[Chimera-users] Phases of the 3D FFT

Tom Goddard goddard at sonic.net
Thu Jun 28 16:27:27 PDT 2012

Hi Denis,

   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?
> Best,
> Denis
> ___________________________
> Université de Rennes 1
> UMR 6290, équipe TIPs
> Campus de Beaulieu, Bât. 13
> 35042 Rennes Cedex
> France

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