[phenixbb] Occupancy larger than 1

Georg Mlynek georg.mlynek at univie.ac.at
Thu Jan 31 14:33:33 PST 2019

Dear Andrew, also look into here


If you need something like example 5 (pdbcode 1EJG)( crambin: crambin 
displays amino acid heterogeneity at
position 22(Pro or Ser) and 25 (Leu or Ile)).

This crashes Coot until you add*


to $HOME/.coot.py in OSX or the appropriate place on Windows. For
Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
directory for configuration - these can be found (added to) the
directory in which Coot was installed (e.g. C:\WinCoot).

Best regards, Georg.

On 31.01.19 05:27, Schnicker, Nicholas J 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.
> https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement
> Cheers,
> Nick
> *From: *<phenixbb-bounces at phenix-online.org> on behalf of Andrew 
> Philip Thompson <andrew.thompson at adelaide.edu.au>
> *Date: *Wednesday, January 30, 2019 at 10:18 PM
> *To: *"phenixbb at phenix-online.org" <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
> Andrew Thompson
> PhD Candidate
> Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide, Australia
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