NavigatetoText>Font,StyleorSize.
SettheformatoptionsontheStyletoolbar.
3. Typethetextinthetextbox.
Theformatisappliedtothetypedtext.Subsequenttextyoutypeusesthedefaultdocumentsettings.
ChangingTextSetting
Youcanchangethetextsettingsforaselectedcaptionoratomlabel.Youcanchoosetohavethesettingsappliedto
theselectedtextandtoallsubsequenttextyoutype.
Tochangethetextsettingsforaselectedcaptionoratomlabel:
1. Selectthetexttochangewithaselectiontool.
2. SettheappropriateoptionsontheTextmenu.
Tochangepartofacaption,selectthepartyouwanttochangeusingtheTexttool.
Tospecifyafontandsizeforselectedtext,dooneofthefollowing:
ChoosethefontandsizefromtheTextmenu.
Right-clickandchoosethefontandsizefromthecontextmenu.
Selectthefontandfont-sizefromthedrop-downlistontheStyleToolbar.
Biopolymersettings
Youcanspecifyhowthesequencesandresiduesappearineithertheentiredocumentorforaspecificsequence,as
follows:
Fortheentiredocument,gotoFile>DocumentSettingsandselecttheBiopolymerDisplaytab.
Foranobject,usetheObjectSettingsdialogbox.
InthebiopolymerDisplaytab,selectfromtheseoptions:
Residuesperline.specifythenumberofresiduestobedisplayedineachlineofthesequence.
Residueperblock.specifythenumberofresiduestobedisplayedineachblockofthesequence.
Amino-acidTermini.SeteitherNH2/COOHorH/OHastheterminiinthesequence.
Note:WhentheterminiaredisplayedusingtheNH2/COOHstyle,theunderlyingatomsareactuallyHandOH.
ThelabelsareintendedtoconveywhethertheNorCterminusispresent.Sincethiscanbeconfusingorambigu-
ous,thisdisplayisnotrecommended,andisprovidedonlyforcompatibilitywithotherproducts.
Specifyingthemarginwidth
Youcanadjustthewhitespacesurroundingtheatomlabelsothatsomeoftheattachedbondishidden.
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Toadjustthewhitespace:
1. GotoFile>DocumentSettings.TheDocumentSettingsdialogboxappears.
2. ClicktheDrawingtab.
3. TypeanewMarginWidthvalue.
4. ClickOK.
Themarginwidthisappliedtoallsubsequentdrawingsinthecurrentdocument.
Settingsfromotherdocuments
Toapplydocumentsettingstotheactivewindowthatarecontainedinadifferentdocument,gotoFile>ApplyDocu-
mentSettingsfromandchoosethedocumentfromwhichtoapplythesettings.
Thesettingsintheactivedocumentwindowchangetothosefoundinthestylesheetthatyouchoose.
Note:Appliedsettingsareforthecurrentdocumentonly.Tomakethemthedefaultsettingsforalldocumentsyou
open,gotoFile>OpenStyleSheets.
Toapplythedocumentsettingsfromadocumentorstylesheetnotlistedinthemenu:
1. GotoFile>ApplyDocumentSettingsfrom>Other.Theselectdocumentdialogboxappears.
2. OpentheappropriatefolderandselectadocumentorStyleSheet.
3. ClickOpen.
Applyingobjectsettings
Youcanapplysettingsfromanotherdocumenttoselectedobjectsinthecurrentdocument.Youcanapplythechosen
settingstotheselectedobjects,ortoallnewobjectsdrawninthecurrentdocument.
Toapplyobjectsettings:
1. Selecttheobject.
2. GotoObject>ApplyObjectSettingsfromandchoosethedocumentfromwhichtoapplythesettings.Adialog
boxappears.
3. Dooneofthefollowing:
Toselectedobjectonly,clickNo.
Toselectedobjectandanynewobjectsyoudraw,clickYes.
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CustomizingHotkeys
IfyouarefamiliarwithXML,youcanedittheChemBioDrawHotkeys,orcreateyourown.
TocustomizeHotkeys,opentheHotkeys.xmlfileinatexteditor.Therearetwopaths--dependingonwhetherthisisa
defaultinstallationoracustominstallation.Thepreferredmethodistoeditthisfilefromacustominstallationloc-
ation.
l
IfaDefaultInstallation,thepathis:
Go > Applications > Right-click on ChemBioDraw > Choose Show Package Contents > Con-
tents > Resources > SpecialPurpose > ChemDraw Items > Hotkeys.xml
l
IfaCustomInstallation,thepathis:
Custom location folder > ChemDraw Items > Hotkeys.xml
Note:ItissafesttoedittheHotkeys.xmlfilefromacustominstallationlocation,ratherthanfromthedefaultinstall-
ationlocation.SincewheneditingtheHotkeys.xmlfromthedefaultinstallationlocation,thiscanaffectthewhole
ChemBioDrawpackagecontent.
TheHotkeyswithinthefileareorganizedbyobjecttype:
“Atom”:Hotkeysthatmodifyatoms.
“Bond”:Hotkeysthatmodifybonds.
"AA1":Hotkeysthatsetsthelabelforthesingleletteraminoacids.
"DNA":HotkeysthatsetsthelabelfortheDNAsequence.
"RNA":HotkeysthatsetsthelabelfortheRNAsequence.
“Generic”:Hotkeysthatselecttoolsandopendialogboxes.
EachHotkeyisencodedinthisformat:
<Hotkey key="{key}" command="{command}" value="{value}" description="{description}”/>
Key
Keyisthekeyboardkeythatinvokesthecommand.Youcanassignthesamekeytodifferentfunctionsaslongasthe
functionsaredefinedfordifferentobjecttypes.Forexample,‘b’changesanatomtoBoronintheAtomobjecttype,a
bondtoboldintheBondobjecttype,andcouldbeassignedtotheBenzenetoolintheGenericobjecttype.Youcan
useanykeyexceptthehard-codedkeys:functionkeys,ENTER,SPACE,BACKSPACE,andarrowkeys.
Note:Hotkeysarecasesensitve.Forexample,youcandefinethehotkeys"S"and"s"todifferentfunctions
withinanobjecttype.
Ifakeyappearsmorethanonceinthefileforthesameobjecttype,theoneclosesttotheendofthefiletakespre-
cedence.
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Command
Commandisanyoneofthepredefinedcommandnames.Allavailablecommandsaredescribedinthehotkeys.xml
file.ThecommandID'saredefinedbasedontheobjecttypesasfollows:
ObjectType
CommandID
Description
Atom
LABELTEXT
Setsthelabelfortheatomstext
SPROUT
Additionofbondstoanatom
CHARGE
Changesthechargeofanatom
FREE_SITE
Increment/decrementfreesitesofanatom
UPTO_SITE
Increment/decrementtheUpTonumberofsub-
stituentsofanatom
EXACT_SITE
Increment/decrementthenumberofsub-
stituentsofanatom
ATOMNUMBER
Show/hidetheatomnumbers
ATTACHMENTPOINT
Setsthevalueoftheattachmentpoint
Bond
BONDORDER
Setsthebondorder
BONDDISPLAY
Setsthebonddisplay
BONDPOSITION
Setsthepositionofbonds
BONDDOUBLEPOSITION
Setsthealignmentfordoublebonds
FUSERING
Fusesaringtoabond
Generic
DIALOG
Displayadialog
TOOLMODE
Changesthecurrenttool
AA1
AA1
Setsthelabelforthesingleletteraminoacids
DNA
DNA
SetsthelabelfortheDNAsequence
RNA
RNA
SetsthelabelfortheRNAsequence
Note:Youcannotaddtothecommandlist.
Value
Thisistheparametervalueassociatedwiththecommand.Forexample,ifthecommandisLABELTEXT,thevalueis
thelabelthatappears.IfthecommandisBONDDISPLAY,thevaluecorrespondstothebonddisplaytype.
Tocreateahotkeythatswitchestoaparticulartool,chooseTOOLMODEforacommandanduseanyofthesecom-
mandnamesforavalue:
LASSO
TLCPLATE
MARQUEE
BENZENE
3DTRACKBALL
CYCLOPENTADIENE
MASSFRAG
CYCLOHEXANECHAIR2
ERASER
CYCLOHEXANECHAIR1
TEXT
CYCLOOCTANE
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SOLIDBOND
CYCLOHEPTANE
MULTIBOND
CYCLOHEXANE
DASHEDBOND
CYCLOPENTANE
PEN
CYCLOBUTANE
HASHEDBOND
CYCLOPROPANE
ARROW
TEMPLATE
HASHEDWEDGEDBOND
SNAKINGCHAIN
ORBITAL
ACYCLICCHAIN
BOLDBOND
QUERY
DRAWINGELEMENTS
TABLE
WEDGEDBOND
ARC
BRACKET
WAVYBOND
HOLLOWWEDGEDBOND
CHEMICALSYMBOLS
Note:ThefeaturesthatareavailabledependsonthelevelofChemBioDrawyouhave.
Description
Thetooldescriptionexplainswhateachhotkeydoes.
EditingtheHotkeys.xmlfile
ToeditChemBioDrawhotkeys:
1. Openthehotkeys.xmlfileinatexteditor.
2. Navigatetotheappropriatehotkeylistinthehotkeys.xmlfile.
3. Eitheraddanewhotkeyentryusingtheappropriateformatandvaluesoreditanexistinghotkeyinthelist.
4. Savethehotkeys.xmlfile.
5. ExitandrestartChemBioDraw.
Caution:Exercisecautionwheneditinghotkeys.xmlfile,sinceiftheformattingisincorrect,itwillnotberead,and
somefunctionsofChemBioDrawmayceasetoworkcorrectly.Makeabackuptheoriginalcopyofthefilepriorto
makinganychanges.
WorkingwithColor
Youcancreatefullcolorpresentationsofyourchemicaldrawingstoappearonyourmonitor,printonacolorprinter,or
create35mmslidesusingafilmprinter.
Mostcomputerscandisplayupto16millioncolors,butthenumberofcolorsmaybelimitedbyyourmonitoranddis-
playcard.
WhatYouCanColor
InChemBioDraw,youcanchangethecolorofthebackground,foreground,orindividualobjectsandelements:
Backgroundcolor.Thecolorofthedocumentwindow.Bydefault,thebackgroundiswhite.
Foregroundcolor.Thecolorofobjectsthatyoudraw.Bydefault,theforegroundisblack.
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Individualobjects.Youcanassigncolorstoobjectstohelpthenstandoutfromotherobjects.
Individualelements.Youcanassigncolorstospecificatomsorelementsinastructure.
Tochangethebackgroundandforegroundcolors:
1. NavigatetoFile>DocumentSettingsandselecttheColorstab.
2. Selectthebackgroundandforegroundcolors.
3. ClickOK.
ColorbyElement
Youcannowcoloratomlabelsusingcolorsassociatedwiththeiratomicsymbols.Youcanassigncolorstoelements
intheperiodictable.Wheneveryouuseaparticularelementinyourdrawing,theelementappearsinsamecoloryou
assignedtoitintheperiodictable.
Toassigndifferentcolorstoelementsinaperiodictable:
1. NavigatetoView>ShowPeriodicTableWindow.Theperiodictableappears.
2. Double-clickanelement.Thecolorpaletteappears.
3. SelectacolorandclickOK.
Note:ThemodifiedcolorsaresavedwhenyouexitChemBioDraw.
Toapplyacolortoastructure:
1. Selectthestructure.
2. NavigatetoColor>ByElement.
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Note:Theatomcolorsarenotdynamicallyset,hencechangingthelabeldoesnotresetthecolor.
TheColorPalette
Usethecolorpalettetospecifythecolorofobjectsandtextinthedocumentintheactivewindow.Apaletteisstored
ineverydocumentandstylesheet.Youcanusestylesheetstocreateaseriesofdocumentswiththesamecolor
scheme.
CustomizingColors
Changesyoumaketothecolorpaletteaffectthecurrentdocumentonly.Youcansaveupto20colors.Formore
information,see"DocumentandObjectSettings"onpage23.
Note:Ifyouselectanobjectorgroupthatcontainsmultiplecolors,acheckmarkappearsnexttoeachofthecol-
orsintheColormenu.Thecheckmarkalertsyouthatachangewouldaffectmorethanonecolor.
Tochangethecolorpaletteinthecurrentdocument:
1. NavigatetoFile>DocumentSettings.TheDocumentSettingsdialogappears.
2. ClicktheColorstab.
3. Clickthecolortochange(eitherbackgroundorforeground)andselectOther.TheColordialogopens.
4. ClickthenewcolorintheBasicColorsortheCustomColorssection.
5. ClickOK.ThecolorchangestothenewcolorandappearsontheColormenu.
Toaddacustomizedcolor:
Figure4.2:Settingcustomcolors.A)Colorrefinerbox;B)Luminositybox.
6. ClickacolorintheColorRefinerboxtosetthehueandsaturation.
Thepointerturnsintoacrosshairwhenyouclick.Youcandragtoadifferentregiontochangethehueandsat-
uration.
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7. ClickintheLuminosityboxtosetthecolorbrightness.
8. Ifnecessary,changethehue,saturation,luminosity,andRGBcomponentsbytypingthevaluesinthetextboxes.
9. ClickAddtoCustomColors.
10.ClickOK.
TemplatesandColor
Thebackgroundandforegroundcolorsinatemplatefromthetemplatepop-uppalettearenotusedwhenthetemplate
isdrawninadocumentwindow.However,othercolorsinthetemplateareaddedtothecolorpaletteofthedocument
iftheyarenotalreadypresent.Formoreinformation,see"Autoscaling"onpage270.
SavingColorPaletteSettings
Youcansavethecolorpaletteinastylesheet.Thecolorpaletteissavedwithotherdocumentsettingssuchaspage
setupsettings,textsettings,anddrawingsettings.
PrintingBackgroundColor
Tochangewhetherthebackgroundcolorisprinted:
1. NavigatetoFile>Preferences.
2. Selectorde-selectPrintBackgroundColorontheGeneraltab.
3. ClickOK.
DocumentSettings
ChemBioDrawincludesalibraryofdocumentsettingsbasedonthosefoundinmanywell-knownscientificpub-
lications.Forexample,somejournalsmayrequiresubmittedarticlesbeformattedwithspecificmargins,fonts,page
size,andsoon.Ifyouplantosubmityourdocumenttoaspecificjournal,openinChemBioDrawthestylesheetfor
thatjournal.Youcanalsocreatestylesheetsofyourown.
Note:Thechangesyoumaketothedocumentsettingsisreflectedonlyinthecurrentdocumentandisnotavail-
ablethroughouttheapplication.
Tocreateyourownstylesheet:
1. Createanewdocument.
2. EnterthesettingsinthePageSetup,Drawing,TextSettings,andColorpalettedialogboxes.
3. NavigatetoFile>SaveAs.
4. IntheSaveAsdialogbox:
a. SelecttheChemBioDrawstylesheetsfileformat.
b. Typeanameforthedocument.
c. SavethetemplateintheChemDrawItemsfolder.
5. ClickOK
.
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ACSDocument1996
FixedLength:14.4pt
BoldWidth:2pt
LineWidth:0.6pt
MarginWidth:1.6pt
HashSpacing:2.5pt
ChainAngle(degrees):120
BondSpacing(%oflength):18
AtomLabelFont:
AtomLabelSize:10pt
CaptionFont:
CaptionSize:10pt
DrawingArea(WidthxHeight):540ptx720pt
PageSize:USLetter
Reduction(%):100
Adv.SynthCatal.
FixedLength:17pt
BoldWidth:2pt
LineWidth:1pt
MarginWidth:1.6pt
HashSpacing:2.5pt
ChainAngle(degrees):120
BondSpacing(%oflength):18
AtomLabelFont:
AtomLabelSize:10pt
CaptionFont:
CaptionSize:12pt
DrawingArea(WidthxHeight):540ptx720pt
PageSize:USLetter
Reduction(%):100
J.Chin.Chem.Soc.
FixedLength:18pt
BoldWidth:2.5pt
LineWidth:1pt
MarginWidth:2pt
HashSpacing:2.5pt
ChainAngle(degrees):120
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BondSpacing(%oflength):20
AtomLabelFont:
AtomLabelSize:12pt
CaptionFont:
CaptionSize:12pt
DrawingArea(WidthxHeight):693ptx918pt
PageSize:USLetter
Reduction(%):80
J.Mol.Mod.(1column)
FixedLength:14.4pt
BoldWidth:2pt
LineWidth:0.6pt
MarginWidth:1.6pt
HashSpacing:2.5pt
ChainAngle(degrees):120
BondSpacing(%oflength):18
AtomLabelFont:TimesNewRoman
AtomLabelSize:10pt
CaptionFont:TimesNewRoman
CaptionSize:10pt
DrawingArea(WidthxHeight):8.5cmx25.4cm(1
column);17cmx25.4cm(2column)
PageSize:USLetter
Reduction(%):100
NewDocument
FixedLength:30pt
BoldWidth:2pt
LineWidth:1pt
MarginWidth:2pt
HashSpacing:2.7pt
ChainAngle(degrees):120
BondSpacing(%oflength):12
AtomLabelFont:
AtomLabelSize:10pt
CaptionFont:
CaptionSize:12pt
DrawingArea(WidthxHeight):7.5inx10in
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