example3

Example 3

Modifying an existing ColBuilder-generated fibril to decrease crosslink density

Files and Usage

• config_replace.yaml
  → Input config file for colbuilder
  → Usage:

  colbuilder -f config_file config_replace.yaml

Output Files

• collagen_fibril_homo_sapiens.pdb
  → Main structure output

• homosapiens_N_HLKNL_C_HLKNL_original.pdb
  → From sequence/geometry/crosslink settings

• homosapiens_N_HLKNL_C_HLKNL.pdb
  → Modified/processed version

• NC/
  → Directory containing additional outputs (e.g., chains or fragments)

• output_terminal.txt
  → Captured example terminal output