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.
----
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz
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