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: color schemes, 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 and <200,000 atoms: coloring by model, simple lighting, atoms as sticks with heteroatom coloring

  If there are 10-4999 biopolymer residues, they are shown as cartoons and atoms are hidden, except for:

  • ligand residues
  • residues within 3.6 Å of ions (metals only) or ligand, with the ions shown as spheres

  Any hydrogens on carbons, however, are kept hidden.

  Nucleotide sidechains are colored by base type and shown as tube/slab in models with ≤100 nucleic acid residues, ladder in those with 101-2000 nucleic acid residues.
  
  

• 5-249 chains and/or 200,001-999,999 atoms: all atoms as spheres (space-filling) except sticks for ligand and balls for solvent, coloring by polymer except by chain for homomultimers, full lighting (except if ≥ 300,000 atoms, ambient shadows from 16 instead of 64 directions)
  
  
• 250+ chains and/or 1,000,000+ atoms: all atoms as spheres (space-filling), coloring by model, soft lighting (except if ≥ 300,000 atoms, ambient shadows from 16 instead of 64 directions)