Frealix: modes

Here is an incomplete listing of useful Frealix modes

Mode Description
FILAMENT_REFINE The workhorse of helical refinement. Takes existing 3D and alignment parameters and refines them
FILAMENT_STARTUP Given picked coordinates (EMAN Boxer or IMOD 3dmod), CTFFIND or CTFTILT results, helical parameters, etc., output an alignment parameter file (and an initial 3D structure, optionally).
APPLY_CTF Apply a CTF to an image
BFACTOR Apply a Bfactor filter and/or cosine-falloff high/low pass filters to an image or volume
CALC_FSC Compute the FSC or FRC between two volumes or images
CROP Resize a volume or image
FINALISE_3DS Combine a number of 3D reconstructions (output by FILAMENT_REFINE, for example) into a single 3D reconstruction
FREALIGN_STACK_TO_FREALIX_ALI Given Frealign inputs (a stack of images, an alignment parameter file), and the location of micrograph images, CTF results etc., output Frealix alignment parameters. Facilitates transition from Frealign to Frealix.
FREALIGN_STACK_TO_THREED Compute a 3D reconstruction from a Frealign alignment parameter file and stack of images. Equivalent to Frealign's mode 0. Implements helical reconstructions in same way as Frealign.
STACK_FROM_PAR Given Frealix alignment parameters, output a stack of images and Frealign alignment parameters. Facilitates transition from Frealix to Frealign.
HEXTEND Impose helical symmetry on a volume. Two alternative algorithms are availble. One is the same as used in Frealign, the other is much faster.
HMASK Given a helical structure, apply an envelope mask. Should be used for example before computing FSCs.
MASK Apply masks
PAD Pad, crop, resize an image or volume to new dimensions
RANDOMIZE_WAYPOINTS Add random perturbations to the waypoints in an alignment parameter file
REBUILD_SEAM Given a microtubule reconstruction, re-impose the symmetry in real-space so that the seam is restored.
ROTATE Rotate and/or shift an image or volume
RPS Compute the rotationally-averaged (1D) power spectrum of an image or volume
SPLIT_PAR Split a long alignment parameter file into shorter files. Used for parallelising refinement cycles.
STACK_ALIGN_TO_SUM Iteratively align images in a stack to their average
SYNTH_MICROGRAPH Generate a simulated micrograph of a filament. Useful in testing algorithms etc.