diff --git a/jmol.mnu b/jmol.mnu index 2e1007a..3f6a619 100644 --- a/jmol.mnu +++ b/jmol.mnu @@ -1,146 +1,33 @@ -# Jmol.mnu Jmol version 11.7.21_dev 2009-01-10 -# -# 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, -# +# popupMenu.mnu Jmol version 14.3.3_2014.08.01 2014-08-01 07:38 # 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 SIGNEDloadMenu SIGNEDwriteMenu FRAMESbyModelComputedMenu configurationComputedMenu - selectMenuText viewMenu renderMenu colorMenu - surfaceMenu SYMMETRYUNITCELLMenu - zoomMenu spinMenu VIBRATIONMenu FRAMESanimateMenu - measureMenu pickingMenu - JVM12showConsole JVM12showMenu - languageComputedMenu aboutComputedMenu -selectMenuText | Select ({0}) = hideNotSelectedCheckbox showSelectionsCheckbox - selectAll selectNone invertSelection - elementsComputedMenu SYMMETRYComputedMenu - PDBproteinMenu PDBnucleicMenu PDBheteroMenu PDBcarboMenu PDBnoneOfTheAbove +popupMenu = fileMenu modelSetMenu FRAMESbyModelComputedMenu configurationComputedMenu - selectMenuText viewMenu renderMenu colorMenu - surfaceMenu FILEUNITMenu - sceneComputedMenu zoomMenu spinMenu VIBRATIONMenu spectraMenu FRAMESanimateMenu - measureMenu pickingMenu - showConsole JSConsole showMenu computationMenu - languageComputedMenu aboutMenu +fileMenu | File = loadMenu saveMenu exportMenu SIGNEDJAVAcaptureMenuSPECIAL +loadMenu | Load = SIGNEDloadFile SIGNEDloadUrl SIGNEDloadPdb SIGNEDloadScript - reload SIGNEDloadFileUnitCell +saveMenu | Save = writeFileTextVARIABLE writeState writeHistory SIGNEDwriteJmol SIGNEDwriteIsosurface +exportMenu | Export = SIGNEDNOGLwriteGif SIGNEDNOGLwriteJpg SIGNEDNOGLwritePng SIGNEDNOGLwritePngJmol SIGNEDNOGLwritePovray - SIGNEDNOGLwriteVrml SIGNEDNOGLwriteX3d +selectMenuText | Select ({0}) = hideNotSelectedCB showSelectionsCB - selectAll selectNone invertSelection - elementsComputedMenu SYMMETRYSelectComputedMenu - 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_UNITCELL]Menu +viewMenu | View = best front left right top bottom back - axisX axisY axisZ - axisA axisB axisC +renderMenu | Style = perspectiveDepthCB showBoundBoxCB showUNITCELLCB showAxesCB stereoMenu - renderSchemeMenu - atomMenu labelMenu bondMenu hbondMenu ssbondMenu - PDBstructureMenu [set_axes]Menu [set_boundbox]Menu [set_UNITCELL]Menu renderSchemeMenu | Scheme = renderCpkSpacefill renderBallAndStick renderSticks renderWireframe PDBrenderCartoonsOnly PDBrenderTraceOnly -atomMenu | Atoms = showHydrogensCheckbox - atomNone - atom15 atom20 atom25 atom50 atom75 atom100 +atomMenu | Atoms = showHydrogensCB - 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 +hbondMenu | Hydrogen Bonds = hbondCalc 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 +VIBRATIONvectorMenu | Vectors = vectorOff vectorOn vibScale20 vibScale05 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 +colorMenu | Color = colorrasmolCB - [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 @@ -159,84 +46,51 @@ colorMenu | Color = colorrasmolCheckbox - [color_atoms]Menu [color_bonds]Menu [c [color_boundbox]Menu | Boundbox = @AXESCOLOR [color_UNITCELL]Menu | Unit cell = @AXESCOLOR colorPDBStructuresMenu | Structures = [color_backbone]Menu [color_cartoon]sMenu [color_ribbon]sMenu [color_rockets]Menu [color_strands]Menu [color_trace]Menu -schemeMenu | By Scheme = cpk - formalcharge partialcharge#CHARGE - altloc#PDB amino#PDB chain#PDB group#PDB molecule monomer#PDB shapely#PDB structure#PDB relativeTemperature#BFACTORS fixedTemperature#BFACTORS +schemeMenu | By Scheme = cpk - formalcharge partialcharge#CHARGE - altloc#PDB amino#PDB chain#PDB group#PDB molecule monomer#PDB shapely#PDB structure#PDB relativeTemperature#BFACTORS fixedTemperature#BFACTORS property_vxyz#VIBRATION 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 +VIBRATIONMenu | Vibration = vibrationOff vibrationOn vibration20 vibration05 VIBRATIONvectorMenu +spectraMenu | Spectra = hnmrMenu cnmrMenu FRAMESanimateMenu | Animation = animModeMenu - play pause resume stop - nextframe prevframe rewind - playrev restart - FRAMESanimFpsMenu FRAMESanimFpsMenu | Set FPS = animfps5 animfps10 animfps20 animfps30 animfps50 -measureMenu | Measurements = 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 -SIGNEDloadMenu | Load = loadPdb loadFileOrURL loadFileUnitCell - loadScript -SIGNEDwriteMenu | Save = writeFileTextVARIABLE writeState writeHistory - writeJpg writePng writePovray - writeIsosurface writeVrml writeMaya +measureMenu | Measurements = showMeasurementsCB - measureOff measureDistance measureAngle measureTorsion PDBmeasureSequence - measureDelete measureList - distanceNanometers distanceAngstroms distancePicometers +pickingMenu | Set picking = pickOff pickCenter pickIdent pickLabel pickAtom pickMolecule pickElement - pickSpin - modelKitMode - PDBpickChain PDBpickGroup SYMMETRYpickSite +computationMenu | Computation = minimize modelkit +showMenu | Show = showHistory showFile showFileHeader - showOrient showMeasure - showSpacegroup showState SYMMETRYshowSymmetry UNITCELLshow - showIsosurface showMo - extractMOL +SIGNEDJAVAcaptureMenuSPECIAL | Capture = SIGNEDJAVAcaptureRock SIGNEDJAVAcaptureSpin - SIGNEDJAVAcaptureBegin SIGNEDJAVAcaptureEnd SIGNEDJAVAcaptureOff SIGNEDJAVAcaptureOn SIGNEDJAVAcaptureFpsSPECIAL SIGNEDJAVAcaptureLoopingSPECIAL [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 +surfaceMenu | Surfaces = surfDots surfVDW surfSolventAccessible14 surfSolvent14 surfMolecular CHARGEsurf2MEP CHARGEsurfMEP surfMoComputedMenuText - surfOpaque surfTranslucent surfOff +FILEUNITMenu | Symmetry = SYMMETRYShowComputedMenu SYMMETRYhide FILEMOLload FILEUNITone FILEUNITnine FILEUNITnineRestricted FILEUNITninePoly [set_axes]Menu | Axes = off#axes dotted - byPixelMenu byAngstromMenu [set_boundbox]Menu | Boundbox = off#axes dotted - byPixelMenu byAngstromMenu [set_UNITCELL]Menu | Unit cell = 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 +aboutMenu | About... = jmolMenu systemMenu +jmolMenu | Jmol = APPLETid version date - help - mouse translations jmolorg +systemMenu | System = os javaVender javaVersion JAVAprocessors JAVAmemMax JAVAmemTotal # 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 | Boundbox = -showHydrogensCheckbox | Show Hydrogens = -showMeasurementsCheckbox | Show Measurements = -showSelectionsCheckbox | Selection Halos = -showUNITCELLCheckbox | Unit cell = +jmolorg | http://www.jmol.org = show url "http://www.jmol.org" +help | Jmol Script Commands = help +mouse | Mouse Manual = show url "http://wiki.jmol.org/index.php/Mouse_Manual" +translations | Translations = show url "http://wiki.jmol.org/index.php/Internationalisation" +colorrasmolCB | RasMol Colors = +hideNotSelectedCB | Display Selected Only = set hideNotSelected true | set hideNotSelected false; hide(none) +perspectiveDepthCB | Perspective Depth = +showAxesCB | Axes = set showAxes true | set showAxes false;set axesMolecular +showBoundBoxCB | Boundbox = +showHydrogensCB | Show Hydrogens = +showMeasurementsCB | Show Measurements = +showSelectionsCB | Selection Halos = +showUNITCELLCB | Unit cell = selectAll | All = SELECT all selectNone | None = SELECT none invertSelection | Invert Selection = SELECT not selected @@ -267,20 +121,27 @@ 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 +Ligand | Ligand = 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 +best | Best = rotate best -1.0 +front | Front = if (showBoundBox or showUnitcell) {moveto 2.0 front;delay 1} else {boundbox on;moveto 2.0 front;delay 1;boundbox off} +left | Left = if (showBoundBox or showUnitcell) {moveto 1.0 front;moveto 2.0 left;delay 1} else {boundbox on;moveto 1.0 front;moveto 2.0 left;delay 1;boundbox off} +right | Right = if (showBoundBox or showUnitcell) {moveto 1.0 front;moveto 2.0 right;delay 1} else {boundbox on;moveto 1.0 front;moveto 2.0 right;delay 1;boundbox off} +top | Top = if (showBoundBox or showUnitcell) {moveto 1.0 front;moveto 2.0 top;delay 1} else {boundbox on;moveto 1.0 front;moveto 2.0 top;delay 1;boundbox off} +bottom | Bottom = if (showBoundBox or showUnitcell) {moveto 1.0 front;moveto 2.0 bottom;delay 1} else {boundbox on;moveto 1.0 front;moveto 2.0 bottom;delay 1;boundbox off} +back | Back = if (showBoundBox or showUnitcell) {moveto 1.0 front;moveto 2.0 back;delay 1} else {boundbox on;moveto 1.0 front;moveto 2.0 back;delay 1;boundbox off} +axisA | Axis a = moveto axis a +axisB | Axis b = moveto axis b +axisC | Axis c = moveto axis c +axisX | Axis x = moveto axis x +axisY | Axis y = moveto axis y +axisZ | Axis z = moveto axis z +renderCpkSpacefill | CPK Spacefill = restrict bonds not selected;select not selected;spacefill 100%;color cpk +renderBallAndStick | Ball and Stick = restrict bonds not selected;select not selected;spacefill 23%AUTO;wireframe 0.15;color cpk +renderSticks | Sticks = restrict bonds not selected;select not selected;wireframe 0.3;color cpk +renderWireframe | Wireframe = restrict bonds not selected;select not selected;wireframe on;color cpk +PDBrenderCartoonsOnly | Cartoon = restrict bonds not selected;select not selected;cartoons on;color structure +PDBrenderTraceOnly | Trace = restrict bonds 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% @@ -295,7 +156,7 @@ bond150 | 0.15 bond200 | 0.20 � = wireframe .2 bond250 | 0.25 � = wireframe .25 bond300 | 0.30 � = wireframe .3 -PDBhbondCalc | Calculate = hbonds calculate +hbondCalc | Calculate = hbonds calculate hbondNone | Off = hbonds off hbondWireframe | On = hbonds on PDBhbondSidechain | Set H-Bonds Side Chain = set hbonds sidechain @@ -324,6 +185,8 @@ 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 +vibration20 | *2 = vibrationScale *= 2 +vibration05 | /2 = vibrationScale /= 2 vectorOff | Off = vectors off vectorOn | On = vectors on vector3 | 3 pixels = vectors 3 @@ -387,8 +250,9 @@ measureOff | Double-Click begins and ends all measurements = set pickingstyle ME 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 +PDBmeasureSequence | Click two atoms to display a sequence in the console = set pickingstyle MEASURE; set picking MEASURE SEQUENCE measureDelete | Delete measurements = measure delete -JVM12measureList | List measurements = console on;show measurements +measureList | 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 @@ -399,11 +263,14 @@ pickLabel | Label = set picking label pickAtom | Select atom = set picking atom PDBpickChain | Select chain = set picking chain pickElement | Select element = set picking element +modelKitMode | modelKitMode = set modelKitMode 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 +SYMMETRYpickSymmetry | Show symmetry operation = set picking symmetry +showConsole | Console = console +JSConsole | JavaScript Console = JSCONSOLE showFile | File Contents = console on;show file showFileHeader | File Header = console on;getProperty FileHeader showHistory | History = console on;show history @@ -414,35 +281,55 @@ 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 -loadPdb | File from PDB = load ?PdbId? -loadFileOrURL | File or URL = load ? -loadFileUnitCell | Load full unit cell = load ? {1 1 1} -loadScript | Script = script ?.spt -writeFileTextVARIABLE | File {0} = write file "?FILE?" -writeState | Script with state = write state "?FILEROOT?.spt" -writeHistory | Script with history = write history "?FILEROOT?.his" -writeIsosurface | JVXL Isosurface = write isosurface "?FILEROOT?.jvxl" -writeJpg | JPG Image = write image "?FILEROOT?.jpg" -writePng | PNG Image = write image "?FILEROOT?.png" -writePovray | POV-Ray Image = write POVRAY "?FILEROOT?.pov" -writeVrml | VRML 3D Model = write VRML "?FILEROOT?.vrml" -writeMaya | Maya 3D Model = write MAYA "?FILEROOT?.maya" +reload | Reload = load "" +SIGNEDloadPdb | Open from PDB = load ?PdbId? +SIGNEDloadFile | Open local file = load ? +SIGNEDloadUrl | Open URL = load http://? +SIGNEDloadFileUnitCell | Load full unit cell = load ? {1 1 1} +SIGNEDloadScript | Open script = script ?.spt +SIGNEDJAVAcaptureRock | Capture rock = animation mode loop;capture '?Jmol.gif' rock y 10 +SIGNEDJAVAcaptureSpin | Capture spin = animation mode loop;capture '?Jmol.gif' spin y +SIGNEDJAVAcaptureBegin | Start capturing = capture '?Jmol.gif' +SIGNEDJAVAcaptureEnd | End capturing = capture '' +SIGNEDJAVAcaptureOff | Disable capturing = capture off +SIGNEDJAVAcaptureOn | Re-enable capturing = capture on +SIGNEDJAVAcaptureFpsSPECIAL | Set capture replay rate = animation fps @{0+prompt('Capture replay frames per second?', animationFPS)};prompt 'animation FPS ' + animationFPS +SIGNEDJAVAcaptureLoopingSPECIAL | Toggle capture looping = animation mode @{(animationMode=='ONCE' ? 'LOOP':'ONCE')};prompt 'animation MODE ' + animationMode +writeFileTextVARIABLE | Save a copy of {0} = if (_applet && !_signedApplet) { console;show file } else { write file "?FILE?"} +writeState | Save script with state = if (_applet && !_signedApplet) { console;show state } else { write state "?FILEROOT?.spt"} +writeHistory | Save script with history = if (_applet && !_signedApplet) { console;show history } else { write history "?FILEROOT?.his"} +SIGNEDwriteJmol | Save as PNG/JMOL (image+zip) = write PNGJ "?FILEROOT?.png" +SIGNEDwriteIsosurface | Save JVXL isosurface = write isosurface "?FILEROOT?.jvxl" +SIGNEDNOGLwriteGif | Export GIF image = write image "?FILEROOT?.gif" +SIGNEDNOGLwriteJpg | Export JPG image = write image "?FILEROOT?.jpg" +SIGNEDNOGLwritePng | Export PNG image = write image "?FILEROOT?.png" +SIGNEDNOGLwritePngJmol | Export PNG+JMOL image = write PNGJ "?FILEROOT?.png" +SIGNEDNOGLwritePovray | Export POV-Ray image = write POVRAY "?FILEROOT?.pov" +SIGNEDNOGLwriteVrml | Export VRML 3D model = write VRML "?FILEROOT?.wrl" +SIGNEDNOGLwriteX3d | Export X3D 3D model = write X3D "?FILEROOT?.x3d" +SIGNEDNOGLwriteIdtf | Export IDTF 3D model = write IDTF "?FILEROOT?.idtf" +SIGNEDNOGLwriteMaya | Export Maya 3D model = write MAYA "?FILEROOT?.ma" SYMMETRYshowSymmetry | Symmetry = console on;show symmetry UNITCELLshow | Unit cell = console on;show unitcell extractMOL | Extract MOL data = console on;getproperty extractModel "visible" +minimize | Optimize structure = minimize +modelkit | Model kit = set modelkitmode 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 +CHARGEsurfMEP | Molecular Electrostatic Potential (range ALL) = isosurface delete resolution 0 vdw color range all map MEP translucent +CHARGEsurf2MEP | Molecular Electrostatic Potential (range -0.1 0.1) = isosurface delete resolution 0 vdw color range -0.1 0.1 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 +SYMMETRYhide | Hide Symmetry = draw sym_* delete +FILEMOLload | Reload (molecular) = save orientation;load "";restore orientation;center +FILEUNITone | Reload {1 1 1} = save orientation;load "" {1 1 1} ;restore orientation;center +FILEUNITnine | Reload {444 666 1} = save orientation;load "" {444 666 1} ;restore orientation;center +FILEUNITnineRestricted | Reload {444 666 1} + Display 555 = save orientation;load "" {444 666 1} ;restore orientation; unitcell on; display cell=555;center visible;zoom 200 +FILEUNITninePoly | 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 @@ -452,24 +339,19 @@ UNITCELLninePoly | Reload + Polyhedra = save orientation;load "" {444 666 1} ;re 25a | 0.25 � = 0.25 50a | 0.50 � = 0.50 100a | 1.0 � = 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 -# -# - +version | 14.3.3_2014.08.01 +date | 2014-08-01 07:38 +os | Windows 7 +JAVAmemTotal | ? +JAVAmemMax | ? +JAVAprocessors | ? +javaVender | Java: Oracle Corporation +javaVersion | Java 1.7.0_67 modelSetMenu | No atoms loaded configurationComputedMenu | Configurations elementsComputedMenu | Element @@ -479,8 +361,9 @@ PDBaaResiduesComputedMenu | By Residue Name PDBnucleicResiduesComputedMenu | By Residue Name PDBcarboResiduesComputedMenu | By Residue Name PDBheteroComputedMenu | By HETATM -surfMoComputedMenu | Molecular Orbitals -SYMMETRYComputedMenu | Symmetry +surfMoComputedMenuText | Molecular Orbitals ({0}) +SYMMETRYSelectComputedMenu | Symmetry +SYMMETRYShowComputedMenu | Space Group hiddenModelSetText | Model information allModelsText | All {0} models configurationMenuText | Configurations ({0}) @@ -496,9 +379,13 @@ mainMenuText | Main Menu biomoleculesMenuText | Biomolecules biomoleculeText | biomolecule {0} ({1} atoms) loadBiomoleculeText | load biomolecule {0} ({1} atoms) +sceneComputedMenu | Scenes +hnmrMenu | 1H-NMR +cnmrMenu | 13C-NMR cpk | Element (CPK) altloc#PDB | Alternative Location molecule | Molecule +property_vxyz#VIBRATION | Vectors formalcharge | Formal Charge partialcharge#CHARGE | Partial Charge relativeTemperature#BFACTORS | Temperature (Relative)