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. |
