[phenixbb] occupancy of a part of a ligand

Young-Jin Cho yjcho at brandeis.edu
Wed Feb 10 08:46:04 PST 2010

Hi Maia,
I had the same situation so I can answer a little bit. May be Pavel can help much better than me though.
You can do that while adding "refine.occupancies.constrained_grouop.selection=chain ATP(name of your ATP) and resseq 1 and (name PB or name O1B or name O2B or name O3B)" fyi. check your names on your ligand.

Hopefully, this will help.


----- Original Message -----
From: "Maia Cherney" <chern at ualberta.ca>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Wednesday, February 10, 2010 11:37:38 AM GMT -05:00 US/Canada Eastern
Subject: Re: [phenixbb] occupancy of a part of a ligand

Hi Pavel,

I have a ligand (ADP or ATP) that partially lost the last phosphate 
group. Can I refine a group occupancy for the adenosine part of the 
ligand separately from the phosphate groups of this ligand. If I do 
atomic occupancies, they diminish for the terminal phosphate groups. I 
can imagine that I can refine them as two superposed ligands with 
different numbers of phosphates, but is it possible to do just different 
group occupancies for parts of the ligand?


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Postdoctoral Fellow, Kern Lab
Biochemistry Department/HHMI
Brandeis University

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