Hi Christian,

the Asn side chain is to which the ligand attaches has only 1 conformation – hence the occupancy for all these atoms is 1.

… but using a LINK might be a good option.

Thanks,

Eike

From: Christian Roth <[email protected]>
Date: Tuesday, 17. July 2018 at 15:25
To: Eike-Christian Schulz <eike.schu[email protected]>
Cc: PHENIX user mailing list <[email protected]>
Subject: Re: [phenixbb] FW: Occupancy / alternate conformation Refinement

Hi Eike,

why have some of your ligand atoms have occupancy of 1 and some 0.5.?  I have had thought all atoms of the ligand are 0.5 for the two states and you create a link for one of them to which is the intermediate. You might have to add a constrained group as well, though nowadays phenix might handle that automatically.

Cheers

Christian

On Tue, Jul 17, 2018 at 3:15 PM Schulz, Eike-Christian <[email protected]> wrote:

    Dear all,

    In one of my structures I appear to have a mixed state between a covalently bound intermediate and the free substrate occupying _almost_ the same position. I can model the states nicely in coot, but during refinement the molecules “fly” apart - although the occupancy was limited to 0.5 for their overlapping atoms. 

    I have tried to model the free ligand as an alternate conformation of the covalent intermediate:

    HETATM  852  N   ASB A 110      10.523  15.702  10.022  1.00 14.48           N 
    HETATM  853  CA  ASB A 110       9.974  15.713   8.664  1.00 15.11           C 
    HETATM  854  C   ASB A 110       8.635  16.385   8.683  1.00 14.31           C 
    HETATM  855  O   ASB A 110       8.563  17.443   9.233  1.00 13.03           O 
    HETATM  856  CB  ASB A 110      10.053  14.307   8.091  1.00 11.72           C 
    HETATM  857  CG  ASB A 110       9.774  14.157   6.621  1.00 15.26           C 
    HETATM  858  OD1 ASB A 110      10.688  14.485   5.644  1.00 19.29           O 
    HETATM  859  OD2 ASB A 110       8.693  13.880   6.340  1.00 13.36           O 
    HETATM  860  C1 AASB A 110      10.637  15.649   3.353  0.50 27.61           C 
    HETATM  861  C2 AASB A 110      10.231  14.480   4.266  0.50 32.98           C 
    HETATM  862  O1 AASB A 110      11.505  16.454   3.690  0.50 31.63           O 
    HETATM  863  O2 AASB A 110      10.085  15.787   2.280  0.50 21.80           O 
    HETATM 4742  O2 BASB A 110      10.072  15.815   2.191  0.50 24.78           O 
    HETATM 4743  C1 BASB A 110      10.573  15.717   3.221  0.50 28.20           C 
    HETATM 4744  O1 BASB A 110      11.449  16.458   3.619  0.50 22.71           O 
    HETATM 4745  C2 BASB A 110      10.107  14.567   4.152  0.50 19.02           C 
    HETATM 4746  F  BASB A 110       9.287  13.735   3.610  0.50 34.13           F

    Although I have provided a new CIF file for the ligand named according to the alternate conformation this causes phenix to crash.

    How can I correctly refine these overlapping atoms ?

    Thanks for your advice,

    Eike





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