[Chimera-users] pdb parsing problem-- hydrogen as mercury

[Josh Tasman]

I'm getting errors on reading PDB files containin hydrogens added by 
TRIPOS SYBYL.  For example, the atoms 1677-1679 are parsed as Mercury (HG):


ATOM   1674 HD11 ILE A 107       4.939  -2.338  17.094  1.00  0.00
ATOM   1675 HD12 ILE A 107       6.613  -2.979  16.971  1.00  0.00
ATOM   1676 HD13 ILE A 107       5.703  -3.133  18.512  1.00  0.00
ATOM   1677 HG21 ILE A 107       4.770  -2.095  20.141  1.00  0.00
ATOM   1678 HG22 ILE A 107       6.235  -1.314  20.827  1.00  0.00
ATOM   1679 HG23 ILE A 107       4.630  -0.527  21.006  1.00  0.00
ATOM   1680  H   ILE A 107       5.291   0.799  16.773  1.00  0.00
ATOM   1681  N   TYR A 108       3.267   1.810  19.498  1.00 21.63


Accoring to the table at

http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl
There are descrepencies between PDB-like file formats, and we see that 
the official PDB format would specify "1HG2" instead of "HG21".

Does anyone know of a quick way to deal with this?

I can write a perl search/replace script if need be.

Thanks,

Josh