Convert

usage: convert [-h] [-o OUTPUT] [--from {auto,coord,csv,star,box}]
               [--to {auto,coord,csv,star,json,box}] [--suffix SUFFIX]
               [-t THRESHOLD] [-s DOWN_SCALE] [-x UP_SCALE]
               [--voltage VOLTAGE] [--detector-pixel-size DETECTOR_PIXEL_SIZE]
               [--magnification MAGNIFICATION]
               [--amplitude-contrast AMPLITUDE_CONTRAST] [--invert-y]
               [--imagedir IMAGEDIR] [--image-ext IMAGE_EXT]
               [--boxsize BOXSIZE] [-v VERBOSE]
               files [files ...]

Positional Arguments

files

path to input particle file(s). when multiple input files are given, they are concatentated into a single output file.

Named Arguments

-o, --output

path to output particle file (default: stdout)

--from

Possible choices: auto, coord, csv, star, box

file format of the INPUT file (default: detect format automatically based on file extension)

Default: “auto”

--to

Possible choices: auto, coord, csv, star, json, box

file format of the OUTPUT file. NOTE: when converting to JSON or BOX formats, OUTPUT must specify the destination directory. (default: detect format automatically based on file extension)

Default: “auto”

--suffix

suffix to append to file names when writing to directory (default: none)

Default: “”

-t, --threshold

threshold the particles by score (optional)

Default: -inf

-s, --down-scale

DOWN-scale coordinates by this factor. new coordinates will be coord_new = (x/s)*coord_cur. (default: 1)

Default: 1

-x, --up-scale

UP-scale coordinates by this factor. new coordinates will be coord_new = (x/s)*coord_cur. (default: 1)

Default: 1

--voltage

voltage metadata (optional)

Default: -1

--detector-pixel-size

detector pixel size metadata (optional)

Default: -1

--magnification

magnification metadata (optional)

Default: -1

--amplitude-contrast

amplitude contrast metadata (optional)

Default: -1

--invert-y

invert (mirror) the y-axis particle coordinates. requires also specifying –imagedir.

Default: False

--imagedir

directory of images. only required to invert the y-axis - sometimes necessary for particles picked on .tiff images

--image-ext

image file extension. required for converting to STAR and BOX formats and to find images when –invert-y is set. (default=.mrc)

Default: “.mrc”

--boxsize

size of particle boxes. required for converting to BOX format.

Default: 0

-v, --verbose

verbosity of information printed (default: 0)

Default: 0