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
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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