Import tomograms

This section shows how to import a data set whose tomograms have already been aligned using IMOD and the CTF estimated with CTFFind or CtfPlotter.

The first step to do is to import the tomogram set into the pipeline. To do that, we must first create a description .star file containing the required information, one row per tomogram. The basic fields are the tilt series stack filename, CTF estimated data filename and IMOD project folder. As an example, the tomograms_descr.star file used in this tutorial contains the following fields:

# tomograms_descr.star

data_

loop_
_rlnTomoName
_rlnTomoTiltSeriesName
_rlnTomoImportCtfFindFile
_rlnTomoImportImodDir
_rlnTomoImportFractionalDose

 TS_01   tomograms/TS_01/01.mrc   tomograms/TS_01/01_output.txt   tomograms/TS_01   3.0
 TS_03   tomograms/TS_03/03.mrc   tomograms/TS_03/03_output.txt   tomograms/TS_03   3.0
 TS_43   tomograms/TS_43/43.mrc   tomograms/TS_43/43_output.txt   tomograms/TS_43   3.1
 TS_45   tomograms/TS_45/45.mrc   tomograms/TS_45/45_output.txt   tomograms/TS_45   3.1
 TS_54   tomograms/TS_54/54.mrc   tomograms/TS_54/54_output.txt   tomograms/TS_54   3.0

The rlnTomoName label is a unique identifier per tomogram, automatically created if not provided in this description file (More information can be found in relion_tomo_import_tomograms program help). Note that in this dataset the electron dose is not constant so it should be provided in the description file instead of as a global parameter when importing tomograms.

In the GUI, select Tomo import from the jobt-type browser on the left and fill in the following parameters on the Tomograms tab:

Import tomograms?

Yes

STAR file with tomograms description:

input/tomograms_descr.star

Append to tomograms set

(This field can be used to add new tomograms to an existing tomograms.star. This is usefull when subsets of tomograms have different values for pixel size, voltage … )

Pixel size (Angstrom):

1.35

Voltage (kV):

300

Spherical aberration (mm):

2.7

Amplitude contrast:

0.07

Frame dose (e/A^2):

(If this value varies among the input tomograms, then specify it using its own column in the description input STAR file.)

Ordered list:

input/order_list.csv

(A 2-column, comma-separated file with the frame-order list of the tilt series, where the first column is the frame (image) number (starting at 1) and the second column is the tilt angle (in degrees). If this value varies among the input tomograms, then specify it using its own column in the description input STAR file.)

Flip YZ?

Yes

Flip Z?

Yes

Tilt handedness:

-1

On the Coordinates tab, make sure the following is set:

Import coordinates?

No

On the Others tab, make sure the following is set:

Import other node types?

No

You may provide a meaningful alias (for example: tomograms) for this job in the white field named Current job: Give_alias_here. Clicking the Run! button will launch the job. A directory called ImportTomo/job001/ will be created, together with a symbolic link to this directory that is called ImportTomo/tomograms. Inside the newly created directory a tomogram set tomograms.star file is created. It contains a table with general tomogram properties and a specific table for each tomogram including projection matrices, astigmatic defocus, cumulative radiation dose and deformations per tilt frame. (See relion_tomo_import_tomograms program help).