ctffindplot

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.

Requires

• ctffind4
• python3
• gnuplot
• curl (for installing ctffind4)

Installation

Linux

1. 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/'

2. 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

Windows (Cygwin)

1. 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.

2. 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

3. Install ctffindplot

• python3 -m pip install ctffindplot

Usage

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.