[phenixbb] Ligand occupancy and conformational change

Edward A. Berry BerryE at upstate.edu
Tue Jul 24 08:25:58 PDT 2018

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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