> Is there a way to have unconnected atoms automatically represented as > crosses (or something) when cpk=off?
As I understand it, the problem you are trying to solve is that unconnected atoms are not visible with 'cpk off; wireframe on'
There is currently no mechanism to represent these atoms.
Q: how do other packages deal with this?
RasMol 2.6 and Chime leave unbonded atoms invisible when only the wireframe display is on. I agree that this is undesirable. In Protein Explorer, I show such atoms as small-diameter spacefills in certain situations. I agree that some sort of crosses sounds like a good idea for Jmol because spacefill (as a default) takes up too much visual space and becomes obscuring.
-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop Biochem Structure Tutorials http://MolviZ.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532
http://www.umass.edu/molvis/martz
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