Path: blob/master/build/pkgs/jmol/patches/appletweb/SageMenu.mnu
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# Jmol.mnu Jmol version 11.3.15_dev 2007-08-28 7:23 AM 9/3/2007 Bob Hanson [email protected] # # 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