[Jmol-users] sprouting Hydrogens, coloring isosurfaces

[Byrne P. <bp...@jp...>]

I am resurrecting some RasMol/Chime scripts and have a couple commands I
can't duplicate. I have extensively searched the archives, documentation and
experimented to no avail.

The "sprout hydrogen" command (Chime?) would calculate positions for
hydrogen atoms not resident in a pdb file so they could be displayed. I see
Jmol seems capable of such calculations for producing isosurfaces but I
can't find how to display them in simple spacefill mode. (I am trying to
emphasize the substrate-active site fit in a protein structure tutorial.)



I also cannot get the isosurface command to generate any other than a
uniformly colored surface. I previously generated, and colored, surfaces
with the "molesurface" command with such ancillary commands as:

surface molsurface white 0.45; set mep distance 99.0; set charge function
gasteiger; calculate charges refresh; list molsurface color potential;

(I probably copied and tweaked this from others so don't think I'm ready for
too erudite a response on this!) The purpose here was to paint a picture of
the protein as this unique electromagnetic landscape ready to interact with
its environment in unique ways. The other purpose was, of course, because it
looks cool.

I have tried the "colorscheme" parameter (again on a pdb file) without luck.
The "Jmol interactive scripting documentation" seems a bit short on how some
of these parameters should be specifically coded. For instance, it shows the
argument of COLORSCHEME in quotes which certainly doesn't work within a
jmolRadio call.

Thanks for any help on this.

Byrne Pedit
bp...@jp...