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.