load "files" "caffeine.xyz" "cyclohexane_movie.xyz"
frame all
display 1.1
display 2.1,2.7
select 2.1,2.10;color yellow
select C1*/2.0;color green # all C-1 carbons in all models in the cyclohexane movie
frame range 2.1 2.10;display *
animation play
animation rewind
load caffeine.xyz;connect (_C) (_O) double modify;select none;selectionHalos on
select connected(double)
select connected(double, carbon)
select connected(0,single)
select connected(2,3,single)
load caffeine.xyz
connect 1.405 1.425 (_C) (_N) red
connect (_C) (_H) radius 0.05
connect 1.5 2.5 (_H) (_O) hbond radius 0.1 translucent yellow create
load 1crn.pdb;cartoon on;isosurface sasurface
slab plane x=10;slab on;moveto /* time, axisAngle */ 1.0 { 28 -880 474 56.2} /* zoom, translation */  100.0 0.0 0.0  /* center, rotationRadius */ {9.268828 9.787275 6.9670877} 17.6;
slab off
load quartz.cif {2 2 2};moveto /* time, axisAngle */ 1.0 { -997 -20 -72 30.0} /* zoom, translation */  100.0 0.0 0.0  /* center, rotationRadius */ {2.5324771 4.257381 5.4054003} 10.7;slab on;
isosurface p1 hkl {1/2 1/2 1/2};isosurface p2 hkl {1/4 1/4 1/4};
isosurface;isosurface off
depth plane $p1;
slab plane $p2;
select not clickable;color translucent yellow;
slab off
depth plane none;slab hkl {1/3 1/3 1/3};slab on
slab plane none;depth hkl {1/2 1/2 1/2};slab on
load quartz-slab.cif
load 1crn.pdb;select *;cartoon on;color group;
set navigationMode; # Automatically loads perspective model 11, which included navigation. Now use the arrow keys
navigate 3 depth 50;
navigate 3 center (*);
navigate 2 trace (*);
set navigationMode off; set perspectiveModel 10
show set


# new0:

 
show defaultDirectory
set debugscript true;show debugscript;set debugscript false
set myvariable true;show myvariable
set dataSeparator "~~~";data "model test"|2|test|C 0 0 1|N 0 1 0|~~~2|test2|Al 0 0 3|Fe 0 4 0|end "model test";moveto 1.0 { -32 -999 23 82.0} 100.0 0.0 0.0 {0.0 2.0 1.5} 4.6;frame 0;labels on
frame 1001
frame 2001
frame 0
save state A
show state A
zap
restore state A
console; show state
save state A
save state B
console; show state A
console; show state B
zap;set echo top left;echo now go load some other model,|then come back here and|click on "restore state A"
restore state A
restore state B
load caffeine.xyz;select _O;set labelOffset 20 10;labels on
set labelpointer on;
background labels yellow
set labelpointer background;
background labels none
load 1myg.cif;color chain
subset *:B;select *;cartoons on;subset all
subset *:A
subset *:B
restrict none;select *;cartoons on;
restrict none;select *;trace on;
subset *:A   # now click on or off chain A.
subset all
load 1crn.pdb;restrict none;select *;cartoons on;color structure;moveto 1.0 { -777 -626 -64 44.0} {10.5935 10.2105 6.079}  17.4;
set traceAlpha off
set sheetSmoothing 0
set sheetSmoothing 1
set traceAlpha
load 1crn.pdb;restrict none;select *;cartoons on;color structure;moveto 1.0 { 140 -957 -255 50.6} 277.4 {10.5935 10.2105 6.079}  17.4;
set hermitelevel 1
set hermitelevel 2
set hermitelevel 3
set hermitelevel 4 # rotate the model to see how this looks.
set hermitelevel 5
set hermitelevel 6
set hermitelevel 7
set hermitelevel 8
set hermitelevel -4 # now rotate -- the smoothness stays
load 1crn.pdb;restrict none;select *;cartoons on;color structure;moveto 1.0 { -777 -626 -64 44.0} {10.5935 10.2105 6.079}  17.4;
set highResolution
set highResolution off
load 1mbo.cif;restrict none;select *;cartoons on;color structure;select HEM;wireframe 0.1;color cpk;set hermitelevel 4;moveto 1.0 { 422 126 898 117.4} 192.2 {15.027501 19.463001 6.660001}  35.7;
set hermitelevel 0
set hermitelevel 4
load 1crn.pdb;restrict none;select *;cartoons on;color structure;set hermiteLevel -4
set ribbonAspectRatio 8
set ribbonAspectRatio 16
set traceAlpha #default
set traceAlpha off
set ribbonAspectRatio 0
cartoons off;ribbons on;
set ribbonAspectRatio 8
set ribbonAspectRatio 16
load caffeine.xyz;selectionhalos on;select *;labels on;background labels yellow;set labeloffset 15 5;set labelfront;labels off;select none
select *;labels off;select C13;labels on
select *;labels off;select C*;labels on
select *;labels off;select C?;labels on
load 1crn.pdb;selectionhalos on;select none
select AL*
select [AS*]
load caffeine.xyz
selectionhalos on;select none
select C3
draw line1 (C3) (C6)
draw plane1 plane perp (C3) (C6)
draw plane2 250 plane (N2) (N4) (N8); color $plane2 translucent red
frame 0
load 1JGQ.pdb;restrict none;select *;cartoons on
moveto 1.0 { 126 -986 109 76.4} 3048.5 {-9.250999 93.968506 300.17548}  133.8;
moveto 1.0 { 126 -986 109 76.4} 30480 {-9.250999 93.968506 300.17548}  133.8;
moveto 1.0 { 126 -986 109 76.4} 10000 {-9.250999 93.968506 300.17548}  133.8;
set echo myecho {1/1 1/1 1/1};echo (1 1 1)
set echo myecho (atomno=10) or (atomno=8);echo x
load 1mbo.cif;restrict not protein and not solvent;select protein;cartoon on
select (HEM);color yellow; zoomTo (selected) *3
moveto 1.0 { 497 381 780 146.4} 700.0 {15.948377 28.639738 0.4097555}  35.7;
zoomTo /2
set picking center
set windowCentered false  # try this, too
if (showBoundBox); set showBoundBox off;set showUnitCell;else;set showUnitCell off;set showBoundBox;endif;
load 1cdr.pdb # carbohydrate
load 114d.cif; # DNA
load quartz.cif {1 1 1} #symmetry
load 04369a.cif {1 1 1};display molecule=1 or molecule=3;color altloc #configuration
load 1crn.pdb;restrict none;select *;cartoons on;select 5-;color yellow;moveto 1.0 -119 993 -3 64.3;
select 10-;color red
select 15-;color white
load benzene.c3xml;mo 1 ;moveto 1.0 212 -928 -306 128.7;
load benzene.c3xml;isosurface molecular color absolute -0.01 0.01 map MEP;moveto 1.0 212 -928 -306 128.7;
load ethanol.c3xml;isosurface molecular map MEP translucent
load quartz.cif {444 666 1} # 27 cells
load quartz.cif {555 555 1} # just one cell
load quartz.cif {555 555 0} # just one cell; # without normalizing
load 1mbo.cif;display HEM;center (displayed);moveto 1.0 -772 -621 -135 158.1 309;select none;set labelpointer on
display within(group, within(3.0, hem));select displayed and *.ca;label %n %r;color labels yellow
select within(group, within(4.0, hem)) and not displayed and *.ca;label %n %r;color labels red;display within(group, within(4.0, hem));
display within(group, within(3.0, hem));
load quartz.cif {444 676 1};display cell=555 or cell=565;polyhedra 4 collapsed yellow;center displayed;moveto 1.0 -200 863 -464 45.0 252;spin y 10
load 2ptn.cif;delay 2;slab 35;slab on;refresh;select not clickable;spacefill off;color translucent grey;slab off;delay 2;moveto 3.0 -976 76 204 77.4 100; # cool, eh?
load 2ptn.cif;slab 35;slab on;refresh;restrict clickable;slab off;center visible;moveto 1.0 -976 76 204 77.4 213;isosurface "2ptn-molecular_slice1.jvxl";moveto 3.0 -308 401 863 108.1 213;
load 2ptn.cif;isosurface plane {1 0 10} {0 1 10} {1 1 10} solvent
load 2ptn.cif;isosurface "2ptn-molecular_slice2.jvxl";moveto 1.0 -976 76 204 77.4 100;isosurface "2ptn-molecular_slice3.jvxl"
load nacl.cif {2 2 2};axes 0.2;boundbox on;moveto 1.0 -402 -582 -706 127;delay 1;restrict none;
select *;isosurface delete hkl {1 1 1} resolution 4 solvent 0;
select *;isosurface delete hkl {1/2 1/2 1/2} resolution 4 solvent 0;
select *;isosurface delete hkl {1 1 0} resolution 4 solvent 0;
select *;isosurface delete hkl {1 0 1} resolution 4 solvent 0;
select *;isosurface delete hkl {1 0 0} resolution 4 solvent 0;
load maleic.cif 7 {2 1 1};moveto 1.0 -995 89 43 71.8;selectionHalos on;select none;
select symop=1
select symop=2
select symop=3
select symop=1555
select symop=1655
select symop=2555
select symop=2655
select symop=3555
select symop=3655
select symop=4555
select symop=4655
select symop>1555
select symop!=2555
select not symop=2555
load 2ptn.cif;moveto 1.0 245 959 140 66.2;
isosurface sasurface
isosurface delete;slab 60;restrict none;select *;set echo top left;echo "standby...";refresh;isosurface solvent colorscheme "sets"; echo;delay 2;slab 60; slab on;
slab off;
zap;delay 2;set echo myecho 50% 50%;set echo myecho center;echo You sure couldn't|do this|before in Jmol,|could you?;delay 2;draw plane1 {-5 -5 -5} {-5 0 -2} {0 -4 -1};delay 2;rotate on
console on # now add your data and press Load
console on;show history
set history 10 # set the history to only 10 lines, not the default 100
history off; # turn history recording off, perhaps at the beginning of a script file
history on; # turn history recording back on
load caffeine.xyz;selectionHalos
select _C
save selection X
save orientation X
load caffeine.xyz;restore orientation X 1;restore selection X;selectionHalos
load caffeine.xyz;select _N
selectionHalos on
color selectionHalos red
color halos blue
select *
color selectionHalos yellow
color halos none
color selectionHalos none
load CH3F.smol;isosurface delete resolution 6 mep
load C6H6.smol;isosurface delete resolution 6 mep
load CH3F.smol;isosurface delete resolution 6 solvent map mep
load C6H6.smol;isosurface delete solvent map mep
load C6H6.smol;isosurface delete resolution 3 solvent map mep
load C6H6.smol;isosurface delete resolution 6 solvent map mep
console on;show isosurface
load C6H6-mep.jvxl;isosurface ""
console on;getProperty fileContents
console on;show orientation
load caffeine.xyz
color _C RasMol
color _C Jmol
set echo top left;echo testing 1
set echo echo1 50 50;echo test 2
set echo all;font echo 30;color echo green;background echo white
load caffeine.xyz;set labelfront;select none; # the way to select NO labels
font label 20 serif bold
color label yellow
background label blue
set labeloffset 30 30
select atomno=3;label "%0.2x %0.2y %0.2z"
select atomno=5;label "this is atom 5"
set echo none
font echo 15 sansserif italic;color echo white;background echo blue
set echo echo1 40 40;set echo echo1 center;echo this is|a test of echo defaults
set echo echo2 100 100;echo another|label |here
load caffeine.xyz;polyhedra 4 bonds translucent red
load 1AL4.pdb; restrict none; conformation 1; cartoons 0.5;color cartoons group;
select *;connect; calculate structure;restrict none; conformation 1;cartoons 0.5; color cartoons yellow;
restrict none;conformation 2;cartoons 0.5;wireframe;select not protein;color yellow
restrict none;conformation 1;cartoons 0.5;wireframe;select not protein;color yellow
load caffeineDT.xyz;select none;set display selected;
select _D;label %e %i
select _C;color yellow
load caffeineDT.xyz;select none;set display selected;
select deuterium;label %e %i
select tritium
select substructure("[C][C][N][C][2H]")
select substructure("[3H][C][2H]")
select substructure("[C][C][N][C][H]")
select substructure("[N][C][1H]")
select hydrogen; color green
select deuterium; color cpk
color deuterium yellow
load caffeineDT.xyz;
load 1cdr.pdb;select carbohydrate;color group; select not carbohydrate; spacefill off; wireframe off;set cartoonRockets;cartoons on;
frame next
frame previous
set forceAutobond false;load 1AL4.pdb;restrict none;select not *%B;wireframe on;spacefill 0.1;cartoons 0.5;color cartoons group
save orientation;set forceAutobond true;load 1AL4.pdb;restore orientation;restrict none;select * and not *%B;wireframe on;spacefill 0.1;cartoons 0.5;color cartoons group
load caffeine.xyz;save orientation 0;save bonds originalBonds
moveto 1.0 -867 -310 -391 108.3;save orientation view1
moveto 1.0 -5 259 966 170.4 40 28 -35;save orientation view2
restore orientation 0
restore orientation view1 2.0
restore orientation view2 2.0
restore orientation 0 2.0
connect (carbon) (hydrogen) delete;save bonds noCH
restore bonds originalBonds
wireframe 0.1;save bonds lineBonds
restore bonds originalBonds
restore bonds lineBonds
load caffeine.xyz;set pickingStyle MEASURE ON;set echo top left
set picking MEASURE DISTANCE;echo now click on any two atoms 
set picking MEASURE ANGLE;echo now click on any three atoms
set picking MEASURE TORSION;echo now click on any four atoms
set pickingStyle MEASURE OFF
console on; show measurements
load 1mbo.cif; set echo top left;echo lots of water molecules here
isosurface delete ignore(none) sasurface; echo no good -- includes the water molecules
isosurface delete select(not solvent) ignore(none) sasurface; echo still a problem
isosurface delete sasurface;echo much better
isosurface delete select(1-10) ignore(none) sasurface;echo a fragment with the same problem
isosurface delete select(1-10) sasurface;echo a better fragment
load cyclohexane_movie.xyz; set backgroundModel 1;moveto 2.0 774 -616 146 112.3;animation on;
set backgroundModel 0
load 1crn.pdb
color surfacedistance # sort of like "color temperature"
select surfacedistance=0;color white # surface atoms
select within(group,surfacedistance=0);color white # surface residues
select not within(group, surfacedistance=0);color red   # interior groups
load 1crn.pdb
calculate surface +2.0;select surfacedistance=0;color yellow # custom solvent-accessible surface.
load caffeine.xyz
select nitrogen
color halos red
halos 20% # default is 20% of Van der Waals radius
halos 0.5
select oxygen
color halos blue
select *;halos on # resets to the default size
halos off
select atomno<10
selectionHalos ON
color selectionHalos yellow # only affect the uncolored ones
color selectionHalos none # back to atom-based colors
select nitrogen;color halos violet;select * # overriding
color halos none # back to the ORIGINAL atom colors
color selectionHalos gold # the original settings
selectionHalos OFF
load 1crn.pdb
color halos group; halos on
color halos amino;
halos off
background white;stereo red cyan
stereo red
stereo redgreen
stereo red green
stereo red lime
stereo [xFF0000]
stereo [xFF0000] [xFFFF00]
background black;stereo off
load "quartz.cif" {1 1 1};select silicon;labels "%0.2X %0.2Y %0.2Z|%U";set labelalignment CENTER;set labeloffset 0 35
set echo myecho 30% 10%;echo this is quartz
set echo myecho 0% 0%
set echo myecho 100% 0%
set echo myecho 100% 100%
set echo myecho 0% 100%
set echo myecho 50% 100%; set echo myecho CENTER
set echo myecho 200% 50%
echo "this|is quartz"
set echo myecho 0 0;echo quartz
set echo myecho 240 100%;echo quartz
echo a|quartz|crystal;
set echo myecho right
set echo myecho center
set echo myecho left
color echo yellow
set echo myecho2 50 50;echo from AMS
color echo white
font echo 18 serif italic
set echo myecho2 250 250
set echo myecho off
set echo myecho2 off
set echo top center
echo top|center
set echo top 200 0
help
help echo
load "team0104a.ccdc.cif" {1 1 1};moveto 0  -689 -707 -161 145.1 60;
select symop = 1;color white
translateSelected {0 -1/1 0}
translateSelected {0 1/1 0}
load "caffeine.xyz" {1 1 2} spacegroup "P 4" unitcell {10 10 10 90 90 90}
load "1crn.pdb"
load "1crn.pdb" {1 1 1}
load "1crn.pdb" {1 2 1};select symop=1;color red
load "1crn.pdb" {1 2 1} spacegroup "P 21:a"
load "1crn.pdb" {1 2 1} spacegroup "P 21:b" # the real one ?
load "1crn.pdb" {1 2 1} spacegroup "P 21:c"
load "quartz.cif" {1 1 2};moveto 0.0 -999 38 -2 73.7;
load "quartz.cif" {1 1 2} unitcell {6.00 6.00 6.00 90 90 120};moveto 0.0 -999 38 -2 73.7;
load "quartz.cif" {1 1 2} spacegroup "P 32 2''" unitcell {6.00 6.00 6.00 90 90 120};moveto 0.0 -999 38 -2 73.7;
load "quartz.cif" {1 1 2} spacegroup "P 32 2'' (0 0 4)" unitcell {6.00 6.00 6.00 90 90 120};moveto 0.0 -999 38 -2 73.7;
load 1crn.pdb;spacefill on;select *.CA;labels "%r";color labels group;
set labelGroup
set labelFront
set labelAtom;
background red;data "model example"|2|testing|C 1 1 1|O 2 2 2|end "model example";show data
load "quartz.cif" {1 1 1}
set display selected
select symop=1
select symop<3
select not symmetry
select specialposition
set display normal;select *;label "%o"
show symmetry
load "team0104a.ccdc.cif" {1 1 1}
show spacegroup
show spacegroup "Pmmn"
show spacegroup "P 32 2'' (0 0 4)"
load "team0104a.ccdc.cif" {1 1 1} spacegroup "ignoreOperators"
load "team0104a.ccdc.cif" {1 1 1} spacegroup "Pmmm";rotate y 90; show spacegroup
load "team0104a.ccdc.cif" {1 1 1} spacegroup "P21/m";rotate y 90; show spacegroup
load "team0104a.ccdc.cif" {1 1 1} spacegroup "P21/c";rotate y 90; show spacegroup;centerAt absolute {1/2 1/2 1/2};set scale3d 6.0;
load "team0104a.ccdc.cif" {1 1 1} spacegroup "-x,y+1/2,-z+1/2";rotate y 90;;centerAt absolute {1/2 1/2 1/2};set scale3d 6.0;
load "team0104a.ccdc.cif" {1 1 1} spacegroup "-x,-y,-z";rotate y 90;centerAt absolute {1/2 1/2 1/2};set scale3d 6.0;
load "team0104a.ccdc.cif" {1 1 1} spacegroup "-x+1/2,y,z+1/2";rotate y 90;centerAt absolute {1/2 1/2 1/2};set scale3d 6.0;
load caffeine.xyz;set dotSurface ON; set dotsSelectedOnly FALSE; dots +1.2
select oxygen;dots off
select *;dots off;
select oxygen;set dotSurface OFF;dots 1.0
dots off; select hydrogen;set dotSurface ON; set dotsSelectedOnly;dots 150%
load 1crn.pdb;restrict none;select *;set cartoonRockets;cartoons ON;
rockets on;trace off;cartoons off;
rockets off;trace off;cartoons on;
rockets off;trace on;cartoons off;
load 1qys.pdb;restrict none;select *;cartoons on;
hbonds calculate
set hovercallback "alert" # Now hover over an atom.
set hovercallback "none"; set messageCallback "alert"
set pickcallback "alert"; set messagecallback "none" # Now click on an atom.
set pickcallback "alert"; set messagecallback "none"; set picking distance # Now click on pairs of atoms.
set pickcallback "none"; set messagecallback "alert"; set picking distance # Now click on pairs of atoms.
set pickcallback "none"; set messagecallback "showmsg" # the default function for this page
load 1bkx.pdb;restrict none;select *;cartoons on;color group; set picking center;
set cartoonRockets on
set cartoonRockets off
rockets off;cartoons on;set picking center
rockets on;cartoons off;set picking center
load "quartz.cif" {3 3 3}; restrict cell=666;unitcell 666;zoom 300
select within(site,atomno=1) # 105 atoms selected.
select within(site,atomno=1 and visible) # nothing selected, because atomno=1 is not visible
select within(site,atomno=1) and visible;color green
select site=2 and visible;color yellow
frame next
frame previous
load "maleic.cif" {2 1 1};unitcell 655;center visible;zoom 400;select none;set display selected
select none;set picking ELEMENT # now start picking atoms
select none;set picking SITE # now start picking atoms
select none;set picking ON # normal picking
set display normal # normal display
load caffeine.xyz;color red;message This script is running;delay 5;color green;message this script is done;
load Water!Liquid.xodydata;connect 2.5 (oxygen) (hydrogen) hbond create;
load ZnSO4!Solution.odydata;select water;spacefill off;wireframe 0.06;color white;
load caffeine.xyz
moveto 3 1 0 0 30 
moveto 3 0 1 0 50
moveto 3 0 0 1 80
moveto 3 1 0 0 30 
moveto 3 0 1 0 50
moveto 3 0 0 1 80
load 1p84.cif;select not solvent;color yellow;spacefill +1.2;select solvent;spacefill 1.2;color red;spin y -10
load caffeine.xyz
spacefill 100%
spacefill +1.2
spacefill 1.2
spacefill 25%
spacefill off
load caffeine.xyz
dots 100%
dots +1.2
dots 1.2
dots 25%
dots off
load 1crn.pdb;geosurface 100%
geosurface +1.2
geosurface off
set display selected; load 1crn.pdb;color white;select within("CIII",*.ca);
set display normal;load 114d.cif;spacefill off;color white;select within("TTAG",*);cartoon on; wireframe off;color red;select selected and *.P;set labelFront;label %n;color labels yellow;moveto 1.0 -301 744 597 142.2;
load "water-G03W.out";frame 2;center visible;moveto 1.0 -571 -817 -75 120.5;set axesmolecular;axes on
mo 4
mo cutoff 0.02
mo cutoff 0.08
mo color yellow purple
mo color red blue
mo resolution 3
mo resolution 6
mo resolution 10
mo color red blue
mo translucent
mo next
mo plane "xy"
mo plane "xz"
mo plane "yz"
mo plane {1 1 1 0}
mo noplane
mo prev
load methanol.spartan;getProperty "auxiliaryinfo"
frame 1;mo cutoff 0.008 ; mo translucent
mo 12
mo next
mo prev
frame 2;vibration scale 0.1; vibration on
frame next
frame prev
load ethene.spartan
load "acetic%20acid.spartan"
load cscl.mol2
load zinc.mol2 # several models
model next
set axesMolecular; axes on
set axesUnitcell; axes on
set axesWindow; axes on
axes 5;set axes scale 1.5;
axes dotted;set axes scale 1.0;
axes off
boundbox on
boundbox off
unitcell on
unitcell off
frank on
frank off
load caffeine.xyz
measure all 1.0 1.3 (carbon) (hydrogen)
color measures green; # same as before
color measures red;measure all 1.0 1.3 (carbon) (oxygen) # only new, since others are already colored
color measures blue;measure all 1.0 1.4 (carbon) (nitrogen) # again, only new
color measures none; # resets all measure colors
color measures yellow; # sets all measure colors (because now all are color "none")
measures off # clears all measurements
load caffeine.xyz
load caffeine.xyz
load xxxx.pdb;
restrict none;select *; cartoon;
set rangeSelected false; #standard default
select protein;cartoon;color temperature
restrict none;select *;cartoon; color grey;
set rangeSelected true;
select protein and *:A;cartoon;color temperature
load 5hvp.cif;restrict *%1,*%2;color altloc;label %A  # alternate Location "%A"
load "quartz.cif" {1 1 1};label %.2X %.2Y %.2Z # fractional coordinates "%X" "%Y" "%Z"
load "agFUPMOS.cif" {1 1 1};color molecule;label %N # molecule number "%N"
load "agFUPMOS.cif" {1 1 1};color molecule;select fluorine;label %S # crystallographic site "%S"
load 1JGQ.pdb;color insertion;restrict none;select *;cartoon on