This is a personal preference. I do model at low sigma levels if there IS
some indication of where to put atoms, always try to keep the correct
sequence even if some atoms are missing, and just for coot convenience keep
atoms with occ = 0, rather than delete them altogether. (COOT will refine a
residue with occs = 0, but not one where atoms are missing.. Paul?? Why
not!)
At deposition the wwwPDB are welcome to (and I think do) strip out all
ocs=0..
Eleanor
On Mar 26 2012, Gregory Bowman wrote:
But what about the issue of resolution? As was previously pointed out, at
say 3.2 Å resolution, many side chains will fail to fit, but it doesn't
seem appropriate to trim them all down. The users need to also be aware
of the quality/resolution of the structures that they are looking at.
Greg
On Mar 26, 2012, at 9:28 AM, Ed Pozharski wrote:
I agree with Eleanor 100%...
In my biased opinion, only the atoms supported by electron density
should be included in deposited models. To satisfy the "but this will
mess up the electrostatic potential coloring" argument (a valid one, of
course), the "projected model" can be deposited alongside which must be
clearly advertised as the unconstrained interpretation by the
structure's author.
Cheers,
Ed.
On Sun, 2012-03-25 at 08:36 +0100, Eleanor Dodson wrote:
As Garib says - an atom with occupancy 0.00 is treated as a marker -
useful
for coot - but is not included in any X-ray refinement at all.. Maybe
it
would be more aesthetic to maintain geometry but as crystallographers
I
think we should be interested in the fit of model to experiment -
right? -
and not in reporting a pseudo fit related to geometric parameters
only..
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
--
Department of Biophysics
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Phone: (410) 516-7850 (office)
Phone: (410) 516-3476 (lab)
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--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
