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.

• CTFFIND Main Page (Grigorieff Lab)

• Module Name: ctffind (see the modules page for more information)
• Multithreaded

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 ~]$

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