**PURPOSE**- Create FFT of search volume, FFT of squared search volume, and FFT of rotated padded mask, as requested. These files are needed for: 'LO LSD' and 'LO'.

**SEE ALSO****LO LSD**[Prepare LSD volume for Locating motif inside volume] **LO**[Locate motif inside a search volume]

**USAGE**- .OPERATION: LO I

- .CREATE SEARCH FFT'S (S), MASK FFT (M), OR BOTH (B): B

[Select type of output files to be created. For a motif with a rotationally invariant mask, both types of output can be created initially before the motif is rotated. For a rotationally varying mask the mask fft must be recalculated at each orientation.].SEARCH VOLUME FILE: BIG000

[For efficiency this volume must be padded, if necessary, to even number of rows and slices before the operation can be used.] - If answer to initial question was 'S' or 'B' then following two
queries appear:
- .SEARCH VOLUME FFT OUTPUT FILE: search_fft

[Enter name for FFT of search volume.].SEARCH VOLUME SQ. FFT OUTPUT FILE: search_sq_fft

[Enter name for FFT of search volume squared.] - If answer to initial question was 'M' or 'B' then following two
queries appear:
- .ROTATED MOTIF MASK INPUT FILE: rot_mask

[Enter name of rotated motif mask.].PADDED MOTIF MASK FFT OUTPUT FILE: mask_fft

[Enter name for padded rotated motif mask FFT file.]

**NOTES**

- The following procedures:

sigs_settings.spi, sigs_pub.spi, and sigsloop.spi for an example of usage. - For futher info see:

RAMOS (RApid MOtif Search) / Signature Search / Docking

- References:

B.K. Rath et al. (2003) Journal of Structural Biology 144, 95-103.

Alan Roseman (2003) Ultramicroscopy 94, 225-236.

**SUBROUTINES**- MOTIF_INIT

**CALLER**- MOTIF1

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