[phenixbb] adding sutrates in phenix.refine

[Maia Cherney]

Have you tried replacing ' with *?

Maia


Rune wederkinck Andersen wrote:
> Hi everyone
> I'm running a refinement in phenix.refine. I'm now trying to ad two 
> subtrates AMP and RP5. The phenix.refine  seams  to reconise AMP but 
> not the RP5 molecules. It seams as if this molecules is well known for 
> the program  
> (phenix-1.4-3/ext_ref_files/chemical_components/r/data_RP5.cif).
> In my PDB file the two molecules are described like this:
> ...
> HETATM   19  C6  AMP A 301      35.852  19.986  36.427  1.00 22.32      A
> HETATM   20  N6  AMP A 301      35.448  19.736  37.693  1.00 24.44      A
> HETATM   21  N7  AMP A 301      36.400  17.540  35.616  1.00 23.01      A
> HETATM   22  C8  AMP A 301      36.853  17.097  34.416  1.00 21.98      A
> HETATM   23  N9  AMP A 301      37.034  18.126  33.560  1.00 19.84      A
> HETATM    1  P'  RP5 A 302      30.291  24.910  31.815  0.25 10.66      A
> HETATM    2  C5' RP5 A 302      32.348  25.416  30.301  0.25 14.76      A
> HETATM    3  O5' RP5 A 302      31.481  24.448  30.868  0.25 12.67      A
> HETATM    4  C4' RP5 A 302      33.260  24.753  29.307  0.25 15.58      A
> HETATM    5  C3' RP5 A 302      33.017  25.227  27.872  0.25 15.17      A
> HETATM    6  O3' RP5 A 302      33.951  26.264  27.522  0.25 14.15      A
> HETATM    7  C2' RP5 A 302      33.282  23.935  27.083  0.25 16.11      A
> HETATM    8  O2' RP5 A 302      34.571  23.963  26.478  0.25 13.68      A
> HETATM    9  C1' RP5 A 302      33.351  22.848  28.160  0.25 16.92      A
> HETATM   10  O1' RP5 A 302      32.775  23.415  29.296  0.25 16.62      A
> HETATM   11  O1  RP5 A 302      32.631  21.639  27.867  0.25 20.12      A
> HETATM   12  O1X RP5 A 302      29.112  25.373  30.809  0.25 10.53      A
> HETATM   13  O2X RP5 A 302      29.912  23.844  32.781  0.25 10.59      A
> HETATM   14  O3X RP5 A 302      30.793  26.258  32.567  0.25  9.63      A
> ATOM      1  N   MET B   1      63.305   2.511  45.667  1.00 64.80      B
> ATOM      2  CA  MET B   1      62.528   3.463  46.463  1.00 68.29      B
> ATOM      3  C   MET B   1      62.555   4.863  45.882  1.00 65.73      B
> ATOM      4  O   MET B   1      63.607   5.325  45.446  1.00 64.47      B
> ...
>
> I have tried with phenix.elbow as well but didn't work...
>
> Please help...
>
> Rune
>
>
>
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