Re: [PyMOL] DSSP

[Ben H. <bh...@ex...>]

Warren -

Just up front I want to state that I don't think DSSP is the best possible
way to algorithmically determine secondary structure.  My position is that
secondary structure is a subjective assignment anyway - so it will always be
open to interpretation.  In that case, you are better off assigning to the
standard this is in most common usage.

Great example of where DSSP fails, but perhaps a bit contrived.

First of all, DSSP is assigning this as a "H" helix and "G" 3-10 helix - not
really a single continuous helix (although one could interpret it this way).
Second, you point about it not really being a 3-10 helix is not strong..

3-10 helix (-49/-26).  (ideal)
residue 101 (-63/-12)

+/- 15 degrees is pretty difficult to see - so I think that DSSPs assignment
in this case, while liberal, is certainly acceptable.

Finally the difference between a 3 residue "helix" and a reverse turn is not
really easy to quantitate.  In fact, any single turn of any helix is
basically, well, a turn.  Any algorithm that "allows" 3-4 residue helices is
going to make such assignments, and in fact any realistic (human)
interpretation is going to make the equivalence of short "helices" with
turns.

Your last point in the URL is critical.  There will presumably be "errors"
in dss, or stride, or any other algorithm, because frankly, the problem is
not very well defined.  Hence, it's probably best to just implement
something, and leave the interpretation to the user.  The reason that
consistency is of paramount importance in assigning secondary structure is
so that different scientists can talk about the same protein in context.  If
everyone uses the same definition of secondary structure - "helix 1" is
always "helix 1".

Ben


--
Ben Hitz                                    Exelixis
Computational Biology and Informatics
bh...@ex...                   650-837-8137
----- Original Message -----
From: "Warren L. DeLano" <wa...@de...>
To: "'Ben Hitz'" <bh...@ex...>; <pym...@li...>
Sent: Monday, November 03, 2003 10:39 AM
Subject: RE: [PyMOL] DSSP


> Ben,
>
> Granted -- and there are certain times when it makes sense for everyone
> to be "wrong" in order to be consistent.  But is this one such case?  I
> think not.  If DSSP "helices" aren't actually helices, then of what use
> is the standard?  Neither the resulting statistics nor the cartoon
> figures will be correct.
>
> I've put up one particularly egregious DSSP example on the web at
>
> http://www.pymol.org/not_helix
>
> for inspection.  If you are comfortable with obvious turn regions (such
> as this one) being assigned as helix, then by all means, go right ahead
> and continue using DSSP via rTools or the PDB.
>
> But for me, I am not going to lose sleep over deviating from an existing
> standard in PyMOL.  As I said before, the DSSP paper wasn't even written
> in such a way as to enable exact reproduction of their research other
> than by running their proprietary (1000 EURO) software program or by
> analyzing their source code.
>
> PyMOL's new "dss" algorithm is nowhere near validated enough to become a
> standard, but I do think that if we are going to agree upon a standard
> for secondary structure assignment, that the standard should reflect
> common notions of secondary structure, be exactly described, be
> reproducible, and be available in an open-source reference
> implementation.  Does DSSP meet these criteria?  No, but STRIDE might
> (if one could find it), and "dss" probably could in time.
>
> Cheers,
> Warren
>
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax   (650)-593-4020
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of Ben Hitz
> > Sent: Monday, November 03, 2003 8:28 AM
> > To: pym...@li...
> > Subject: [PyMOL] DSSP
> >
> >
> > Warren -
> > The advantage of using DSSP over another heuristic method, is
> > that it is a standard. A DSSP helix is a DSSP helix
> > everywhere, even if a crystallographer might extend the end a bit.
> >
> > Ben
> > --
> > Ben Hitz                                    Exelixis
> > Computational Biology and Informatics
> > bh...@ex...                   650-837-8137
> >
> >
> >
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