What I would like to do is then to add the ligand. But in the apo state it clashes with one residue of the loop.

So I thought fixing the occupancy to 0 (zero), for one ALT of the ligand (with apo loop) and having a second ALT with an occupancy <1 (bound loop) to try to prevent atom clashing.

Is it the right strategy ? And how to do it ?

Moreover, it seems to get more complicated as the bound ligand can also exist with at least 2 different alternatives (different orientation of a central indole ring).

Le 24 juil. 2018 à 09:49, G_Kontopidis <[email protected]> a écrit :

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

Xavier Brazzolotto, PhD

[email protected]

Département de Toxicologie et Risques Chimiques

Unité Neurotoxiques

Institut de Recherche Biomédicale des Armées

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