[phenixbb] Ligand occupancy and conformational change
gkontopidis at vet.uth.gr
Tue Jul 24 00:49:51 PDT 2018
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
ANISOU 258 CA AGLN A 35 4942 7133 5533 0 946 -219
ATOM 259 CA BGLN A 35 3.127 -4.246 69.643 0.60 47.74
ANISOU 259 CA BGLN A 35 5152 7285 5702 0 930 -219
The alternative atom specified with letter A and B before the amino acid
From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Xavier Brazzolotto
Sent: Tuesday, July 24, 2018 9:50 AM
To: phenixbb at phenix-online.org
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
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
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