Jmol.mnu
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# Jmol.mnu Jmol version 11.3.15_dev 2007-08-28 7:23 AM 9/3/2007 Bob Hanson hansonr@stolaf.edu
#
# This file is in three parts.
#
# Part I contains the menu structure.
# Part II contains all the Jmol scripts that correspond to a menu click.
# Part III contains additional words that will be translated.
#
# This file is not normally read by Jmol.
#
# Jmol APPLETS: If you want it to be read, then include
#
# jmolSetCallback("menuFile", "Jmol.mnu") // or whatever filename you choose
#
# just after jmolInitialize() and before the jmolApplet() call.
#
# Jmol APPLICATION: use the -m filename startup flag.
#
#
# Part I: Menu Structure
# ----------------------
#
# Each definition consists of
#
# key | label = [menu list]
#
# for example:
#
# zoomMenu | Zoom = zoom50 zoom100 zoom150 zoom200 zoom400 zoom800 - zoomIn zoomOut
#
# The words used for the key are arbitrary designations, but they must end with the
# letters "Menu". They must not contain spaces. They are case sensitive.
#
# The label is what the user sees. Or, rather, the translation of that label
# (see below) is what the user sees.
#
# The menu list is a space-separated list of submenu keys or item keys (see Part II)
# or, if not listed in Part II, a single-word Jmol script word, such as "cpk".
#
# A hyphen indicates the location for a horizonatal menu separator
#
# menu items starting with @ are predefined sets. For example:
#
# [color_atoms]Menu | Atoms = schemeMenu - @COLOR - opaque translucent
#
# Here @COLOR is a predefined set:
#
# @COLOR = black white red orange yellow green cyan blue indigo violet
#
# You can create your own predefined terms and use them anywhere you want.
# Predefined terms may contain more predefined terms.
#
# DON'T DO THIS: @COLOR = something something @COLOR
#
# "Checkbox" at the end of a menu item creates a check box. These objects operate
# by setting Jmol true/false parameters. The name of the checkbox must correspond
# to the name of a valid Jmol parameter.
#
# atomMenu | Atoms = showHydrogensCheckbox - atomNone - atom15 atom20 atom25 atom50 atom75 atom100
#
#
# A note about language translation
# ---------------------------------
#
# The way translation works is that a code preprocessor identifies text that
# in the CODE is written as GT._("...."). This is called *internationalization*,
# and it occurs when the Jmol distribution is built.
#
# Then, when that method is executed in the running Jmol program, the table for
# the selected language is looked up. If that phrase has been translated into
# that particular language by a human volunteer, then the translated phrase is
# returned. This is called *localization*.
#
# All menu labels will be sent through the GT._() method. If you change a menu label to
# a phrase that has not been internationalized, then it won't be localized. It will appear
# in the language in which you have written it here. Just be aware of that.
#
#
# Computed Menus
# --------------
#
# Menu keys containing the term "Computed" are modified after the fact.
# You should be able to omit them, but this needs additional testing (by YOU!)
#
#
# Special identifiers in this section
# -----------------------------------
#
# Certain all-capitalized words anywhere in a key are significant. They relate to
# specific Jmol data options. If a model set does not involve data that are relevant to this
# option, then this menu item will be present but disabled (greyed out). Note that if a menu
# key is greyed out, then submenu items of that key are not visible, so those item keys do
# not need the identifier as well. This is the case with many PDB identifiers -- if you
# move them to another menu, make sure that menu has "PDB" in it or add PDB somewhere in the name.
#
# The following options exist as of Jmol 11.3.15:
#
# CHARGE data set includes partial charge information
# FRAMES data set includes multiple frames
# PDB data set is PDB file format information (HETERO, etc.)
# SYMMETRY data set includes symmetry information
# UNITCELL data set contains a unit cell
# VIBRATION data set includes vibration data
#
# A key may contain multiple option identifiers.
#
# In addition, APPLET indicates that this item should
# show up only in the Jmol applet menu, not the Jmol application menu
#
# If a key includes a phrase in square brackets, as in
#
# [color_atoms]Menu | Atoms = schemeMenu - @COLOR - opaque translucent
#
# then for all menu and submenu items under this menu
# the script given in Part II is PREPENDED with that phrase, with
# underscore replaced with space. For example,
#
# Part I -- Menu Structure
# ------------------------
#
@COLOR = black white red orange yellow green cyan blue indigo violet
@AXESCOLOR = gray salmon maroon olive slateblue gold orchid
popupMenu = modelSetMenu FRAMESbyModelComputedMenu configurationComputedMenu - selectMenu viewMenu renderMenu colorMenu - surfaceMenu SYMMETRYUNITCELLmenu - zoomMenu spinMenu VIBRATIONMenu FRAMESanimateMenu - measureMenu pickingMenu - JVM12showConsole JVM12showMenu - languageComputedMenu aboutComputedMenu
selectMenu | Select = hideNotSelectedCheckbox showSelectionsCheckbox - selectAll selectNone invertSelection - elementsComputedMenu SYMMETRYComputedMenu - PDBproteinMenu PDBnucleicMenu PDBheteroMenu PDBcarboMenu PDBnoneOfTheAbove
PDBproteinMenu | Protein = PDBaaResiduesComputedMenu - allProtein proteinBackbone proteinSideChains - polar nonpolar - positiveCharge negativeCharge noCharge
PDBcarboMenu | Carbohydrate = PDBcarboResiduesComputedMenu - allCarbo
PDBnucleicMenu | Nucleic = PDBnucleicResiduesComputedMenu - allNucleic nucleicBackbone nucleicBases - DNA RNA - atPairs auPairs gcPairs
PDBheteroMenu | Hetero = PDBheteroComputedMenu - allHetero Solvent Water - Ligand exceptWater nonWaterSolvent
viewMenu | View = front left right top bottom back
renderMenu | Style = perspectiveDepthCheckbox showBoundBoxCheckbox showUNITCELLCheckbox showAxesCheckbox stereoMenu - renderSchemeMenu - atomMenu labelMenu bondMenu hbondMenu ssbondMenu - PDBstructureMenu [set_axes]Menu [set_boundbox]Menu [set_UNITCEL]menu
renderSchemeMenu | Scheme = renderCpkSpacefill renderBallAndStick renderSticks renderWireframe PDBrenderCartoonsOnly PDBrenderTraceOnly
atomMenu | Atoms = showHydrogensCheckbox - atomNone - atom15 atom20 atom25 atom50 atom75 atom100
bondMenu | Bonds = bondNone bondWireframe - bond100 bond150 bond200 bond250 bond300
hbondMenu | Hydrogen Bonds = PDBhbondCalc hbondNone hbondWireframe - PDBhbondSidechain PDBhbondBackbone - hbond100 hbond150 hbond200 hbond250 hbond300
ssbondMenu | Disulfide Bonds = ssbondNone ssbondWireframe - PDBssbondSidechain PDBssbondBackbone - ssbond100 ssbond150 ssbond200 ssbond250 ssbond300
PDBstructureMenu | Structures = structureNone - backbone cartoon cartoonRockets ribbons rockets strands trace
VIBRATIONvectorMenu | Vectors = vectorOff vectorOn vector3 vector005 vector01 - vectorScale02 vectorScale05 vectorScale1 vectorScale2 vectorScale5
stereoMenu | Stereographic = stereoNone stereoRedCyan stereoRedBlue stereoRedGreen stereoCrossEyed stereoWallEyed
labelMenu | Labels = labelNone - labelSymbol labelName labelNumber - labelPositionMenu
labelPositionMenu | Position Label on Atom = labelCentered labelUpperRight labelLowerRight labelUpperLeft labelLowerLeft
colorMenu | Color = colorrasmolCheckbox - [color_atoms]Menu [color_bonds]Menu [color_hbonds]Menu [color_ssbonds]Menu colorPDBStructuresMenu [color_isosurface]Menu - [color_labels]Menu [color_vectors]Menu - [color_axes]Menu [color_boundbox]Menu [color_UNITCELL]Menu [color_background]Menu
[color_atoms]Menu | Atoms = schemeMenu - @COLOR - opaque translucent
[color_bonds]Menu | Bonds = none - @COLOR - opaque translucent
[color_hbonds]Menu | Hydrogen Bonds = none - @COLOR - opaque translucent
[color_ssbonds]Menu | Disulfide Bonds = none - @COLOR - opaque translucent
[color_labels]Menu | Labels = none - @COLOR - opaque translucent
[color_vectors]Menu | Vectors = none - @COLOR - opaque translucent
[color_backbone]Menu | Backbone = none - schemeMenu - @COLOR - opaque translucent
[color_cartoon]sMenu | Cartoon = none - schemeMenu - @COLOR - opaque translucent
[color_ribbon]sMenu | Ribbons = none - schemeMenu - @COLOR - opaque translucent
[color_rockets]Menu | Rockets = none - schemeMenu - @COLOR - opaque translucent
[color_strands]Menu | Strands = none - schemeMenu - @COLOR - opaque translucent
[color_trace]Menu | Trace = none - schemeMenu - @COLOR - opaque translucent
[color_background]Menu | Background = @COLOR
[color_isosurface]Menu | Surface = @COLOR - opaque translucent
[color_axes]Menu | Axes = @AXESCOLOR
[color_boundbox]Menu | Boundbox = @AXESCOLOR
[color_UNITCELL]Menu | Unitcell = @AXESCOLOR
colorPDBStructuresMenu | Structure = [color_backbone]Menu [color_cartoon]sMenu [color_ribbon]sMenu [color_rockets]Menu [color_strands]Menu [color_trace]Menu
schemeMenu | By Scheme = cpk altloc molecule formalcharge partialcharge#CHARGE - amino#PDB structure#PDB chain#PDB
zoomMenu | Zoom = zoom50 zoom100 zoom150 zoom200 zoom400 zoom800 - zoomIn zoomOut
spinMenu | Spin = spinOn spinOff - [set_spin_X]Menu [set_spin_Y]Menu [set_spin_Z]Menu - [set_spin_FPS]Menu
VIBRATIONMenu | Vibration = vibrationOff vibrationOn VIBRATIONvectorMenu
FRAMESanimateMenu | Animation = animModeMenu - play pause resume stop - nextframe prevframe rewind - playrev restart - FRAMESanimFpsMenu
FRAMESanimFpsMenu | Set FPS = animfps5 animfps10 animfps20 animfps30 animfps50
measureMenu | Measurement = showMeasurementsCheckbox - measureOff measureDistance measureAngle measureTorsion - measureDelete JVM12measureList - distanceNanometers distanceAngstroms distancePicometers
pickingMenu | Set picking = pickOff pickCenter pickIdent pickLabel pickAtom pickMolecule pickElement PDBpickChain PDBpickGroup SYMMETRYpickSite pickSpin
JVM12showMenu | Show = showHistory showFile showFileHeader - showOrient showMeasure - showSpacegroup showState SYMMETRYshowSymmetry UNITCELLshow - showIsosurface showMo - extractMOL
[set_spin_X]Menu | Set X Rate = s0 s5 s10 s20 s30 s40 s50
[set_spin_Y]Menu | Set Y Rate = s0 s5 s10 s20 s30 s40 s50
[set_spin_Z]Menu | Set Z Rate = s0 s5 s10 s20 s30 s40 s50
[set_spin_FPS]Menu | Set FPS = s0 s5 s10 s20 s30 s40 s50
animModeMenu | Animation Mode = onceThrough palindrome loop
surfaceMenu | Surfaces = surfDots surfVDW surfSolventAccessible14 surfSolvent14 surfMolecular CHARGEsurfMEP surfMoComputedMenu - surfOpaque surfTranslucent surfOff
SYMMETRYUNITCELLmenu | Symmetry = UNITCELLone UNITCELLnine UNITCELLnineRestricted UNITCELLninePoly
[set_axes]Menu | Axes = off#axes dotted - byPixelMenu byAngstromMenu
[set_boundbox]Menu | Boundbox = off#axes dotted - byPixelMenu byAngstromMenu
[set_UNITCEL]menu | Unitcell = off#axes dotted - byPixelMenu byAngstromMenu
byPixelMenu | Pixel Width = 1p 3p 5p 10p
byAngstromMenu | Angstrom Width = 10a 20a 25a 50a 100a
aboutComputedMenu | About Jmol = APPLETjmolUrl APPLETmouseManualUrl APPLETtranslationUrl
# Part II -- Key Definitions
# --------------------------
#
# This section contains the Jmol equivalents of all action items.
#
# Each definition consists of
#
# key | label = [Jmol script]
#
# or
#
# someCheckbox | label = [on script] | [off script]
#
# for example:
#
# stereoNone | None = stereo off
#
# showAxesCheckbox | Axes = set showAxes true | set showAxes false;set axesMolecular
#
# Each key should be referred to explicitly in at least one menu list in Part I.
#
# The label is what the user sees. Or, rather, the translation of that label
# (see above) is what the user sees.
#
# For checkboxes, the on and off scripts are not required if the action is simply to
# turn a Jmol parameter on or off.
#
#
# Special identifiers in this section
# -----------------------------------
#
#
# "SELECT" at the beginning of a definition wraps the definition with "select thisModel and ()";
#
# For example: invertSelection | Invert Selection = SELECT not selected
#
#
#
# "#" anywhere in a definition indicates that the script evaluation should be done in "silent"
# mode -- that is, without sending messages to the console or status line
# Note that checkboxes are always executed in silent mode.
colorrasmolCheckbox | RasMol Colors =
hideNotSelectedCheckbox | Display Selected Only = set hideNotSelected true | set hideNotSelected false; hide(none)
perspectiveDepthCheckbox | Perspective Depth =
showAxesCheckbox | Axes = set showAxes true | set showAxes false;set axesMolecular
showBoundBoxCheckbox | Bound Box =
showHydrogensCheckbox | Show Hydrogens =
showMeasurementsCheckbox | Show Measurements =
showSelectionsCheckbox | Selection Halos =
showUNITCELLCheckbox | Unit Cell =
selectAll | All = SELECT all
selectNone | None = SELECT none
invertSelection | Invert Selection = SELECT not selected
allProtein | All = SELECT protein
proteinBackbone | Backbone = SELECT protein and backbone
proteinSideChains | Side Chains = SELECT protein and not backbone
polar | Polar Residues = SELECT protein and polar
nonpolar | Nonpolar Residues = SELECT protein and not polar
positiveCharge | Basic Residues (+) = SELECT protein and basic
negativeCharge | Acidic Residues (-) = SELECT protein and acidic
noCharge | Uncharged Residues = SELECT protein and not (acidic,basic)
allCarbo | All = SELECT carbohydrate
allNucleic | All = SELECT nucleic
DNA | DNA = SELECT dna
RNA | RNA = SELECT rna
nucleicBackbone | Backbone = SELECT nucleic and backbone
nucleicBases | Bases = SELECT nucleic and not backbone
atPairs | AT pairs = SELECT a,t
gcPairs | GC pairs = SELECT g,c
auPairs | AU pairs = SELECT a,u
A = SELECT a
C = SELECT c
G = SELECT g
T = SELECT t
U = SELECT u
allHetero | All PDB "HETATM" = SELECT hetero
Solvent | All Solvent = SELECT solvent
Water | All Water = SELECT water
nonWaterSolvent | Nonaqueous Solvent (solvent and not water) = SELECT solvent and not water
exceptWater | Nonaqueous HETATM (hetero and not water) = SELECT hetero and not water
Ligand | Ligand (hetero and not solvent) = SELECT ligand
PDBnoneOfTheAbove | None of the above = SELECT not(hetero,protein,nucleic,carbohydrate)
front | Front = if not(showBoundBox);if not(showUnitcell);boundbox on;moveto 2.0 front;delay 1;boundbox off;else;moveto 2.0 front;delay 1;endif;endif;
left | Left = if not(showBoundBox);if not(showUnitcell);boundbox on;moveto 1.0 front;moveto 2.0 left;delay 1;boundbox off;else;moveto 1.0 front;moveto 2.0 left;delay 1;endif;endif;
right | Right = if not(showBoundBox);if not(showUnitcell);boundbox on;moveto 1.0 front;moveto 2.0 right;delay 1;boundbox off;else;moveto 1.0 front;moveto 2.0 right;delay 1;endif;endif;
top | Top = if not(showBoundBox);if not(showUnitcell);boundbox on;moveto 1.0 front;moveto 2.0 top;delay 1;boundbox off;else;moveto 1.0 front;moveto 2.0 top;delay 1;endif;endif;
bottom | Bottom = if not(showBoundBox);if not(showUnitcell);boundbox on;moveto 1.0 front;moveto 2.0 bottom;delay 1;boundbox off;else;moveto 1.0 front;moveto 2.0 bottom;delay 1;endif;endif;
back | Back = if not(showBoundBox);if not(showUnitcell);boundbox on;moveto 1.0 front;moveto 2.0 back;delay 1;boundbox off;else;moveto 1.0 front;moveto 2.0 back;delay 1;endif;endif;
renderCpkSpacefill | CPK Spacefill = restrict not selected;select not selected;spacefill 100%;color cpk
renderBallAndStick | Ball and Stick = restrict not selected;select not selected;spacefill 20%;wireframe 0.15;color cpk
renderSticks | Sticks = restrict not selected;select not selected;wireframe 0.3;color cpk
renderWireframe | Wireframe = restrict not selected;select not selected;wireframe on;color cpk
PDBrenderCartoonsOnly | Cartoon = restrict not selected;select not selected;cartoons on;color structure
PDBrenderTraceOnly | Trace = restrict not selected;select not selected;trace on;color structure
atomNone | Off = cpk off
atom15 | 15% van der Waals = cpk 15%
atom20 | 20% van der Waals = cpk 20%
atom25 | 25% van der Waals = cpk 25%
atom50 | 50% van der Waals = cpk 50%
atom75 | 75% van der Waals = cpk 75%
atom100 | 100% van der Waals = cpk on
bondNone | Off = wireframe off
bondWireframe | On = wireframe on
bond100 | 0.10 Å = wireframe .1
bond150 | 0.15 Å = wireframe .15
bond200 | 0.20 Å = wireframe .2
bond250 | 0.25 Å = wireframe .25
bond300 | 0.30 Å = wireframe .3
PDBhbondCalc | Calculate = hbonds calculate
hbondNone | Off = hbonds off
hbondWireframe | On = hbonds on
PDBhbondSidechain | Set H-Bonds Side Chain = set hbonds sidechain
PDBhbondBackbone | Set H-Bonds Backbone = set hbonds backbone
hbond100 | 0.10 Å = hbonds .1
hbond150 | 0.15 Å = hbonds .15
hbond200 | 0.20 Å = hbonds .2
hbond250 | 0.25 Å = hbonds .25
hbond300 | 0.30 Å = hbonds .3
ssbondNone | Off = ssbonds off
ssbondWireframe | On = ssbonds on
PDBssbondSidechain | Set SS-Bonds Side Chain = set ssbonds sidechain
PDBssbondBackbone | Set SS-Bonds Backbone = set ssbonds backbone
ssbond100 | 0.10 Å = ssbonds .1
ssbond150 | 0.15 Å = ssbonds .15
ssbond200 | 0.20 Å = ssbonds .2
ssbond250 | 0.25 Å = ssbonds .25
ssbond300 | 0.30 Å = ssbonds .3
structureNone | Off = backbone off;cartoons off;ribbons off;rockets off;strands off;trace off;
backbone | Backbone = restrict not selected;select not selected;backbone 0.3
cartoon | Cartoon = restrict not selected;select not selected;set cartoonRockets false;cartoons on
cartoonRockets | Cartoon Rockets = restrict not selected;select not selected;set cartoonRockets;cartoons on
ribbons | Ribbons = restrict not selected;select not selected;ribbons on
rockets | Rockets = restrict not selected;select not selected;rockets on
strands | Strands = restrict not selected;select not selected;strands on
trace | Trace = restrict not selected;select not selected;trace 0.3
vibrationOff | Off = vibration off
vibrationOn | On = vibration on
vectorOff | Off = vectors off
vectorOn | On = vectors on
vector3 | 3 pixels = vectors 3
vector005 | 0.05 Å = vectors 0.05
vector01 | 0.10 Å = vectors 0.1
vectorScale02 | Scale 0.2 = vector scale 0.2
vectorScale05 | Scale 0.5 = vector scale 0.5
vectorScale1 | Scale 1 = vector scale 1
vectorScale2 | Scale 2 = vector scale 2
vectorScale5 | Scale 5 = vector scale 5
stereoNone | None = stereo off
stereoRedCyan | Red+Cyan glasses = stereo redcyan 3
stereoRedBlue | Red+Blue glasses = stereo redblue 3
stereoRedGreen | Red+Green glasses = stereo redgreen 3
stereoCrossEyed | Cross-eyed viewing = stereo 5
stereoWallEyed | Wall-eyed viewing = stereo -5
labelNone | None = label off
labelSymbol | With Element Symbol = label %e
labelName | With Atom Name = label %a
labelNumber | With Atom Number = label %i
labelCentered | Centered = set labeloffset 0 0
labelUpperRight | Upper Right = set labeloffset 4 4
labelLowerRight | Lower Right = set labeloffset 4 -4
labelUpperLeft | Upper Left = set labeloffset -4 4
labelLowerLeft | Lower Left = set labeloffset -4 -4
zoom50 | 50% = zoom 50
zoom100 | 100% = zoom 100
zoom150 | 150% = zoom 150
zoom200 | 200% = zoom 200
zoom400 | 400% = zoom 400
zoom800 | 800% = zoom 800
zoomIn | Zoom In = move 0 0 0 40 0 0 0 0 1
zoomOut | Zoom Out = move 0 0 0 -40 0 0 0 0 1
spinOn | On = spin on
spinOff | Off = spin off
s0 | 0 = 0
s5 | 5 = 5
s10 | 10 = 10
s20 | 20 = 20
s30 | 30 = 30
s40 | 40 = 40
s50 | 50 = 50
onceThrough | Play Once = anim mode once#
palindrome | Palindrome = anim mode palindrome#
loop | Loop = anim mode loop#
play | Play = anim play#
pause | Pause = anim pause#
resume | Resume = anim resume#
stop | Stop = anim off#
nextframe | Next Frame = frame next#
prevframe | Previous Frame = frame prev#
playrev | Reverse = anim playrev#
rewind | Rewind = anim rewind#
restart | Restart = anim on#
animfps5 | 5 = anim fps 5#
animfps10 | 10 = anim fps 10#
animfps20 | 20 = anim fps 20#
animfps30 | 30 = anim fps 30#
animfps50 | 50 = anim fps 50#
measureOff | Double-Click begins and ends all measurements = set pickingstyle MEASURE OFF; set picking OFF
measureDistance | Click for distance measurement = set pickingstyle MEASURE; set picking MEASURE DISTANCE
measureAngle | Click for angle measurement = set pickingstyle MEASURE; set picking MEASURE ANGLE
measureTorsion | Click for torsion (dihedral) measurement = set pickingstyle MEASURE; set picking MEASURE TORSION
measureDelete | Delete measurements = measure delete
JVM12measureList | List measurements = console on;show measurements
distanceNanometers | Distance units nanometers = select *; set measure nanometers
distanceAngstroms | Distance units Angstroms = select *; set measure angstroms
distancePicometers | Distance units picometers = select *; set measure picometers
pickOff | Off = set picking off
pickCenter | Center = set picking center
pickIdent | Identity = set picking ident
pickLabel | Label = set picking label
pickAtom | Select atom = set picking atom
PDBpickChain | Select chain = set picking chain
pickElement | Select element = set picking element
PDBpickGroup | Select group = set picking group
pickMolecule | Select molecule = set picking molecule
SYMMETRYpickSite | Select site = set picking site
pickSpin | Spin = set picking spin
JVM12showConsole | Console = console
showFile | File Contents = console on;show file
showFileHeader | File Header = console on;getProperty FileHeader
showHistory | History = console on;show history
showIsosurface | Isosurface JVXL data = console on;show isosurface
showMeasure | Measure = console on;show measure
showMo | Molecular orbital JVXL data = console on;show mo
showModel | Model = console on;show model
showOrient | Orientation = console on;show orientation
showSpacegroup | Space group = console on;show spacegroup
showState | Current state = console on;show state
SYMMETRYshowSymmetry | Symmetry = console on;show symmetry
UNITCELLshow | Unit cell = console on;show unitcell
extractMOL | Extract MOL data = console on;getproperty extractModel "visible"
surfDots | Dot Surface = dots on
surfVDW | van der Waals Surface = isosurface delete resolution 0 solvent 0 translucent
surfMolecular | Molecular Surface = isosurface delete resolution 0 molecular translucent
surfSolvent14 | Solvent Surface (1.4-Angstrom probe) = isosurface delete resolution 0 solvent 1.4 translucent
surfSolventAccessible14 | Solvent-Accessible Surface (VDW + 1.4 Angstrom) = isosurface delete resolution 0 sasurface 1.4 translucent
CHARGEsurfMEP | Molecular Electrostatic Potential = isosurface delete resolution 0 molecular map MEP translucent
surfOpaque | Make Opaque = mo opaque;isosurface opaque
surfTranslucent | Make Translucent = mo translucent;isosurface translucent
surfOff | Off = mo delete;isosurface delete;select *;dots off
UNITCELLone | Reload {1 1 1} = save orientation;load "" {1 1 1} ;restore orientation;center
UNITCELLnine | Reload {444 666 1} = save orientation;load "" {444 666 1} ;restore orientation;center
UNITCELLnineRestricted | Reload {444 666 1};display 555 = save orientation;load "" {444 666 1} ;restore orientation; unitcell on; display cell=555;center visible;zoom 200
UNITCELLninePoly | Reload + Polyhedra = save orientation;load "" {444 666 1} ;restore orientation; unitcell on; display cell=555; polyhedra 4,6 (displayed);center (visible);zoom 200
1p | 1 px = on
3p | 3 px = 3
5p | 5 px = 5
10p | 10 px = 10
10a | 0.10 Å = 0.1
20a | 0.20 Å = 0.20
25a | 0.25 Å = 0.25
50a | 0.50 Å = 0.50
100a | 1.0 Å = 1.0
APPLETjmolUrl | http://www.jmol.org = show url "http://www.jmol.org"
APPLETmouseManualUrl | Mouse Manual = show url "http://wiki.jmol.org/index.php/Mouse_Manual"
APPLETtranslationUrl | Translations = show url "http://wiki.jmol.org/index.php/Internationalisation"
# Part III -- Word Translations
# -----------------------------
#
# This section contains a few additional words that are translated as menu labels.
# They are menu items that do not otherwise have Jmol script definitions listed in Part II.
#
# Each definition consists of
#
# key | label
#
#
modelSetMenu | No atoms loaded
configurationComputedMenu | Configurations
elementsComputedMenu | Element
FRAMESbyModelComputedMenu | Model/Frame
languageComputedMenu | Language
PDBaaResiduesComputedMenu | By Residue Name
PDBnucleicResiduesComputedMenu | By Residue Name
PDBcarboResiduesComputedMenu | By Residue Name
PDBheteroComputedMenu | By HETATM
surfMoComputedMenu | Molecular Orbitals
SYMMETRYComputedMenu | Symmetry
hiddenModelSetText | Model information
selectMenuText | Select ({0})
allModelsText | All {0} models
configurationMenuText | Configurations ({0})
modelSetCollectionText | Collection of {0} models
atomsText | atoms: {0}
bondsText | bonds: {0}
groupsText | groups: {0}
chainsText | chains: {0}
polymersText | polymers: {0}
modelMenuText | model {0}
viewMenuText | View {0}
mainMenuText | Main Menu
cpk | Element (CPK)
altloc | Alternative Location
molecule | Molecule
formalcharge | Formal Charge
partialcharge#CHARGE | Partial Charge
amino#PDB | Amino Acid
structure#PDB | Secondary Structure
chain#PDB | Chain
none | Inherit
black | Black
white | White
cyan | Cyan
red | Red
orange | Orange
yellow | Yellow
green | Green
blue | Blue
indigo | Indigo
violet | Violet
salmon | Salmon
olive | Olive
maroon | Maroon
gray | Gray
slateblue | Slate Blue
gold | Gold
orchid | Orchid
opaque | Make Opaque
translucent | Make Translucent
off#axes | Hide
dotted | Dotted
