[phenixbb] Phenix.refine and Unusual residues
Katherine Sippel
katherine.sippel at gmail.com
Mon Jun 27 18:02:32 PDT 2011
I don't know if this helps but you have TER cards in the middle of chains E
and G. This might be confusing the program.
Good Luck,
Katherine Sippel
Postdoctoral Associate
Baylor College of Medicine
On Mon, Jun 27, 2011 at 6:01 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
>
>
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