|LO LSD||[Prepare LSD volume for Locating motif inside volume]|
|LO I||[Initialize files for Locating motif inside volume]|
.MOTIF INPUT FILE: motif
[Enter name of motif volume which is already rotated to the above orientation.]
.MASK FOR MOTIF INPUT FILE: motif_mask
[Enter name of motif mask file. If the mask varies with orientation then the mask must be already rotated to the above orientation.]
.SEARCH VOLUME FFT INPUT FILE: search_fft
[Enter name of FFT of search volume. This can be prepared with: 'LO I'.]
.LOCAL STANDARD DEV. INPUT FILE: lsd
[Enter name of local standard deviation file. This can be prepared with: 'LO LSD'.]
.NUMBER OF PEAKS WANTED: 20
[Enter number of peaks to be reported.]
.PEAK OUTPUT FILE: peakht
[Enter name for cross correlation peaks file.]
.PEAK OUTPUT DOCUMENT FILE: peak_doc
[Enter name for document file listing current orintation, peak location and cross correlation peak heights. Locations are upper left corner of motif as found within the search volume. This is the main output produced by this operation. (Appends to existing output file of same name).
It contains 7 register columns:
1. Eulerian angle (psi) of current rotation.
2. Eulerian angle (theta) of current rotation.
3. Eulerian angle (psi) of current rotation.
4. X location of peak within search volume.
5. Y location of peak within search volume.
6. Z location of peak within search volume.
7. Normalized cross correlation coefficient from