STAR file utilities: Difference between revisions
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= Overview of utilities = | |||
For any of the programs below, instructions on how to use them are printed to the screen if no arguments are given. | For any of the programs below, instructions on how to use them are printed to the screen if no arguments are given. | ||
Revision as of 14:53, 6 October 2011
Overview of utilities
For any of the programs below, instructions on how to use them are printed to the screen if no arguments are given.
- relion_star_loopheader : generates the header of STAR-file (with given labels)
- relion_star_datablock_stack : generates the datablock for a given number of images in a stack
- relion_star_datablock_singlefiles : generates the datablock for all images represented by a wildcard
- relion_star_datablock_ctfdat : generates the datablock for all images inside an XMIPP-style
ctfdatfile. - relion_star_printtable : prints the contents of specified labels of a given datablock to the screen.
- relion_star_plottable : uses gnuplot to produce XY-plots of columns in a datablock
Example use
- Generate a STAR file for images that are stored per-micrograph and in single-file SPIDER format:
relion_star_loopheader rlnImageName rlnMicrographName rlnDefocusU rlnDefocusV rlnDefocusAngle rlnVoltage rlnSphericalAberration rlnAmplitudeConstrast > all_images.star relion_star_datablock_singlefiles "micrograph1/images*.spi" micrograph1 10000 10500 34 200 2.26 0.1 >> all_images.star relion_star_datablock_singlefiles "micrograph2/images*.spi" micrograph2 15000 14500 37 200 2.26 0.1 >> all_images.star relion_star_datablock_singlefiles "micrograph3/images*.spi" micrograph3 22300 22000 43 200 2.26 0.1 >> all_images.star
- Generate a STAR file for images that are as an individual stack for each micrograph:
relion_star_loopheader rlnImageName rlnMicrographName rlnDefocusU rlnDefocusV rlnDefocusAngle rlnVoltage rlnSphericalAberration rlnAmplitudeConstrast > all_images.star relion_star_datablock_stack 126 mic1.mrcs mic1.mrcs 10000 10500 34 200 2.26 0.1 >> all_images.star relion_star_datablock_stack 102 mic2.mrcs mic2.mrcs 15000 14500 34 200 2.26 0.1 >> all_images.star relion_star_datablock_stack 135 mic3.mrcs mic3.mrcs 22300 22000 34 200 2.26 0.1 >> all_images.star
- Generate STAR file from an XMIPP-style
ctfdatfile:
relion_star_loopheader rlnImageName rlnMicrographName rlnDefocusU rlnDefocusV rlnDefocusAngle rlnVoltage rlnSphericalAberration rlnAmplitudeContrast> all_images.star relion_star_datablock_ctfdat all_images.ctfdat>> all_images.star