---
title: "UC #3 : CryoEM Proteasome"
url: "https://help.dectris.cloud/en/article/uc-3-cryoem-proteasome"
language: "en"
last_updated: "2026-08-10T16:52:25.352Z"
---

# UC #3 : CryoEM Proteasome

### Solve the structure of the proteasome!

Learn how to easily repeat a CryoSPARC refinement in RELION.

![](https://cdn-assets.productfruits.com/94b93b00-8795-4b69-aa5f-c2c194339dbb)![](https://cdn-assets.productfruits.com/627572a6-9e83-4b6a-a1d8-28021182888b)

### Get access to the necessary Job Templates here:

[https://app.dectris.cloud/sections/user/share-links/7ZDmN\_J98cZUK6bhZQcF6](https://app.dectris.cloud/sections/user/share-links/7ZDmN_J98cZUK6bhZQcF6)

  

### Extended License Information

Click on your initials in the top right and go to "My Licenses" > "ACTIVATE LICENSE".

You will be prompted to add the following details:

Licence ID: **LCID-IUCR-WORK**

Activation code: **62411364**

  

### Step-by-step

1.  **Create a new Project**
2.  1.  Go to Projects
    2.  Create New Project
    3.  Choose Region **US**
3.  **Run CryoSPARC to RELION conversion**
4.  1.  Go To Library > My Templates
    2.  Find the “CryoSPARC to RELION conversion” Job
    3.  Select and click “Run Job” on the bottom right
    4.  For “cryosparc\_project\_dir” enter Project “**IUCr Workshop : Group A/B/C/D**” by double-clicking and navigate to the CryoSPARC project dir: **processed/CS-automated-workflow**
    5.  For “output\_parent\_dir” enter your **newly created Project** and select the "processed" subfolder
    6.  Click CONTINUE
    7.  Check “Show advanced”
    8.  Set “**DC\_COPY\_IMAGE\_DATA**” to True
    9.  Click CONTINUE
    10.  Stick to the defaults and click RUN JOB
    11.  Wait for the Job to finish (~8 min)
5.  **Run Relion Refine3D**
6.  1.  Go To Library > My Templates
    2.  Find the “Run RELION Job” Job
    3.  Select and click “Run Job” on the bottom right
    4.  Browse to and select the RELION project dir at “**<your new project>/processed/relion\_from\_cryosparc**”
    5.  Click CONTINUE
    6.  Enter this as “DC\_RELION\_COMMAND”:
    7.  `relion_refine_mpi --o Refine3D/job011/run --auto_refine --i Refine3D/job010/run_data.star --ref Refine3D/job010/run_class001.mrc --firstiter_cc --trust_ref_size --ini_high 60 --dont_combine_weights_via_disc --scratch_dir /scratch --ctf --particle_diameter 190 --healpix_order 4 --sym D7 --j 5 --pipeline_control Refine3D/job011/`
    8.  Click CONTINUE and click RUN JOB
7.  **Share the Job**
8.  1.  After the Job is finished (~30 min), check if CryoSPARC’s resolution was reproducible by RELION
    2.  Why did the resolution differ from the CryoSPARC result?
    3.  Share the link on social media and tag us!
9.  Optional: Refine the Refine3D parameters to see if you can get a better resolution!

  

  

**References**:

Campbell, M. G., Veesler, D., Cheng, A., Potter, C. S., & Carragher, B. (2015). 2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy. *eLife*, *4*. [https://doi.org/10.7554/elife.06380](https://doi.org/10.7554/elife.06380)

Punjani, A., Rubinstein, J. L., Fleet, D. J., & Brubaker, M. A. (2017). cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. *Nature Methods*, *14*, 290–296. [https://doi.org/10.1038/nmeth.4169](https://doi.org/10.1038/nmeth.4169)

Scheres, S. H. W. (2012). RELION: Implementation of a Bayesian approach to cryo-EM structure determination. *Journal of Structural Biology*, *180*, 519–530. [https://doi.org/10.1016/j.jsb.2012.09.006](https://doi.org/10.1016/j.jsb.2012.09.006)

Asarnow, D., Palovcak, E., Cheng, Y. UCSF pyem v0.5. Zenodo [https://doi.org/10.5281/zenodo.3576630](https://doi.org/10.5281/zenodo.3576630) (2019).