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cryoSPARC is a CryoEM software suite.

Tutorials: https://cryosparc.com/docs/tutorials/

The cryoEM facility cryoSPARC installation is available at the public analysis PC (when booted in Linux mode): http://cssbhpi047.desy.de:39000/

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

Quick start

The public analysis PC has a 9TB local drive for processing data which is available to everybody as /data.

If you have an extracted particle set and you just need a fast 3D ab-initio reconstruction in cryoSPARC you can transfer your full Relion folder or create a simpler 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 PC. Please ask for the password of the dataprocessor user.

rsync -av cryoem_testsuite_job006.* dataprocessor@cssbhpi047.desy.de:/data/cryoSPARC2/username

The select the cryoem_testsuite_job006.star for metadata and the cryoem_testsuite_job006.mrcs as data location.

Important Note

The public analysis PC has no SSD drive to accelerate cryoSPARC GPU computing. So you have to disable in the Compute settings the Cache particle images on SSD if available.

MotionCor2

cryoSPARC can use MotionCor2 instead of its own implementation.

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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