Chimera Commands Index

Usage:
alias [ [^]name [ wordlist... ] ]

Usage:
~alias [ [^]name ]

Alias assigns to name the specified wordlist. Subsequent occurrences of name (space- and/or semicolon-delimited) in commands will be replaced with wordlist. Using ^name indicates that only occurrences as a command (at the beginning of a line, following a semicolon, or as a command argument of perframe) should be replaced. This is useful for aliasing a long command to a short string without having to worry about that string appearing (and being expanded) in the middle of some other command. Conversely, aliases defined without ^ are useful for atom specification strings that are tedious to type. See also: namesel, perframe, preset, rmfalias

Aliases are saved in sessions. Aliases defined with ^name and that do not require arguments (see below) are also saved in the preferences file and listed in a top-level Aliases menu. Choosing an entry in the Aliases menu executes the alias. Aliases can be set up automatically by placing alias commands in a startup command file (see the Command Line preferences).

The alias command without any arguments shows the definitions of all current aliases in the Reply Log. The definition of a specific alias can be shown with alias name.

The command ~alias without arguments deletes all aliases, whereas a specific alias can be deleted with ~alias name (^name should be used instead of name if the alias was defined that way).

Within wordlist, 1ドル, 2ドル, 3ドル ... may be used to indicate the first, second, third ... arguments of name. To have a string with spaces in it handled as a single argument, replace each space with an underscore. Any underscore (unless escaped by a preceding backslash) will be replaced with a space before the command is executed. For example,

alias ^colorsrf color 1,ドルs 2ドル
alias helix5 :200-228.a
colorsrf light_sea_green helix5

is equivalent to

color light sea green,s :200-228.a

which colors the molecular surface of the specified residues light sea green.

Note that wordlist may contain multiple commands separated by semicolons, for example:

alias ^inspect ~rl; show 1ドル z<4; align 1ドル protein; focus 1ドル z<4; rl 1ドル
inspect :26.A

Avoid embedding semicolons in an alias by accident. For example, the following will not color anything red because the entire line is interpreted as merely creating an alias:

alias others ligand | ions | solvent; color red others

In this case, the aliasing and coloring commands should be on separate lines.