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                                gu...@uwosh.edu
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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