[phenixbb] a double conformation residue included in metal coordination file

Pavel Afonine pafonine at lbl.gov
Tue Jun 7 13:34:48 PDT 2011


Hello,

I just tried this:

- saved the ATOM/ANISOU lines provided below into a file zz.pdb
- and then ran the command:

phenix.pdb_atom_selection zz.pdb "name  OD2 and altid A and chain B and 
resname ASP and resseq  271"

which supposed to select the atom with the above selection string, and 
so it did it:

(...)
name  OD2 and altid A and chain B and resname ASP and resseq  271
   1 atom selected
     ATOM   6107  OD2AASP B 271     -19.758  19.638  48.708  
0.50156.92           O
(...)

So, I'm not sure I understand what's happening. Can you make sure you 
are using the correct PDB file in phenix.refine run? There must be 
something obvious like this.

If nothing helps, you can send me the full PDB file and phenix.refine 
command you used so I can reproduce this problem (I don't need data file 
- I can fake it).

Pavel.

> HI all,
>
> In my structure, there is a double conformation residue and on
> conformation is coordinated to a metal.
> I use phenix.metal_coordination to generate a elbow.edits file. In
> such file the restraint listed as:
> refinement.geometry_restraints.edits {
>    bond {
>      action = *add
>      atom_selection_1 = name MG   and chain B and resname MG and resseq 2001
>      atom_selection_2 = name  OD2 and altid A and chain B and resname
> ASP and resseq  271
>      distance_ideal = 2.070000
>      sigma = 0.100
>    }
> }
>
> But when I use this file for refinement, I got an error message:
>
> Sorry: No atom selected: "name OD2 and altid A and chain B and resname
> ASP and resseq 271"
>
>
> I also check my PDB file:
> ATOM   6100  N  AASP B 271     -19.420  19.064  51.907  0.50115.36           N
> ANISOU 6100  N  AASP B 271    14002  14643  15186   -598    738  -1235       N
> ATOM   6101  CA AASP B 271     -18.016  18.977  51.528  0.50127.08           C
> ANISOU 6101  CA AASP B 271    15508  16123  16656   -585    725  -1202       C
> ATOM   6102  C  AASP B 271     -17.194  19.859  52.460  0.50105.81           C
> ANISOU 6102  C  AASP B 271    12832  13418  13952   -583    730  -1182       C
> ATOM   6103  O  AASP B 271     -17.750  20.593  53.277  0.50 67.89           O
> ANISOU 6103  O  AASP B 271     8027   8614   9153   -586    738  -1193       O
> ATOM   6104  CB AASP B 271     -17.818  19.429  50.080  0.50154.71           C
> ANISOU 6104  CB AASP B 271    18986  19641  20157   -560    689  -1204       C
> ATOM   6105  CG AASP B 271     -18.871  18.868  49.141  0.50167.83           C
> ANISOU 6105  CG AASP B 271    20622  21317  21830   -559    682  -1230       C
> ATOM   6106  OD1AASP B 271     -18.804  17.661  48.823  0.50157.05           O
> ANISOU 6106  OD1AASP B 271    19265  19945  20462   -568    691  -1224       O
> ATOM   6107  OD2AASP B 271     -19.758  19.638  48.708  0.50156.92           O
> ANISOU 6107  OD2AASP B 271    19211  19952  20460   -550    666  -1256       O
> ATOM   6108  N  BASP B 271     -19.303  18.972  52.212  0.50115.36           N
> ANISOU 6108  N  BASP B 271    14002  14643  15186   -598    738  -1235       N
> ATOM   6109  CA BASP B 271     -17.822  18.681  52.128  0.50127.08           C
> ANISOU 6109  CA BASP B 271    15508  16123  16656   -585    725  -1202       C
> ATOM   6110  C  BASP B 271     -17.006  19.773  52.851  0.50105.81           C
> ANISOU 6110  C  BASP B 271    12832  13418  13952   -583    730  -1182       C
> ATOM   6111  O  BASP B 271     -17.610  20.704  53.419  0.50 67.89           O
> ANISOU 6111  O  BASP B 271     8027   8614   9153   -586    738  -1193       O
> ATOM   6112  CB BASP B 271     -17.514  18.729  50.592  0.50154.71           C
> ANISOU 6112  CB BASP B 271    18986  19641  20157   -560    689  -1204       C
> ATOM   6113  CG BASP B 271     -16.455  17.692  50.152  0.50167.83           C
> ANISOU 6113  CG BASP B 271    20622  21317  21830   -559    682  -1230       C
> ATOM   6114  OD1BASP B 271     -16.846  16.720  49.601  0.50157.05           O
> ANISOU 6114  OD1BASP B 271    19265  19945  20462   -568    691  -1224       O
> ATOM   6115  OD2BASP B 271     -15.310  17.950  50.520  0.50156.92           O
> ANISOU 6115  OD2BASP B 271    19211  19952  20460   -550    666  -1256       O
>
>
> Is there something wrong?
>
> Thank you very much!
>
> yamei yu
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