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Double and triple bonds To see other biotech frequently asked questions,
please visit http://biotech.fyicenter.com/faq/
(Continued from previous question...) 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". (Continued on next question...)
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