CTFFIND
CTFFIND
CTFFIND [1] is a program for finding CTFs of electron micrographs. The program CTFFIND4 is an updated version of the program CTFFIND2, which was developed in 1998 by Nikolaus Grigorieff at the MRC Laboratory of Molecular Biology in Cambridge, UK with financial support from the MRC. This software is licensed under the terms of the Janelia Research Campus Software Copyright 1.1. A new version of ctffind is available, which should run significantly faster than ctffind3 and may give slightly improved results when processing data from detectors other than scanned photographic film. More information is avaible on the ctffind4 page [2].
Important Notes
The image/video files in .mrc format can be huge which can occupy your home space. So, temporary scratch space is used for the sample example. Please refer to HPC Storage & Quota for details.
If you want space to store these files permanently, you need to purchase storage. Please refer to HPC Guest/Member access policy for details.
Installed Versions
All the available versions of CTFFIND for use can be viewed by issuing the following command. This applies for other applications as well.
module avail ctffind
output:
---------- /usr/local/share/modulefiles/MPI/intel/17/openmpi/2.0.1--------------
ctffind/4.1.10
The default version is identified by "(D)" behind the module name and can be loaded as:
module load ctffind
The other versions of NAMD can be loaded as:
module load namd/<version>
Running CTFFIND
Create a user directory at /scratch/pbsjobs/ and cd to it
mkdir <caseID>
cd <caseID>
Download the apoferritin test dataset (consists of bunch of movi files in .mrc format) from https://cistem.org/documentation#tab-1-1 transfer it to the scratch
or copy the exisitng apoferritin_data.tar.gz file from /usr/local/doc/CISTEM to /scratch/pbsjobs/<caseID>
cp /usr/local/doc/CISTEM/apoferritin_data.tar.gz .
Untar the zipped file
tar -xzvf apoferritin_data.tar.gz
Copy ctffind shell script to the working directory
cp /usr/local/doc/CTFFIND/ctffind.sh .
Submit the job:
sbatch --mem=5gb ctffind.sh
Check the output in slurm-<jobid>
** Welcome to Ctffind **
Version : 4.1.10
Compiled : Jan 18 2018
Mode : Scripted
Input image file name : ./apoferritin_data/May08_03.05.02.bin.mrc
Input is a movie (stack of frames) : no
Output diagnostic image file name : diagnostic_output.mrc
...
Estimating CTF parameters...
100% [=================] done! (0h:11m46s)
100% [=================] done! (0h:11m41s)
...
Summary of results : diagnostic_output.txt
Diagnostic images : diagnostic_output.mrc
Detailed results, including 1D fit profiles : diagnostic_output_avrot.txt
Use this command to plot 1D fit profiles : ctffind_plot_results.sh diagnostic_output_avrot.txt
Execute the command to generate the plot
ctffind_plot_results.sh diagnostic_output_avrot.txt
output:
Neither pdftk nor exiftool were found on your system. Please install one of them to get improved metadata in your output PDF file.
Generated plots of 1D profiles and fits: diagnostic_output_avrot.pdf
Open PDF:
evince diagnostic_output_avrot.pdf
