[Chimera-users] Phases of the 3D FFT
goddard at sonic.net
Thu Jun 28 16:27:27 PDT 2012
I enhanced the "vop fourier" command so that it provides a map of
phase values (-pi to pi) in addition to the Fourier transform magnitude
map that it already provides. Use
vop fourier #0 phase true
to get the phase map and the same command without the phase option gives
the magnitude map. This will be in tonight's daily builds. Chimera only
handles real-valued maps so the magnitudes and phases need to be treated
as two real-valued maps instead of a single complex-valued map. I'm not
sure what will be an effective way to look at the phases. The phases
can vary rapidly across the map looking almost like noise. You could
try a contour surface of the FT magnitude colored to depict the phases
on that surface (use Surface Color tool) but it is not clear that it
will tell you anything.
> Dear all,
> I'm new to this list, so maybe this question has been raised
> previously. Sorry if this is the case.
> We are using the capability of Chimera to perform 3D Fourier
> transforms, in order to analyse the effect of the missing wedge on
> cryo-electron tomograms of microtubules. The "layer lines" of the
> microtubules are nicely revealed in 3D, showing rings corresponding to
> the amplitudes of their FFT. Yet, it would be really nice to have the
> phases displayed, e.g. using colors. Would that be possible to be
> implemented into the "vop Fourier" command of Chimera?
> Université de Rennes 1
> UMR 6290, équipe TIPs
> Campus de Beaulieu, Bât. 13
> 35042 Rennes Cedex
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