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):

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:

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:

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:

Color

There are many color choices, as well as the special options

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

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:

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:

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:

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: