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cg_high_res_chromatin_setup

Setup scripts for high-resolution chromatin model in https://doi.org/10.1038/s41467-021-23090-3.

  1. first look at https://github.com/CollepardoLab/CollepardoLab_Chromatin_Model.

  2. This repo contains the python script to make the initial nucleosome structure and the lammps script to replicate it into a fiber.

  3. setup.sh contains the steps (bash setup.sh):

  • create a single nucleosome:

    python creation.py
    

    change the value of NRL in creation.py to set the nucleosome NRL. this creates nucl.txt - the lammps data file. And in.nucl - the first part of the lammps input script.

  • setup the replication settings:

    python replicate_dna_seq.py $N > replicate_settings.txt
    cp new_DNA_sequence.txt DNA_sequence.txt
    

    where $N is the number of nucleosomes in the fiber

  • make the input script with the run settings in run_settings.txt

    cat in.nucl run_settings.txt > run.in
    
  • run the simulation:

    ./lmp -in run.in
    

The prodecure uses the lammps fix drag to pull the DNA linkers, it then uses replicate to create more nucleosomes, finally it uses create_bonds to join the nucleosomes together.

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