You can make very general alternate conformations with the "constrained_group" construction.
Say the loop is N12:14 and ligand is R221 present only in A conformation. You can also add waters
to either conformation. The following is for running from .eff script, but I expect it is available from the Gui. There is a detailed description of handling alt conf in one of the newsletters.

  refine {
    occupancies {
      constrained_group {
        selection = ((chain N and resseq 12:14) or (chain R and resid 221)) \
                    and altloc A
        selection = (chain N and resseq 12:14) and altloc B

      }

}}
On 07/24/2018 02:49 AM, Xavier Brazzolotto wrote:

I am struggling with a ligand bound structure.
The ligand seems to induce a small conformational change of one loop. However, despite my efforts I did not get any data with a full occupancy for this ligand yet.

As a result, I have to deal with a loop in apo state (where ligand occupancy = 0) and a loop with a bound ligand (where ligand occupancy <1) and where the ligand is clashing with the modelled loop in the apo state.
Hope I did myself clear.

How to deal with this situation ? I am sure that phenix.refine can do it but how ?
What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X
Maybe something specific in a parameter file ?

Thank you for your help
Xavier

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