ctffind on Biowulf
CTFFIND and CTFTILT are two programs for finding CTFs of electron micrographs.
References:
- Mindell, JA, Grigorieff N. 2003. Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol. 142:334-47.
- Rohou, A, Grigorieff N. 2015. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J Struct Biol. 192:216–221.
Documentation
Important Notes
- Module Name: ctffind (see the modules page for more information)
- Multithreaded
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive 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 ctffind [user@cn3144 ~]$ ctffind --help [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. ctffind.sh). For example:
#!/bin/bash module load ctffind time ctffind3.exe << eof micrograph.mrc montage.pow 2.0,200.0,0.07,60000,7.0 !CS[mm],HT[kV],AmpCnst,XMAG,DStep[um] 128,200.0,8.0,5000.0,30000.0,1000.0,100.0 !Box,ResMin[A],ResMax[A],dFMin[A],dFMax[A],FStep[A],dAst[A] eof
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] ctffind.sh