Grouping procedure: Difference between revisions
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== | == Overview == | ||
Despite that RELION groups are NOT the same as defocus groups (see this [[FAQs#What_are_groups_for_anyway.3F | FAQ]]) | We will generate a text file with the rlnMicrographName for each micrograph in our data set. To allow grouping them in a convenient manner, we will sort this list either based on defocus values or on previously refined intensity scale-factors inside RELION. We will then insert empty lines in the list, which will indicate the start of a new group. Fibnally, we will run a csh script to generate a new particles_grouped.star file with the corresponding rlnGroupName labels. | ||
=== Defocus-based groups === | |||
Despite that RELION groups are NOT the same as defocus groups (see this [[FAQs#What_are_groups_for_anyway.3F | FAQ]]), it appears that particles with similar defocus values often have similar scale intensity factors and noise power spectra. Therefore, you may sort your micrographs on defocus and use this as a guideline for grouping. You could sort your micrographs for example by using the following command: | |||
relion_star_printtable particles.star data_ _rlnDefocusU _rlnMicrographName | sort | uniq -f 1 | awk '{print $2, $1}' > split_mics_defocus.dat | |||
Note that this sorting will disregard any increase in noise due to contamination. If you think contamination may play an important role in your data set, then you might want to consider an alternative sorting (one that takes defocus AND aquisition time into account). | |||
=== Intensity scale-factor-based groups === | |||
Alternatively, if you have already ran a RELION refinement (either 2D class averages or 3D classification/refinement), you may group your particles based on their refined intensity scale-factor. | |||
Revision as of 12:24, 27 March 2013
Overview
We will generate a text file with the rlnMicrographName for each micrograph in our data set. To allow grouping them in a convenient manner, we will sort this list either based on defocus values or on previously refined intensity scale-factors inside RELION. We will then insert empty lines in the list, which will indicate the start of a new group. Fibnally, we will run a csh script to generate a new particles_grouped.star file with the corresponding rlnGroupName labels.
Defocus-based groups
Despite that RELION groups are NOT the same as defocus groups (see this FAQ), it appears that particles with similar defocus values often have similar scale intensity factors and noise power spectra. Therefore, you may sort your micrographs on defocus and use this as a guideline for grouping. You could sort your micrographs for example by using the following command:
relion_star_printtable particles.star data_ _rlnDefocusU _rlnMicrographName | sort | uniq -f 1 | awk '{print $2, $1}' > split_mics_defocus.dat
Note that this sorting will disregard any increase in noise due to contamination. If you think contamination may play an important role in your data set, then you might want to consider an alternative sorting (one that takes defocus AND aquisition time into account).
Intensity scale-factor-based groups
Alternatively, if you have already ran a RELION refinement (either 2D class averages or 3D classification/refinement), you may group your particles based on their refined intensity scale-factor.