Bonding

  • connect_bonded (boolean, default: off) controls whether or not bonds can be detected between atoms with explicit bonds in the PDB file.
  • connect_cutoff (float, default: 0.4) affects how close atoms need to be in order for bonds to be created.
  • connect_mode (integer, default: 0) controls how bonds are detected when PDB files are loaded.
    • 0 = auto-connect and use explicit valences
    • 1 = use explicit valences only
    • 2 = reserved
  • half_bonds (boolean, default: off) controls whether or not half-bonds are shown when only one of the two atoms is visible.
  • hide_long_bonds (boolean, default: off) controls whether or not PyMOL hides bonds longer than 90% of the sum the vdw radii.
  • heavy_neighbor_cutoff (float, default: 3.5) boundary at which neighboring heavy atoms are no longer considered ‘neighbors’.
  • trace_atoms_mode (integer 0-5, default: 0) affects how cartoon and ribbon traces are performed.
  • valence (boolean, default: off) controls whether or not bond valences are shown.
  • valence_size (float, default: 0.06) controls how far apart bond valences are drawn.
 
setting/connect.txt
 
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