Nucleosome resolution Chromatin Model (NuChroM)

Python scripts for conducting nucleosome resolution MD simulations of chromatin structures.

This script uses OpenMiChroM and openMM packages. Please refer to these packages for installation guide and dependency requirements.

This script is adapted from the tutorial of OpenMiChroM, Single Chromosome Simulation.

Usage

python3 NuChroM.py [--iclist] [--type2type] [--inputseq] [--sysname] [--outpath] [--outfilename]

Required arguments

• --iclist: Parameters for setting ideal chromosome (IC) potentials. Trained IC parameters for NuChroM: Trained_parameters/IC_gammas.
• --type2type: Parameters for setting type-to-type interactions. For example, when only A and B compartments are used in the simulation, interactions between A-A, A-B and B-B are defined in this file. Trained type-to-type parameters for NuChroM: Trained_parameters/Type_to_type_alphas.
• --inputseq: The file that contains the sequence of types for the simulated chromatin segment. An example file for chromatin 7 39.5-42.5 Mb region can be found: examples/chr7_39.5-42.5_AB_beads.txt.

Optional arguments

• --sysname: Name the chromatin segments that is simulated. Default: chrom_unknown.
• --outpath: Path for saving the output files. Default: output.
• --outfilename: Prefix of the output files. Default: chrom_unknown.

Example:

python3 NuChroM.py \
  --iclist Trained_parameters/IC_gammas \
  --type2type Trained_parameters/Type_to_type_alphas \
  --sysname test_chr7 \
  --outpath test_out \
  --outfilename test_chr7_file \
  --inputseq ./examples/chr7_39.5-42.5_AB_beads.txt