[ccp4bb]: Re: Ramachandran Idealization

["Gerard \"CD\" Kleywegt" <gerard@xray.bmc.uu.se>]

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your metaphor is besides the point. standard geometry
includes bond lengths and angles, planar groups,
getting your chirality right and not letting two atoms
occupy the same part of space - things we "know" and
which we don't really need xtallographic or nmr data for
to confirm. however, the conformational torsion angles
in proteins (phi, psi, chi1, ...) contain the essential
information about the structure of the protein - determining
their values is what experimental structural biology is
all about; predicting their values is what homology modelling 
is about. since these torsion angles do not have a unimodal
distribution (i.e., more than one "ideal" value) you cannot
impose "standard values". moreover, the ramachandran plot
in particular is often used as a hallmark of structural
quality in x-ray/nmr work, so "fudging" its appearance
might convey a false message - which i'm sure you wouldn't
want to happen

a better analogy would be the following: you build a model
of *my* house ! now, it's a safe bet that my house has a
front door and windows. but what you are trying to do is
decide what colour my wall paper is, without any experimental
observations of said wall paper ... sure, you modelling
my wall paper as "pink with elephants on it" makes your
prediction look very precise and detailed - but it is in
fact wholly inaccurate ! (honest!)

--dvd

On Fri, 11 Feb 2000, Paul Hubbard wrote:

> Hello,
> 
> I feel I ought to explain my last e-mail regarding ramachandran
> idealization. As I mentioned, yes its a predicted structure, and so there
> is no way of knowing whether the correct angles have been introduced.
> However, why build a model at all if it violates standard geometry of
> proteins. Thats like making a model of a house which doesn't have a front
> door or any windows (bad analogy - but you get the point!). Why not
> introduce beta phi/psi angles to a region which is predicted to be a
> beta-strand?
> 
> Just wanted to get that off my chest.
> 
> ags
> 
> *******************************************************************************
> Paul Hubbard
> Department of Biochemistry
> Medical College of Wisconsin
> 8701 Watertown Plank Rd.
> Milwaukee
> Wisconsin. 53226
> 
> Tel: 414-456-4305
> Fax: 414-456-6510
> WWW: http://141.106.40.30
> *******************************************************************************
> 
> On Fri, 11 Feb 2000, Gerard "CD" Kleywegt wrote:
> 
> > Date: Fri, 11 Feb 2000 11:37:30 +0100 (MET)
> > From: "Gerard \"CD\" Kleywegt" <gerard@xray.bmc.uu.se>
> > To: Paul Hubbard <phubbard@post.its.mcw.edu>
> > Cc: CCP4 News Group <ccp4bb@dl.ac.uk>,
> >     O News Group <o-info@kaktus.imsb.au.dk>
> > Subject: Re: Ramachandran Idealization
> > 
> > 
> > i think the question should not be "how" but "why on Earth".
> > without any experimental data, the best any program can do
> > is to pull residues into the nearest favourable area, but
> > there is no guarantee that this will be the *correct* area
> > (see our 'databases' paper in acta cryst d, 1998, for an
> > example of this -even with x-ray data- and a discussion).
> > all this would amount to is (at best) cosmetic nonsense.
> > moreover, it could give a false impression of the quality
> > of the model.
> > 
> > --dvd
> > 
> > ******************************************************************
> >                         Gerard J.  Kleywegt
> > Dept. of Cell & Molecular Biology  Bolshevik University of Uppsala
> >                 Biomedical Centre  Box 596
> >                 SE-751 24 Uppsala  SWEDEN
> > 
> >     http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
> > ******************************************************************
> >    The opinions in this message are fictional.  Any similarity
> >    to actual opinions, living or dead, is purely coincidental.
> > ******************************************************************
> > 
> 
> 

******************************************************************
                        Gerard J.  Kleywegt
Dept. of Cell & Molecular Biology  Bolshevik University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
******************************************************************
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
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