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 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
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