[phenixbb] FW: Occupancy / alternate conformation Refinement

[Christian Roth]

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 <
eike.schulz at mpsd.mpg.de> 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 <christianroth034 at gmail.com>
> *Date: *Tuesday, 17. July 2018 at 15:25
> *To: *Eike-Christian Schulz <eike.schulz at mpsd.mpg.de>
> *Cc: *PHENIX user mailing list <phenixbb at phenix-online.org>
> *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 <
> 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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