STAR file 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

This script generates the header of STAR-file with the given labels, in that order. Note that the order of the labels in the STAR header should be the same as the order of the entries on each line of the following datablock!!

Example:

relion_star_loopheader rlnImageName rlnDefocusU rlnDefocusV rlnDefocusAngle rlnVoltage rlnSphericalAberration rlnAmplitudeConstrast

will yield:

data_
loop_
_rlnImageName
_rlnDefocusU
_rlnDefocusV
_rlnDefocusAngle
_rlnVoltage
_rlnSphericalAberration
_rlnAmplitudeConstrast

relion_star_datablock_stack

Generates the datablock for N images in a stack, any number of additional data values (such as DefocusU/V, AmplitudeConstrast, etc values) are in subsequent arguments.

Example (N=3):

relion_star_datablock_stack 3 my_images.mrcs 10000 10500 0.0 200 2 0.1

will yield:

000001@my_images.mrcs 10000 10500 0.0 200 2 0.1
000002@my_images.mrcs 10000 10500 0.0 200 2 0.1
000003@my_images.mrcs 10000 10500 0.0 200 2 0.1

relion_star_datablock_singlefiles

Generates the datablock for all images represented by the wildcard in the first argument, any number of additional data values (such as DefocusU/V, AmplitudeConstrast, etc values) are in subsequent arguments.

Example:

relion_star_datablock_singlefiles "tmp/*.spi" 10000 10500 0.0 200 2 0.1

will yield:

tmp/t1.spi 10000 10500 0.0 200 2 0.1
tmp/t2.spi 10000 10500 0.0 200 2 0.1
tmp/t3.spi 10000 10500 0.0 200 2 0.1

relion_star_datablock_ctfdat

Generates the STAR datablock for all images in an xmipp-format CTFDAT file. Note that the sign for XMIPP's defocusU, defocusV and Q0 values is reversed. Also note that all xmipp-format CTFPARAM files that are referred to in the CTFDAT file should have the same order of the labels.

Example:

/public/EM/RELION/relion/bin/relion_star_datablock_ctfdat all_images.ctfdat