[phenixbb] C=O-D(+) and COOD restraints for phenix.refine

Thu Jul 28 09:38:47 PDT 2011

Maxime

I appears you wish to deuterate your model. Start with a
hydrogen/deuterium free model (phenix.reduce -Trim model.pdb >
new.pdb) and use

phenix.ready_set new.pdb perdeuterate=True

to all deuteriums to your model. You can also add exchange deuterated
sites using

phenix.ready_set new.pdb neutron_exchange_hydrogens=True

Nigel

On Thu, Jul 28, 2011 at 8:54 AM, Maxime Cuypers <cuypers at ill.fr> wrote:
> Hello,
>
> Apologies if this problem has been asked previously, but i can t seem to
> find a solution online.
> I have added deuterium atoms in an exotic part of amide group (main chain)
> R2-C=O-D (+) bond and on a side chain Glu R-COOD to my pdb. i need to get  a
> .cif that would account for it and work with phenix.refine. However,
> ready_set does not create a .cif file for it as it does not find
> unrestrained atoms.
>
> "No unknown residues"
>
> i have formatted the pdb the following way, adding DX for example (see ***):
>
>
> ATOM    778  N   GLU A  51       8.057  40.510  -2.596  1.00  9.23
> N
> ATOM    779  CA  GLU A  51       8.846  41.709  -2.789  1.00 10.29
> C
> ATOM    780  CB  GLU A  51       8.151  42.937  -2.157  1.00 10.64
> C
> ATOM    781  CG  GLU A  51       6.672  43.097  -2.610  1.00 14.50
> C
> ATOM    782  CD  GLU A  51       6.543  43.007  -4.130  1.00 12.87
> C
> ATOM    783  OE2 GLU A  51       6.056  42.014  -4.689  1.00 12.79
> O
> ATOM    784  OE1 GLU A  51       6.987  43.967  -4.788  1.00 14.44
> O
> ATOM    785  C   GLU A  51      10.293  41.604  -2.286  1.00  8.42
> C
> ATOM    786  O   GLU A  51      10.961  42.627  -2.213  1.00 11.96
> O
> ATOM    787  D   GLU A  51       7.625  40.435  -1.776  1.00 10.15
> D
> ATOM    788  DA  GLU A  51       8.957  41.874  -3.812  1.00 12.62
> D
> ATOM    789  DB2 GLU A  51       8.172  42.833  -1.173  1.00 11.93
> D
> ATOM    790  DB3 GLU A  51       8.654  43.758  -2.380  1.00 13.79
> D
> ATOM    791  DG2 GLU A  51       6.159  42.376  -2.149  1.00 11.66
> D
> ATOM    792  DG3 GLU A  51       6.340  43.998  -2.326  1.00 14.27
> D
> ***ATOM    793  DE1 GLU A  51       8.271  44.322  -5.268  1.00
> 30.00           D
>
> ATOM    850  N   LEU A  56      20.084  37.831  -2.359  1.00 10.58
> N
> ATOM    851  CA  LEU A  56      21.370  38.483  -2.643  1.00 11.42
> C
> ATOM    852  CB  LEU A  56      21.801  39.360  -1.449  1.00 12.58
> C
> ATOM    853  CG  LEU A  56      20.783  40.461  -1.081  1.00 14.37
> C
> ATOM    854  CD1 LEU A  56      21.278  41.264   0.152  1.00 16.71
> C
> ATOM    855  CD2 LEU A  56      20.512  41.416  -2.257  1.00 17.46
> C
> ATOM    856  C   LEU A  56      22.415  37.441  -2.957  1.00 14.27
> C
> ATOM    857  O   LEU A  56      23.025  36.818  -2.093  1.00 30.34
> O
> ATOM    858  D   LEU A  56      19.954  37.597  -1.492  1.00 11.35
> D
> ATOM    859  DA  LEU A  56      21.249  39.065  -3.470  1.00 11.59
> D
> ATOM    860  DB2 LEU A  56      21.898  38.760  -0.652  1.00 14.27
> D
> ATOM    861  DB3 LEU A  56      22.681  39.834  -1.676  1.00 14.15
> D
> ATOM    862  DG  LEU A  56      19.925  39.988  -0.873  1.00 15.72
> D
> ATOM    863 DD11 LEU A  56      20.622  41.969   0.365  1.00 17.87
> D
> ATOM    864 DD12 LEU A  56      21.385  40.668   0.910  1.00 17.46
> D
> ATOM    865 DD13 LEU A  56      22.131  41.691  -0.060  1.00 18.41
> D
> ATOM    866 DD21 LEU A  56      19.968  42.175  -1.959  1.00 18.01
> D
> ATOM    867 DD22 LEU A  56      21.384  41.721  -2.564  1.00 16.67
> D
> ATOM    868 DD23 LEU A  56      20.043  40.956  -2.972  1.00 18.06
> D
> ***ATOM    869 DX   LEU A  56      22.482  36.144  -2.004  0.20
> 30.00           D
>
> I suspect i need to find a correct name for the D atoms, but i tried several
> already unsuccessfully.
>
> phenix.refine complains about 2 unrestrained atoms, the 2 D.
> Does someone know if there is a way to solve this issue or a workaround,
> please?
>
> thanks,
> Maxime
>
>
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>
>

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov