On Thu, Sep 24, 2009 at 12:52 PM, Jason Grout
<jason-s...@creativetrax.com> wrote:
>
> I updated the jmol spkg to 11.8.6 at #7003 (ready for review!).
I just want to comment that I want jmol to just be part of the
standalone sage notebook. If you look in the
sagenb/data/java
directory of the current standalone notebook you'll see that jmol is
sitting right there. It's the only thing not under revision control
in there.
I think having 3d graphics work right there as a standard part of the
Sage Notebook will be a big plus for people using it outside of Sage
(e.g., maybe Enthought).
And yes, I'll try to make this standalone notebook transition happen ASAP!
William
> Here
> are some new things since the current version of jmol we have in Sage.
> I post this here because some people might be interested in
> exposing/using some of these in Sage:
>
> These come from: http://chemapps.stolaf.edu/jmol/docs/examples-11/new8.htm
>
>
> 48. unit cell coordinates
> Jmol 11.7.37 introduces coordinate transformation functions .fxyz,
> .uxyz, and .xyz, and coordinate functions .ux, .uy, and .uz. The u-based
> functions allow selecting atoms and specifying coordinates based on unit
> cell coordinates within the range [0,1). The .xyz function now can be
> used to transform a fractional coordinate in decimal, {0.5, 1, 1} for
> instance, to Cartesian coordinates. The unit cell used for the .xyz
> function is the one currently set using unitcell nnn.
>
> 74. draw ARC
> Jmol 11.7.47 allows drawing of arcs in 3D based on center position and
> either a defined axis point or a plane. The default scale is an overall
> diameter (SCALE) of 1.0 Angstrom and a line diameter (DIAMETER) of 0.1
> Angstroms.
>
>
> 80. VRML and X3D support
> Jmol 11.8.1 adds nearly full VRML and X3D support. Caveates include: no
> label backgrounds, no background image, label sizes are approximations,
> no ellipsoid quadrant cutouts, and slightly irregular trace when
> displayed with a very small diameter
>
>
> 45. Jmol and Flot
> See jmol-flot.htm and jmol-flot-energy.htm for an interesting way to get
> graphical output from Jmol in an easily programmable way using Flot. The
> files used for this are in the flot subdirectory. Note that I did need
> to adapt the jquery.flot.js a bit to do the sort of plotting I was
> interested in. I added axes.majorTicks for the bold lines in the
> Ramachandran plot, added an options.grid.hoverDelay variable, and also
> added a selection.hoverMode option to allow hovering over a vertical
> stripe, not just a point. Note how the callbacks from Flot are used to
> highlight groups on the structure. This little experiment shows that we
> have a bit of work to do on straightness. We are working on that and may
> end up modifying the straightness(c) definition, as it seems to be off
> by one residue in comparison to DSSP (plot straightness(c) or
> straightness(p) and structure to see how that works).
>
> 33. isosurface OBJ "filename"
> # Jmol 11.7.27 adds the capability to read surfaces of the Wavefront OBJ
> type. Only the vertex, group, and face records are used. The group
> records define sets of faces that can be loaded selectively using an
> integer after the filename. In addition, if the group name is of the
> form "g kRRGGBB", then RRGGBB is interpreted as a hexidecimal color key.
> The generated isosurface may be saved as a JVXL file using a new
> extension of that format that allows compression of face-color data. The
> surfaces may also be mapped or recolored in a solid color as can any
> other surface. Future versions of Jmol may utilize the Material (.mtl)
> file associated with these objects to better specify color. zap;center
> {105 45 0};isosurface OBJ "sample.obj";set antialiasdisplay true
> # isosurface OBJ "sample.obj" 2
> # isosurface OBJ "sample.obj" 3
> # isosurface OBJ "sample.obj" 4
>
>
> 32. isosurface CONTOUR and CONTOURLINES|NOCONTOURLINES
> Jmol 11.7.27 adds contour lines for mapped data. Hovering over these
> lines displays the value of the mapped function at this point. The
> default is 10 contour lines.
>
> 2. draw LINE {pt1} {pt2} {pt3} ...
> Jmol 11.7.1 introduces the LINE keyword for the draw command. Line
> segments are drawn from point to point for a series of points.
>
> Jason
>
>
> --
> Jason Grout
>
>
> >
>
--
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org
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