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 *Date: *Tuesday, 17. July 2018 at 15:25 *To: *Eike-Christian Schulz *Cc: *PHENIX user mailing list *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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Hi Eike -  There is no space between the altloc and residue name fields in the PDB format (per HETATM specification).  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 ([email protected]) 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 Date: Tuesday, 17. July 2018 at 16:03 To: Eike-Christian Schulz Cc: PHENIX user mailing list 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 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 Date: Tuesday, 17. July 2018 at 15:25 To: Eike-Christian Schulz Cc: PHENIX user mailing list 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 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

It did. Many thanks to both of you! From: Christian Roth Date: Tuesday, 17. July 2018 at 18:44 To: "[email protected]" Cc: Eike-Christian Schulz , PHENIX user mailing list Subject: Re: [phenixbb] FW: Occupancy / alternate conformation Refinement I think Jareds line should do the trick. Christian On Tue, Jul 17, 2018 at 6:28 PM Jared Sampson mailto:[email protected]> wrote: Hi Eike - There is no space between the altloc and residue name fields in the PDB format (per HETATM specificationhttp://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#H...). 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 ([email protected]mailto:[email protected]) 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 mailto:[email protected]> Date: Tuesday, 17. July 2018 at 16:03 To: Eike-Christian Schulz mailto:[email protected]> Cc: PHENIX user mailing list mailto:[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 mailto:[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 mailto:[email protected]> Date: Tuesday, 17. July 2018 at 15:25 To: Eike-Christian Schulz mailto:[email protected]> Cc: PHENIX user mailing list mailto:[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 mailto:[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 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]