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I/Draw
TheI/DrawthemechangesthelookoftheMaintoolbar.However,besideschangingthetoolbar,youcanselectthe
I/Drawmodetoactivatetwootherhelpfulfeatures:
Sproutrings(asopposedtospirorings).
ThedefaultstylesheetischangedtoI/DrawStyles.cds.
ToactivatetheI/Drawmode,navigatetoFile>PreferencesandclickI/DrawMode.
DefaultDocumentLocation
Youcansetthedefaultfiledirectoryforeachtimeyouopenafile.
Tosetthedefaultfiledirectory:
1. NavigatetoFile>Preferences.ThePreferencesdialogappears.
2. ClicktheDirectoriestab.
3. ClicktheUseDocumentsLocationcheckboxandtypeinorbrowsetothelocationtouse.
DefaultOpenFileFormat
TosetthedefaultfileformatintheOpendialogbox:
1. NavigatetoFile>Preferences.ThePreferencesdialogappears.
2. ClicktheOpen/Savetab.
3. ClickUseDefaultFileFormatintheOpeningFilessection,andchoosethefileformat.
SettingtheDefaultTool
Youcanchoosewhichtoolisselectedwhenyouopendocuments.
1. NavigatetoFile>Preferences.ThePreferencesdialogappears.
2. ClicktheOpen/Savetab.
3. UnderOpeningFiles,selectatool.
NewLinesandClosingTextBoxes
Tocreateanewlineinacaptiontextboxpresseither<Enter>or<Return>.Tocreateanewlineinanatomlabel
press<Alt>+<Enter>.Toclosethetextbox,clickoutsidethetextboxorselectanothertool.
Tochangethedefault:
1. NavigatetoFile>Preferences.
2. ChoosetheappropriateoptionontheBuilding/Displaytab,tochangethedefaultfor:
AtomLabelText-Require<Alt>+<Enter>tocreatenewlineinAtomlabels.
CaptionText-Require<Alt>+<Enter>tocreatenewlineinCaptions.
3. ClickOK.
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HighlightBoxTolerance
Tolerancedeterminesthesizeofthehighlightboxandhowcloseyoumovethecursortoanobjecttoactivateit.The
defaultsettingfortheToleranceis5pixels.Atthissetting,thehighlightboxappearsonbondsifthepointerislocated
5pixelsorlessfromanypointonthebond.
Tosetthetolerance:
1. NavigatetoFile>Preferences.
2. OntheGeneraltab,selectortypethetolerance.Thischangeaffectsalldocuments.
TheChemDrawItemsFolder
Thefoldercontainsthepreferences,hotkeys,nicknames,andisotopesfiles;scripts,andthegenericnicknamesfile.
ItalsocontainstemplatedocumentsandtemplateStationeryPads.YoucanhavemultipleChemDrawItemsfolders.
Thisisusefulincorporateinstallationsformaintainingpersonalfilessuchasnicknamesandstandardtemplates.
ThelocationoftheChemDrawItemsfolderisbasedonyouroperatingsystem.IfyouareusingChemOffice2014,the
folderisat:
C:\ProgramData\CambridgeSoft\ChemOffice2014\ChemDraw\ChemDrawItems
ToaddapathtoaChemDrawItemsfolder:
1. NavigatetoFile>Preferences.ThePreferencesdialogappears.
2. ClicktheDirectoriestab.
3. ClickAddNew,browsetoalocation,andclickOK.Anewpathisaddedtothelist.
4. Torearrangethesearchorder,clickMoveUpandMoveDown.
5. Todeleteapath,clickRemove.Todeletealladdedpaths,clickDefaultPaths.
DefaultStyles
ChemBioDrawsavesdefaultstylesasastylesheet.WhenyoulaunchChemBioDraw,thelaststylesheetyouuse
opensasthedefault.Ifyouchoosedifferentone,thatfilebecomesthedefault.
Youcansetadefaultthatisnotchanged:
1. NavigatetoFile>Preferences.
2. OntheOpen/Savetab,browsetothedefaultstylesheet.
3. DeselectOpeningAnyStyleSheetChangesDefault.
4. ClickOK.
Toviewthedefaultstyle,clicktheFilemenu.TheNewmenuitemdisplaysthenameoftheStyleSheet.
SavingCustomizedStyles
Everynewdocumentyoucreateusesastylesheetfileforitsdocumentsettings.Thesefilescanalsocontainpre-
definedobjects.Whenyoucreateanewdocument,youactuallycreateanuntitledcopyofthestylesheet.Changes
youmaketothecopydonotaffectthefile.
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YoucancreateastylesheetwithyourowncustomizedsettingbysavingitasaCDSfile.IfyoustoretheCDSfilein
theChemDrawItemsfolder,itappearsintheOpenTemplatesmenu(undertheFilemenu).
Tosaveadocument’ssettingasastylesheet:
1. NavigatetoFile>SaveAs.TheSaveAsdialogappears.
2. Namethefileandchangethetype(inOSX:format)toCDStyleSheet(cds)
3. TosavethefileintheChemDrawitemsfolder,clickGoToChemDrawItems.
4. ClickSave.
CustomizingToolbars
ThelookandarrangementoftoolbarsaredefinedbyasetofXMLfiles.IfyouarefamiliarwitheditingXMLfiles,your
canmodifythetoolbarforthewayyouwork.Youcanremove,rename,andresizebuttons;changebuttonicons,or
movethemfromonetoolbartoanother.Youcanalsocreateordeletetoolbars.
TheToolbarSchema
TheToolbars.xsdfilecontainstheschemadefinitionsforallthetoolbars.Theseincludedefinitions(butnotthecon-
tent)forthetoolbars,thepop-uptext,andthestatusbartext.
TheToolbarXMLFiles
TheToolbarsdirectoryatC:\Documents and Settings\All Users\Application Data\Cam-
bridgeSoft\ChemOffice2014\ChemDraw\GUI\Common\XML\Toolbars,containsthesubdirectorywhere
thetoolbarsxmlfilesarestored.Thefilesarestoredaccordingtotheskinsinwhichtheyareused.Thesearethefiles
youwillmostcommonlyedittocustomizethetoolbars.TheXMLfilewhenlaunched,validatesitselfagainsttheTool-
bars.xsdfilestoredonline.
EditingtheXMLFiles
Youcaneditthefilesusinganyxmlortexteditor.Afteryousavethefiles,exitandrestartChemBioDraw.Your
changeswilltakeeffect.
CreateabackupofallXMLfilesyouintendtoedit.
Note:Allimagesfilesyouuseasiconsmustbein.pngformat.
DocumentandObjectSettings
Youcanapplydocumentandobjectsettingstothecurrentdocument.Thechangesyouspecifyinthedocumentset-
tingsareapplicableonlywithinthedocumentandarenotapplicablethroughouttheapplication.Thechangesyouspe-
cifyintheobjectsettingsarespecifictotheselectedobject.
Settingsinclude:
Drawingsettings.Setdrawingoptionssuchasthefixedlengthusedtodrawbonds.
Captionandlabeltextsettings.Settextoptionssuchasthefontusedforatomlabelsandcaptions.
Colorsettings.Setavailablecolorsforobjectsandthedocumentbackground.
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Print/PageSetup.Setoptionssuchasthepagesizeusedandtextdisplayedinfooters.
Youcanapplydocumentsettingsinthefollowingways:
CustomizesettingsfortheentiredocumentusingtheDocumentSettingsdialog.
Applysettingstotheentirecurrentdocumentfromanexistingdocument.
Applysettingstoselectedobjectsinthecurrentdocumentfromanexistingdocument.
DrawingSettings
Drawingsettingsaffecthowbondsandotherobjectsaredrawn.Youcanconfigurethedrawingsettingsforanentire
documentorforaparticularobjectasfollows:
Fortheentiredocument,navigatetoFile>DocumentSettingsandselecttheDrawingcategory.
Foranobject,usetheObjectSettingsdialogbox.
Changesyoumaketothedrawingsettingsaffecttheactivedocumentwindowonly.Youcansavedrawingsettingsin
stylesheets.
Toapplysettingsfromotherdocumentstoyourdocument,navigatetoFile>ApplyDocumentSettings.
ThevariousoptionsavailableunderDrawingcategoryincludes:
FixedLength.Constrainthebondsdrawntothelengthyouspecify.Thisalsoadjuststhepreferredbondlengthwhen
youusetheCleanUpStructurecommand.See"DrawingFixedLengthBonds"onpage56and"AttachmentPoints"
onpage122.
BondSpacing.Setthedistancebetweenthelinesindoubleortriplebonds.Thedistanceisseteitheras:
Thepercentofthelengthofthebond(between1and100).Thisallowsforproportionalspacingifdifferentbond
lengthsareused.
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Anabsolutevalueyouchooseintheunitsspecifiedforyourdocument.
BoldWidth.Setthewidthofthelineusedwhenboldandwedgebondsaredrawn.TheBoldWidthsettingmustbe
greaterthantheLineWidthsetting.Theendofawedgeis1.5timestheboldwidth.
LineWidth.Setthewidthofallbonds,lines,andarrowheadsinthedrawing.
MarginWidth.Changetheamountofspacesurroundingallatomlabelsthatwilleraseportionsofthebondstowhich
theyareattached.Themarginwidthalsodeterminestheamountofwhitespacesurroundingthefrontbondsinabond
crossing.See"BondCrossing"onpage55.
HashSpacing.Setthespacingbetweenthehashedlinesusedwhenwedgedhashedbonds,hashedbonds,dashed
bonds,dashedarrows,ordashedcurvesaredrawn.
ChainAngle.Settheangle(from1to179degrees)betweenbondscreatedbytheAcyclicchaintoolormodifiedby
theCleanUpStructurecommand.See"Chains"onpage69and"AttachmentPoints"onpage122.
Units.SettheunitsusedintheObjectSettingsdialogboxtocentimeters,inches,points,orpicas.
AtomandBondIndicators.Setwhichindicatorstodisplay.See"AtomNumbering"onpage124.
ConfiguringDocuments
1. NavigatetoFile>DocumentSettings.
2. ClicktheDrawingcategoryandconfigurethesettings.
3. ClickOK.
TerminalCarbonLabels
Bydefault,ChemBioDrawdoesnotdisplayterminalcarbons.
Todisplayterminalcarbonlabels:
1. NavigatetoFile>DocumentSettings.
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2. SelecttheAtomLabelscategory.
3. SelectShowLabelsOnTerminalCarbons.Seefigurebelow:
ConfiguringObjects
Toconfigurethedrawingsettingsforaselectedobject:
1. Selecttheobject.
2. NavigatetoObject>ObjectSettings.
3. ConfigurethesettingsandclickOK.Thesettingsyouchoseareappliedonlytotheselectedobject.
AnalysisandProperties
Youcanpastefundamentalstructurepropertiesintoyourdrawing.Youcanalsorenamethesepropertieswhen
desired.Forinstance,youmayconsiderrenaming“MolecularWeight”to“MW”tosaveroomonthepage.The
changesyoumakeapplyonlytothepropertiesyoupasteinyourdrawing.ThenamesintheAnalysisandChemical
Propertiesdialogboxesremainunaffected.
Tochangethenamesoftheproperties:
1. NavigatetoFile>DocumentSettings.
2. SelectthePropertyLabelscategory.Seefigurebelow:
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3. IntheAnalysiswindow,selectthepropertytorename.
4. ClickEditLabelandtypeanewnameintheEditLabeltextbox.ClickOK.
5. Typethenewname,andclickOK.
6. Repeatstep4forotherproperties.
7. ClickOK.
FormattingCaptions
Textsettingsaffecthowcaptionsandatomlabelsforthecurrentdocumentaredrawnandformatted.
Formattingoptionsinclude:
Font(fonttype)
Size(fontsize)
Style(fontandbaselinestyle)
Linespacing
Alignment
SettingFontParameters
ChangingtextformatsintheDocumentSettingsdialogaffectsthecurrentdocumentonly.Youcanalsochangeset-
tingsforindividualobjectsbyusingtheObjectSettingsdialog,theTextmenu,ortheStyletoolbar.
Toeditthedocumenttextsettingsforcaptionsandatomlabels:
1. ClickFile>DocumentSettings.
2. IntheDocumentSettingsdialog,clickTextCaptionsorAtomLabels.
3. Changethesettingsasdesired.Theoptionsaredescribedinthefollowingsections.
4. ClickOK.Theformattingisappliedtothecurrentdocument.
SettingtheBaselineStyle
Youcanspecifythesebaselinestyles:
Normal.Usethisforstandardtext.
Superscript.Reducesthetextsizebyabout25 percentandraisesitsbaseline.
Subscript.Reducesthetextsizebyabout25 percentandlowersthebaseline.
Formula.Formatsinawaythatisappropriateformostchemicalformulas,thatis,numbersaresubscripted.You
must,however,manuallycapitalize.
Youcanalsoapplymultiplestylestodifferentportionsofasinglecaption.
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StyleIndicators
SelectanytextinthedocumentwindowandnavigatetoText>Styletoviewthestylesthathavebeenapplied.A
checkindicatesthestyleappliestoalltheselectedtext.Ahyphenindicatesthestyleappliestosomeoftheselected
text.
SpecifyingLineSpacing
Youcanspecifythesetypesoflinespacing:
Automatic.Consistentlyspacedlinesoftextbasedontheheightofthetallestcharacterinthecaption.Thisisthe
defaultlinespacing.
Variable.Linesoftextwithdifferentspacingbasedonthetallestcharacterandthelowestdescenderineachline.
Fixed.Consistentlyspacedlinesusingaspacingthatyouspecify.
AligningText
Youcanaligncaptionsandatomlabelstojustifytexttosuityourneeds.Theoptionsavailabledependonwhetheryou
arealigningcaptionsoratomlabels.ApplysettingsintheObjectSettingsdialog.
Toopentheobjectsettingsdialog:
1. Selectacaptionoratomlabel.
2. NavigatetoObject>ObjectSettings.TheObjectSettingsdialogappears.
Captions
YouspecifythecaptionjustificationandlinespacingontheTextCaptionstaboftheObjectSettingsdialog.Alltextin
asinglecaptionmusthavethesamejustificationandlineSpacing.
Therearefouravailablejustifications:
FlushLeft.Createsleft-justifiedcaptiontext.
Centered.Createscenteredcaptiontext.
FlushRight.Createsright-justifiedcaptiontext.
Justified.Createsright-leftjustifiedcaptiontext.
AtomLabels
UsetheCentered,FlushLeft,FlushRight,StackedAbove,orAutomaticjustificationstocreatelabelsthat
identifyatomsandfunctionalgroupsinyourchemicalstructurewithoutobscuringbondsorotheratomlabels.
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Note:WhenusingStackedAbovejustification,enterthetokensfromtoptobottomusing<alt>+<enter>togotoa
newline.Ifyouchangethejustificationafterthelabelisentered,warningmayappear.
Examplesoftheatomlabeljustificationsareshownbelow.
Figure4.1:Atomlabeljustification.A)stackedabove;B)centered;C)flushleft;D)flushright.
AutomaticAlignment
Whenyoujustifyatomlabelsautomatically,ChemBioDrawbreaksthelabelintotokens.Atokenconsistsofanupper-
caseletterfollowedbyanynumbersorlowercaseletters.Thefirsttokenisattachedtotheatomandtherestofthe
labelappearswithoutobscuringotherpartsofthechemicalstructure.
Forexample,tocreateN-methylpiperidine,labelanatomincyclohexaneasNCH
3.
Thislabelhasthreetokens,N,C
andH
3
.IfyoulabelC3,thetokensareplacedfromlefttorightbecausetherearebondstotheleftoftheatom.
IfyoulabelC5,thetokensappearfromrighttoleftbecausetherearebondstotherightoftheatom:
Youcanforceanentiremulti-atomlabeltobeatokenbydefiningitasanickname.Thispreventsthelabelfromflip-
pingwhenappliedtotheleftsideofastructure.
Forexample,ifyoudefinethenicknameCH
3
,andlabelC5withthecombinedlabelandnicknameNCH
3
,thefinalori-
entationisCH
3
NinsteadofH
3
CN.Inthiscase,thenickname,CH
3
,isatoken.
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IfyoulabelC1,thesecondandthirdtokensareplacedabovethefirsttokensincetherearebondsbelowtheatom.
IfyoulabelC4,thesecondandthirdtokensareplacedbelowthefirsttoken.
ChangingDefaultFormats
Eachnewcaptionoratomlabelusesdefaultdocumentsettingsforthefont,font-size,andstyleofcaptionsandatom
labels.
Youcanchangetheformatby:
Changingthedocumentsettingsforsubsequentdrawingsinthecurrentdocument.
ChoosinganewformatforanindividualcaptionorlabelfromtheTextmenuortoolbarbeforeyoutype.
Selectingtextandapplyinganewformattoanindividuallabelafteryoutype.
SettingsforNewText
Tospecifythetextsettingsfornewcaptionsandatomlabelsinthecurrentdocument:
1. NavigatetoFile>DocumentSettings.
2. ClickTextCaptionsorAtomLabelsintheDocumentSettingsdialog.
3. Selecttheappropriateoptions.
4. ClickOK.
Thesesettingsaffectallnewcaptionsoratomlabelsinthecurrentdocument.Tousethesesettingsinnewdoc-
uments,savetheminastylesheet.Formoreinformation,see"DocumentandObjectSettings"onpage23.
FormattingaCaptionorLabel
Youcansetthetextformatforanindividualcaptionoratomlabelbeforeyoutype.Theformatchangeisappliedonly
tothecurrenttext.
Tosetthetextformatbeforeyoutype:
1. SelecttheTexttoolandclickinthedocumentwindow.Atextboxappears.
2. Tosetthetextformatdooneofthefollowing:
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