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RasMol and Chime FAQ (Frequently Asked Questions) - B
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Double and triple bonds
Beginning with RasMol 2.6 beta-2 (and also in Chime 2) the PDB file needs to
specify CONECT records only for the double or triple bonds (not for all
bonds in the entire molecule as in the previous version of RasMol), and the
default is to display double bonds (set bonds on). Beware that
if the sticks get too large, the double bonds will disappear (reduce
the size of your graphics window, or zoom to smaller size).
Here is a sample PDB file with three double bonds,
fumarate.pdb. The heavily commented
contents of this file may
be viewed as fumarate.txt, which may be
used as an example for constructing your own such file.
A stereo image showing double
bonds is provided for the drug Alprazolam.
For purposes of showing delocalized double bonds (as in
COO-) it would be ideal to draw the second
bond in each pair as a broken line, but neither RasMol nor Chime can presently do
this. The command wireframe dash draws the selected bonds as
dashed (dotted) lines, but is presently incapable of showing double
bonds, and the dashed bonds cannot be thick (sticks).
For historic details, use your browser's Find capability to search the
RasMol email discussion history for February and July 1996
for the phrase "double bond".
Mouse Control Summary
These click-and-drag controls work similarly for RasMol
and for Chime. In RasMol, the set mouse command mode
defaults to set mouse rasmol, which gives the controls
summarized below. However, there are also set mouse insight
and set mouse quanta modes (not shown below).
| Action |
Windows |
Macintosh |
| Rotate X,Y |
Left |
Unmodified |
| Translate X,Y |
Right |
Command* |
| Rotate Z |
Shift-Right |
Shift-Command* |
| Zoom |
Shift-Left |
Shift |
| Slab Plane |
Ctrl-Left |
Ctrl |
*On some Macs, the Option (Alt) key has the same
effect on RasMol as the Command key.
If you use unix, send your mouse information to
me for inclusion
in the above table.
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