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Dear Chris,
did you check the map looks like what you expect it to be? If I remember
correctly, I had difficulties covering the Tl+/K+ ions from these data
because they lie at the very edge of the asymmetric unit. I used mapmask
as in the attached script in order to extend the map to cover the Tl+
atoms.
Note that the 1D-profile (as well as the 3D-profile) depends on the
B-values of the ions, and a dip in the anomalous signal could be
accounted for by an increased vibrational motion. That's why I did
not interprete the map but the diffraction data in my re-analysis of
these data in
http://www.sciencemag.org/content/346/6207/352
with modern means.
Kind regards,
Tim
On 04/14/2015 11:15 PM, Chris K wrote:
> Dear all,
>
> I was trying to generate a one-dimensional electron density
> profile along the Z axis from an anomalous difference map (similar
> to Fig. 1 of Zhou, Y., & Mackinnon, R. (2003), Journal of Molecular
> Biology, 333(5), 965–975) using the program MAPMAN, but I think I’m
> missing something.
>
> This is what I tried: - I’ve generated the anomalous difference
> map covering all the atoms in the pdb file using FFT from the CCP4
> gui, doubling the grid space. - I fed MAPMAN with that anomalous
> map and ran the command “1d mymap”. - I then selected the Z axis. -
> I converted the O2D plot file into a PS file.
>
> But I think what I’m getting is only noise. Is there a way to plot
> the profile only for signals above 4 sigma?
>
>
> Cheers,
>
> Chris
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149
GPG Key ID = A46BEE1A
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