Hi Joe,
For translation try SHIFT-double-click and drag. For mouse gestures
in general see this Jmol wiki page,
http://wiki.jmol.org:81/index.php/Mouse_Manual
HTH,
Frieda
///////////////////////////////////////////
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
///////////////////////////////////////////
On Aug 7, 2007, at 12:57 PM, Joe Ivanic - Contractor & Foreign
National/bioanalysis wrote:
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
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