As a general note here, and I think this seems to come up regularly, one
should only use something like PyMol as a quick tool. If anything in PyMol
looks wrong, one should initially assume it is PyMol, and load the output
coordinates and parameters using something like VMD. I would generally
only use .pdb files if you want to show data to someone who may not be
familiar with software like VMD and needs the extreme user-friendliness of
PyMol.
On Tue, Feb 14, 2012 at 10:08 PM, case <case.biomaps.rutgers.edu> wrote:
> 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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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Feb 14 2012 - 20:00:02 PST
