On Tue, Feb 14, 2012, Lachele Foley (Lists) wrote:
>
> The two ways of specifying hydrogens are just two different
> conventions. Not all software recognizes both. So, it isn't really
> correct or incorrect, just different. I don't know how the two
> conventions arose, but they both seem fairly common. Perhaps there is
> a historian among us. :-)
Designations like "1H6" were use in PDB version 2. Several years ago,
the PDB (and Amber starting at version 10 or 11) moved to the "version 3"
naming convention, where all hydrogens begin with "H". "Real" pdb file
(from www.rcsb.org) will have a "REMARK" line like this:
REMARK 4 1UBQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
PDB-like files from other sources (especially from older software) may still
use the version 2 atom nomenclature. It's hard to tell how you might have
done the "cleanup", or why some files are different than others. But it
sounds like the problem is primarily cosmetic, and can be fixed.
...good luck...dac
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Received on Tue Feb 14 2012 - 19:30:02 PST
