[Molvis-list] exporting _good_ h-bonds (was: export Chime h-bonds)

Raymond Keller rsk at misinformation.org
Mon Jan 2 19:32:54 EST 2006

* Kevin Karplus (karplus at soe.ucsc.edu) [20060102 14:32]:
> I'm not familiar with the programs available, because I wrote my own
> for the undertaker program.  It turns out to be fairly tricky to get
> "real" hbonds, and there is always an arbitrary cutoff for whatever
> properties are measured (distances, angles, ...).  There are also
> questions about whether weak Hbonds (such as donor hydrogens on
> araomatic carbons, or acceptors in the center of an aromatic ring)
> should be counted.
> I would be a bit uncomfortable using someone else's code, unless I
> spent many hours reading it carefully and seeing how all the arbitrary
> decisions had been made.

I should clarify my situation.

I'm a commercial contractor responsible for rendering client
representations of proteins into different forms, including physical
media.  My needs are not academic, and as such they are not subject
to the ostensibly ardent dedication to truth that should typify
academic research.  Interestingly, while the academic search for
truth may be tainted by the need for securing grants, my primarily
commercial efforts are tainted by a personal desire to be accurate.

Clients get to dictate secondary structure assignments as suits
them.  I find it odd that many don't seem concerned about how the
determinations are made.  I've come to assume that the "standards"
are in flux (if glacially so).

A current client is interested in having his RasMol representation
processed, including h-bonds, and this explains my request for all
y'all's advice.

Here the taint of desire for accuracy comes into play:  If I can't
get RasMol's data, I may opt for an alternative.  I have been able
to hack Stride's sources to make it output its internal h-bond
information (normally it only outputs residues).  Presumably a
program that uses phi and psi values should be more accurate than
one that uses bond distance alone.  (I'm having a hard time finding
a description of the method(s) employed by RasMol, so the
insinuation of method should be taken as slander until proven.)  I
am but a simple trained primate.  Your advanced biomolecular science
frightens and confuses me.  Still, the Stride sources appear to take
advantage of torsion angles (and empirically-derived hydrogen bond
energy)--necessarily so, it seems, for the computation of "Baker"
and "Rose" h-bonds.  From this and my assumptions about RasMol I
believe that Stride's output is of higher quality, and will use this
alternative for my client, barring his refusal.

Do you think it's a better choice?

Raymond Scott Keller
independent molecular visualization contractor
Santa Cruz, California, United States

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