I updated the jmol spkg to 11.8.6 at #7003 (ready for review!). 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 --~--~---------~--~----~------------~-------~--~----~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -~----------~----~----~----~------~----~------~--~---
