[phenixbb] adding sutrates in phenix.refine

Rune wederkinck Andersen andersenrune at hotmail.com
Wed Aug 12 05:11:39 PDT 2009


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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