Walkthrough on command line based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)

From Dynamo
Jump to navigation Jump to search


Dynamo includes a package for automated alignment and reconstruction of tilt series. This walkthrough guides users through a series of steps on how to use it in command line based mode. The GUI based alignment walkthrough shows how to operate this procedure through the GUI. Here, we go through each command one by one (for advanced applications, all commands can also be summarized in a Matlab script and run at once).

Data

We use a binned version of the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). You can download it directly from EMPIAR, then bin it, or simply follow this link to download a 600Mb file. In this course, the data for this walkthrough is in: 

 /home/student/data/AlignmentOfTiltSeries/

and the tomogram with the data is in the link: 

 /home/student/data/AlignmentOfTiltSeries/b001ts001.mrc
Retrieved from "https://www.dynamo-em.org//w/index.php?title=Walkthrough_on_command_line_based_tilt_series_alignment_(I2PC_–_Instruct_Course_on_Electron_Tomography_and_Subtomogram_Averaging_2025)&oldid=5789"