the model with both the ligand and chloride ions present and have been trying to do this with altLoc flags but so far with no luck.  I'm assuming that since the Cl ions more-or-less directly overlay atoms from the ligand positional refinement keeps pushing them out of the density.  I'm sure there is a simple way to get around this and I would be grateful for any suggestions.

Best wishes,

Steve

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email [email protected]
tel 01235 567717

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