Hey everyone,

I've done some more digging into pdb_atomtypes.xml, and (with some pointers from #cdk and the google), managed to trace down the source of the pdb_atomtypes van der Waals data.
It all comes from Emboss's Evdw.dat file. I've been going through it and noticed a pattern to the 'odd' radii mentioned above:
The radius is reduced only for branched carbons attached to at least one hetero-atom, it is then consistently 1.7 (so the branching C-Delta in Leucine is 1.9, the branching C-Delta in asparagine is 1.7)

There are also some additional "atom-types" listed in the Emboss file, such as Deuterium isotopes (at least, I _think_ they're supposed to indicate Deuterium...), and labels for "unknown-flip-state" of asymmetric residues (e.g. "This is either the terminal N-delta OR the terminal O-delta of asparagine).

I'm now rewriting pdb_atomtypes.xml from scratch, and was wondering a few things:
1) how to represent the deuteriums? Just with element-type="H", or is there a way to indicate the isotope?

2) what to do with the "unknown flip-state" labels? Obviously they have no defined element-type (unless you count "C or N", "N or O", etc.), but I think it's wasteful to just skip them outright.

What are this list's opinions on this?

Cheers,
Jules

On 24 March 2011 16:16, Andreas Schueller <aschueller@bio.puc.cl> wrote:
RebondTool.java cites "Miguel Howard <miguel@jmol.org>" as the author.

Does somebody know Miguel better and could ask about the PDB atom type
definitions?

Cheers,
Andreas

On 24/03/2011 09:48, gilleain torrance wrote:
>>
>> Where are these radii used anyway? In the RebondingTool?
>>
> Yes, they are used in the rebond tool (if that option is set) to bond
> the protein and DNA residues. Or only the ones with types defined in
> that xml file.
>
> gilleain
>
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