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README.md

CTF Analysis

This app will display interactive scatterplots allowing you to check the quality of data following collection and output a star file that is subsetted to only include the data you want.

Requires installation of numpy, pandas and bokeh. This can be done through pip or conda.

Data Plotted

Four fields are plotted:

  • Estimated resolution that thon rings extend to
  • Defocus (average of DefocusU and DefocusV)
  • Defocus difference (absolute difference between DefocuU and DefocusV)
  • Cross correlation score

Running

Requires either the path to your CTF log files (e.g. Micrographs/*ctffind3.log) or the star file output after CTF estimation (e.g. micrographs_all_gctf.star) as long as it contains the resolution.

The command is bokeh serve --show /path/to/.../ctf_analysis/ --args input (e.g. bokeh serve --show /path/to/.../ctf_analysis/ --args Micrographs/*.log). I would make an alias in your .bashrc (e.g.alias ctf_analysis='bokeh serve --show /path/to/.../ctf_analysis/ --args') and then you can just run ctf_analysis Micrographs/*.log.

Result

This command should automatically open your browser to localhost:5006 (or else open manually). The main page should look similar to below: alt text

A summary of the complete dataset is given and you can generate one for your current subset by clicking the Summary Stats button.

Output a csv with the extracted values (e.g. if you want to plot in another program) with either the Save all csv or Save subset csv. This will be written with the name given in the text box above.

Output a star file to read into relion containing just your current subset with the Save star button. This requires an input star to be provided in the text box above (defaults to micrographs_all_gctf.star or the input star file you ran the program with) that contains all the information you would want in the output file (e.g. what was output from GCTF or CTFFIND (if it was run through relion)).

There is a second tab (Summary) that just contains histograms to show your overall data distribution. These don't do anything fun. alt text

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