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

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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
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