[phenixbb] Occupancy larger than 1

Andrew Philip Thompson andrew.thompson at adelaide.edu.au
Wed Jan 30 21:13:44 PST 2019

Hi Nick,

Explicitly inputting my intended occupancy groups into phenix seems to have done the trick, thanks very much!


Andrew Thompson
PhD Candidate
Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide

On 31 Jan 2019, at 2:57 pm, Schnicker, Nicholas J <nicholas-schnicker at uiowa.edu<mailto:nicholas-schnicker at uiowa.edu>> wrote:

Hi Andrew,

You should use group constrained refinement to link the occupancies of each isomer. You can see the documentation for how to implement it.


From: <phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>> on behalf of Andrew Philip Thompson <andrew.thompson at adelaide.edu.au<mailto:andrew.thompson at adelaide.edu.au>>
Date: Wednesday, January 30, 2019 at 10:18 PM
To: "phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>" <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Subject: [phenixbb] Occupancy larger than 1

Hi Phenix BB,

We discovered that a fragment had degraded in our crystallography condition and the product was observed bound in the resulting crystal structure. Unfortunately we have been unable to separate certain stereoisomers of this compound or its analogues, and so are looking to simultaneously model two of the isomers into the crystal structure. I have made a .cif file corresponding to each isomer and modelled them into my crystal structures with altloc tags A & B, however after refinement, the occupancy of the two adds up to more than 1 in some instances (ie. 0.51 and 0.53). I’ve never had this before when trying to model dual conformations of the stereoisomers. I tried to make the ligands the same residue number as discussed in a previous thread (http://www.phenix-online.org/pipermail/phenixbb/2011-March/016859.html), however neither coot or pymol will open the pdb file after refinement if I do this. Unfortunately I am unable to share the pdb file as we do not want to disclose the compound structure.

Does anyone have any suggestions as to how to proceed?

Thanks in advance,

Andrew Thompson
PhD Candidate
Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide, Australia

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