Description
This app requires the clip command from IMOD.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[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 novactf IMOD [user@cn3144 ~]$ clip flipyz input.ali output.ali [user@cn3144 ~]$ novaCTF -Algorithm defocus -InputProjections input_stack.st -FULLIMAGE 464,464 -THICKNESS 140 -TILTFILE angles.tlt -SHIFT 0.0,0.0 -CorrectionType phaseflip -DefocusFileFormat ctffind4 -CorrectAstigmatism 1 -DefocusFile defocus_file.txt -PixelSize 0.135 -DefocusStep 15 -DefocusShiftFile file_with_additional_defocus.txt [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. novactf.sh). For example:
#!/bin/bash set -e module load novactf IMOD novaCTF -Algorithm defocus -InputProjections input_stack.st -FULLIMAGE 464,464 -THICKNESS 140 -TILTFILE angles.tlt -SHIFT 0.0,0.0 -CorrectionType phaseflip -DefocusFileFormat ctffind4 -CorrectAstigmatism 1 -DefocusFile defocus_file.txt -PixelSize 0.135 -DefocusStep 15 -DefocusShiftFile file_with_additional_defocus.txt
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] novactf.sh