ccpem (The Collaborative Computational Project for electron cryo-microscopy) is a suite of separate programs lanuched from the ccpem GUI, including but not limited to: Buccaneer, Coot, Flex-EM, LAFTER, Model Validation, LocScale, Haruspex and Refmac-Servalcat

To use the programs the user must allocate lscratch for interactive session.

References:

• Please see https://www.ccpem.ac.uk/index.php for details on citing ccpem programs.

• ccpem Tutorial Documentation

• Module Name: ccpem (see the modules page for more information)
• Multithreaded/Singlethreaded
• environment variables set
  • CCPEM -- base directory for ccpem, set to /usr/local/apps/ccpem/1.6.0/ccpem-20220526 for interactive and batch jobs.

  ccpem depends on CCP4 which requires the allocation of local scratch space. Please see https://hpc.nih.gov/docs/userguide.html#local for more information.

  Interactive job
  Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

  This example shows the Refmac-Servalcat GUI of ccpem.

  Allocate an interactive session and run the program. Sample session:

  [user@biowulf]$ sinteractive -c8 --gres=lscratch:10
  salloc.exe: Pending job allocation 46116226
  salloc.exe: job 46116226 queued and waiting for resources
  salloc.exe: job 46116226 has been allocated resources
  salloc.exe: Granted job allocation 46116226
  salloc.exe: Waiting for resource configuration
  salloc.exe: Nodes cn3144 are ready for job
  
  [user@cn3144 ~]$ module load ccpem
  [user@cn3144 ~]$ ccpem &
  [user@cn3144 ~]$ exit
  salloc.exe: Relinquishing job allocation 46116226
  [user@biowulf ~]$