[phenixbb] FW: Occupancy / alternate conformation Refinement

[Christian Roth]

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 <
eike.schulz at mpsd.mpg.de> 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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