Marking up molecules with Chime and CSML

[Rzepa, Henry]

More on the use of Chime;

 O. Casher, G. Chandramohan, M. Hargreaves, C. Leach, P. Murray-Rust,
 R. Sayle, H. S. Rzepa and B. J. Whitaker, "Hyperactive Molecules and the
World-Wide-Web Information System", J. Chem. Soc., Perkin Trans 2, 1995, 7.
describe a simple way of sending rendering instructions to e.g. a RasMol
browser,  called CSML (chemical structure markup language).
 It appears this is fully implemented in the Chime plug in.

For example, a molecule in-lined as;

<embed src="http://www.ch.ic.ac.uk/hyperactive/1prc.pdb" align=abscenter
width=250 height=250 spiny=360 startspin=true display3D=ribbons
PLUGINSPAGE="http://www.ch.ic.ac.uk/cgi-bin/plugin.cgi" name="1prc"></embed>

can be marked up using
<embed src="1prc_1.csml" width=12 height=12 target="1prc" button=push>

where the csml looks like  e.g.

all grey backbone on
607 red spacefill on
608 grey spacefill on
his217 blue spacefill on
atomno=6519 blue spacefill on HIS:217

If you go to our  "molecule of the month for March"

on http://www.ch.ic.ac.uk/motm/1prc.html
you can see all this in action. It appears stable and works well on
Windows-95. For a system as big as this, one really needs to use
non-scrolling frames.
A version implementing this is on its way!!

Dr Henry Rzepa,  Dept. Chemistry,  Imperial College,  LONDON SW7 2AY;
rzepa at ic.ac.uk; Tel  (44) 171 594 5774; Fax: (44) 171 594 5804.
URL: http://www.ch.ic.ac.uk/rzepa/  


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