Actions Menu - Detailed Explanation
The Actions menu is described here in detail;
for a more terse description, see the
Actions menu listing.
Functions in the Actions menu are applied to items that
have been selected.
Actions... Inspect opens the
Selection Inspector, which lists
what items are selected, shows their properties, and allows their
properties to be changed.
The other operations
(Color,
Display,
Label,
Represent,
Surface):
- act on everything at the level specified by the
Target setting when nothing is selected
- act only on molecule-type models and will not affect other kinds of models
Target and Realm
When atoms and/or bonds have been selected,
it is often useful for an action to apply to a broader set. There
are two different issues to consider:
- should the action apply to more atoms/bonds, for example,
all atoms/bonds in the residues containing the selection
or all atoms/bonds in the models containing the selection?
- should the action apply not only to atom/bond properties, but also to
properties at the residue and/or model level?
The latter is important because there can be separate property
assignments at the atom, residue, and model levels. There is a
coloring hierarchy in which atom colors
override residue colors, which in turn overrule model colors.
Similarly, there is a
display hierarchy in which the atom display settings
are only revealed when display is enabled at the model level.
Possible Target settings are:
- selected atoms/bonds
- selected residues
- selected models
- unselected atoms/bonds
- unselected residues
- unselected models
Target settings
will be explained further as they apply to the different actions.
The term indicated will be used to describe items
containing or not containing a selection when the Target
category is selected or unselected, respectively.
Realm only applies when the Target setting
is unselected atoms/bonds or unselected residues;
possible values are:
- selected models - only act on unselected parts of models
containing selections
- all models - act on unselected parts of models containing
selections and on models not containing any selections
Color
There are many color choices,
as well as the special options
- by element
- use a built-in
color-by-element scheme; these colors are always applied at the
atom level regardless of the Target and Color... applies to
settings
- from editor - use the current
Color Editor color
- none - remove color assignments;
color assignments at other levels may become visible
(see coloring hierarchy);
when applied to models, the models will revert to a default color
If Color... applies to is set to default:
When the Target is atoms/bonds, only the
indicated atoms/bonds are colored.
When the Target is residues, the residue-level color of
the indicated residues is changed
and the atom/bond colors are set to none, making the residue color
visible. When the Target is models, the model-level color of
the indicated models is changed
and the residue and atom/bond colors are set to none,
making the model color visible
(see coloring hierarchy).
If Color... applies to is set to residues only:
When the Target is atoms/bonds or residues,
only the residue-level color of
the indicated residues is changed;
the atoms/bonds retain their individual assignments.
When the Target is models, the color is again changed only at the
residue level, but for all residues in each model
indicated.
The residues only setting allows residue color (thus
ribbon color) and atom/bond color to be controlled independently.
If Color... applies to is set to atoms/bonds only:
This setting differs from default only when the
Target is residues or models.
When the Target is residues, the color is changed only at the atom/bond
level, but for all atoms/bonds in each residue
indicated.
When the Target is models, the color is again changed only at the
atom/bond level, but for all atoms/bonds in each model
indicated.
If Color... applies to is set to surfaces only:
The per-atom surface color (but not the atom color) is changed for all atoms
in the indicated instances of the specified
Target level. For example, if the Target is residues,
the per-atom surface color is changed for all atoms in each residue
indicated.
If Color... applies to is set to labels only, atom labels
only, or bond labels only:
The color of labels (atom and bond labels, just the atom labels,
or just the bond labels) is changed for all atoms/bonds in the
indicated instances of the specified Target
level. For example, if the Target is residues, the color of
the atom and/or bond labels is changed for all atoms and/or bonds in
each residue indicated.
It should be noted that currently,
"residue labels" are actually extra atom labels; the labeled
atom is CA in amino acid residues, C4' in nucleic acid residues,
and in other residue types, the atom with the name that falls first
in alphabetical order.
The labels only and atom labels only settings thus include
residue labels.
The colors of pseudobond labels cannot
be changed here, but they can be changed using the
Selection Inspector.
Display
The Display options
are applied at the per-atom level regardless of the Target level.
Display at the model level is not affected. Note that when model-level
display is off, atoms/bonds will not be visible even if display is turned
on at the atom level
(see display hierarchy).
The first two options
are applied to atoms/bonds comprising the Target.
When the Target is atoms/bonds, only the
indicated atoms/bonds are displayed or undisplayed.
When the Target is residues, all atoms/bonds in the
indicated residues are displayed or undisplayed.
When the Target is models, all atoms/bonds in the
indicated models are displayed or undisplayed.
The remaining options
- backbone only
- side chain/base only
- chain trace only
are applied to atoms/bonds
within the indicated residues.
Only residues in bonded chains containing
amino acid or nucleic acid moieties are affected.
A chain trace includes only one atom per residue, CA in each
amino acid and C4' in each nucleic acid residue.
A backbone includes a continuous series of bonded atoms
connecting the chain trace atoms (-[N-CA-C]n- in
peptides and -[O5'-C5'-C4'-C3'-O3'-P]n- in nucleic acids).
Each amino acid side chain includes any side chain
atoms from CB outward, plus the atom CA (for connectivity purposes);
similarly, each nucleic acid base includes the base
plus the sugar atom to which it is bonded, usually named C1'.
Choosing side chain/base only turns
auto-chaining off,
whereas choosing chain trace only turns
auto-chaining on.
Label
The first set of options affect atom labels regardless of the
Target level:
- clear - undisplay atom labels
- name - label atoms by name
- element - label atoms by element
- IDATM type - label atoms by
atom type
- other... label atoms with other atom-associated information
When the Target is atoms/bonds, only the
indicated atoms are labeled or unlabeled.
When the Target is residues, all atoms in the
indicated residues are labeled or unlabeled.
When the Target is models, all atoms in the
indicated models are labeled or unlabeled.
Options under residue affect residue labels regardless of the
Target level:
- clear - undisplay residue labels
- name - label residues by name
- number - label residues by sequence number (including the
chain ID, if any)
- both - label residues by name and sequence number
When the Target is atoms/bonds or residues, the
indicated residues are labeled or unlabeled.
When the Target is models, all residues in the
indicated models are labeled or unlabeled.
Currently, "residue labels" are actually extra atom labels; the labeled
atom is CA in amino acid residues, C4' in nucleic acid residues,
and in other residue types, the atom with the name that falls first
in alphabetical order.
Represent
The first set of representations
are applied at the atom/bond level regardless of the
Target level:
- wire (wireframe)
- stick
- ball & stick
- sphere (CPK)
When the Target is atoms/bonds, only the representations
of the indicated atoms/bonds are changed.
When the Target is residues, all atom/bond representations
in the indicated residues are changed.
When the Target is models, all atom/bond representations
in the indicated models are changed.
Options under ribbon refer to the 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.
Options under ribbon are applied to residues regardless of the
Target level:
When the Target is atoms/bonds or residues, the ribbon representation
of the indicated residues is changed.
When the Target is models, the ribbon representation of
all residues in the indicated models is changed.
The surface representation
options are applied to entire surfaces regardless of the Target level:
Changes in line width are applied to the entire models
indicated regardless of the Target level.
Surface
The first set of Surface options
is applied at the per-atom surface level
regardless of the Target level:
When the Target is atoms/bonds, only the surfaces
of the indicated atoms in the appropriate
category are displayed or undisplayed.
When the Target is residues, the surfaces of all atoms in
the appropriate category
in the indicated residues are displayed
or undisplayed.
When the Target is models, the surfaces of all atoms in
the appropriate category
in the indicated models are displayed
or undisplayed.
The style section of Surface
(same as Actions... Represent... surface)
affects the representation
of entire surfaces regardless of the Target level: