Any idea how I can select only 1 out of the 2 alternate conformations ?

My PDB file:

HETATM 5039  OT AFAH C   1      10.082  15.814   2.201  0.50 24.78           O 

HETATM 5040  C  AFAH C   1      10.568  15.712   3.241  0.50 28.20           C 

HETATM 5041  O  AFAH C   1      11.451  16.466   3.591  0.50 22.71           O 

HETATM 5042  C3 AFAH C   1      10.136  14.590   4.170  0.50 19.02           C 

HETATM 5043  F  AFAH C   1       9.265  13.714   3.608  0.50 34.13           F 

HETATM 5044  OT BFAH C   1      10.119  15.728   2.366  0.50 24.78           O 

HETATM 5045  C  BFAH C   1      10.613  15.673   3.487  0.50 28.20           C 

HETATM 5046  O  BFAH C   1      11.519  16.468   3.737  0.50 22.71           O 

HETATM 5047  C3 BFAH C   1      10.307  14.473   4.424  0.50 19.02           C 

I provide

refinement.geometry_restraints.edits {

   bond {

     action = *add

     atom_selection_1 = chain A and resseq 110 and name OD2

     atom_selection_2 = chain C and resseq 1 and resname BFAH and name C3

     distance_ideal = 1.43

     sigma = 0.04

     slack = None

   }

  }

But the result is:

Sorry: No atom selected: "chain C and resseq 1 and resname BFAH and name C3"

Cheers,

Eike

From: Christian Roth <[email protected]>
Date: Tuesday, 17. July 2018 at 16:03
To: Eike-Christian Schulz <[email protected]>
Cc: PHENIX user mailing list <[email protected]>
Subject: Re: [phenixbb] FW: Occupancy / alternate conformation Refinement

Ahh I see. Yes I think you are better off letting the Asn be an amino acid and have the ligand on its own. with an appropriate link record.

Good luck!

Christian

On Tue, Jul 17, 2018 at 3:52 PM Schulz, Eike-Christian <[email protected]> wrote:

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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