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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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Hello all,
Some time ago, I deposited a C-ALPHA model (check in the data base that
holds old PDB entries). The reason there was that there was no sequence
information available, the only sequence information available came only
from the electron density map (at 2.25 A resolution).
Even though all authors were confident of the work carried out, WE KNEW
that there were model errors due to this lack of essential information.
Hence the decision to deposit only the C-ALPHAS (anyone wishing to obtain
the complete coordinate file could obtain it on request). The point was to
indicate that there was something missing there (a protein sequence).
I still think (14 years later) that this was the only way we could go
about it. Not deposit a structure complete with side chains, when these
side chains were deduced from visual inspection of electron density maps.
Fred.
PS as far as I know, the sequence is still not available to date...
--
s-mail: F.M.D. Vellieux (B.Sc., Ph.D.)
Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: (+33) (0) 438789605
Fax: (+33) (0) 438785494
e-mail: vellieux@ibs.fr
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Don't even think of asking me: "I would Het leven is genieten
if I could, but I can't" (L.R., 1998) (to live is to enjoy)
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