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Re: Time for CA-only models to be abolished ? (was: Re: [ccp4bb]:Howto deal with sidechainatoms with low electron density?)
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that's all nice and dandy, but:
(a) what good is information that is unreliable and unverifiable ? is a
CA-only model with tracing errors really of any use ? is it (biological)
signal or is it (biological) noise ? i tell students to compare 1PTE and 3PTE.
then i ask them to have a look at 2PTE ... how much research effort and money
has gone wasted due to incorrect models we'll probably never know.
(b) there are cases of CA-only models with obviously refined temperature
factors. this suggests that people have 'grep'-ed the CA lines out of their
PDB file and hence intentionally obfuscated their results.
for a very recent example to which both (a) and (b) apply (plus absence of
structure factors of course), see FEBS Letters, vol 525, pp 174-175 (2002)
[plus the reply by the crystallographers on pp 176-178 which, if it wasn't so
serious a matter, would be laughable]
a question for the industrial crystallographers - how do you address issues of
quality and reliability ? surely you folks must take this stuff more seriously
than some of your academic colleagues who demand to be believed on the power
of their word/reputation/elephantine behaviour ? or am i being blue-eyed ?
--gerard
On Mon, 25 Nov 2002, Edward Berry wrote:
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>
> Gerard DVD Kleywegt wrote:
> >
> > Speaking of which - isn't it time for a grass-roots movement to root out that
> > abomination that is CA-only models ?
>
> No, I think there is a valid use for CA-only models - when the
> resolution is 4-5 A and the side chains don't show up but the
> transmembrane helices do, and the protein is of such importance
> that the biologists would prefer a TMH + Cofactors model
> at 5 A to any number of mutant HEW lysozyme structrures at 1.2 A.
>
> 2PPS (Photosystem I) was such a case and in my opinion one of the
> most exciting structures of the last decade. I believe some of the
> early cryo-EM structures of bacteriorhodopsin were C-a only,
> and were a huge improvement over the transmembrane-blob
> structures we had been working with since 1977.
>
> It would have cut decades off the time it took for Ron Kaback
> to solve the structure of lac permease (1M2U) by non-crystallographic,
> non-NMR means, if he had had a good C-a trace available to
> thread his structure onto.
>
> And the ribosome- even more exciting- surely they don't have
> side-chains at that resolution. There is an immense amount of
> useful information in a C-a trace, especially when it shows the
> juxtaposition of cofactors or nucleic acids and the backbone.
> For a lot of biologists, the first thing to do when one looks at
> a structure in RASMOL is to set the display to "backbone" or
> "ribbons" to see how the thing folds. All those messy side
> chains just get in the way!
>
> Ed
>
--gerard
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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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