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
- model-level display - whether display is enabled at the model level
(see display hierarchy)
- 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 depiction - type of secondary structure
ribbon shown (see also resrepr).
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.
- none
- 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.
- 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.
- 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.
- 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)
- 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
- length of odd dashes - if dashed lines are enabled,
the unscaled pixel length of every other "dash" (can be a dot)
- length of even dashes - if dashed lines are enabled,
the unscaled pixel length of the alternate set of "dashes" (can be dots)
- dash/space scale - multiplicative scale factor for
all dashes and spaces if dashed lines are enabled
If the model was read from a PDB file with information preceding
the coordinates, a button marked PDB Headers... will be present
at the bottom of the attributes panel. Clicking this button displays the
information in a separate window. The lines of information are not in their
original order, but are sorted alphabetically
by record type (for example, AUTHOR records
precede HEADER records). Within a record type, however, the lines are
in their original order.
MSMS (Molecular Surface) Model Attributes
VRML, Volume, and
Surface Model Attributes