This latest rendition of Jmol also expands the (undocumented) capability of
Jmol to render "compiled graphical objects" such as GL/PyMOL-type
LINE_LOOP/VERTEX business and now relatively simplistic PostScript. VERTEX
coordinates can be given in 3D, in 2D 0-100% screen coordinates, absolute
screen coordinates, or "UV-mapping" coordinates, which map 2D vector
graphics onto a specified 3D-specified plane.
Examples are given below.
JmolVersion="14.3.12_2015.01.27"
bug fix: select thisModel does not select all atoms in visible frame set
bug fix: configuration 1 broken
bug fix: display configuration=1 broken (in Jmol 12.0, 2011)
new feature: @@3 for "atomno=3 and thisModel"
-- provides a function distinct from @3 when there are multiple models
-- includes all atoms in current frame set
-- example:
load "cyclohexane_movie.xyz"
select @10
35 atoms selected
select @@10
1 atom selected
frame [1 2 4 6]
select @@10
4 atoms selected
@@10.label = "atom 10"
new feature: frame [1 3 5 6]
-- sets limited number of frames for animation and frame *
-- same as animation frame [1 3 5 6]; frame *
new feature: CGO SCREEN option
-- CGO [SCREEN z ...]
-- reads CGO 2D VERTEX records as screen coordinates, installing them at a
depth of z
- where z > 0 indicates a percent (0.01 far back; 100 front)
- z < 0 indicates an absolute screen z value as -z.
- uses 2D VERTEX and other CGO point elements, not 3D
-- example: a static border 20% from the back of the model
cgo test2 [ SCREEN 20
BEGIN LINE_LOOP
VERTEX 10 10
VERTEX 90 10
VERTEX 90 90
VERTEX 10 90
END
]
new feature: CGO UVMAP option
-- CGO [UVMAP @origin @x @y x0 y0 x1 y1 scaleX scaleY ...]
-- 2D VERTEX records are scaled and mapped to a plane defined by @origin
@x @y
-- example: a parallelogram based on atoms 1, 6, and 11
cgo test1a [ UVMAP @1 @6 @11 0 0 80 80 1 1
BEGIN LINE_LOOP
VERTEX 0 0
VERTEX 80 0
VERTEX 80 80
VERTEX 0 80
END
]
new feature: CGO PostScript option
-- CGO [ PS @origin @x @y ] data "PS" [primitive encapsulated postscript
data] end "PS"
-- maps 2D EPS data onto a plane defined by an origin point, an x-axis
point, and a y-axis point.
-- somewhat similar to UV mapping of textures in other programs
-- allows 2D data to be superimposed on a model.
-- a crude implementation still in development; doesn't properly implement
stroke;
-- just for drawing lines; does not implement PS fill, gsave, grestore
-- just moveto, lineto, newpath, closepath, setlinewidth, scale
-- uses %%BoundingBox x0 y0 x1 y1 prolog record
to map [x0 y0] to @origin, [x1 0] to @x, and [0 y1] to @y
-- used for NBO contour mapping
CGO[ PS @{point(-5,-5,0)} @{point(5,-5,0)} @{point(-5,5,0)] data "PS"
%!PS-Adobe-2.0 EPSF-1.2
%%Creator: Bob Hanson (from NBO)
%%Title: nbo orbital slice
%%CreationDate: 1/26/2015 5:36 AM
%%DocumentFonts: Helvetica
%%BoundingBox: 211 300 428 518
%% note: above numbers are from 0.24*881 0.24*1781 0.24*1256 0.24*2156
%%EndComments
%%EndProlog
0.2400 0.2400 scale
newpath
3 setlinewidth
newpath
881 1256 moveto
1781 1256 lineto
1781 2156 lineto
881 2156 lineto
closepath
stroke
1241 1717 moveto
1250 1713 lineto
...
stroke
%%Trailer
showpage
end "PS"
bug fix: CGO LINE_LOOP not closing
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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