Jmol Code

Fah

draw support for animation:

(1) absolute [x,y,z] coordinates are "fixed" in space
in all frames.

(2) (atom sets) are calculated freshly for EACH frame
unless the FIXED keyword is present. In that case,
what is displayed is an average value for all frames.

(3) [objectID] references are fixed or free to move, as
defined in the initial "draw objectID" specification.

(4) fixed coordinates and free (atom sets) can be mixed.

Examples:

load cyclohexane_movie.xyz
draw axis1 250 (atomno=2) (atomno=5)
#between two atoms

draw axis2 200 (atomno=4 or atomno=3) (atomno=1 or atomno=6)
#between two bonds

draw axis2 200 FIXED (atomno=4 or atomno=3) (atomno=1 or atomno=6)
#average position shown throughout animation

draw axis2 200 [0.,0.,0.] (atomno=4 or atomno=3) (atomno=1 or atomno=6)
# one fixed point and two moving points forming a triangle.

animation on



see http://www.stolaf.edu/people/hansonr/jmol/test/json/pmesh.htm

FollowSymLinks added for the wiki

adding detail to getProperty("shapeInfo") and getProperty("ModelInfo")

(1) augmenting pmesh "inline" and draw to allow a friendlier
flow of data -- [x,y,z] -- really anywhere [,] are ignored.

(2) allowing for identifier access to draw objects as
[point1], [line1], etc., in square brackets. It's a simple,
clean method that doesn't require anything in the compiler.

examples:

http://www.stolaf.edu/people/hansonr/jmol/test/json/pmesh.htm

pmesh test1 "inline" "1 [0. 0. .5] 0";color pmesh white;pmesh test1 dots
pmesh test2 "inline" "2 [0. 0. 0.] [1. 0. 0.] 1 [3 0 1 0]";color pmesh orange
pmesh test3 "inline" "3 [-0.49, -2.8, -1.2] [-2.2, 0.80, 1.09] [1.89, 2.12, 0.42] 1 [4 0 1 2 0]";color pmesh yellow
pmesh test4 "inline" "4 [0., 0., 0.] [0., 2., 0.] [2., 2., 0.] [2., 0., 0.] 1 [5 0 1 2 3 0]";color pmesh translucent red
load caffeine2.xyz;draw triangle1 150 (atomno=1) (atomno=14) (atomno=15);draw line2 200 [triangle1] (atomno=9) (atomno=11);color draw translucent green
draw line1 120 (atomno=1) (atomno=2);color draw white
draw line1 300 (oxygen) (nitrogen)
draw triangle1 400
draw line1 100;draw triangle1 100
draw triangle1;color draw red;draw line1;color draw blue
draw line2 200 [triangle1] (atomno=9) (atomno=11);color pmesh green
draw square1 [1.0 1.0 1.0] [1.0 0.0 1.0] [0.0 0.0 1.0] [0.0 1.0 1.0]

just removing dangling debug comment I had forgotten to remove

fixes select resno < nnn problem.
created Atom.getResno() and Group.getResno()
as distinct from Group.getSeqcode().
Involves returning seqcode >> 8 instead of seqcode

Fah

adjustments to new "draw" command
oh, and I see I didn't commit Draw or DrawRenderer last time.

adds drawing support for points, lines, and planes (triangles and quadralaterals).

(1) new classes Draw and DrawRenderer

(2) new script command "draw" based on pmesh

draw line1 (atomno=1) (atomno=2)
#a line from atom 1 to atom 2

draw line1 120 (atomno=1) (atomno=2)
#a line from atom 1 to atom 2, scaled to 120%

draw point1 (all)
#geometric center of the model

draw point2 (oxygen)
#center of all oxygens

draw line2 1.0 1.0 1.0 3.0 3.0 3.0
#draw a line from (1,1,1) to (3,3,3)

just a start....

Bob Hanson