Dear All,
For my master thesis I am busy with neutron crystallography. For refinement,
the software used is phenix.refine and COOT for manual corrections.
However, it seems that deuterium atoms will not correctly refine because there
are no restraints available in the COOT dictionary.
Thus we set out to introduce restraints to COOT by creating cif files for each
amino acid with restraints for deuteriums.
This seems to work for perdeuterated proteins, but not for those that are
H/D-exchanged.
The cause of this problem seems to be in the way H/D positions are defined:
phenix.refine assigns H and D to alternative conformations A and B,
while the other part of the residue remains normal (eg. has no alternative
conformation assigned).
ATOM 1080 N ALA A 67 16.629 -3.415 9.989 1.00 7.92
N
ATOM 1081 CA ALA A 67 15.560 -3.601 9.012 1.00 10.82
C
ATOM 1082 C ALA A 67 14.894 -4.957 9.211 1.00 8.09
C
ATOM 1083 O ALA A 67 14.918 -5.812 8.329 1.00 6.06
O
ATOM 1084 CB ALA A 67 16.119 -3.459 7.599 1.00 7.64
C
ATOM 1085 HA ALA A 67 14.801 -2.842 9.167 1.00 9.05
H
ATOM 1086 HB1 ALA A 67 15.405 -3.583 6.954 1.00 9.12
H
ATOM 1087 HB2 ALA A 67 16.502 -2.575 7.490 1.00 9.97
H
ATOM 1088 HB3 ALA A 67 16.806 -4.129 7.454 1.00 9.88
H
ATOM 1089 H AALA A 67 17.253 -4.214 10.089 0.50 9.73
H
ATOM 1090 D BALA A 67 17.253 -4.214 10.089 0.50 9.73
D
The restraints we introduced in the cif files do work when deuterium and the
corresponding hydrogen have not been assigned to an alternative conformation.
When they are, they (both hydrogen and deuterium) refuse to refine. Does
someone know a way around this problem?
Thanks in advance and kind regards,
Toon Van Thillo
