Molecule Model Attributes

Once a model has been chosen in the left side of the Model Panel, clicking the attributes... button in the right side of the panel brings up a window that lists model attributes and allows them to be changed. Molecule-type models are of class Molecule.

• active - whether the model is activated for motion
  • false
  • true
• model-level display - whether display is enabled at the model level (see display hierarchy)
  • false
  • true
• atom-level display - whether display is enabled at the atom level (see display hierarchy). If some but not all atoms are displayed, the value is reported to be -- multiple --.
  • -- multiple --
  • false
  • true
• ribbon display - whether a secondary structure ribbon is shown; ribbons are only drawn for proteins and nucleic acids. Protein secondary structure is determined from HELIX and SHEET records in the input file, or if these are not present, using ksdssp.
  • off
  • on
• ribbon depiction - type of secondary structure ribbon shown (see also ribrepr)
  • flat ribbon
  • edged ribbon
  • rounded ribbon
• atom style - atom draw mode. Since this is an attribute of individual atoms, a variety of values may be present simultaneously; if so, the value is reported to be -- multiple --. If one of the other options is selected, then all atoms in the model will be changed accordingly.
  • -- multiple --
  • dot (as in the wireframe representation)
  • ball (as in the ball-and-stick representation)
  • endcap (as in the stick representation)
  • sphere (as in the sphere representation)
• bond style - bond draw mode. Since this is an attribute of individual bonds, a variety of values may be present simultaneously; if so, the value is reported to be -- multiple --. If one of the other options is selected, then all bonds in the model will be changed accordingly.
  • -- multiple --
  • wire (as in the wireframe representation)
  • stick (as in the stick, ball-and-stick, and sphere representations)
• line width - pixel thickness of lines drawn to show bonds in the wire draw mode
• vdw dot size - pixel size of dots in any VDW surfaces
• stick diameter - angstrom thickness of bonds in the stick draw mode
• ball size - fraction of VDW radius used for ball radius when atoms are in the ball draw mode
• vdw density - relative density of dots used in any VDW surfaces (as with the command vdwdensity)
• halfbond mode - whether the two halves of a bond are handled as separate entities; when halfbond mode is on, the color of each halfbond matches that of the attached atom. Since this is an attribute of individual bonds, a variety of values may be present simultaneously; if so, the value is reported to be -- multiple --. If one of the other options is selected, then all bonds in the model will be changed accordingly.
  • -- multiple --
  • on
  • off
• model-level color - color at the model level; see coloring hierarchy
• auto-chaining - whether to connect atoms that precede and follow undisplayed segments (whether to draw pseudobonds between them)
  • off
  • on
• current coordinate set - which frame is currently featured, if the model contains a trajectory
• dashed lines enabled - whether lines drawn to show bonds in the wire draw mode are broken
  • false
  • true
• length of odd dashes - if dashed lines are enabled, the unscaled pixel length of every other "dash" (can be a dot)
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • 7
• length of even dashes - if dashed lines are enabled, the unscaled pixel length of the alternate set of "dashes" (can be dots)
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • 7
• dash/space scale - multiplicative scale factor for all dashes and spaces if dashed lines are enabled