By Vinzenz Unger and Anchi Cheng

This program calculates an autocorrelation map from a small piece of the filtered image. The central autocorrelation peak is later used to search the cross-correlation map for the position and height of the cross-correlation peaks. Like the cross-correlation (program: TWOFILE) the autocorrelation is calculated in reciprocal space and includes the following separate operations

• transforming a small square area excised from the filtered image. For simplicity, the centre of this area is the same as for the reference.
• placing the transform into a larger box to obtain a finer sampling of the profile. In this step, the phase origin is also shifted to centre the autocorrelation peak about the centre of the expanded map.
• multiplying with the complex conjugate transform and backtransforming to give the real space autocorrelation map (name of file in script: “auto$image.cor”).

The program is dimensioned to handle areas with a final size of 520×520 pixel for the entire autocorrelation map. While in principle there is some flexibility in choosing the size of input and amount of oversampling, it should be noted that the current settings (26×26 pixel input and 20x oversampling) are “hard-wired” into the QUADSERCHB source code. Furthermore, QUADSERARCHB expects a (101×101 pixel) profile array that is generated by excising the central autocorrelation peak using LABEL. These settings will be adequate for most cryo applications. However, if problems occur a likely source is that the image was sampled either too finely or too coarse. Depending on the particular case, rescanning the image at a more appropriate step size should void the problem.