# this script is the first of its kind -- demonstrating the use of # variables in Jmol 11.1.12. We use the variable "auRadius" here to # smoothly adjust the gold radius in the spacefill command. # The idea is that @auRadius in any command inserts the value of # auRadius at the time that command is executed. load gold.cif {5 5 5};wireframe off;spacefill 1.45;draw off;axes off;unitcell off; # rotate to orientation moveto /* time, axisAngle */ 5.0 { 329 816 -476 154.9} /* zoom, translation */ 100.0 0.0 0.0 /* center, rotationauRadius */ {10.196499 10.1965 9.176849} 18.8; # create the clipping planes draw plane1 (atomno=1) (atomno=2) (atomno=6) draw plane2 (atomno=1) (atomno=6) (atomno=5) draw plane3 (atomno=1) (atomno=2) (atomno=5) draw plane4 (atomno=513) (atomno=532) (atomno=429) # select tetrahedron select within(999,plane,$plane1) and within(999,plane,$plane2) and within(-999,plane,$plane3) and within(-999,plane,$plane4) # fade unwanted atoms select not selected auRadius = 1.45 message _here1 auRadius = auRadius - 0.02 spacefill @auRadius refresh if (auRadius > 0.02);goto _here1;endif display not selected #reorient moveto /* time, axisAngle */ 5.0 { -180 497 -849 149.7} /* zoom, translation */ 100.0 -6.0 15.1 /* center, rotationRadius */ {10.196499 10.1965 9.176849} 18.8; #fade in nontetrahedral atoms select not displayed;color translucent white; display (atomx < 20 && atomy < 20) auRadius = 0.05 message _here2 auRadius = auRadius + 0.02 spacefill @auRadius refresh if (auRadius < 1.45);goto _here2;endif