How to upload particle stacks into COSMIC²

To help users learn expectations for data uploads and downloads, we have provided a tutorial dataset using a subset of micrographs from EMPIAR-10025 (Campbell et al. 2015).

Right now, we have a binned particle stack and a 3D volume both at a pixel size of 1.32Å/pixel and a box size = 256 x 256.

Step 1: How to access tutorial data for COSMIC²

We have publicly shared the tutorial data on Globus (more info on Globus here). Search for the endpoint ‘COSMIC2 tutorial’ and click ‘Add’ to add your endpoint list:

Now that you added it, you can list the shared endpoint contents by navigating to ‘My endpoints’ and then clicking ‘List’ next to the endpoint name ‘COSMIC2 tutorial’:

NOTE: You’ll see that the Source Endpoint is listed as COSMIC2 tutorial (the data you want to upload) where as the Destination Endpoint is listed as the COSMIC2 Science Gateway on XSEDE Comet.

Step 2: Upload tutorial particle stack

Using this endpoint, you can upload the particle stack by clicking on the ‘Extract’ folder checkbox and then click ‘Transfer’:

After you click transfer you can monitor the Transfer Status tab to watch your job status.

When the job is successfully uploaded, you’ll see the files listed on the data menu:

Click here to watch a video walking you through the upload process:


Step 3: Submit test 2D classification job

Using this example dataset, submit a 2D classification job using the tool “Relion 2D classification” such as that shown in this tutorial video:

You can check on the job status while the job is running to see which iteration the job is on.

Step 4: Download results

After the job is finished you will see the job action button change from ‘View Status’ to ‘Output’, where you will see the run.out (output information from RELION) and run.err (any errors associated with job running) output files available for viewing or download:

To download the output results, you will use Globus for moving the output files back to your local machine: