Re: [Jmol-users] first peak at update to Jmol in SAGE (3-D function plotting)...

[Jonathan G. <gu...@uw...>]

Most of the issues relate to the user interface I'm trying to  
generate.  For example, to have clean control of the axes they've  
drawn from the user interface draw items need to have labels.  Sage  
Worksheets created so far don't name draw items in scripts, so I have  
to make some assumptions.  Another example is that as we fix bugs or  
enhance things they don't work exactly as they once did.  I already  
pointed out that there was an issue with the angle of frontlit between  
11.6 and 11.8, which is obvious when playing with simple SAGE  
surfaces.  I've worked around that in my code by issuing a pmesh o*  
fullylit command.  But this depends on the fact that presently SAGE  
names all the surfaces obj_XXXXXXX.  Anyway, I expect issues like this  
to continue.  I also find it very hard to build a web interface based  
on a moving set of features, so I'm playing with the 11.9 features,  
but expect the next version of Jmol in SAGE to be 11.8 (I hope very  
soon) and want to be ready to put 11.10 in when it comes out.  I'd  
like to see that include a plot primitive.

Since Jason is lurking here too maybe he can add to the following list  
of what it might contain.  My preliminary thoughts are a structure  
that contains:

1) An arbitrary number of isosurfaces, with attributes color,  
transparency, visibility, mesh color, mesh visibility, lighting state  
(fullylit default).  The range for the numbers in these isosurfaces  
should be limited only by the number range available for floating point.
2) Strings to title the X, Y and Z axes
3) Based on the range of the isosurfaces (pmeshes) provided Jmol would  
determine the bounding box and the scale adjustment for display.
4) This structure would have scriptable functions for turning on and  
off each of the edges of the bounding box, the axis titles and  
automatically computed numerical ranges on the axes (a real bonus  
would be if the tick numbers could be associated with any of four  
equivalent axes).  I think the SAGE solution of a minimum of 3 numbers  
per axis is pretty good.  Really big displays (> 600 px square) could  
benefit from 5 numbers per axis.

So ideally SAGE can just generate an unscaled list of isosurfaces,  
planes, etc.. Then Jmol would worry about making the plot pretty.

I think that the arbitrary intersections of planes and surfaces should  
continue to be accessed using the script methods already defined.

Part of the problem for me when dealing with lots of new features is  
that I don't have a whole lot of time to work on this.  I do it in  
five minute bits and pieces or for a while before bed instead of a  
crossword puzzle or reading a book....

Jonathan

P.S. Did all the fixes related to an applet label of '0' get into  
Jmol.js?


On Dec 15, 2009, at 8:39 PM, jmo...@li...  
wrote:

> Date: Tue, 15 Dec 2009 20:39:02 -0600
> From: Robert Hanson <ha...@st...>
> Subject: Re: [Jmol-users] first peak at update to Jmol in SAGE (3-D
> 	function	plotting)...
> To: jmo...@li...
> Message-ID:
> 	<ba9...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Why would there be any compatibility issue, Jonathan? There should  
> not be
> any. Please let me know of any you are aware of.
>
> Bob

                          Dr. Jonathan H. Gutow
Chemistry Department                                 gu...@uw...
UW-Oshkosh                                           Office:920-424-1326
800 Algoma Boulevard                                 FAX:920-424-2042
Oshkosh, WI 54901
                  http://www.uwosh.edu/facstaff/gutow