[Jmol-users] Translation with mouse and labeling of nodes (atoms)

[Joe I. - C. & F. National/b. <ji...@bi...>]

Hi, 
 
I am a quantum chemistry theory and program developer (mainly GAMESS),
plenty of experience with Fortran and C, but none really with Java. My
questions may be very simple but I have to ask them.
 
Jmol is fantastic for visualizing almost everything. However, I still
have not found a way to translate a molecule with the mouse. There are
the move, moveto, and translate Jmol commands, however, being able to
move the molecule sideways with the mouse, rather than only rotation and
zoom, helps to accurately focus in on very specific parts of a system.
Is there a way to translate with the mouse?
 
The above question is asked mainly because I am also using Jmol to
visualize very large networks. So I trick Jmol (with a .gpr file) into
thinking I have lots of atoms (difference for each type of node) and
then specify their connections (with bonds). This has proven very
useful. Being able to translate, though, would make network
visualization and "navigation" that much better. Being able to select a
node (atom) with the mouse, or script, and then recentering the network
(molecule) about this node would also be extremely useful, very similar
to the free translation.
 
My last query is about the labeling of the nodes (atoms). There is the
script command "label" which can do this very efficiently. However,
being able to have the pointer on top of a node (or atom) and then
automatically include showing of the label (not the atom, e.g. H, Li,
rather a string label) would be nice. I'm not sure how to do this within
Jmol. It seems to have the flexiblity to have an "atom name" shown,
rather than an "atom label" but I am not able to figure out just how to
accomplish this. Certainly not within the .gpr format anyway. Typing an
atom label (node label) into the script window, with the relevant
command, and this being highlighted would also be extremely useful. I
guess I am asking if we can input other types of nodes, rather than just
atoms, into Jmol.
 
Any help with the above would be very much appreciated.
 
Joe
 
---
 
Dr. Joe Ivanic 
Scientist
Biotechnology HPC Software Applications Institute
ATTN: MCMR-ZB-T (Joe Ivanic)
Building 363, Miller Drive
Ft. Detrick, MD 21702-5012
 
Voice: (301) 619 1976
Fax: (301) 619 1983