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

[Maxime Cuypers]

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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