# HG changeset patch # User Jonathan H. Gutow +JmolHelp

Brief Help for the Jmol 3-D viewer

Reorient View
To reorient the view place cursor over the image, hold down the mouse button and drag.
Zoom View
To +zoom place the cursor over the image hold down the shift key and the +mouse button while dragging down to zoom in or up to zoom out.
Adding annotation
Annotation +may be added using the Jmol scripting language.  To do this +right-click (control-click) in the applet window to get the applet +pop-up menu.  In the advanced submenu select "Console".  You +can type Jmol script commands into the console.  See the jmol scripting documentation, the jmol web site and the jmol wiki for more information.
By Jonathan Gutow
November 2009
\ No newline at end of file diff -r d12daf8c85a8 -r b0a0157ab2ad sagenb/data/jmol/appletweb/SageMenu.mnu --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sagenb/data/jmol/appletweb/SageMenu.mnu Wed Mar 16 03:40:25 2011 -0700 @@ -0,0 +1,591 @@ +# 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 = viewSageMenu renderSageMenu colorSageMenu - zoomMenu spinMenu - advancedMenu - aboutComputedMenu + +viewSageMenu | View = standardview xyplane xzplane yzplane + +renderSageMenu | Style = perspectiveDepthCheckbox showBoundBoxCheckbox showAxesCheckbox stereoMenu - [set_axes]SageMenu [set_boundbox]SageMenu + +stereoMenu | Stereographic = stereoNone stereoRedCyan stereoRedBlue stereoRedGreen stereoCrossEyed stereoWallEyed + +colorSageMenu | Color = [color_background]Menu [color_axes]Menu [color_boundbox]Menu + +[color_background]Menu | Background = @COLOR + +[color_axes]Menu | Axes = @AXESCOLOR + +[color_boundbox]Menu | Boundbox = @AXESCOLOR + +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 + +[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 + +[set_axes]SageMenu | Axes = off#axes dotted - byPixelMenu byCoordinateMenu +[set_boundbox]SageMenu | Boundbox = off#axes dotted - byPixelMenu byCoordinateMenu + +byPixelMenu | Pixel Width = 1p 3p 5p 10p +byCoordinateMenu | Width = 10d 20d 50d 100d +aboutComputedMenu | About Jmol = APPLETjmolUrl APPLETmouseManualUrl APPLETtranslationUrl + + +### ORIGINAL MENUS +advancedMenu | Advanced = modelSetMenu FRAMESbyModelComputedMenu configurationComputedMenu - selectMenu viewMenu renderMenu colorMenu - surfaceMenu SYMMETRYUNITCELLmenu - zoomMenu spinMenu VIBRATIONMenu FRAMESanimateMenu - measureMenu pickingMenu - JVM12showConsole JVM12showMenu - languageComputedMenu aboutComputedMenu + +viewMenu | View = front left right top bottom back + +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 +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 +[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_UNITCELL]Menu | Unitcell = @AXESCOLOR + +VIBRATIONMenu | Vibration = vibrationOff vibrationOn VIBRATIONvectorMenu + +SYMMETRYUNITCELLmenu | Symmetry = UNITCELLone UNITCELLnine UNITCELLnineRestricted UNITCELLninePoly +[set_UNITCEL]menu | Unitcell = off#axes dotted - byPixelMenu byAngstromMenu +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 +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 + +labelMenu | Labels = labelNone - labelSymbol labelName labelNumber - labelPositionMenu +[color_isosurface]Menu | Surface = @COLOR - opaque translucent + +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 +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 +FRAMESanimateMenu | Animation = animModeMenu - play pause resume stop - nextframe prevframe rewind - playrev restart - FRAMESanimFpsMenu +animModeMenu | Animation Mode = onceThrough palindrome loop + +FRAMESanimFpsMenu | Set FPS = animfps5 animfps10 animfps20 animfps30 animfps50 +JVM12showMenu | Show = showHistory showFile showFileHeader - showOrient showMeasure - showSpacegroup showState SYMMETRYshowSymmetry UNITCELLshow - showIsosurface showMo - extractMOL +surfaceMenu | Surfaces = surfDots surfVDW surfSolventAccessible14 surfSolvent14 surfMolecular CHARGEsurfMEP surfMoComputedMenu - surfOpaque surfTranslucent surfOff +[set_axes]Menu | Axes = off#axes dotted - byPixelMenu byAngstromMenu +[set_boundbox]Menu | Boundbox = off#axes dotted - byPixelMenu byAngstromMenu +byAngstromMenu | Width = 10a 20a 25a 50a 100a + + + + +# 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) + +xzplane | XZ plane = if (showBoundBox);if (showAxes);moveto 2.0 bottom;else;axes on;moveto 2.0 bottom;delay 1;axes off;endif;else;boundbox on;if (showAxes);moveto 2.0 bottom;else;axes on;moveto 2.0 bottom;delay 1;axes off;endif;boundbox off;endif; + +xyplane | XY plane = if (showBoundBox);if (showAxes);moveto 2.0 front;else;axes on;moveto 2.0 front;delay 1;axes off;endif;else;boundbox on;if (showAxes);moveto 2.0 front;else;axes on;moveto 2.0 front;axes off;delay 1;endif;boundbox off;endif; + +yzplane | YZ plane = if (showBoundBox);if (showAxes);moveto 1.0 { -1 -1 -1} 120;else;axes on;moveto 1.0 { -1 -1 -1} 120;axes off;delay 1;endif;else;boundbox on;if (showAxes);moveto 1.0 { -1 -1 -1} 120;else;axes on;moveto 1.0 { -1 -1 -1} 120;delay 1;axes off;endif;boundbox off;endif; + +standardview | Positive octant = if (showBoundBox);if (showAxes);moveto 1.0 { -210 -550 -800 145};else;axes on;moveto 1.0 { -210 -550 -800 145};delay 1;axes off;endif;else;boundbox on;if (showAxes);moveto 1.0 { -210 -550 -800 145};else;axes on;moveto 1.0 { -210 -550 -800 145};delay 1;axes off;endif;boundbox off;endif; + +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 + +#For the Sage units above +10d | 1 = 0.1 +20d | 2 = 0.20 +50d | 5 = 0.50 +100d | 10 = 1.0 + + +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