Automatic Styling (Smart Initial Display)

Automatic styling or smart initial display refers to automatically adjusting the appearance of a newly opened atomic model based on its contents, as described below. The lighting is only adjusted if no other atomic models are already open. If only a volume model is opened, full lighting is used.

The process includes chemical perception, which can be slow and unnecessary for pseudoatom data not meant to be interpreted as atoms in molecules (e.g., a SAXS bead model in PDB format). Generating the initial representation can also be slow, for example, drawing ribbons for a very large number of models. Automatic styling can be circumvented by using the open command with autoStyle false. See also: initial colors, markers and links, presets, model information

• 0 chains: all atoms shown as sticks, coloring by model for carbons and by element for heteroatoms, simple lighting
  
  
• 1-4 chains: cartoons, coloring by model, simple lighting, monatomic ions as spheres, atoms as sticks with heteroatom coloring (hydrogens on carbons hidden) for:
  • ligand residues
  • residues within 3.6 Å of ligand or ions
  Nucleotide sidechains are colored by base type and shown as tube/slab in models with <100 nucleic acid residues, ladder in those with 100+ nucleic acid residues.
  
  
• 5-249 chains: all atoms as spheres (space-filling) except sticks for ligand and balls for solvent, coloring by chain, full lighting (except if ≥ 300,000 atoms, ambient shadows from 16 instead of 64 directions)
  
  
• 250+ chains: all atoms as spheres (space-filling), coloring by model, soft lighting (except if ≥ 300,000 atoms, ambient shadows from 16 instead of 64 directions)