CryoSPARC¶

CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state of the art HPC software solution for complete processing of single-particle cryo-electron microscopy (cryo-EM) data. CryoSPARC is useful for solving cryo-EM structures of membrane proteins, viruses, complexes, flexible molecules, small particles, phase plate data and negative stain data.

Policy¶

CryoSPARC™ and CryoSPARC Live™ are available free of charge for non-profit academic use. To use it at HPC2N, you need to acquire a license from the CryoSPARC website (one working day for the processing).

When you have received your license ID, copy it, create a file in your home directory (change u/username to the first letter in your username and your username), using your favourite editor.

This example use nano:

nano /home/u/username/.cryosparc-license 

and then paste your licence ID in the first line of this file. In the second line of the file, write your email address. Save it (Ctrl-X with nano).

Overview¶

CryoSPARC enable:

• Ultra-fast end-to-end processing of raw cryo-EM data and reconstruction of 3D maps, ready for ingestion into model building software
• Optimized algorithms and GPU acceleration at all stages, from pre-processing through particle picking, 2D particle classification, 3D ab-initio structure determination, high resolution refinement, and heterogeneity analysis
• Specialized and unique tools for therapeutically relevant targets, membrane proteins, continuously flexible structures

A longer description of CryoSPARC features can be found here on the CryoSPARC guide page.

CryoSPARC at HPC2N¶

On HPC2N we have CryoSPARC available as a module on Kebnekaise. To see the available versions, login to Kebnekaise and do ml spider cryosparc.

Usage at HPC2N¶

To use, load the CryoSPARC module to add it to your environment. You give this command to see which versions of CryoSPARC are available:

ml spider cryosparc

and then this command to see how to load a specific version and its prerequisites:

ml spider cryosparc/<version> 

ml GCC/13.2.0  OpenMPI/4.1.6 cryosparc/4.5.3-CUDA-12.4.0 

Example¶

1. Create a suitable folder in your project storage directory, for instance /proj/nobackup/hpc2n202X-XYZ/cryosparc (change to the name of your own project storage directory) and change to this folder.
2. Download the tarball lanes.tar.gz to the cryosparc folder you just created and untar it there (tar -zxvf lanes.tar.gz). You get some tar files named lane_TYPE.tar. Untar each one of them with tar -xvf lane_TYPE.tar where TYPE is either A100. CPU, H100, L40S, or V100.
3. Change the string Project_ID in the file lane*/cluster_script.sh to reflect your current project.
4. Also, the time was set to 20 min. in these files but for your realistic simulations you can change it to longer times (change -t 00:20:00 to what suits your case).
5. The lanes should be recognized by CryoSPARC when it starts running.
6. Load the CryoSPARC module and prerequisites if you have not already. Start CryoSPARC and accept the request which asks about continuing using cryostart and that the folder was not used before. List the users on the server (which should be only yourself for this type of license), check the email address that is displayed for this user (it should be the one you added in the license file) and reset the password to. These steps are summarized here:

   $cryosparc start
   ...
   Do you wish to continue starting cryosparc? [yN]: y
   ...
   CryoSPARC master started.
    From this machine, access CryoSPARC and CryoSPARC Live at
       http://localhost:39007
   ...
   
   $cryosparc listusers
   cryosparc resetpassword --email "myemail@mail.com" --password "choose-a-password"
   

7. Copy and paste the line which has the localhost port (notice that port number can change) to a browser on Kebnekaise:
8. After loging in, you will be able to see the CryoSPARC’s dashboard.

Additional info¶

Additional information can be obtained from a tutorial given during a workshop on Berzelius and also from the NSC documentation.

Notice that although the guidelines are for machines different to Kebnekaise, the systems are very similar and you could get ideas from them. For instance, the cryosparc copylanes is not supported on Kebnekaise and you will need to follow the step above (manually copying the lanes) for getting lanes working.

There are several tutorials at the CryoSPARC website, in the previous picture we followed the Introductory Tutorial (v4.0+). More details about this example can be found in the Intro Course to Kebnekaise.