[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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