Getting Started

Connect to the EC2 Instance

• Follow instrucions specified by the UMich Cryo-EM Facility to connect to the EC2 instance .

CryoSPARC Setup

• Start cryoSPARC on your EC2 instance if you haven't already:
  • module load cryosparc
  • cryosparcm start
• You can access cryoSPARC via EC2_INSTANCE_URL:39000
• Create an empty directory for your cryoSPARC projects:
  • mkdir -p /scratch/cryosparc_projects
• Case study data is available in the following directory: /scratch/data
  • Tri-snRNP, EMPIAR-10073: /scratch/data/10073/CryoSPARC
  • Staph Helicase, EMPIAR-10881: /scratch/data/10881/CryoSPARC
  • Apo-CGRP, EMPIAR-10668: /scratch/data/10668/CryoSPARC

Port Forwarding

It's recommended to set up port forwarding to access cryoSPARC from your local machine. You can do this using SSH:

• Open a terminal on your local machine.
• Run the following command, replacing EC2_INSTANCE_URL with your instance's public DNS or IP address:
  • ssh -L 39000:localhost:39000 participant@EC2_INSTANCE_URL
• This command forwards port 39000 on your local machine to port 39000 on the EC2 instance.
• Now, you can access cryoSPARC by navigating to http://localhost:39000 in your web browser.

CryoSPARC Tools

We will be working with CryoSPARC Tools as part of the EMPIAR-10881 case study – detailed instructions are outlined on that page.

UCSF ChimeraX Commands

We will be using UCSF ChimeraX for visualization and analysis. Here are some useful commands to get started:

• Open a volume series (after unzipping):
  • open ~/Downloads/cryosparc_P1_J1_component_000/* vseries true
• Play a volume series in a loop:
  • vseries play #1 direction oscillate loop true
  • Adjust the #1 to match the volume series number in your session. You can also specify multiple series by separating them with spaces or using a range (e.g., #1-3 ).
• Stop the playback:
  • vseries stop #1
• Tile a set of volumes
  • tile #1-3
  • Adjust the #1-3 to match the volume series numbers you want to tile.