CTFFIND5 provides improved insight into quality and geometry of cellular cryo-EM samples

Johannes Elferich, Lingli Kong, Ximena Zotttig, Nikolaus Grigorieff

This repository contains the raw text, figures, and scripts used to generate a manuscript describing improvements to the CTFFIND program targeted at cryo-EM imaging of cellular samples.

Get started

Clone this repository

git clone https://github.com/GrigorieffLab/ctffind5_manuscript.git ./

Make sure Git LFS is setup

git lfs install

Setup the conda environment

conda env create -f build/environment.yml

Activate the environment:

source activate ctffind5_manuscript

Build the manuscript:

./build/build.sh

Tools

The following tools are used for this purpose:

pandoc to convert the markdown files into Word or PDF files
manubot-cite-pandoc to manage citations
miniconda to maintain a virtual environment for the required tools
inkscape to assemble panels into figures
python and matplotlib to generate plots
tikz to generate flowcharts
git-lfs to maintain image files

Files and directories

manuscript.md the manuscript file.
output/ contains the rendered manuscript.
figures/ contains the inkscape .svg files and .png files created from them.
panels/scripts contains python scripts that create plots.
panels/images contains the image files resulting from the scripts. IMages could be placed directly in there, but the preference is to have them generated by code.
scripts/ contains scripts that do data processing, but do not directly result in a panel.

TODO items

Choose pixel size for fitting better
Find datasets for tomo vs thickness verification
Fix OverlayCTF
Just change FRC threshold?
Find out why it fails for certain images atm
Options for
- McMullan vs CTFFIND style model
- Reduce weight of node area in fitting

Dataset for tomo thickness verification

Tomos

Pixel Size 4.1746
/data/elferich/CryoTEM/Johannes_20210412/0401_grid10/st011.mrc
/data/elferich/CryoTEM/Johannes_20210412/0401_grid10/st003.mrc
/data/elferich/CryoTEM/Johannes_20210412/0401_grid10/st008.mrc
Pixel Size 2.0873
/data/elferich/CryoTEM/Johanes_20210614/144diff_NP2/s003.mrc
/data/elferich/CryoTEM/Johanes_20210614/144diff_NP1/s001.mrc
/data/elferich/CryoTEM/Johanes_20210614/120diff_Y12/s003.mrc
/data/elferich/CryoTEM/Johanes_20210614/120diff_Y12/s006.mrc

Exposures

Undiff
/data/elferich/CryoTEM/Johannes_20210412/0401_grid10/frames/stack_record_40_00000_-0.0.tif -> 2843A
/data/elferich/CryoTEM/Johannes_20210412/0401_grid10/frames/stack_record_25_00000_-0.0.tif -> 1002A
/data/elferich/CryoTEM/Johannes_20210412/0401_grid10/frames/stack_record_32_00000_-0.0.tif -> 2215A
144
/data/elferich/CryoTEM/Johanes_20210614/144diff_NP2/frames/s_records_20_00000_-20.0.tif -> 2147A
/data/elferich/CryoTEM/Johanes_20210614/144diff_NP1/frames/s_records_29_00000_-20.0.tif -> 1866A
120
/data/elferich/CryoTEM/Johanes_20210614/120diff_Y12/frames/s_record_25_00000_-20.0.tif -> 2383
/data/elferich/CryoTEM/Johanes_20210614/120diff_Y12/frames/s_record_36_00000_-20.0.tif -> 2184