[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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