NovaCTF Quick Scripts

This repository contains a set of Python scripts designed to simplify the process of running NovaCTF, a software for correcting CTF artifacts in cryo-EM tilt series data.

Overview

novactf_bin_prep.py Prepare files to run NovaCTF with a binned stack.
novactf_paral_auto.py Run different steps of NovaCTF using a script template for each tomogram individually.
novactf_process_list.py Using novactf_paral_auto.py to run NovaCTF for many tomograms using a tomogram list
step 1 to 7 .script files Template for running novaCTF steps. #n = defocus file number & #ts tilt series name.

Requirements

Python 3.3
NovaCTF (https://github.com/turonova/novaCTF)
Imod (https://bio3d.colorado.edu/imod/)

Directory Structure

ProjectDir (.)
	├── Tilt series folder (TS_001, TS_002, etc.)
	│   ├── Stack (.st or .mrc)
	│   ├── IMOD files (.xf, .tlt, .xtilt)
	│   └── Defocus file (must be named defocus_file.txt)
	├── Script template (step1 to step7 with appropriate NovaCTF binary and parameters, especially focusing on THICKNESS and IMAGESIZE if you use binned stack)
	└── Tomolist file (contains a list of tomograms to process)

Tomolist File Format

TS_001/TS_001_dose-filt.st
TS_002/TS_002_dose-filt.st
...

Running the Scripts

1. Binning the Stack

Use novactf_bin_prep.py to prepare the files for NovaCTF with a binned stack. This step significantly reduces computational and storage requirements.

python novaCTF_quick_scripts/novactf_bin_prep.py tomolist bin_factor no_proc

Example:

python novaCTF_quick_scripts/novactf_bin_prep.py tomolist.txt 2 10

Output: bin2 stack file, bin2 xf, .tlt, and .txtilt files, and tomolist list file bin 2 (tomolist_bin2.txt).

2. Running Individual Steps for NovaCTF

Edit the .script files in the main project folder with the appropriate parameters. Then, navigate to the tomogram folder (e.g., TS_001) and run each step sequentially: NOTE: Step5 does not deal with xaxistilt right now

Step 1: Generating defocus file

python novactf_paral_auto.py ../step1_gendeffile.script TS_001 1

Step 2: CTF correction

python novactf_paral_auto.py ../step2_ctfcorr.script TS_001 10

Step 3: Aligning and flipping the stack

python novactf_paral_auto.py ../step3_align_flip_stack.script TS_001 10

Step 4: Filtering projections

python novactf_paral_auto.py ../step4_filter_proj.script TS_001 10

Step 5: Reconstruction (Make sure to check the output to ensure correctness before proceeding with further steps)
```
python novactf_paral_auto.py ../step5_recon.script TS_001 1
```

Step 6: Cleaning

python novactf_paral_auto.py ../step6_clean.script TS_001 1

Step 7: Binning to bin 2 and bin 4 using Fourier3D

python novactf_paral_auto.py ../step7_bin.script TS_001 1

3. Running for All Tomograms Simultaneously

This script will iterate through each tomogram and perform NovaCTF correction using novactf_paral_auto.py from steps 1 to 7.

Note: Choose the binned tomolist if you want to perform CTF correction on a binned volume.

python novactf_process_list.py tomolist no_proc