Model Attributes: Molecule

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.

The list includes the attributes of the molecule model and selected attributes of its component atoms, bonds, and residues. Descriptions in the dialog are not necessarily identical to the attribute names (used in the code and in various commands).

Molecule Attributes

• active - whether the model is activated for motion
  • false
  • true
• aromatic color (a color well) - color of aromaticity displays; No Color indicates matching the corresponding atoms
• aromatic display - whether to show aromaticity of displayed aromatic rings (see also the command aromatic)
  • false
  • true
• aromatic line style - line style of circles drawn to indicate aromaticity:
  • –––
  • – –
  • ·  ·
  • – ·
  • – ··
• aromatic ring style - style of aromaticity display (see also the command aromatic)
  • circle
  • disk
• auto-chaining - whether to connect atoms that precede and follow undisplayed segments (whether to draw pseudobonds between them)
  • off
  • on
• ball scale - scale factor for atoms in the ball draw mode. The ball scale is multiplied by individual atom VDW radii to generate ball radii in angstroms.
• color (a color well) - color at the model level; see coloring hierarchy
• current coordinate set - which frame is currently featured, if the model contains a trajectory
• displayed - whether display is enabled at the model level (see display hierarchy)
  • false
  • true
• line style - how to show bonds in the wire draw mode:
  • –––
  • – –
  • ·  ·
  • – ·
  • – ··
• line width - pixel width of lines depicting bonds (when in the wire draw mode)
• residue label positioning - which method is used to compute residue label position (see rlabel for more details):
  • centroid - geometric center of displayed atoms
  • centroid of backbone - geometric center of displayed backbone atoms, as defined by ribbon residue class (geometric center of displayed atoms for residues without a residue class)
  • primary atom - adjacent to the primary atom, generally CA in an amino acid, C5' in a nucleotide, the first nonhydrogen atom in residues of other types
• ribbon (cardinal) smoothing - whether to perform additional smoothing of cardinal spline ribbon, and if so, for which types of secondary structure
  • none
  • strand (peptide/protein strand)
  • coil (peptide/protein nonhelix, nonstrand; nucleic acid)
  • both (strand and coil)
• ribbon (cardinal) stiffness - “resistance” to changes in the path direction of cardinal spline ribbon (range 0.0-1.0)
• ribbon hides backbone atoms - whether showing ribbon for residues within the model hides backbone atoms for those residues (see the command ribbackbone for details)
  • false
  • true
• ribbon inside color (a color well) - if assigned, this color will be used for the insides of all protein helix ribbon segments in the model regardless of how the rest of the ribbon is colored; No Color restores the default behavior of matching interior and exterior
• ribbon spline - method used to determine ribbon path (see also the command ribspline)
  • B-spline - path smoothed over five successive residues, may not coincide exactly with any mainchain atoms
  • cardinal - path smoothed over four successive residues, follows guide atom positions exactly unless additional smoothing is applied
• stick scale - scale factor for bonds in the stick draw mode. The stick scale is multiplied by individual bond radii (default 0.2 angstroms) to generate stick radii in angstroms. Changing stick scale is preferable to changing all of the bond radii in a model, because the former will also scale singleton atoms in the endcap draw mode appropriately. Either way, the other endcap atoms (those participating in bonds) will be scaled to match the thickest of the attached bonds.
• surface color (a color well) - model-level surface color; see coloring hierarchy
• surface opacity - model-level surface opacity, ranging from 0 (completely transparent) to 1 (completely opaque); a negative value indicates that the opacity included in the definition of the model-level surface color should be used instead
• vdw density - relative density of dots used in any VDW surfaces (as with the command vdwdensity)
• vdw dot size - pixel size of dots in any VDW surfaces

Component Atom Attributes

Attributes of individual atoms within a molecule model can be set independently. When different atoms within the model have different attribute values, the value is reported to be -- multiple --. If one of the other options is chosen, all atoms in the model will be changed accordingly.

• atom style - atom draw mode
  • -- multiple --
  • dot
  • ball
  • endcap
  • sphere
• color (a color well) - color at the atom level; see coloring hierarchy
• displayed - whether display is enabled at the atom level (see display hierarchy)
  • -- multiple --
  • false
  • true
• surface color (a color well) - atom-level surface color; see coloring hierarchy
• surface opacity - atom-level surface opacity, ranging from 0 (completely transparent) to 1 (completely opaque); a negative value indicates that the opacity included in the definition of the atom-level surface color(s) should be used instead

Component Bond Attributes

Attributes of individual bonds within a molecule model can be set independently. When different bonds within the model have different attribute values, the value is reported to be -- multiple --. If one of the other options is chosen, all bonds in the model will be changed accordingly.

• bond style - bond draw mode
  • -- multiple --
  • wire
  • stick
• 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 (can also be controlled with the command bondcolor).
  • -- multiple --
  • on
  • off

Component Residue Attributes

Attributes of individual residues within a molecule model can be set independently. When different residues within the model have different attribute values, the value is reported to be -- multiple --. If one of the other options is chosen, all residues in the model will be changed accordingly.

• ribbon color (a color well) - residue-level ribbon color; see coloring hierarchy
• ribbon cross section - ribbon style (see also ribrepr)
  • -- multiple --
  • edged
  • flat
  • rounded
  • supersmooth
    (any additional styles created and named with the Ribbon Style Editor will also be listed)
• ribbon display - whether ribbon is shown; ribbons are only drawn for proteins and nucleic acids. Protein helix and strand assignments are taken from the input structure file or generated with ksdssp.
  • -- multiple --
  • off
  • on
• ribbon scaling - ribbon scaling (see also ribscale)
  • -- multiple --
  • Chimera default
  • licorice
    (any additional scalings created and named with the Ribbon Style Editor will also be listed)

If the model was read from a PDB file with information preceding the coordinates, there will be a button marked PDB Headers... at the bottom of the attributes panel. Clicking this button displays the information in a separate window. The Record Type Order can be Alphabetical (AUTHOR precedes COMPND, etc.) or PDB (the stereotyped order used by the Protein Data Bank). Either way, lines of the same record type will be shown in their original order.