[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[ccp4bb]: Re: Ramachandran Idealization

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***


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

Just wanted to get that off my chest.


Paul Hubbard
Department of Biochemistry
Medical College of Wisconsin
8701 Watertown Plank Rd.
Wisconsin. 53226

Tel: 414-456-4305
Fax: 414-456-6510

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.
> ******************************************************************