another 3D viewer
a free molecule viewer widely used in chemistry. It is rich in features
and fast. CaGe supports Rasmol for its popularity and speed, but there
are two problems we have with the program: we can't be fully certain that
Rasmol can actually run, and there is no guarantee that Rasmol will show
a molecule exactly as CaGe wants to show it.
that Rasmol is installed and usable, CaGe starts the simple command
"rasmol", writes a few basic Rasmol commands to it through
a pipe (which won't cause a window to open), and then checks if the
command has terminated successfully. This happens before CaGe dares
to offer Rasmol to you as a viewer option. But it isn't actually a
complete test that Rasmol will successfully run on the system. Most
versions of Rasmol for the X Windows system are compiled for a particular
display bit depth, and on the wrong kind of display Rasmol will accept
CaGe's testing commands, but it will refuse to open a display window
when asked to actually display a molecule.
is quite "intelligent" in terms of chemistry. Given a detailed
representation of a molecule, it can display it using many different
chemical models and viewing modes. But there is no way of convincing
Rasmol that it should not use its intelligence to second-guess
where a molecule has a bond and where it doesn't. We want to display
molecules that are originally graphs, and because of that context
we want our graphs' edges to be faithfully shown by our viewers, with
no edges left out and none added.
is this uncertainty about Rasmol, CaGe shows a warning message when the
Rasmol viewer is requested for the first time in a CaGe session. Click
"Ok" in the message box and CaGe will continue.
This screenshot shows Rasmol displaying the "buckyball" C60
fullerene as generated by CaGe. As with Jmol, you can drag the mouse to
rotate the molecule around its center, Shift-drag to zoom it, and Control-drag
to translate it. You can use the menus as well, changing into different
display modes. There are some menu items that cause Rasmol to ask for
additional information. Rasmol does this by writing a prompt string to
its output. CaGe checks this output at regular intervals (the length of
these is set in the configuration file CaGe.ini).
If a question is found, CaGe will present it to the user in a small dialog
window. A response must be given (Rasmol is waiting for one on its input),
and you give it by filling in the dialog's text field and pressing Return.
To cancel the interaction, don't type anything and press Return, or close
the dialog window.
You can reset
Rasmol's display options by viewing a different graph, or by redisplaying
the current one (click into the "view/goto" field in the results
window, don't change the number, and press Return).