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cryoSPARC is a CryoEM software suite.

Documentation and Tutorials: https://guide.cryosparc.com/

The cryoEM facility cryoSPARC installation is available inside the DESY network at: http://cssb-cryosparc.desy.de:39000/. You can use DESY VPN access or Firefox in the FastX2 virtual desktop from outside the network.

If you are an academic user you can get an account. Please contact Wolfgang Lugmayr .

First-time Setup

Once you have your cryoSPARC account you have to login to max-cssb-display.desy.de with your DESY username and password.

Open a terminal or ssh console and call:

cryosparc_create_projects_folder.sh

This will create your personal cryoSPARC project location with the correct access rights like: 

/beegfs/cssb/user/${LOGNAME}/cryoSPARC2

All files and folders copied into /beegfs/cssb/user/${LOGNAME}/cryoSPARC2/Import can then be imported with the cryoSPARC user interface.

If you want to import larger datasets from different locations ask Wolfgang Lugmayr for instructions to set the correct access rights.

Note:

  • cryoSPARC keeps all your information in the project folder like: /beegfs/cssb/user/${LOGNAME}/cryoSPARC2/P14
  • You can transfer this folder to a different cryoSPARC instance and use the Import button to continue with the analysis on a different location.

Getting started

Tutorial and sample workflow

cryoSPARC provides a sample workflow and a good tutorial at: https://cryosparc.com/docs/tutorials/t20s

For first-time users ist recommend to run the sample workflow so you get a good impression of an cryoEM analysis cycle in cryoSPARC. Once started the workflow runs by itself to the end of the analysis and you can use this as a guide for your own first analysis.

How to run the sample workflow:

  • Create a project
  • Create a workspace inside the project
  • Activate both so the buttons are green like in the following image

  • On the right side choose

  • Click the Queue button on the lower right corner and choose the default queue called lane in cryoSPARC. Ignore the location of the input files. If cryoSPARC does not find them they are downloaded on-the-fly.

  • Now wait until the run is finished
  • You can look at the results e.g. project P1 and job J20 as follows:

    cd  /beegfs/cssb/user/${LOGNAME}/cryoSPARC2/P1/J20
    chimerax choose_a.mrc

Quick start with your own particle stack

If you have an extracted particle set and you just need a fast 3D ab-initio reconstruction in cryoSPARC you create a combined particle stack (e.g. cryoem_testsuite_job006):

relion_stack_create --i Extract/job006/particles.star --o cryoem_testsuite_job006

Now you transfer the created stack and the corresponding metadata to the cryoSPARC Import folder:

cp cryoem_testsuite_job006.* /beegfs/cssb/user/${LOGNAME}/cryoSPARC2/Import

The select the cryoem_testsuite_job006.star for metadata and the cryoem_testsuite_job006.mrcs as data location in the Job Builder user interface.

MotionCor2

cryoSPARC can use MotionCor2 1.3 instead of its own implementation. Version 1.4.0 is not supportet yet.

When asked for the path to the MotionCor2 executable choose:

/beegfs/cssb/software/em/motioncor2/1.3/bin/MotionCor2

Topaz

cryoSPARC can use now the deep learning particle picker Topaz.

When asked for the path to the Topaz executable choose:

/beegfs/cssb/software/anaconda3/envs/topaz-0.2/bin/topaz
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