Aliases are abbreviations or shortcuts for entering commands. For example, examining the list of current aliases, you will find s next to select and l next to ligand . This means that if you type s l in the command input slot, it will be automatically replaced with select ligand .
The message window shows the expanded alias as it is sent to Chime.
Occasionally you may need to prevent an alias from being expanded. To prevent expansion, simply capitalize one or more letters in it. For example, suppose your molecule happens to contains a ligand designated spl. Since spl is aliased to set picking label, the command
s splexpands to an unwanted and meaningless
select set picking labelwhereas
s Splis sent to Chime as
select SplChime doesn't distinguish case in commands (so 'Spl' is the same as 'spl' to Chime), with the exception of labels, where case is shown in the label text. Alternatively, you can disable all alias expansion with the Preferences page. The link to Preferences is below the message box.
If you want to define a term which is already an alias, just use a capital letter in the defined term. (See the previous section for explanation of why changing the case works.) For example, if you want to define cot selected, since cot is already an alias for color temperature, you'll need to define Cot (note the capital C). Now you will be able, for example, to select Cot.
To add, change, or delete aliases, edit the file shared\alias.js making sure to save the modified version as plain MS-DOS/ASCII text.