I try to answer your questions below. In summary, now that you've changed the
isosurface slab command so that it can be done after the surface is defined I
am mostly concerned with building a GUI that is intuitive enough that people
don't have to understand the details of the isosurface and slab commands to
look at a section through the displayed object. My first goal is to get this
working well for isosurfaces, but I don't think it will be hard to extend it to
do everything.
On Jun 30, 2011, at 1:07 AM, Robert Hanson wrote:
> well, the molecular coordinates are just the molecular coordinates. This
> "slicing" is by them, right? Not the screen coordinates? There are three
> coordinate systems:
>
> -- molecular coordinates
> -- relation of those by rotation to the original view (the orientation
> quaternion/matrix)
> -- translation of that into screen coordinates (the transformation matrix)
>
> I'd sure like to hear more about what the specs are going to be on this
> "slice" command. Before you go too far, Jonathan, can you remind us of what
> exactly it is going to do?
>
> Q: Are we slicing in molecular coordinates (like isosurface slab plane... and
> slab plane...) or screen coordinates (like slab/depth and isosurface slab
> nnn)?
The first draft will be slicing in molecular coordinates, although I think some
people might also like a GUI for slab/depth like behavior.
>
> Q: Does the slab change when you rotate the model, or is it fixed? (Basically
> the same as the previous question.)
People wanted to be able to look at the slice from different angles so that's
why molecular coordinates.
>
> Q: What functionality does this add that does not already exist in the other
> commands?
Other than a ghost feature, which presently requires building a duplicate
surface, I cannot think of anything.
Anyway, the issue is that people want the ability to specify the slice in a way
that is logical relative to the view. Tentatively, I am going to make the
controls relative to the origin of the boundingbox. If they are relative to
the view orientation, things change on rotation and translation. I think that
would be confusing. I think there should also be an option to do everything
relative to the absolute coordinates (molecular). I'll just set a switch. So
I am still at my original question, which is will the boundbox coordinates
always be parallel to the molecular coordinates?
>
> There is no point in adding a new command unless it makes *scripting* far
> easier. This sounds a lot more like a GUI thing -- which would use the
> already-existent commands, possibly with a few modifications to suit.
I agree. Initially as I began looking at what Jmol could do, I thought it
would help. Now I'm not sure.
>
> It seems to me a popup window is a nice idea -- at least for the application.
> Not convinced with respect to the applet -- we don't do that, so far, except
> with the signed applet for file read/write. A good dialog can take lots and
> lots of code to produce and work with. If possible, with the applet, we
> should do that in JavaScript, not Java. (My opinion.)
I agree for another usability reason as well. When you have more than one
applet on a page it is difficult to tell which one the pop-ups go with. A
javascript tool that is anchored on the page in the vicinity of the applet is
much easier to understand. That is one of the reasons, I thought about a
special command. The idea being that the smaller the scripts that have to be
passed the better the potential for speed.
>
> By the way, you asked about the possibility of duplicating an isosurface so
> there was a translucent "shadow." Since rendering is a two-pass system, a
> better way
I like your idea and have sent a comment in a separate message.
Jonathan
Dr. Jonathan H. Gutow
Chemistry Department [email protected]
UW-Oshkosh Office: 920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
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