[phenixbb] Ligand occupancy and conformational change

[G_Kontopidis]

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: 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
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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