newExam('.animation','','','animation.htm')
newExam('.atom expressions','select atomno=1;color purple;spacefill 600||select nitrogen;color yellow||select [PRO];color green||select within(5.0,[PRO]62) and not [PRO]62;color white||select within(group,within(5.0,[PRO]));color yellow||select substructure("[Fe][S]");wireframe 1.0||select 95:L^a # selects residue 95 of chain L, insertion code a','1blu.pdb','select.htm,examples-11/altloc.htm')
newExam('.center','select [CYS]32;center selected;select *;','1','')
newExam('.cpk','cpk 0.2;spacefill 80%','','atoms.htm')
newExam('.define','define ~mygroup within(5.0,[FS4]102);select ~mygroup;color atoms white','1blu.pdb','select.htm')
newExam('.depth','slab 50; depth 0;slab on; # show the back half of the molecule||slab 100;depth 50; slab on;# show the front half of the molecule||slab 75; depth 25;slab on; # show middle 50% of the molecule||slab 50;depth 50;slab on; # show a plane that is 1 pixel deep','1crn.pdb; ribbons on; spacefill off; wireframe off; color ribbons group','')
newExam('.echo','set echo top left;font echo 20 serif bolditalic;color echo green||echo "I am green top left|20 serif bolditalic"||set echo myecho 350 150||echo this is|myecho; set echo myecho center||echo this|is|a|test||set echo myecho right||set echo myecho left|| set echo top center|| set echo top right||set echo top 70 320','caffeine.xyz','')
newExam('.centerAt','centerAt absolute 1.0 2.0 3.0;centerAt boundbox 1.0 2.0 -3.0;centerAt average 0.0 0.0 0.0;','','')
newExam('.label','select nitrogen;label %a: %x %y %z','1','labels.htm')
newExam('.loop','color bonds red;delay 3;color bonds green;loop 1','1blu.pdb','')
newExam('.moveto','moveto 0 1 0 0 -90; #view from top||moveto 0 0 1 0 90; #view from right||moveto 0 0 1 0 -90; #view from left||moveto 2 1 0 0 90; #view from bottom with smooth 2-second transition||moveto 0 0 0 0 0 200; #default orientation with instantaneous transition and a zoom of 200%','1crn.pdb; ribbons on; spacefill off; wireframe off','moveto.htm')
newExam('.pmesh','pmesh myPlane "10x10pmesh.txt"; # load a pmesh with ID myPlane;color pmesh translucent yellow; # make it translucent yellow;pmesh myWave "wave.pmesh"; # load another pmesh, with ID myWave;pmesh dots; # turn on dots on all loaded pmeshes;pmesh myWave;# select pmesh myWave;color pmesh white; # color it white;pmesh myPlane mesh; # only display the mesh for myPlane;pmesh myPlane nodots; # no dots for myPlane','caffeine.xyz; rotate x 100','examples-11/pmesh.htm')
newExam('polyhedra1','select *;polyhedra BONDS; color polyhedra grey||select atomno=19; select hydrogen; polyhedra RADIUS 3.0 ;color polyhedra yellow||polyhedra RADIUS 2.0 (*) COLLAPSED #all three||polyhedra (*) DELETE||polyhedra RADIUS 2.0 (*) TO (not within (1.1225, carbon)) #note how this disallows one of the three||select *;color polyhedra translucent; # now we can see the carbons inside||polyhedra (*) EDGES; # highlight the edges||select *; color polyhedra translucent orange;||polyhedra (*) OFF','caffeine.xyz','')
newExam('.display','display protein||display not solvent||display within(3.0,[FS4]102)','1blu.pdb','')
newExam('.select','select carbon;color white||select protein;ribbons on||select *:D;color blue||select [HIS]:D;spacefill 300||select [HIS]92:D.N;spacefill 600||select [HIS]92:D.C?;color orange||select [HIS]92.N;color [255,196,196]||select elemno<7;spacefill 200||select within(group, within(10.0, :a));color green;select :a;color red||select within(chain, [HIS]92);color white;||select within(chain, within(3.0,[HIS]92:D));color purple;||select within(chain,within(5.0,[HIS]92));color white||select 95^a:L # selects chain L, residue 95, insertion code a','1a3n.pdb','select.htm')
newExam('.slab','slab 50; depth 0;slab on; # show the back half of the molecule||slab 100;depth 50; slab on;# show the front half of the molecule||slab 75; depth 25;slab on; # show middle 50% of the molecule||slab 50;depth 50;slab on; # show a plane that is 1 pixel deep','1crn.pdb; ribbons on; spacefill off; wireframe off; color group','')
newExam('.wireframe','wireframe 0.2||wireframe off','','bonds.htm')
newExam('coloratoms','select oxygen;color atoms green||select carbon;color atoms TRANSLUCENT white;color bonds green;||select carbon;color bonds OPAQUE [255,196,196]','caffeine.xyz','atoms.htm,bonds.htm')
newExam('colorrasmol','define ~myset (*.N?);select ~myset;color green;select *;color cartoons structure;color rockets chain;color backbone blue','','')
newExam('colortext','select [CYS]32 ;label %a: %x %y %z;color labels white;||set axes on;color axes green||set axes on;color axes [xFF00FF];','1','')
newExam('comment','# color by polarity||color background [xffa0a0] # pink||#jx set perspectiveDepth on; #executed only in Jmol, not Chime or Rasmol||zoom 125 #jc; # zoom to 125% in Chime and Rasmol but not in Jmol','kaolin.mol','')
newExam('lighting','','','lighting.htm')
newExam('models','model 1||model NEXT||model PREVIOUS||model 0;select *;wireframe 0.1;spacefill 0.2||anim on||model 0;select *;wireframe off;spacefill off;||select 1.1 # in Jmol10 use */1||wireframe 0.1;spacefill 0.2;color atoms red;||select 1.35;wireframe 0.1;spacefill 0.2;color atoms blue','cyclohexane_movie.xyz','animation.htm')
newExam('setsolvent','set radius 2.0;set solvent ON;select 1-10;dots ON','1','')
newExam('orientation','','','moveto.htm')
newExam('polyhedra2','# build tetrahedrons around silicon||polyhedra BONDS (silicon)||# make some of them green||select atomno<50; color polyhedra translucent green|| ||# delete some of them||polyhedra (atomno>75 and atomno<100) DELETE|| ||# now build octahedrons where oxygens are within 2.0 Angstroms of a central aluminum atoms||polyhedra BONDS (atomno<75) FRONTEDGES||select aluminum and atomno > 75; color polyhedra red','kaolin.mol','examples-11/poly.htm')
newExam('scale3d','','','scaletest.htm')
newExam('setbonds','','','bonds.htm')
newExam('structure','','','structure.htm')
newExam('.isosurface','isosurface pos05 0.05 "ethene-HOMO.cub.gz";isosurface neg05 -0.05 "ethene-HOMO.cub.gz";||# now load some other surface further out;||isosurface pos01 0.01 "ethene-HOMO.cub.gz";isosurface neg01 -0.01  "ethene-HOMO.cub.gz";color isosurface translucent; # make neg01 translucent||isosurface pos01 nofill mesh; # make pos01 a mesh;||color isosurface translucent; # make the pos01 mesh translucent, too||isosurface neg01 dots; # make neg01 show dots, too||isosurface neg01 nofill; # only dots||isosurface nodots nomesh fill; #everybody is back to a solid ...;color isosurface opaque; # ... and opaque||isosurface neg01; #select neg01;||color isosurface green;||isosurface pos01;color isosurface violet;||slab on; slab 50; # slab in order to see the inside||slab off; # all done!','ethene-HOMO.cub.gz; rotate x -60;rotate y -30','examples-11/isosurface.htm')
newExam('.star','select *.S?;star ON||select 40;star 1.0;color star red||select *;color star NONE||select *;star OFF','1','')
newExam('.stereo','zoom 50;background white;stereo ON||stereo 90||stereo 5||stereo -5||zoom 100;background grey;stereo REDCYAN||stereo REDBLUE 3||stereo REDGREEN;stereo OFF','1crn.pdb; ribbons on; spacefill off; wireframe off; background grey','')
newExam('pickd','(pdb data in this case);Atom #1:[VAL]8.CA #49;Atom #2:[GLU]23.OE2 #169;Distance [VAL]8.CA #49 - [GLU]23.OE2 #19 : 16.765396','','')
newExam('picka','(xyz data in this case);Atom #1:C 2 #2;Atom #2:C 3 #3;Atom #3:C 4 #4;Angle C 2 #2 - C 3 #3 - C 4 #4 : 122.3754','','')
newExam('pickt','(cml data in this case);Atom #1:a7 #7;Atom #2:a3 #3;Atom #3:a1 #1;Atom #4:a2 #2;Torsion a7 #7 - a3 #3 - a1 #1 - a2 #2 : -4.15209','','')
newExam('.connect','# two ways to link atom #1 with atom#2|| connect (atomno=1) (atomno=2) DOUBLE || select atomno=1,atomno=2; connect (selected)|| ||# connect all carbons with hydrogens that are within the range 1.0 to 1.2 angstroms and are not already connected||connect 1.0 1.2 (carbon) (hydrogen) PARTIAL CREATE|| ||# change all bonds to single bonds||connect (all) (all) SINGLE MODIFY|| ||# connect every atom with every other atom that is within 1.5 angstroms whether it is connected already or not||connect 1.5 (all) (all) ModifyOrCreate|| ||# delete all bonds WITHIN a selected atom set||connect (selected) (selected) DELETE || ||# delete all bonds TO a selected atom set||connect (selected) (not selected) DELETE','caffeine.xyz','')
newExam('.mo','','_blank','examples-11/mo.htm')
newExam('.draw','','_blank','examples-11/draw.htm')
newExam('.load','','_blank','examples-11/sym.htm')
newExam('.lcaoCartoon','','_blank','examples-11/lcao.htm')
newExam('.dipole','','_blank','examples-11/dipole.htm')
newExam('.fractional coordinates','','_blank','examples-11/fraction.htm')
newExam('.measure','','_blank','examples-11/measure.htm')
newExam('.translateSelected','select molecule=1;translateSelected {0 0 1/1}','','')
newExam('.if_else_endif','if (showBoundBox);||&nbsp;&nbsp;set showBoundBox off;set showUnitCell;||else;||&nbsp;&nbsp;set showUnitCell off;set showBoundBox;||endif;','','')
newExam('quaternions','# set to final state||moveto 0.0 { -46 -870 492 142.18} 300.0 0.0 0.0 {61.260506 38.7915 44.659} 50.97134 {0.0 0.0 0.0} 281.9351 50.269466 50.0||qfinal = quaternion(script("show rotation"))||# set to initial state||moveto 0.0 { -142 866 480 107.35} 100.0 0.0 0.0 {61.260506 38.7915 44.659} 50.97134 {0.0 0.0 0.0} 8.481314 102.86942 50.0;||qinitial = quaternion(script("show rotation"))||# calculate steps||dq = qfinal / qinitial / 20||# now loop and save||write image "image0.jpg"||for (i = 1; i <= 20; i = i+1)||   rotate quaternion @dq||   f = "image"+i+".jpg"||   write image @f||end for','','')
newExam('.rotateSelected','select connected(C19) and not N8;||rotateSelected {N8} {C19} 30  # CH3 rotates 30 degrees around that bond other options might be rotateSelected {0 0 0} {1 1 1} 30,  rotateSelected axisangle {1 1 1 30}, or rotateSelected molecular x 30','caffeine.xyz','')
newExam('.spin','spin branch {N8} {C19} 50 # CH3 starts spinning around the N8-C19 bond','caffeine.xyz','')
newExam('writeframes','write frames {*} "all.jpg"|| write frames {1.0} "allModelsInFirstFile.jpg"||write frames {1.0,2.0} "firstTwoFiles.jpg" || write frames {1.0} 200 200 "smallFile.jpg"','','')
newExam('.bind','bind "CTRL-ALT-LEFT" "_rotate";||bind "CTRL-ALT-LEFT-DOUBLE" "spin @{!_spinning}"','','')
newExam('.unbind','unbind "CTRL-SHIFT-LEFT";||unbind "_clickFrank";unbind "_popupMenu";||unbind "LEFT" "_rotate"','','')