Properties

The following table lists builtin properties. Builtin properties are properties that are set from within the program. You are free to use them for making selections, but you should normally avoid modifying builitin properties (with the excpetion of selected, movable and displayed), some of them are used by the program itself, and the results of the user modifying them may be unpredictable.

item name description

any all Always set for all items. Do not modify!

any selected Set for selected items. Most commands operate on items that have this property set.

any displayed Only items with this property set are displayed. Can be useful for making items (especially molecules) temporarily visible/invisible, use the Molecule Dialog for a convenient way of setting it.

mol movable Only molecules with this property set are affected by interactive manipulations and commands that transform molecules. Useful for moving molecules relative to each other, use the Molecule Dialog for a convenient way of setting it.

atom visible Set for all atoms that have a display style that makes them visible. Convenient to restrict a selection to only visible items.

bond visible Set for all bonds that have a display style that makes them visible.

dist visible Set for all distances that have a display style that makes them visible.

prim visible Set for all primitives that have a display style that makes them visible.

item	name	description
any	`all`	Always set for all items. Do not modify!
any	`selected`	Set for selected items. Most commands operate on items that have this property set.
any	`displayed`	Only items with this property set are displayed. Can be useful for making items (especially molecules) temporarily visible/invisible, use the Molecule Dialog for a convenient way of setting it.
mol	`movable`	Only molecules with this property set are affected by interactive manipulations and commands that transform molecules. Useful for moving molecules relative to each other, use the Molecule Dialog for a convenient way of setting it.
`atom`	`visible`	Set for all atoms that have a display style that makes them visible. Convenient to restrict a selection to only visible items.
`bond`	`visible`	Set for all bonds that have a display style that makes them visible.
`dist`	`visible`	Set for all distances that have a display style that makes them visible.
`prim`	`visible`	Set for all primitives that have a display style that makes them visible.

The following table lists predefined properties. Predefined properties are properties whose definitions are read from a file (by default setup/PropDef in the installation directory) and evaluated whenever new data is added, e. g. a new molecule loaded.

item name description

atom bb Backbone atoms of a protein or nucleic acid.

bond bb Backbone bonds of a protein or nucleic acid.

atom sc Side chain atoms of a protein or nucleic acid.

bonds sc Side chain bonds of a protein or nucleic acid.

atom heavy Heavy atoms.

bond heavy Bonds between two heavy atoms.

atom heavysc Heavy side chain atoms of a protein or nucleic acid.

bond heavysc Bonds between two heavy side chain atoms of a protein or nucleic acid.

atom phos Atoms in phosphate group of a nucleic acid.

bond phos Bonds in phosphate group of a nucleic acid.

atom sugar Atoms in sugar group of a nucleic acid.

bond sugar Bonds in sugar group of a nucleic acid.

atom base Atoms in base of a nucleic acid.

bond base Bonds in base of a nucleic acid.

atom proton Hydrogen atoms.

atom ca Atoms with name CA.

atom pseudo Pseudo atoms (name starting with Q).

atom lonepair Lone pair (name starting with LP).

item	name	description
`atom`	`bb`	Backbone atoms of a protein or nucleic acid.
`bond`	`bb`	Backbone bonds of a protein or nucleic acid.
`atom`	`sc`	Side chain atoms of a protein or nucleic acid.
`bonds`	`sc`	Side chain bonds of a protein or nucleic acid.
`atom`	`heavy`	Heavy atoms.
`bond`	`heavy`	Bonds between two heavy atoms.
`atom`	`heavysc`	Heavy side chain atoms of a protein or nucleic acid.
`bond`	`heavysc`	Bonds between two heavy side chain atoms of a protein or nucleic acid.
`atom`	`phos`	Atoms in phosphate group of a nucleic acid.
`bond`	`phos`	Bonds in phosphate group of a nucleic acid.
`atom`	`sugar`	Atoms in sugar group of a nucleic acid.
`bond`	`sugar`	Bonds in sugar group of a nucleic acid.
`atom`	`base`	Atoms in base of a nucleic acid.
`bond`	`base`	Bonds in base of a nucleic acid.
`atom`	`proton`	Hydrogen atoms.
`atom`	`ca`	Atoms with name CA.
`atom`	`pseudo`	Pseudo atoms (name starting with Q).
`atom`	`lonepair`	Lone pair (name starting with LP).

Last modified: Mon Jan 20 19:44:57 CST 2003

Reto Koradi, kor@mol.biol.ethz.ch