Without F000 we cannot get absolute density level vs zero, but still
I think electron density in units of e-/a^3 above the mean is much more
meaningful than sigma above the mean. I think the last one of these
mystery density questions generated a lot of discussion until someone
pointed out that there was no 2Fo-Fc density for the feature.
eab
Pavel Afonine wrote:
For map in e-/A^3 units to make sense one needs to obtain F000, which
may be more tricky than one may think. Interesting, how Coot does this
given just a set of Fourier map coefficients?
Pavel
On Wed, Nov 28, 2012 at 12:21 PM, Greg Costakes <gcost...@purdue.edu
<mailto:gcost...@purdue.edu>> wrote:
You stated that the map is set to 3 sigma, but what is the e-/A^3?
In Coot I often find that my fo-fc map needs to be maxed out (max
sigma) in order to get to an acceptable e-/A^3. It is possible that
your fo-fc map at 3 sigma has an e-/A^3 of 0.04 or something low
like that.
-------------------------------------------------------------------------------
Greg Costakes
PhD Candidate
Department of Structural Biology
Purdue University
Hockmeyer Hall, Room 320
240 S. Martin Jischke Drive, West Lafayette, IN 47907
--------------------------------------------------------------------------------
------------------------------------------------------------------------
*From: *"Jon Read" <jon.r...@astrazeneca.com
<mailto:jon.r...@astrazeneca.com>>
*To: *CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Sent: *Wednesday, November 28, 2012 10:48:04 AM
*Subject: *[ccp4bb] Strange density
Anyone see anything like this before? The data is 1.7Angstrom data
with good statistics. The picture shows the solid FoFc density
contoured at 3 Sigma in light brown and -3 Sigma in purple. The
density is odd as it appears to be bound to a peptide carbonyl with
no other obvious interactions with the protein. There is a
characteristic tail at one end.
------------------------------------------------------------------------
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