Guidelines for running RELION

  • All data will be uploaded in the form of directories using Globus (read more about Globus here)
  • COSMIC² expects either of the following input data structures:
    1. Uploaded directory has RELION extracted particles with STAR file within uploaded directory named particles.star
    2. Uploaded directory has subdirectories, where each subdirectory has a STAR file named particles.star 
      • Each subdirectory will be listed as a separate dataset
  • For all cases the particle paths specified in the particles.star file must include the name of the uploaded directory
  • For RELION2 users, this means you just have to upload Extract directory and then every sub-directory (job001, job002, etc) will be listed as separate datasets

Example #1: 

  • Uploaded directory name: Extracted_particles
  • Location of particles.star file: Extracted_particles/particles.star
  • Location of extracted particle images, anywhere within uploaded directory: Extracted_particles/particles/
  • Example particle entry line from particles.star: Extracted_particles/particles/file001.mrcs  
  • Will be displayed as the following on COSMIC²: Extracted_particles/particles.star

Example #2: 

  • Uploaded directory name: Extract
    • With subdirectories: Extract/job001, Extract/job002
  • Location of particles.star file: Extract/job001/particles.starExtract/job002/particles.star
  • Location of extracted particle images (anywhere within subdirectory: Extract/job001/Micrographs, Extract/job002/Micrographs/
  • Example particle entry line from particles.star: Extract/job001/Micrographs/file001.mrcs  
  • Will be displayed as the following on COSMIC²:Extract/job001/particles.starExtract/job002/particles.star

Output data guidelines for RELION

  • All output data will be delivered back to the user via a compressed file: output.tar.gz
  • Download and decompress by double clicking on the file