From 0a29244a79009feeecbfcc488692a1cb0dd8bbd3 Mon Sep 17 00:00:00 2001 From: Jasenko Zivanov Date: Thu, 19 Nov 2020 15:39:27 +0100 Subject: [PATCH] import_tomograms and import_particles documented --- .../tomography/programs/import_particles.html | 29 +++++++++++ .../tomography/programs/import_tomograms.html | 48 ++++++++++++------- 2 files changed, 59 insertions(+), 18 deletions(-) create mode 100644 documentation/tomography/programs/import_particles.html diff --git a/documentation/tomography/programs/import_particles.html b/documentation/tomography/programs/import_particles.html new file mode 100644 index 000000000..00ad7d99b --- /dev/null +++ b/documentation/tomography/programs/import_particles.html @@ -0,0 +1,29 @@ + + + + + + Import Particles + + + + +

relion_tomo_import_particles

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This program imports a set of 3D coordinates and (optionally) Euler angles to construct a new particle set. The 3D coordinates can be provided either in one big .star file, or as a set of shorter files, one for each tomogram.

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If all the coordinates are provided as one .star file, it has to contain at least the following columns:

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Optionally, the file may also contain the particle angles: rlnAngle<Rot/Tilt/Psi>

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In case the other format is chosen, then the input file only needs to contain the following columns: rlnTomoName and rlnTomoImportParticleFile. The latter column points to a set of files (one for each tomogram) that contain the coordinates (rlnCoordinate<X/Y/Z>) and (optionally) angles (rlnAngle<Rot/Tilt/Psi>)

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relion_tomo_add_tomo

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relion_tomo_import_tomograms

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This program adds a new tilt series to a tomogram set. It is typically the first program to be used to create a Relion tomography data set. It imports an existing alignment from IMOD and the initial CTF parameters from either CTFFind or CtfPlotter. Additional parameters, such as the fractional electron dose and the chronological sequence of frames have to be supplied through the command line. The default parameters correspond to default IMOD output file names, so they can be omitted if the program is pointed to an IMOD project directory (--id argument).

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This program imports a set of tilt series to form a tomogram set. It is typically the first program to be used when creating a Relion tomography data set. It imports an existing alignment from IMOD and the initial CTF parameters from either CTFFind or CtfPlotter. Additional parameters, such as the fractional electron dose and the chronological sequence of frames have to be supplied by the user.

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The tilt series alignment effectively defines an arbitrary 3D coordinate system, as well as a set of projections that map those 3D coordinates to the individual 2D images of the tilt series. The aim of this program is to translate that alignment into the Relion nomenclature. If used successfully, this will produce an equivalent 3D coordinate system inside Relion that will allow particle positions already defined in an IMOD tomogram to be used unchanged.

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The tilt series alignment effectively defines an arbitrary 3D coordinate system, as well as a set of projections that map those 3D coordinates to the individual 2D images of the tilt series. The aim of this program is to translate that alignment into a format readable by Relion. If used successfully, this will produce an equivalent 3D coordinate system inside Relion that will allow particle positions already defined in an IMOD tomogram to be used unchanged.

Optimally, the tilt series would be imported into Relion right after alignment, and the particles would be picked in a low-magnification tomogram generated by relion_tomo_reconstruct_tomogram. That way, the particle positions would be guaranteed to be correct.

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Note: the user is advised to call this program from a script, inside a loop running over all tilt series.

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The primary input to relion_tomo_import_tomograms is a .star file containing one row for each tilt series and at least the following columns:

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The following additional columns may be present. If they are not, then the corresponding command line arguments will be used. In that case, they will be identical for all tilt series.

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General program arguments:

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