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.


== relion_star_loopheader ==
* '''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 <code>ctfdat</code> file.
* '''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


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!!'''
Examples on how to use these utilities are given on the [[Prepare input files]] and [[Analyse results]] pages.
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, optional labels (such as DefocusU/V, AmplitudeConstrast, etc values) can be given for each stack.
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, and then adds (optional) data values in subsequent arguments.
relion_star_datablock_singlefiles "tmp/*" 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 ==
 
== relion_star_printtable ==
 
== relion_star_plottable ==

Latest revision as of 14:59, 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 ctfdat file.
  • 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

Examples on how to use these utilities are given on the Prepare input files and Analyse results pages.

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