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Nat Echols wrote:
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A new student showed me how to build in Coot the other day and I was
impressed enough to spend three hours trying to install it on my
laptop. Works great, but I'm a little confused by the inconsistent
electron density. In Coot, some water molecules don't have any 2Fo-Fc
density around them; in O, most of them have density although most are
pretty marginal.
So, which program is right? I assume they're calculating the
distribution of electron density, or else the default cutoff means
something different in each. I had thought everyone used 1 sigma,
with some standard formula for calculating this, but obviously that's
not the case. What should I go by in deciding whether to kill the
waters?
thanks,
Nat
Your question should maybe be posted to [EMAIL PROTECTED], but you
already have the solution to your "problem" the different contour levels.
You should also have a look at the validation tools in Coot, there's an
optio to validate waters.
Juergen
--
--------------------------------------------
Jürgen Bosch
University of Washington
STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA
Health Science Building
Dept. of Biochemistry, K-418
Box 357742
1705 NE Pacific Street
Seattle, WA 98195-7742
Phone: 206-616-4542
FAX: 206-685-7002
Web: www.sgpp.org
