Setup for 2026 U of M Workshop

These instructions are for setting up your system to run this tutorial in the 2026 University of Michigan cryo-ET workshop.

First, use DCV Viewer to connect to your AWS instance using the provided IP address, username, and password. Right click on the desktop to start a terminal window.

Load Modules

The instances we are using for this tutorial have all the required software installed as Lmod modules. In terminals where you will run TOMOMAN or STOPGAP, load them with:

module load aretomo2 chimera ctffind/4.1.14 motioncor3/1.2.4 novactf stopgap tomoman

NOTE: To paste into a terminal, you can use the keyboard shortcut CTRL + Shift + V.

You can see what packages are loaded with module list.

NOTE: loading modules makes software accessible as well as defining paths and aliases appropriately to run them.

Tutorial Data

The test data we will be using for this workshop is tilt series 1 (TS_01) from the EMPIAR-10164 dataset. The /work/data/EMPIAR-10164/data/ directory contains frames/ and mdoc-files/ subfolders. The frames/ subfolder contains the raw .mrc frames for the tilt series, while the mdoc-files/ folder contains the SerialEM .mdoc files for the tilt series. With a larger dataset there would be one mdoc file for each tilt series. Here, we will generate symbolic links for the files relevant to TS_01.

mkdir ~/HIV_dataset/
cd ~/HIV_dataset/
mkdir tomo/
cd tomo/
ln -s /work/data/EMPIAR-10164/data/frames/ frames
ln -s /work/data/EMPIAR-10164/data/mdoc-files/ rawdata

You are now ready to begin the tutorial.