ctffindplot generates a real-time graph of the summary results of ctffind4. It watches the current directory for files ending in ali.mrc
, runs ctffind using a parameters file, creates a png, then moves the original mrc file into a different folder.
- ctffind4
- python3
- gnuplot
- curl (for installing ctffind4)
- Install ctffind4 if not already installed
sudo sh -c 'curl http://grigoriefflab.umassmed.edu/sites/default/files/ctffind-4.1.10-linux64.tar.gz | tar xvz -C /usr/local/'
- Install ctffindplot
Ubuntu
sudo apt update && sudo apt install -y curl gnuplot python3-pip && sudo python3 -m pip install ctffindplot
Centos
sudo yum install -y --enablerepo=extras epel-release && sudo yum install -y python36-pip gnuplot curl && sudo python36 -m pip install ctffindplot
- Install Cygwin with required packages
- Download the Cygwin setup-x86_64.exe installer
- Download this repository's cygwin_install_script.bat into the same folder.
- Double click the cygwinInstallScript.bat to start the installer. Continue clicking next until the installation is finished.
- Install ctffind4
- Open Cygwin terminal
curl http://grigoriefflab.umassmed.edu/sites/default/files/ctffind-4.1.10.tar.gz | tar xz && cd ctffind-4.1.10 && ./configure --with-wx-config=wx-config-3.0 && make && make install
- Install ctffindplot
python3 -m pip install ctffindplot
usage: ctffindplot [-h] [-o OUTPUT] [-p ALIGNED_MRC_DIR]
[-t CTFFIND_PARAMS_FILE] [-c CTF_FITS_DIR] [-l LOGFILE]
plot summary results from ctffind
optional arguments:
-h, --help show this help message and exit
-o OUTPUT, --output OUTPUT
output png file (default = ctffindplot_plot.png)
-p ALIGNED_MRC_DIR, --aligned_mrc_dir ALIGNED_MRC_DIR
destination for processed mrc files (default =
alignedMRC)
-t CTFFIND_PARAMS_FILE, --ctffind_params_file CTFFIND_PARAMS_FILE
ctffind parameters file (default = ctffindoptions.txt)
-c CTF_FITS_DIR, --ctf_fits_dir CTF_FITS_DIR
destination for ctffind diagnostic images (default =
ctffind_fits)
-l LOGFILE, --logfile LOGFILE
data file for plotting (default = ctffindplot_log.txt)
First, have a ctffindoptions.txt file in the current working directory, or use the -t flag to specify a filename.
Next, type ctffindplot
and ...ali.mrc files will be fed through ctffind and a png graph will be created and continuously updated.
The last
ali.mrc
file in sorted alphabetical order will not be processed since it may be in use by other real-time programs like IMOD's framewatcher.