Initialization

Initial configurations for 1CPN can be generated using input/init_1cpn.py

init_1cpn.py can take various command line arguements:

  • --stemangle (-a) : This is the angle alpha
  • --nrl (-nrl) : Nucleosome Repeat Length
  • --nrlends (-nrlends) : Nucleosome Repeat Length of DNA at beginning and end of fiber. This arguement defaults to set nrlends=nrl if not specified
  • --nnucl (-n): number of nucleosomes
  • --linkerhistone (-lh): turn on linker histones

Note

If you only want to generate a long strand of DNA (without any nucleosomes), you can do this by adding --nnucl 0 to the command line arguements. Then specify the length of DNA (in base pairs) with the --nrl entry.

Note

If you use the -lh flag to turn generate the linker histone, you’ll also need to change a single line in in.1cpn. You’ll want to change this line to

variable lh equal 1