Commands to Chime
Commands sent to Chime control the image of the molecule. To send a command to Chime, type it in the command slot (the one initially labeled "#Enter commands here") and press Enter. Many examples of commands are explained in the tutorial (enter Advaced Explorer, then click on the green question mark near the top of your window).
Previously executed commands can be recalled with the Recall ^ button. If you recall too many, move back down with the v button. 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 PE commands.
Abbreviations for some command words are defined as aliases. For example, s is an alias for select, so the command "s thr" will be sent to Chime as "select thr". To see the list of aliases, and instructions on how to use them, click on Show aliases below the message box.
Chime's command language is a superset of RasMol's. The best place for beginners to start is with the examples in the Protein Explorer Tutorial. To find it, click on any green question mark outside of this help window. 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. All RasMol commands are fully documented in the RasMol Reference Manual. Additional commands available in Chime are documented by Chime's original source, MDL Information Systems. As of May, 1998, the documentation at MDL is incomplete. Some additional information can be found at the UMass Chime Site
Commands to Protein Explorer (PE)
Commands to the 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 the PE, or what PE does. PE commands are short (one or two characters) and use characters which are easy to type (not Shifted, for example).
PE commands are:
.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 which synch's in both directions.