Actually, I think we need to know whether or not it was fixed in the Java
1.5 that shipped with 10.4 Tiger.
I honestly doubt if Apple will be interested in fixing any Java bugs in
anything but their latest release.
OK. This will help push me over the edge to install Tiger pretty soon, but there is one outstanding problem I need to solve before I can upgrade. So for now I need to leave this Mac mouse testing to others, until I can return to it with Tiger.
Actually the next thing wanted to address is related-- slabbing mode, ie, the appearance of the front plane of the slab as it moves through a large molecule such as a protein.
Eric Martz posted on this but I do not see a response when searching the archive. Eric said:
SLAB RENDERING
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:
http://www.umass.edu/microbio/chime/beta/molslides/slab/slab-chime.gif
Here is a snapshot of the same molslide rendered in jmol
http://www.umass.edu/microbio/chime/beta/molslides/slab/slab-jmol.gif
Do these links start to get into the type of thing that would restrict your development efforts, Miguel? Obviously I do not wish to do that. I have little feel for it beyond your not using Chime and not having it installed on your machine- which you have clearly stated.
If it does get into a gray area, perhaps you could show us what solid sphere rendering looks like in Jmol, so we can comment.
Previously, Miguel had said:
<x-tad-bigger> One of the problems I have had with slab is the various "slabbing modes". It is difficult for me to render a solid sphere that has had the front of it sliced off. And when it gets past the midpoint these turn into solid circles. Not difficult to implement, but rather ugly to my eye.
</x-tad-bigger>
Hmm, I don't think the Chime solid sphere slab is at all displeasing, so I imagine that the Jmol version looks rather different... I guess the only point of showing it to us in Jmol would be if it could somehow be modified using our suggestions, or implemented as an optional slabbing mode.
<x-tad-bigger> It seems to me that perhaps one would want the slabbing mode to be different when working with large molecules as opposed to small molecules. That is, with large molecules it may be better for atoms to disappear completely rather than get sliced away.
Q: What slabbing modes are useful when working with large molecules?</x-tad-bigger>
<x-tad-bigger>
Q: What slabbing modes are useful when working with small molecules (or zoomed in on a piece of a large molecule) ?</x-tad-bigger>
For large molecule viewing, having atoms disappear would be superior to having the empty circle (bubble) appearance that is the current default. But I would have to see it in action to say if it could really live up to the clarity of a solid face rendering as I know it.
I don't work much with small molecules so I can't really comment on that. When working with a somewhat small section of a protein, such as a beta sheet, or alpha helix (still a far cry from a typical "small molecule" I think) I found that the solid face rendering continued to be very useful.
Are there any other choices for rendering slab besides the bubble, solid sphere, and disappearing act?
-Frieda
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
