Gctf provides accurate estimation of the contrast transfer function (CTF) for near-atomic resolution cryo electron microscopy (cryoEM) reconstruction using GPUs. The main target of Gctf is to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction.

References:

• Zhang K. Gctf: Real-time CTF determination and correction. J Struct Biol. 2016 Jan;193(1):1-12.

• Gctf Main Site
• Type Gctf --help

• Module Name: Gctf (see the modules page for more information)
• GPU-accelerated
• environment variables set
  • GCTF_HOME
  • RELION_GCTF_EXECUTABLE

Gctf can utilize GPUs. This requires the user load the proper CUDA library for the executables. For example, the executable Gctf-v1.06_sm_30_cu7.5_x86_64 requires module load CUDA/7.5 prior to use.

Alternatively, a wrapper script which automatically loads the correct CUDA library can be used: Gctf

Allocate an interactive session, along with at least one GPU, and run the program. Sample session:

[user@biowulf]$ sinteractive --constraint=gpup100 --gres=gpu:p100:1
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 Gctf CUDA/7.5
[user@cn3144 ~]$ Gctf-v1.06_sm_30_cu7.5_x86_64 --apix 1.07  --kV 300 --Cs 2.7 --ac 0.1  Micrographs/Falcon*.mrc

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. Gctf.sh). For example:

#!/bin/bash
module load Gctf
Gctf --apix 1.07 --kV 300 --Cs 2.7 --ac 0.1 Micrographs/Falcon*.mrc

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] --gres=gpu:p100:1 --partition=gpu Gctf.sh