From: Eric Martz <emartz@mi...> - 2005-06-30 16:10:53
I am trying to see how jmol's slab renderings compare with Chime's. The
long term goal is to be able to make molslides in jmol that show views
equivalent to those for the same molslides in chime. Ultimately, this would
ideally be achieved by feeding the chime script to jmol without
modification. We are presently trying to identify cases where jmol does not
produce an equivalent image to chime. One such case is for slabbed images.
FINDING MOUSE GESTURES
1. After trying to guess a mouse gesture to move the slab plane, I looked
but could not find a list of jmol mouse gestures. (I looked in
documentation, FAQ, and jmol applet guide.)
2. I would like to suggest that Jmol's mouse gestures be listed in a window
that can be opened from the Jmol applet menu. That way they are always
accessible. (Chime has had this for many years, at my request.) I suggest
that "Mouse Gestures" be an item under "About Jmol".
3. If there is no mouse gesture to move the slab-percent, I suggest that
one be added. Being able to slide the slab percent with the mouse is very
useful for finding an optimal slab position.
Control-left mouse did not do anything to my view in jmol (jmol 10.00.11,
Firefox, Windows 98, java 1.5.0-01_b08). This is the mouse gesture used for
slab-percent in Chime.
I note that on 2004-11-15 a mouse gesture for slab-percent had not been
and that Control-left would conflict with something in OSX. A list of all
currently implemented gestures would be helpful in suggesting a gesture for
Chime's default slab rendering shows each atom cut by the slab plane as a
partial sphere with a solid flat face cut by the plane. This is very useful
for one of the most important visualizations in proteins, namely, to see
the distribution of hydrophobic, polar, charged residues within the core of
a domain. Here is a snapshot of an example:
Here is a snapshot of the same molslide rendered in jmol
(The molecule has been moved with the mouse to approximate the same
perspective as in Chime since we have not yet achieved an automatic way to
do equivalent centering and rotations.)
4. Am I correct in believing that jmol's only existing slab rendering mode
shows cut atoms as rings?
It may be worthwhile to implement in jmol a "flat cut face" rendering
similar to Chime's, but I can't be sure until I can experiment with the
views obtained when the jmol slab-percent is moved by the mouse.
5. Has anyone implemented a slider or other control that permits
interactive real-time sliding of the slab-percent?
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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz
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