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

[Greg Couch]

On Fri, 18 Feb 2005, Josh Tasman wrote:

> 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.

We'll take the suggestion under advisement.  Please file a bug report with 
TRIPOS.  We'd be especially happy if they fixed the names, but it would 
also help if they put the atomic element symbol in columns 77-78 as 
allowed by PDB version 2.  A perl script is an excellent workaround.

 	Regards,

 	Greg