Helix/bwVisu/CryoSPARC: Difference between revisions
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== CryoSPARC License == |
== CryoSPARC License == |
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For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The |
For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu. |
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== CryoSPARC in bwVisu == |
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== Information about the CryoSPARC application == |
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=== The application === |
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The |
The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs. |
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=== The database === |
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The CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database. |
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=== Downloads === |
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== CryoSPARC and Topaz == |
== CryoSPARC and Topaz == |
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CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code> |
CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code> |
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== CryoSPARC Documentation == |
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== Documentation and Tutorials == |
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Latest revision as of 23:58, 5 June 2025
CryoSPARC is a scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.
CryoSPARC License
For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to CryoSPARC and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.
CryoSPARC in bwVisu
The application
The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs.
The database
The CryoSPARC application creates a database in the .cryosparc directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.
Downloads
When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.
CryoSPARC and Topaz
CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: /opt/bwhpc/common/bio/topaz/0.25/bin/topaz
CryoSPARC Documentation
You can find usage information and tutorials for CryoSPARC at CryoSPARC Docs.