Commands to Chime
Commands sent to Chime control the image of the molecule. Protein Explorer's buttons and menus operate by generating sequences of commands and sending them to Chime. The commands are displayed in the message box as they are being executed. Thus, a good way to learn about Chime's command language is to watch the commands generated by Protein Explorer's menus and buttons.
Commands may also be entered by hand, although one of the major benefits of using Protein Explorer is that you don't have to learn Chime's command language. To send a command to Chime, type it in the command input slot (the one initially labeled "#Enter commands here") and press Enter. For example, try entering these commands, pressing Enter after each line:
Previously executed commands can be recalled with Commands: Back (near the command input slot). If you recall too many, use Fwd. After you recall a command, you can edit it (if desired), then press Enter to execute it. Command recall can also be done with shortcut commands to PE.
Most commonly used commands have short aliases. These require less typing, and are liable to fewer typing errors. For example, the above three commands can be entered as:
Chime's command language is a superset of RasMol's. An introduction to commands useful for selecting groups of atoms or portions of a molecule is in the document Select Commands in Chime and RasMol. Comprehensive reference manuals begin with the RasMol Reference Manual and continue with the command enhancements in Chime, documented at MDL's Chime Script Commands. The most complete collection of Chime documentation is at MolviZ.Org.
Commands to Protein Explorer (PE)
Commands to PE itself ("PE commands") are entered in the same slot as commands to Chime, but they are not sent to Chime and do not affect the molecular image. Instead, they affect the state of PE. PE commands are short (one or two characters) and use characters that are easy to type (not Shifted, for example).
Because these commands act on PE but are not sent to Chime, they are distinct from command aliases, which can also be one or two characters long.
PE commands are:
.1 Go to the FirstView (1st) control panel.
.a, .x Go to the Advanced EXplorer control panel.
.c Go to the Contact Surfaces control panel in Advanced Explorer.
.f Go to the Features of the Molecule control panel.
.l Go to the molecule Loading page.
.q Go to QuickViews.
.s Go to the Surfaces control panel in Advanced Explorer.
.w Wipe (clear) the message box.
.o Toggle control to the Other molecule (top or bottom).
tb "Top and Bottom". Commands prefixed with tb are sent to both the top and bottom Chimes. For example, tb ssb displays disulfide bonds in backbone mode on the molecules in both the top and bottom Chime frames. The tb prefix simply saves typing the same command twice, and switching the active Chime in between.
See also the alias sy that synch's in both directions.