Eric,
At 8/2/05, you wrote:
I have a feeling that this involves some hidden dictionary. I've
never been clear which HETATOMs they regard as ligands. Seems
arbitrarily wierd, but perhaps I'm missing something obvious.
Dear David,
1. I suggest that you send inquiries about rasmol/chime to
molvis-list, in addition to or instead of to jmol-users.
http://bioinformatics.org/mailman/listinfo/molvis-list
2. A comprehensive list of manuals and tutorials for rasmol/chime is
at molviz.org under 'about chime'
http://www.umass.edu/microbio/chime/abtchime.htm
3. In rasmol/chime, "ligand" means all HETATM's that are not
"solvent". Solvent includes water and ions. "Ions" are defined as
sulfate and phosphate ions. There is a nice Venn diagram, and
definitions of all these terms in the RasMol manual under
"predefined sets".
http://www.umass.edu/microbio/rasmol/distrib/rasman.htm#predefinedsets
4. The requirement to use square brackets on group names containing
numerals is easy to miss ;-) but is documented in "Select commands
in chime and rasmol"
http://www.umass.edu/microbio/rasmol/seleccmd.htm
Again, items 3 and 4 above are linked under About Chime at molviz.org.
Thanks. I am still supporting Chime on our protein motif database
site, so I should check the Chime docs. However I should admit that
my main interest is in the Jmol applet because it runs on all
platforms including Mac OS9 and all flavours of Unix (especially Mac
OS X). I can't see much of a bioinformatics future for a plugin that
only runs on Windows.
David
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