Hi Havier,

You got the formula right

alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X

You may have also some water include in the model correspond to alternate loop A" occupancy = X

I have done it many times using RefMac and SHELX I am sure it is working in Phenix as well .

you do not need something specific in a parameter file for the protein atom.

The PDB file look like the following.

ATOM    258  CA AGLN A  35       2.979  -4.265  69.678  0.40 46.35           C

ANISOU  258  CA AGLN A  35     4942   7133   5533      0    946   -219       C

ATOM    259  CA BGLN A  35       3.127  -4.246  69.643  0.60 47.74           C

ANISOU  259  CA BGLN A  35     5152   7285   5702      0    930   -219       C

The alternative atom specified with letter A and B before the amino acid three letters.

Regards,

George

From: [email protected] [mailto:[email protected]] On Behalf Of Xavier Brazzolotto
Sent: Tuesday, July 24, 2018 9:50 AM
To: [email protected]
Subject: [phenixbb] Ligand occupancy and conformational change

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