Revision: 20108
http://sourceforge.net/p/jmol/code/20108
Author: aherraez
Date: 2014-11-12 19:46:49 +0000 (Wed, 12 Nov 2014)
Log Message:
-----------
updated popup menu content (Jmol 14.3.3)
Modified Paths:
--------------
trunk/Jmol/jmol.mnu
Modified: trunk/Jmol/jmol.mnu
===================================================================
--- trunk/Jmol/jmol.mnu 2014-11-12 15:36:35 UTC (rev 20107)
+++ trunk/Jmol/jmol.mnu 2014-11-12 19:46:49 UTC (rev 20108)
@@ -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 @@
[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 @@
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 @@
bond200 | 0.20 \xC5 = wireframe .2
bond250 | 0.25 \xC5 = wireframe .25
bond300 | 0.30 \xC5 = 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 @@
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 @@
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 @@
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 @@
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 @@
25a | 0.25 \xC5 = 0.25
50a | 0.50 \xC5 = 0.50
100a | 1.0 \xC5 = 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 @@
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 @@
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)
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