[phenixbb] FW: Occupancy / alternate conformation Refinement

Christian Roth christianroth034 at gmail.com
Tue Jul 17 09:44:31 PDT 2018


I think Jareds line should do the trick.

Christian

On Tue, Jul 17, 2018 at 6:28 PM Jared Sampson <jared.sampson at columbia.edu>
wrote:

> Hi Eike -
>
> There is no space between the altloc and residue name fields in the PDB
> format (per HETATM specification
> <http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM>).
> Here, the residue name is FAH, and the altloc is A/B.  Try:
>
>     chain C and resseq 1 and altloc B and resname FAH and name C3
>
> Hope that helps.
>
> Cheers,
> Jared
>
> On July 17, 2018 at 12:11:37 PM, Schulz, Eike-Christian (
> eike.schulz at mpsd.mpg.de) wrote:
>
> 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 <christianroth034 at gmail.com>
> *Date: *Tuesday, 17. July 2018 at 16:03
> *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
>
>
>
> 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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