Ticket #9232: trac_9232_notebook_fixes.patch

File trac_9232_notebook_fixes.patch, 29.6 KB (added by Jonathan Gutow, 12 years ago)

Notebook fixes for launch Jmol from cmd line

  • new file sagenb/data/jmol/appletweb/JmolHelp.html 

    # HG changeset patch
# User Jonathan H. Gutow <gutow@uwosh.edu
# Date 1300272025 25200
# Node ID b0a0157ab2ad8b034004a0950dfaefd440144ac8
# Parent  d12daf8c85a85a184c16dc52f1c9132ee1910f41
Trac 9232: notebook fixes for Jmol launch from cmd line

diff -r d12daf8c85a8 -r b0a0157ab2ad sagenb/data/jmol/appletweb/JmolHelp.html
    - +  
     1<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
     2<html><head><meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"><title>JmolHelp</title><meta content="J. Gutow" name="author"><meta content="Brief Jmol instructions for SAGE math" name="description"></head><body><div style="text-align: center;"><h3>Brief Help for the Jmol 3-D viewer</h3><div style="text-align: left;"><dl><dt>Reorient View</dt><dd>To reorient the view&nbsp;place cursor over the image, hold down the mouse button and drag.</dd><dt>Zoom View</dt><dd>To
     3zoom place the cursor over the image hold down the shift key and the
     4mouse button while dragging down to zoom in or up to zoom out.</dd><dt>Adding annotation</dt><dd>Annotation
     5may be added using the Jmol scripting language. &nbsp;To do this
     6right-click (control-click) in the applet window to get the applet
     7pop-up menu. &nbsp;In the advanced submenu select "Console". &nbsp;You
     8can type Jmol script commands into the console. &nbsp;See the <a href="http://chemapps.stolaf.edu/jmol/docs/">jmol scripting documentation</a>, the <a href="http://www.jmol.org">jmol web site</a> and the <a href="http://wiki.jmol.org">jmol wiki</a> for more information.</dd></dl><div style="text-align: right;"><small><small>By Jonathan Gutow<br>November 2009</small></small></div></div></div></body></html>
     9 No newline at end of file

  • new file sagenb/data/jmol/appletweb/SageMenu.mnu 

    diff -r d12daf8c85a8 -r b0a0157ab2ad sagenb/data/jmol/appletweb/SageMenu.mnu
    - +  
     1# Jmol.mnu Jmol version 11.3.15_dev  2007-08-28  7:23 AM 9/3/2007 Bob Hanson hansonr@stolaf.edu
     2#
     3# This file is in three parts.
     4#
     5# Part I contains the menu structure.
     6# Part II contains all the Jmol scripts that correspond to a menu click.
     7# Part III contains additional words that will be translated.
     8#
     9# This file is not normally read by Jmol.
     10#
     11# Jmol APPLETS: If you want it to be read, then include
     12#
     13#   jmolSetCallback("menuFile", "Jmol.mnu") // or whatever filename you choose
     14#
     15# just after jmolInitialize() and before the jmolApplet() call.
     16#
     17# Jmol APPLICATION: use the -m filename startup flag.
     18#
     19#
     20# Part I: Menu Structure
     21# ----------------------
     22#
     23# Each definition consists of
     24#
     25#  key | label = [menu list]
     26#
     27#  for example:
     28#
     29#   zoomMenu | Zoom = zoom50 zoom100 zoom150 zoom200 zoom400 zoom800 - zoomIn zoomOut
     30#
     31# The words used for the key are arbitrary designations, but they must end with the
     32# letters "Menu". They must not contain spaces. They are case sensitive.
     33#
     34# The label is what the user sees. Or, rather, the translation of that label
     35# (see below) is what the user sees.
     36#
     37# The menu list is a space-separated list of submenu keys or item keys (see Part II)
     38# or, if not listed in Part II, a single-word Jmol script word, such as "cpk".
     39#
     40# A hyphen indicates the location for a horizonatal menu separator
     41#
     42# menu items starting with @ are predefined sets. For example:
     43#
     44#   [color_atoms]Menu | Atoms = schemeMenu - @COLOR - opaque translucent
     45#
     46# Here @COLOR is a predefined set:
     47#
     48#   @COLOR = black white red orange yellow green cyan blue indigo violet
     49#
     50# You can create your own predefined terms and use them anywhere you want.
     51# Predefined terms may contain more predefined terms.
     52#
     53# DON'T DO THIS:  @COLOR = something something @COLOR
     54#
     55# "Checkbox" at the end of a menu item creates a check box. These objects operate
     56# by setting Jmol true/false parameters. The name of the checkbox must correspond
     57# to the name of a valid Jmol parameter.
     58#
     59#   atomMenu | Atoms = showHydrogensCheckbox - atomNone - atom15 atom20 atom25 atom50 atom75 atom100   
     60#
     61#
     62# A note about language translation
     63# ---------------------------------
     64#
     65# The way translation works is that a code preprocessor identifies text that
     66# in the CODE is written as GT._("...."). This is called *internationalization*,
     67# and it occurs when the Jmol distribution is built.
     68#
     69# Then, when that method is executed in the running Jmol program, the table for
     70# the selected language is looked up. If that phrase has been translated into
     71# that particular language by a human volunteer, then the translated phrase is
     72# returned. This is called *localization*.
     73#
     74# All menu labels will be sent through the GT._() method. If you change a menu label to
     75# a phrase that has not been internationalized, then it won't be localized. It will appear
     76# in the language in which you have written it here. Just be aware of that.
     77#
     78#
     79# Computed Menus
     80# --------------
     81#
     82# Menu keys containing the term "Computed" are modified after the fact.
     83# You should be able to omit them, but this needs additional testing (by YOU!)
     84#
     85#
     86# Special identifiers in this section
     87# -----------------------------------
     88#
     89# Certain all-capitalized words anywhere in a key are significant. They relate to
     90# specific Jmol data options. If a model set does not involve data that are relevant to this
     91# option, then this menu item will be present but disabled (greyed out). Note that if a menu
     92# key is greyed out, then submenu items of that key are not visible, so those item keys do
     93# not need the identifier as well. This is the case with many PDB identifiers -- if you
     94# move them to another menu, make sure that menu has "PDB" in it or add PDB somewhere in the name.
     95#
     96# The following options exist as of Jmol 11.3.15:
     97#
     98# CHARGE    data set includes partial charge information
     99# FRAMES    data set includes multiple frames
     100# PDB       data set is PDB file format information (HETERO, etc.)
     101# SYMMETRY  data set includes symmetry information
     102# UNITCELL  data set contains a unit cell
     103# VIBRATION data set includes vibration data
     104#
     105# A key may contain multiple option identifiers.
     106#
     107# In addition, APPLET indicates that this item should
     108# show up only in the Jmol applet menu, not the Jmol application menu
     109#
     110# If a key includes a phrase in square brackets, as in
     111#
     112#   [color_atoms]Menu | Atoms = schemeMenu - @COLOR - opaque translucent
     113#
     114# then for all menu and submenu items under this menu
     115# the script given in Part II is PREPENDED with that phrase, with
     116# underscore replaced with space. For example,
     117#
     118
     119# Part I -- Menu Structure
     120# ------------------------
     121#
     122
     123@COLOR = black white red orange yellow green cyan blue indigo violet
     124@AXESCOLOR = gray salmon maroon olive slateblue gold orchid
     125popupMenu = viewSageMenu renderSageMenu colorSageMenu - zoomMenu spinMenu - advancedMenu - aboutComputedMenu
     126
     127viewSageMenu | View = standardview xyplane xzplane yzplane
     128
     129renderSageMenu | Style = perspectiveDepthCheckbox showBoundBoxCheckbox showAxesCheckbox stereoMenu - [set_axes]SageMenu [set_boundbox]SageMenu
     130
     131stereoMenu | Stereographic = stereoNone stereoRedCyan stereoRedBlue stereoRedGreen stereoCrossEyed stereoWallEyed
     132
     133colorSageMenu | Color = [color_background]Menu [color_axes]Menu [color_boundbox]Menu
     134
     135[color_background]Menu | Background = @COLOR
     136
     137[color_axes]Menu | Axes = @AXESCOLOR
     138
     139[color_boundbox]Menu | Boundbox = @AXESCOLOR
     140
     141zoomMenu | Zoom = zoom50 zoom100 zoom150 zoom200 zoom400 zoom800 - zoomIn zoomOut
     142
     143spinMenu | Spin = spinOn spinOff - [set_spin_X]Menu [set_spin_Y]Menu [set_spin_Z]Menu - [set_spin_FPS]Menu
     144
     145[set_spin_X]Menu | Set X Rate = s0 s5 s10 s20 s30 s40 s50
     146
     147[set_spin_Y]Menu | Set Y Rate = s0 s5 s10 s20 s30 s40 s50
     148
     149[set_spin_Z]Menu | Set Z Rate = s0 s5 s10 s20 s30 s40 s50
     150
     151[set_spin_FPS]Menu | Set FPS = s0 s5 s10 s20 s30 s40 s50
     152
     153[set_axes]SageMenu | Axes = off#axes dotted - byPixelMenu byCoordinateMenu
     154[set_boundbox]SageMenu | Boundbox = off#axes dotted - byPixelMenu byCoordinateMenu
     155
     156byPixelMenu | Pixel Width = 1p 3p 5p 10p
     157byCoordinateMenu | Width = 10d 20d 50d 100d
     158aboutComputedMenu | About Jmol = APPLETjmolUrl APPLETmouseManualUrl APPLETtranslationUrl
     159
     160
     161### ORIGINAL MENUS
     162advancedMenu | Advanced = modelSetMenu FRAMESbyModelComputedMenu configurationComputedMenu - selectMenu viewMenu renderMenu colorMenu - surfaceMenu SYMMETRYUNITCELLmenu - zoomMenu spinMenu VIBRATIONMenu FRAMESanimateMenu - measureMenu pickingMenu - JVM12showConsole JVM12showMenu - languageComputedMenu aboutComputedMenu
     163
     164viewMenu | View = front left right top bottom back
     165
     166selectMenu | Select = hideNotSelectedCheckbox showSelectionsCheckbox - selectAll selectNone invertSelection - elementsComputedMenu SYMMETRYComputedMenu - PDBproteinMenu PDBnucleicMenu PDBheteroMenu PDBcarboMenu PDBnoneOfTheAbove
     167
     168PDBproteinMenu | Protein = PDBaaResiduesComputedMenu - allProtein proteinBackbone proteinSideChains - polar nonpolar - positiveCharge negativeCharge noCharge
     169
     170PDBcarboMenu | Carbohydrate = PDBcarboResiduesComputedMenu - allCarbo
     171
     172PDBnucleicMenu | Nucleic = PDBnucleicResiduesComputedMenu - allNucleic nucleicBackbone nucleicBases - DNA RNA - atPairs auPairs gcPairs
     173
     174PDBheteroMenu | Hetero = PDBheteroComputedMenu - allHetero Solvent Water - Ligand exceptWater nonWaterSolvent
     175atomMenu | Atoms = showHydrogensCheckbox - atomNone - atom15 atom20 atom25 atom50 atom75 atom100
     176
     177bondMenu | Bonds = bondNone bondWireframe - bond100 bond150 bond200 bond250 bond300
     178
     179hbondMenu | Hydrogen Bonds = PDBhbondCalc hbondNone hbondWireframe - PDBhbondSidechain PDBhbondBackbone - hbond100 hbond150 hbond200 hbond250 hbond300
     180
     181ssbondMenu | Disulfide Bonds = ssbondNone ssbondWireframe - PDBssbondSidechain PDBssbondBackbone - ssbond100 ssbond150 ssbond200 ssbond250 ssbond300
     182
     183PDBstructureMenu | Structures = structureNone - backbone cartoon cartoonRockets ribbons rockets strands trace
     184
     185VIBRATIONvectorMenu | Vectors = vectorOff vectorOn vector3 vector005 vector01 - vectorScale02 vectorScale05 vectorScale1 vectorScale2 vectorScale5
     186[color_atoms]Menu | Atoms = schemeMenu - @COLOR - opaque translucent
     187
     188[color_bonds]Menu | Bonds = none - @COLOR - opaque translucent
     189
     190[color_hbonds]Menu | Hydrogen Bonds = none - @COLOR - opaque translucent
     191
     192[color_ssbonds]Menu | Disulfide Bonds = none - @COLOR - opaque translucent
     193
     194[color_labels]Menu | Labels = none - @COLOR - opaque translucent
     195
     196[color_vectors]Menu | Vectors = none - @COLOR - opaque translucent
     197
     198[color_backbone]Menu | Backbone = none - schemeMenu - @COLOR - opaque translucent
     199
     200[color_cartoon]sMenu | Cartoon = none - schemeMenu - @COLOR - opaque translucent
     201
     202[color_ribbon]sMenu | Ribbons = none - schemeMenu - @COLOR - opaque translucent
     203
     204[color_rockets]Menu | Rockets = none - schemeMenu - @COLOR - opaque translucent
     205
     206[color_strands]Menu | Strands = none - schemeMenu - @COLOR - opaque translucent
     207
     208[color_trace]Menu | Trace = none - schemeMenu - @COLOR - opaque translucent
     209
     210[color_UNITCELL]Menu | Unitcell = @AXESCOLOR
     211
     212VIBRATIONMenu | Vibration = vibrationOff vibrationOn VIBRATIONvectorMenu
     213
     214SYMMETRYUNITCELLmenu | Symmetry = UNITCELLone UNITCELLnine UNITCELLnineRestricted UNITCELLninePoly
     215[set_UNITCEL]menu | Unitcell = off#axes dotted - byPixelMenu byAngstromMenu
     216labelPositionMenu | Position Label on Atom = labelCentered labelUpperRight labelLowerRight labelUpperLeft labelLowerLeft
     217
     218colorMenu | 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
     219renderMenu | Style = perspectiveDepthCheckbox showBoundBoxCheckbox showUNITCELLCheckbox showAxesCheckbox stereoMenu - renderSchemeMenu - atomMenu labelMenu bondMenu hbondMenu ssbondMenu - PDBstructureMenu [set_axes]Menu [set_boundbox]Menu [set_UNITCEL]menu
     220renderSchemeMenu | Scheme = renderCpkSpacefill renderBallAndStick renderSticks renderWireframe PDBrenderCartoonsOnly PDBrenderTraceOnly
     221
     222labelMenu | Labels = labelNone - labelSymbol labelName labelNumber - labelPositionMenu
     223[color_isosurface]Menu | Surface = @COLOR - opaque translucent
     224
     225colorPDBStructuresMenu | Structure = [color_backbone]Menu [color_cartoon]sMenu [color_ribbon]sMenu [color_rockets]Menu [color_strands]Menu [color_trace]Menu
     226schemeMenu | By Scheme = cpk altloc molecule formalcharge partialcharge#CHARGE - amino#PDB structure#PDB chain#PDB
     227measureMenu | Measurement = showMeasurementsCheckbox - measureOff measureDistance measureAngle measureTorsion - measureDelete JVM12measureList - distanceNanometers distanceAngstroms distancePicometers
     228
     229pickingMenu | Set picking = pickOff pickCenter pickIdent pickLabel pickAtom pickMolecule pickElement PDBpickChain PDBpickGroup SYMMETRYpickSite pickSpin
     230FRAMESanimateMenu | Animation = animModeMenu - play pause resume stop - nextframe prevframe rewind - playrev restart - FRAMESanimFpsMenu
     231animModeMenu | Animation Mode = onceThrough palindrome loop
     232
     233FRAMESanimFpsMenu | Set FPS = animfps5 animfps10 animfps20 animfps30 animfps50
     234JVM12showMenu | Show = showHistory showFile showFileHeader - showOrient showMeasure - showSpacegroup showState SYMMETRYshowSymmetry UNITCELLshow - showIsosurface showMo - extractMOL
     235surfaceMenu | Surfaces = surfDots surfVDW surfSolventAccessible14 surfSolvent14 surfMolecular CHARGEsurfMEP surfMoComputedMenu - surfOpaque surfTranslucent surfOff
     236[set_axes]Menu | Axes = off#axes dotted - byPixelMenu byAngstromMenu
     237[set_boundbox]Menu | Boundbox = off#axes dotted - byPixelMenu byAngstromMenu
     238byAngstromMenu | Width = 10a 20a 25a 50a 100a
     239
     240
     241
     242
     243# Part II -- Key Definitions
     244# --------------------------
     245#
     246# This section contains the Jmol equivalents of all action items.
     247#
     248# Each definition consists of
     249#
     250#  key | label = [Jmol script]
     251#
     252# or
     253#
     254#  someCheckbox | label = [on script] | [off script]
     255#
     256#  for example:
     257#
     258#   stereoNone | None = stereo off
     259#
     260#   showAxesCheckbox | Axes = set showAxes true | set showAxes false;set axesMolecular
     261#
     262# Each key should be referred to explicitly in at least one menu list in Part I.
     263#
     264# The label is what the user sees. Or, rather, the translation of that label
     265# (see above) is what the user sees.
     266#
     267# For checkboxes, the on and off scripts are not required if the action is simply to
     268# turn a Jmol parameter on or off.
     269#
     270#
     271# Special identifiers in this section
     272# -----------------------------------
     273#
     274#
     275# "SELECT" at the beginning of a definition wraps the definition with "select thisModel and ()";
     276#
     277#   For example:     invertSelection | Invert Selection = SELECT not selected
     278#
     279#
     280#
     281# "#" anywhere in a definition indicates that the script evaluation should be done in "silent"
     282# mode -- that is, without sending messages to the console or status line
     283# Note that checkboxes are always executed in silent mode.
     284 
     285
     286colorrasmolCheckbox | RasMol Colors =
     287hideNotSelectedCheckbox | Display Selected Only = set hideNotSelected true | set hideNotSelected false; hide(none)
     288perspectiveDepthCheckbox | Perspective Depth =
     289showAxesCheckbox | Axes = set showAxes true | set showAxes false;set axesMolecular
     290showBoundBoxCheckbox | Bound Box =
     291showHydrogensCheckbox | Show Hydrogens =
     292showMeasurementsCheckbox | Show Measurements =
     293showSelectionsCheckbox | Selection Halos =
     294showUNITCELLCheckbox | Unit Cell =
     295
     296selectAll | All = SELECT all
     297selectNone | None = SELECT none
     298invertSelection | Invert Selection = SELECT not selected
     299allProtein | All = SELECT protein
     300proteinBackbone | Backbone = SELECT protein and backbone
     301proteinSideChains | Side Chains = SELECT protein and not backbone
     302polar | Polar Residues = SELECT protein and polar
     303nonpolar | Nonpolar Residues = SELECT protein and not polar
     304positiveCharge | Basic Residues (+) = SELECT protein and basic
     305negativeCharge | Acidic Residues (-) = SELECT protein and acidic
     306noCharge | Uncharged Residues = SELECT protein and not (acidic,basic)
     307allCarbo | All = SELECT carbohydrate
     308allNucleic | All = SELECT nucleic
     309DNA | DNA = SELECT dna
     310RNA | RNA = SELECT rna
     311nucleicBackbone | Backbone = SELECT nucleic and backbone
     312nucleicBases | Bases = SELECT nucleic and not backbone
     313atPairs | AT pairs = SELECT a,t
     314gcPairs | GC pairs = SELECT g,c
     315auPairs | AU pairs = SELECT a,u
     316A = SELECT a
     317C = SELECT c
     318G = SELECT g
     319T = SELECT t
     320U = SELECT u
     321allHetero | All PDB "HETATM" = SELECT hetero
     322Solvent | All Solvent = SELECT solvent
     323Water | All Water = SELECT water
     324nonWaterSolvent | Nonaqueous Solvent (solvent and not water) = SELECT solvent and not water
     325exceptWater | Nonaqueous HETATM (hetero and not water) = SELECT hetero and not water
     326Ligand | Ligand (hetero and not solvent) = SELECT ligand
     327PDBnoneOfTheAbove | None of the above = SELECT not(hetero,protein,nucleic,carbohydrate)
     328
     329xzplane | 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;
     330
     331xyplane | 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;
     332
     333yzplane | 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;
     334
     335standardview | 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;
     336
     337front | 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;
     338left | 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;
     339right | 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;
     340top | 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;
     341bottom | 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;
     342back | 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;
     343
     344
     345
     346renderCpkSpacefill | CPK Spacefill = restrict not selected;select not selected;spacefill 100%;color cpk
     347renderBallAndStick | Ball and Stick = restrict not selected;select not selected;spacefill 20%;wireframe 0.15;color cpk
     348renderSticks | Sticks = restrict not selected;select not selected;wireframe 0.3;color cpk
     349renderWireframe | Wireframe = restrict not selected;select not selected;wireframe on;color cpk
     350PDBrenderCartoonsOnly | Cartoon = restrict not selected;select not selected;cartoons on;color structure
     351PDBrenderTraceOnly | Trace = restrict not selected;select not selected;trace on;color structure
     352atomNone | Off = cpk off
     353atom15 | 15% van der Waals = cpk 15%
     354atom20 | 20% van der Waals = cpk 20%
     355atom25 | 25% van der Waals = cpk 25%
     356atom50 | 50% van der Waals = cpk 50%
     357atom75 | 75% van der Waals = cpk 75%
     358atom100 | 100% van der Waals = cpk on
     359bondNone | Off = wireframe off
     360bondWireframe | On = wireframe on
     361bond100 | 0.10 Å = wireframe .1
     362bond150 | 0.15 Å = wireframe .15
     363bond200 | 0.20 Å = wireframe .2
     364bond250 | 0.25 Å = wireframe .25
     365bond300 | 0.30 Å = wireframe .3
     366PDBhbondCalc | Calculate = hbonds calculate
     367hbondNone | Off = hbonds off
     368hbondWireframe | On = hbonds on
     369PDBhbondSidechain | Set H-Bonds Side Chain = set hbonds sidechain
     370PDBhbondBackbone | Set H-Bonds Backbone = set hbonds backbone
     371hbond100 | 0.10 Å = hbonds .1
     372hbond150 | 0.15 Å = hbonds .15
     373hbond200 | 0.20 Å = hbonds .2
     374hbond250 | 0.25 Å = hbonds .25
     375hbond300 | 0.30 Å = hbonds .3
     376ssbondNone | Off = ssbonds off
     377ssbondWireframe | On = ssbonds on
     378PDBssbondSidechain | Set SS-Bonds Side Chain = set ssbonds sidechain
     379PDBssbondBackbone | Set SS-Bonds Backbone = set ssbonds backbone
     380ssbond100 | 0.10 Å = ssbonds .1
     381ssbond150 | 0.15 Å = ssbonds .15
     382ssbond200 | 0.20 Å = ssbonds .2
     383ssbond250 | 0.25 Å = ssbonds .25
     384ssbond300 | 0.30 Å = ssbonds .3
     385structureNone | Off = backbone off;cartoons off;ribbons off;rockets off;strands off;trace off;
     386backbone | Backbone = restrict not selected;select not selected;backbone 0.3
     387cartoon | Cartoon = restrict not selected;select not selected;set cartoonRockets false;cartoons on
     388cartoonRockets | Cartoon Rockets = restrict not selected;select not selected;set cartoonRockets;cartoons on
     389ribbons | Ribbons = restrict not selected;select not selected;ribbons on
     390rockets | Rockets = restrict not selected;select not selected;rockets on
     391strands | Strands = restrict not selected;select not selected;strands on
     392trace | Trace = restrict not selected;select not selected;trace 0.3
     393vibrationOff | Off = vibration off
     394vibrationOn | On = vibration on
     395vectorOff | Off = vectors off
     396vectorOn | On = vectors on
     397vector3 | 3 pixels = vectors 3
     398vector005 | 0.05 Å = vectors 0.05
     399vector01 | 0.10 Å = vectors 0.1
     400vectorScale02 | Scale 0.2 = vector scale 0.2
     401vectorScale05 | Scale 0.5 = vector scale 0.5
     402vectorScale1 | Scale 1 = vector scale 1
     403vectorScale2 | Scale 2 = vector scale 2
     404vectorScale5 | Scale 5 = vector scale 5
     405stereoNone | None = stereo off
     406stereoRedCyan | Red+Cyan glasses = stereo redcyan 3
     407stereoRedBlue | Red+Blue glasses = stereo redblue 3
     408stereoRedGreen | Red+Green glasses = stereo redgreen 3
     409stereoCrossEyed | Cross-eyed viewing = stereo 5
     410stereoWallEyed | Wall-eyed viewing = stereo -5
     411labelNone | None = label off
     412labelSymbol | With Element Symbol = label %e
     413labelName | With Atom Name = label %a
     414labelNumber | With Atom Number = label %i
     415labelCentered | Centered = set labeloffset 0 0
     416labelUpperRight | Upper Right = set labeloffset 4 4
     417labelLowerRight | Lower Right = set labeloffset 4 -4
     418labelUpperLeft | Upper Left = set labeloffset -4 4
     419labelLowerLeft | Lower Left = set labeloffset -4 -4
     420zoom50 | 50% = zoom 50
     421zoom100 | 100% = zoom 100
     422zoom150 | 150% = zoom 150
     423zoom200 | 200% = zoom 200
     424zoom400 | 400% = zoom 400
     425zoom800 | 800% = zoom 800
     426zoomIn | Zoom In = move 0 0 0 40 0 0 0 0 1
     427zoomOut | Zoom Out = move 0 0 0 -40 0 0 0 0 1
     428spinOn | On = spin on
     429spinOff | Off = spin off
     430s0 | 0 = 0
     431s5 | 5 = 5
     432s10 | 10 = 10
     433s20 | 20 = 20
     434s30 | 30 = 30
     435s40 | 40 = 40
     436s50 | 50 = 50
     437onceThrough | Play Once = anim mode once#
     438palindrome | Palindrome = anim mode palindrome#
     439loop | Loop = anim mode loop#
     440play | Play = anim play#
     441pause | Pause = anim pause#
     442resume | Resume = anim resume#
     443stop | Stop = anim off#
     444nextframe | Next Frame = frame next#
     445prevframe | Previous Frame = frame prev#
     446playrev | Reverse = anim playrev#
     447rewind | Rewind = anim rewind#
     448restart | Restart = anim on#
     449animfps5 | 5 = anim fps 5#
     450animfps10 | 10 = anim fps 10#
     451animfps20 | 20 = anim fps 20#
     452animfps30 | 30 = anim fps 30#
     453animfps50 | 50 = anim fps 50#
     454measureOff | Double-Click begins and ends all measurements = set pickingstyle MEASURE OFF; set picking OFF
     455measureDistance | Click for distance measurement = set pickingstyle MEASURE; set picking MEASURE DISTANCE
     456measureAngle | Click for angle measurement = set pickingstyle MEASURE; set picking MEASURE ANGLE
     457measureTorsion | Click for torsion (dihedral) measurement = set pickingstyle MEASURE; set picking MEASURE TORSION
     458measureDelete | Delete measurements = measure delete
     459JVM12measureList | List measurements = console on;show measurements
     460distanceNanometers | Distance units nanometers = select *; set measure nanometers
     461distanceAngstroms | Distance units Angstroms = select *; set measure angstroms
     462distancePicometers | Distance units picometers = select *; set measure picometers
     463pickOff | Off = set picking off
     464pickCenter | Center = set picking center
     465pickIdent | Identity = set picking ident
     466pickLabel | Label = set picking label
     467pickAtom | Select atom = set picking atom
     468PDBpickChain | Select chain = set picking chain
     469pickElement | Select element = set picking element
     470PDBpickGroup | Select group = set picking group
     471pickMolecule | Select molecule = set picking molecule
     472SYMMETRYpickSite | Select site = set picking site
     473pickSpin | Spin = set picking spin
     474JVM12showConsole | Console = console
     475showFile | File Contents = console on;show file
     476showFileHeader | File Header = console on;getProperty FileHeader
     477showHistory | History = console on;show history
     478showIsosurface | Isosurface JVXL data = console on;show isosurface
     479showMeasure | Measure = console on;show measure
     480showMo | Molecular orbital JVXL data = console on;show mo
     481showModel | Model = console on;show model
     482showOrient | Orientation = console on;show orientation
     483showSpacegroup | Space group = console on;show spacegroup
     484showState | Current state = console on;show state
     485SYMMETRYshowSymmetry | Symmetry = console on;show symmetry
     486UNITCELLshow | Unit cell = console on;show unitcell
     487extractMOL | Extract MOL data = console on;getproperty extractModel "visible"
     488surfDots | Dot Surface = dots on
     489surfVDW | van der Waals Surface = isosurface delete resolution 0 solvent 0 translucent
     490surfMolecular | Molecular Surface = isosurface delete resolution 0 molecular translucent
     491surfSolvent14 | Solvent Surface (1.4-Angstrom probe) = isosurface delete resolution 0 solvent 1.4 translucent
     492surfSolventAccessible14 | Solvent-Accessible Surface (VDW + 1.4 Angstrom) = isosurface delete resolution 0 sasurface 1.4 translucent
     493CHARGEsurfMEP | Molecular Electrostatic Potential = isosurface delete resolution 0 molecular map MEP translucent
     494surfOpaque | Make Opaque = mo opaque;isosurface opaque
     495surfTranslucent | Make Translucent = mo translucent;isosurface translucent
     496surfOff | Off = mo delete;isosurface delete;select *;dots off
     497UNITCELLone | Reload {1 1 1} = save orientation;load "" {1 1 1} ;restore orientation;center
     498UNITCELLnine | Reload {444 666 1} = save orientation;load "" {444 666 1} ;restore orientation;center
     499UNITCELLnineRestricted | Reload {444 666 1};display 555 = save orientation;load "" {444 666 1} ;restore orientation; unitcell on; display cell=555;center visible;zoom 200
     500UNITCELLninePoly | Reload + Polyhedra = save orientation;load "" {444 666 1} ;restore orientation; unitcell on; display cell=555; polyhedra 4,6 (displayed);center (visible);zoom 200
     5011p | 1 px = on
     5023p | 3 px = 3
     5035p | 5 px = 5
     50410p | 10 px = 10
     505
     506#For the Sage units above
     50710d | 1 = 0.1
     50820d | 2 = 0.20
     50950d | 5 = 0.50
     510100d | 10 = 1.0
     511
     512
     51310a | 0.10 Å = 0.1
     51420a | 0.20 Å = 0.20
     51525a | 0.25 Å = 0.25
     51650a | 0.50 Å = 0.50
     517100a | 1.0 Å = 1.0
     518APPLETjmolUrl | http://www.jmol.org = show url "http://www.jmol.org"
     519APPLETmouseManualUrl | Mouse Manual = show url "http://wiki.jmol.org/index.php/Mouse_Manual"
     520APPLETtranslationUrl | Translations = show url "http://wiki.jmol.org/index.php/Internationalisation"
     521
     522
     523# Part III -- Word Translations
     524# -----------------------------
     525
     526#
     527# This section contains a few additional words that are translated as menu labels.
     528# They are menu items that do not otherwise have Jmol script definitions listed in Part II.
     529#
     530# Each definition consists of
     531#
     532#  key | label
     533#
     534#
     535
     536modelSetMenu | No atoms loaded
     537configurationComputedMenu | Configurations
     538elementsComputedMenu | Element
     539FRAMESbyModelComputedMenu | Model/Frame
     540languageComputedMenu | Language
     541PDBaaResiduesComputedMenu | By Residue Name
     542PDBnucleicResiduesComputedMenu | By Residue Name
     543PDBcarboResiduesComputedMenu | By Residue Name
     544PDBheteroComputedMenu | By HETATM
     545surfMoComputedMenu | Molecular Orbitals
     546SYMMETRYComputedMenu | Symmetry
     547
     548hiddenModelSetText | Model information
     549selectMenuText | Select ({0})
     550allModelsText | All {0} models
     551configurationMenuText | Configurations ({0})
     552modelSetCollectionText | Collection of {0} models
     553atomsText | atoms: {0}
     554bondsText | bonds: {0}
     555groupsText | groups: {0}
     556chainsText | chains: {0}
     557polymersText | polymers: {0}
     558modelMenuText | model {0}
     559viewMenuText | View {0}
     560mainMenuText | Main Menu
     561
     562cpk | Element (CPK)
     563altloc | Alternative Location
     564molecule | Molecule
     565formalcharge | Formal Charge
     566partialcharge#CHARGE | Partial Charge
     567amino#PDB | Amino Acid
     568structure#PDB | Secondary Structure
     569chain#PDB | Chain
     570none | Inherit
     571black | Black
     572white | White
     573cyan | Cyan
     574red | Red
     575orange | Orange
     576yellow | Yellow
     577green | Green
     578blue | Blue
     579indigo | Indigo
     580violet | Violet
     581salmon | Salmon
     582olive | Olive
     583maroon | Maroon
     584gray | Gray
     585slateblue | Slate Blue
     586gold | Gold
     587orchid | Orchid
     588opaque | Make Opaque
     589translucent | Make Translucent
     590off#axes | Hide
     591dotted | Dotted