STAR file utilities: Difference between revisions
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000003@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 == | === 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. | 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. | ||
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tmp/t3.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_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. | 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. | Also note that all xmipp-format CTFPARAM files that are referred to in the CTFDAT file should have the same order of the labels. | ||
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/public/EM/RELION/relion/bin/relion_star_datablock_ctfdat all_images.ctfdat | /public/EM/RELION/relion/bin/relion_star_datablock_ctfdat all_images.ctfdat | ||
== relion_star_printtable == | === relion_star_printtable === | ||
== relion_star_plottable == | === relion_star_plottable === | ||
Revision as of 14:33, 6 October 2011
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 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