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Re: Time for CA-only models to be abolished ? (was: Re: [ccp4bb]:How to deal with sidechainatoms with low electron density?)



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Mandating that structure factors (amplitudes and phases) are deposited
together with the coordinates should by itself prevent depositions of C-alpha
or polyala models if the data clearly allows a more detailed interpretation.
However, when the chain direction cannot be determined CA-only models may be
the best that can be done.

Bart

On Mon, 25 Nov 2002, Gerard DVD Kleywegt wrote:

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>
> > >...
> > > In the end, however, I agree with the method
> > > discussed by Bart:  delete parts of side chains not seen in electron
> > > density, and keep the residue name as it should be, even if you have to
> > > delete down to the CB.  These residues are flagged in the PDB file.
> > >...
> >
> > Is this not exactly what one does when the main chain cannot be seen in
> > the electron density map?  That is, we seem to have no problem depositing
> > structures with missing residues/atoms at the N- and C-termini and in
> > loops.  Why not be consistent and do the same for other atoms that cannot
> > be visuallized or modelled?
>
> Are you suggesting that people who deposit CA-only models only saw density for
> the CA atoms ? :-) [I know of a few cases were this was probably true,
> actually ...]
>
> Speaking of which - isn't it time for a grass-roots movement to root out that
> abomination that is CA-only models ? The PDB still accepts them, but in this
> day and age I can't see any justification for them. Never mind the fact that
> models for which only CA coordinates have been deposited are statistically
> many times more likely to be seriously wrong (see J Mol Biol 273, 371 (1997),
> reprint: http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=44), such
> models are also considerably less useful (and harder to validate) than
> all-atom models.
>
> If you agree that it is time we abolished CA-only models, please sign the "No
> CA" petition at:
>
>        http://xray.bmc.uu.se/cgi-bin/gerard/no_ca_petition.pl
>
> I am cross-posting this to the PDB and O-info mailing lists; please, forward
> it to any colleagues who might be interested in supporting this initiative.
>
>
> --Gerard Kleywegt
>
>
> PS: this initiative was born during a discussion at the recent course in Cold
> Spring Harbor
>
> ******************************************************************
>                         Gerard J.  Kleywegt
>     [Research Fellow of the Royal  Swedish Academy of Sciences]
> Dept. of Cell & Molecular Biology  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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