[phenixbb] Phenix.refine and Unusual residues
Ralf Grosse-Kunstleve
rwgrosse-kunstleve at lbl.gov
Mon Jun 27 16:34:52 PDT 2011
phenix.refine does recognize all of your residues, it just flags them as
"unusual" for your information. There is also "unknown". If it finds any of
those it will stop.
I think the Coot problem is unrelated; I hope someone else can help.
Ralf
On Mon, Jun 27, 2011 at 4:01 PM, Haytham Wahba <haytham_wahba at yahoo.com>wrote:
>
> Version: 1.7
> Release tag: 650
> Platform: intel-linux-2.6-x86_64 linux
> User: haytham
>
> why phenix does not recognise ACT, PO4 Sn and Br (unusual residue) as you
> see in this part in the Log file.. (see below)
>
> Chain: "C"
> Number of atoms: 4
> Number of conformers: 1
> Conformer: ""
> Number of residues, atoms: 1, 4
> Unusual residues: {'ACT': 1}
> Classifications: {'undetermined': 1}
> Chain: "C"
> Number of atoms: 4
> Number of conformers: 1
> Conformer: ""
> Number of residues, atoms: 1, 4
> Unusual residues: {'ACT': 1}
> Classifications: {'undetermined': 1}
> Chain: "E"
> Number of atoms: 1
> Number of conformers: 1
> Conformer: ""
> Number of residues, atoms: 1, 1
> Unusual residues: {' SN': 1}
> Classifications: {'undetermined': 1}
> Chain: "E"
> Number of atoms: 1
> Number of conformers: 1
> Conformer: ""
> Number of residues, atoms: 1, 1
> Unusual residues: {' SN': 1}
> Classifications: {'undetermined': 1}
> Chain: "F"
> Number of atoms: 1
> Number of conformers: 1
> Conformer: ""
> Number of residues, atoms: 1, 1
> Unusual residues: {' SN': 1}
> Classifications: {'undetermined': 1}
> Chain: "G"
> Number of atoms: 5
> Number of conformers: 1
> Conformer: ""
> Number of residues, atoms: 1, 5
> Unusual residues: {'PO4': 1}
> Classifications: {'undetermined': 1}
> Chain: "G"
> Number of atoms: 5
> Number of conformers: 1
> Conformer: ""
> Number of residues, atoms: 1, 5
> Unusual residues: {'PO4': 1}
> Classifications: {'undetermined': 1}
> Chain: "H"
> Number of atoms: 1
> Number of conformers: 1
> Conformer: ""
> Number of residues, atoms: 1, 1
> Unusual residues: {' BR': 1}
> Classifications: {'undetermined': 1}
> Residues with excluded nonbonded symmetry interactions: 2
> residue:
> pdb=" SN SN E 1 " occ=0.70
> residue:
> pdb=" SN SN E 2 " occ=0.20
> ---------------------------------------------------------
> when i try to refine specially the Tin atom (not other, ACT,...) in coot
> after phenix.refine. coot display ((no restraints Found,...lablabla))
>
> -----------------------------------------------------------
>
>
> this is the PDB (what is the wrong with that)
> HETATM 3552 O HOH S 361 11.670 -4.327 9.559 1.00
> 34.14 O
> TER 3553 HOH S
> 361
> HETATM 3554 OXT ACT C 1 10.133 -3.417 7.937 1.00
> 20.00 O
> HETATM 3555 C ACT C 1 9.911 -2.331 7.357 1.00
> 20.00 C
> HETATM 3556 O ACT C 1 10.897 -1.607 7.183 1.00
> 20.00 O
> HETATM 3557 CH3 ACT C 1 8.550 -1.912 6.905 1.00
> 20.00 C
> TER 3558 ACT C 1
> HETATM 3559 OXT ACT C 2 10.700 -2.628 9.985 1.00
> 20.00 O
> HETATM 3560 C ACT C 2 10.962 -1.952 11.000 1.00
> 20.00 C
> HETATM 3561 O ACT C 2 11.756 -2.461 11.809 1.00
> 20.00 O
> HETATM 3562 CH3 ACT C 2 10.364 -0.601 11.240 1.00
> 20.00 C
> TER 3563 ACT C 2
> HETATM 3564 SN SN E 1 6.346 -4.396 -16.894 0.70 20.00
> SN
> TER 3565 SN E 1
> HETATM 3566 SN SN E 2 6.492 -2.146 -14.779 0.20 20.00
> SN
> TER 3567 SN E 2
> HETATM 3568 SN SN F 1 10.186 0.632 6.366 1.00 30.00
> SN
> TER 3569 SN F 1
> HETATM 3570 P PO4 G 1 5.763 10.047 -3.974 1.00
> 30.00 P
> HETATM 3571 O1 PO4 G 1 6.960 10.924 -4.190 1.00
> 30.00 O
> HETATM 3572 O2 PO4 G 1 4.531 10.872 -4.101 1.00
> 30.00 O
> HETATM 3573 O3 PO4 G 1 5.758 8.978 -5.017 1.00
> 30.00 O
> HETATM 3574 O4 PO4 G 1 5.835 9.456 -2.607 1.00
> 30.00 O
> TER 3575 PO4 G 1
> HETATM 3576 P PO4 G 2 9.060 -4.976 -17.812 1.00
> 30.00 P
> HETATM 3577 O1 PO4 G 2 10.418 -5.179 -18.415 1.00
> 30.00 O
> HETATM 3578 O2 PO4 G 2 8.223 -4.116 -18.710 1.00
> 30.00 O
> HETATM 3579 O3 PO4 G 2 8.412 -6.316 -17.597 1.00
> 30.00 O
> HETATM 3580 O4 PO4 G 2 9.172 -4.280 -16.485 1.00
> 30.00 O
> TER 3581 PO4 G 2
> HETATM 3582 BR BR H 1 9.484 11.317 -29.959 1.00 20.00
> BR
> TER 3583 BR H 1
> END
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20110627/c715b7aa/attachment-0001.htm>
More information about the phenixbb
mailing list