Code for the manuscript Staggering and splaying in nonmuscle myosin II minifilaments by Tom Kaufmann and Ulrich S. Schwarz (Institute for Theoretical Physics and BioQuant, Heidelberg University, Heidelberg, Germany).
Correspondence should be addressed to Ulrich Schwarz at schwarz@thphys.uni-heidelberg.de. (Website)
The project requires the folder structure as shown below
├── data
│ ├── charges
│ ├── paircoil
│ ├── seqs
├── results
│ ├── potentials
│ └── T1
├── scripts
This structure can be created using the command mkdir -p data/{paircoil,charges} results/{potentials,T1} on *nix machines.
The workflow is run using the workflow manager Snakemake.
The workflow uses the standard modules argparse, json and numpy as well as Numba for JIT compilation of the code.
All scripts are in the folder scripts and use functions from the file utils.py.
The amino acid sequences of the NM2 heavy chains found in the folder data/seqs were obtained from the NCBI Protein Database with the accession numbers: NM2A - P35579, NM2B - P35580, NM2C - NP_079005 and M18A - Q92614.
All other data are created in the workflow.
The workflow uses the programm Paircoil2.
Proper execution of the workflow requires the program the paircoil binary paircoil2 as well as the reference data nr90-050325.tb and newcc.tb from the Official paircoil website placed in the main folder.