Enhance the Fourier amplitudes of a reconstructed cryo-EM volume
such that they more closely resemble those of experimental
low-angle X-ray scattering data.
This approach is described in Gabashvili et al., Cell 100:537-549, March 3, 2000.
EM : 1D power spectrum of EM volume.
X-ray : Low-angle of X-ray scattering data, out to 8 Å.
FSC : Fourier shell correlation of the EM volume. The Fourier amplitudes need only be corrected out to the spatial frequency corresponding to the 0.5 FSC level, here 1/14 Å.
The above data were plotted with a gnuplot script. The EM data were first multiplied to be in the same numerical range as the X-ray data (right axis), by running the procedure b06.pww.
These data are in the form of SPIDER document files with 4 columns:
|Frequency (1/Å)||intensity multiplied by 60||(unknown)||frequency in units of 2.93 Å|
|Inputs:||volume to be enhanced,|
|X-ray scattering data|
|Outputs:||1D power spectrum from volume,|
gnuplot> K(x)=A*x*x+B gnuplot> fit K(x) 'fen.dat' using 1:3 via A,B gnuplot> plot 'fen.dat' using 1:3 with lines, K(x) A = 623.42 +/- 20.02 (3.212%) B = 13769.2 +/- 1.153e+04 (83.72%)Or, you can try a 3 parameter expression for a better fit:
gnuplot> K(x)=C*x*x*x+A*x*x+B gnuplot> fit K(x) 'fen.dat' using 1:3 via A,B,CGnuplot script to save parameters to a file, and plot the curves in a gnuplot window.
applyabc.bat using the parameters obtained above, apply the enhancement/correction to the volume, then filter the volume at the resolution level.
applyfen.bat Alternatively, apply the enhancement curve directly to the volume.
Older Procedure files
Back to the documents pageUpdated Feb. 20, 2003