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.

@@ Line 1: / Line 1: @@
-__TOC__
+= 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.
-== List of utilities ==
+* '''relion_star_loopheader''' : generates the header of STAR-file (with given labels)
-=== relion_star_loopheader ===
+* '''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
-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.
-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:
-@my_images.mrcs 10000 10500 0.0 200 2 0.1
-@my_images.mrcs 10000 10500 0.0 200 2 0.1
-@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
-=== relion_star_printtable ===
-=== relion_star_plottable ===

STAR file utilities: Difference between revisions

Latest revision as of 14:59, 6 October 2011

Overview of utilities

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