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. Tom
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