ResizingObjects
Youcanresizeobjectsbydraggingtheresizehandleofaselectedobjectorbyscaling.
Toresizeaselectedobjectproportionately:
1. Selecttheobjectstoresize.Theresizehandleislocatedinthelowerrightcorneroftheselectionrectangle.
2. PointtotheResizehandle.Thecursorbecomesadouble-headedarrow.
3. Dragtheresizehandleuntiltheobjectisthesizeyouwant.
Inmostcases,whenyouresizeanobject,theaspectratiooftheobject(theratiooftheheighttowidth)doesnot
change.However,itispossibletodistortcertainobjectsincludingchemicalstructures,circles,boxes,andovals.
Todistortanobjectinthehorizontalorverticaldirection:
1. Selecttheobject
2. Dooneofthefollowing:
Dragthehandleonthedesiredside
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<Shift>+dragtheResizehandleinthedesireddirection.The<shift>keymodifiestheresizeoperationsothat
youcandistortobjectsalongtheX-axisorY-axis.
RotatingObjects
1. Selectanobjecttorotate.Forobjectsthatcanberotated,therotationhandleappearsatthetopoftheselection
rectangle.
2. Dragtherotationhandleclockwiseorcounterclockwise.
3. Torotateanatomlabelwithastructure,pressthe<control>keywhiledraggingthestructure.
Note:Ifasingleatomisunselectedwhenastructureisrotated,thestructurerotatesaroundtheunselectedatom,
asshownintheexamplebelow:
Torotateaselectedobjectbyaspecifiedangle:
1. Dooneofthefollowing:
NavigatetoObject>Rotate.
Double-clicktherotationhandle.TheRotateObjectsdialogappears.
2. EnteranumberandclickeitherdegreesCWforaclockwiserotationordegreesCCWforcounterclockwiserota-
tion.
3. Torotatetheatomlabeltext,selectRotateAtomLabels.
4. ClickRotate.Objectsarerotatedaroundthecenteroftheselectionrectangle.
Torepeatthesamerotationonanyobjectinthedocumentwindow:
1. Immediatelyafterrotatinganobject,selecttheotherobjectstorotate.
2. NavigatetoEdit>RepeatRotate.
MovingtheCenterofRotation
Bydefault,anobjectturnsarounditscenterwhenyourotateit.However,youcanmovethecenterofrotationsothat
theobjectrotatesaroundanatomorsomeotherlocationonthepage.
Tomovethecenterofrotation:
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1. Selecttheobject.Acenterofrotationindicator(‘+’)appearsinthecenteroftheobject,asshowninthefigure:
Figure6.8:A)Centerofrotation
2. Whilepressingthe<alt>key,clickanddragtheindicatortoanotherlocation.Seetheexamplebelow:
Figure6.9:B)centerofrotationmoved
3. Torotatetheobject,clickanddragtherotationhandle.
Toresetthecenterofrotationtoitsdefaultposition,deselecttheobject.
Note:Ifyoudragclosetoanatom,thecenterofrotationwillsnaptotheatomposition.
MovingObjects
1. Selectanobjecttomoveusingaselectiontool.
2. Clickanddragtheobjecttoanewlocation.
Toconstrainthemovementtothehorizontalorverticaldirection,<shift>+dragtheselectedobjects.
Smallincrementalmovementsareoftenusefulforaligningobjects.
Tomoveanobjectaincrementally:
1. Selecttheobject.
2. Pressanarrowkey.Theselectedobjectmoves1pointinthedirectionofthearrow.
Note:Tomoveinalargerincrement,holddownthe<alt> keywhilepressinganarrowkey.Theselectedobjects
moves10pointsinthedirectionofthearrow.
CopyingObjects
1. Selectoneormoreobjects.
2. <Control>+dragtheobject(s)tocreateacopyandpositionit.
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Toconstrainthecopytomoveonlyverticallyorhorizontallywhilepositioningit,holddownthe<shift>+<control>
keys.
TheInfoWindow
Thiswindowdisplaysthesizeandpositionofthepointerandofanythingyouhaveselected.Toshow,orhide,thewin-
dow,navigatetoView>ShowInfoWindow.
Pointer
XandYdisplaythecurrentmousecoordinates.dXanddYindicatethechangeinXandYofamovedselection.
Selection
XandYdisplaythepositionofaselection.WandHarethewidthandheight.
Other
Angleistheangleofabondorrotationofaselection.Dististhebondlengthorthedistanceaselectionhasmoved.
Whenresizinganobject,%indicatesthecurrentpercentageoftheoriginalsize.
MirrorImages
YoucanreflectstructuresthroughplanesperpendiculartotheX-axisorY-axis.Bycopyingastructure,youcancreate
itsmirrorimagetocreatestereoisomers.
Tocreateamirrorimage:
1. Drawastructurewithdefinedstereochemistry,forexample,wedgedbonds.
2. <control>+dragthestructuretocopyit.
3. Withthecopystillselected,navigatetoObject>FlipHorizontalorFlipVertical.YoucanalsousetheFlipHori-
zontallyorFlipVerticallytoolsontheObjecttoolbar.
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DeletingObjects
Todeleteselectedobjects,dooneofthefollowing:
Pressthe<delete>key.
NavigatetoEdit>Clear.
UsetheErasertool.
JoiningStructures
Tojointwostructuressothattheyshareabond:
1. Selectabondinthefirststructure.
2. <Shift>+clicktoselectthebondinthesecondstructure.
3. NavigatetoObject>Join.
Tojointwostructuressothattheyshareanatom:
1. Positionthetwochemicalstructuressothattheatomsyouwanttofuseareneareachother.
2. Selectthetwoatomstobejoined.
3. NavigatetoObject>Join.
Note:Whenyoujointwodifferentlycoloredbondsoratomlabels,thecolorofthefrontobjectbecomesthecolorof
theresultingjoinedobject.Whenyoujointwoatomsthatarelabeled,thefrontatomlabelbecomestheatomlabel
oftheresultingatom.Formoreinformationaboutfronttobackorderingofobjects,see"PageLayout"onpage10.
GroupingObjects
Agroupisacollectionofobjectsthatactasasingleobject.Youcanselectallgroupedobjectsbydouble-clickingon
anyofthecontainedobjectswithaselectiontool.
Whenyougroupobjectssothattheindividualobjectsinthegroupcannotbeselected,youcreateanintegralgroup.
Whenyouselectanyobjectinanintegralgroup,theentiregroupisselected.Objectswithinanon-integralgroupcan
beselectedindividuallyandmanipulatedwhilestillremainingpartofthegroup.
Youcanchangethepositionororientationofgroupedobjects.Individualobjectswithinthegroupmaintaintheirrel-
ativepositionswhenthegroupedobjectsarerotated,aligned,ordistributed.
Atomsandbondsmakingupasinglechemicalstructurearealwaysgrouped.Ifyougrouppartofastructurewithother
objects,theresultinggroupcontainstheentirestructure.Ifyouaddatomsorbondstoagroupedstructure,thenew
atomsandbondsarepartofthegroup.
Togroupobjects:
1. Selecttheobjectsusingaselectiontool.
2. NavigatetoObject>Group.
Toselectanindividualobjectwithinagroup,movetheselectiontoolovertheobjectuntilitishighlighted,andclick
once.
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Toselectgroupedobjects,movetheselectiontooloveranobjectinthegroupuntilitishighlighted,anddouble-click
it.
UngroupingObjects
Toungroupobjects:
1. Selectagroup.
2. NavigatetoObject>Ungroup,orright-clickthegroupandselectGroup>Ungroup.
Tocreateagroupsothatindividualobjectscannotbeselected(integralgroup):
1. Selecttheobjects.
2. NavigatetoObject>Group.
3. Right-clickthegroupandselectGroup>Integral.
Torestoreanintegralgrouptoaregulargroup:
1. Selecttheintegralgroup.
2. Right-clickthegroupanddeselectGroup>Integral.
Note:Manyoftheshapesanddrawingswithinthetemplatedocumentsareintegralgroups.However,theycanbe
ungroupedandedited.
Scalingobjects
Toscaleoneormoreobjectstoadifferentsize:
1. Selecttheobject(s).
2. Dooneofthefollowing:
GotoObject>Scale.
Double-clickaresizehandle.TheScaleObjectsdialogappears.
3. Dooneofthefollowing:
ToscalebondssothattheFixedLengthbecomesthenewmedianbondlength,selectScaleselectedobjectsso
thatmedianbondisFixedLength(0.4167in).
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Toscalethebondstoanewfixedlengththatyouspecify,selectScaleselectedobjectssothatmedianbond
is,andtypethenewmedianbondlengthinthetextfield.
Toscaletheobjecttoapercentageofthecurrentsize,selectScaleby,andspecifythepercentageinthetext
field.Avaluegreaterthan100%enlargesit;avaluelessthan100%reducesit.
4. ClickScale.
CenteringObjects
Tocenteranobject(orgroupofobjects)onthepage:
1. Selecttheobject.
2. NavigatetoObject>CenteronPage.
Theselectedobjectmovessothatthecenteroftheselectionrectangleisatthecenterofthepage.
AligningObjects
Youcanalignobjectsverticallyandhorizontallyalongtheircentersoredges.
Note:Objectsarealignedwiththeselectedobjectthatappearshighestonthepage.
Toaligntwoormoreobjects:
1. Selecttheobjects.
2. NavigatetoObject>Align.
Note:Ifyouselectonlypartofastructureorgroupwithaselectiontool,onlythatpartisusedforthealignment,
buttheentirestructureorgroupmoves.
DistributingObjects
Usethedistributecommandtodistributeobjectshorizontallyorverticallyandatanequaldistanceapart.
Todistributethreeormoreobjects:
1. Selecttheobjectstodistribute.
2. NavigatetoObject>Distribute,andchooseVerticallyorHorizontally.
Figure6.10:Distributingobjects
Thespacebetweentheobjectsisequalized.Theupper,lower,right,andleftpositionsofobjectsinyourselection
remainunchanged.
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CleanUpStructure
TheCleanUpStructurecommandisusedtoneatentheappearanceofmoleculesbyregularizingbondlengthsand
angles.Graphicobjects,suchasarrowsandaromaticcircles,arenotaffected.Youcanusethiscommandtoredraw
structuresthatyoumayhavedrawnfreehand,ortoneatenstructuresthatyoumayhaveimportedfromanotherapplic-
ation.
Forcertaincompounds,theCleanUpStructurecommandproducesastructurethatextendsbeyondtheboundsof
thepage.Toviewtheentirestructure,scalethestructureorincreasethesizeoftheprintedpage.See"Scaling
objects"onpage86and"PageSetup"onpage12.
TheCleanUpStructurefeaturefollowstheserules:
BondsaresettothetargetFixedLengthspecifiedinthedocumentsettings.Formoreinformation,see"Document
Settings"onpage38.
Aringisredrawnonlyifallofitsbondsareselected.
Multi-attachedatomlabels,variableattachmentpoints,andmulti-centerbondscannotbecleaned.
Structuresarerotatedsothatasmanybondsaspossiblearedirectedatamultipleof15degrees.
CleanUpStructurepreservesstereochemicalmeaningratherthanthepreciseidentityofwedged,orhashed
bonds,asshownbelow.
TouseCleanUpStructure:
1. Selectthestructure,orpartofthestructure,tocleanup.
2. NavigatetoStructure>CleanUpStructure,ortype<shift>+<ctrl>+<K> > .
Note:TheCleanUpStructurecommandredrawsyourstructureiniterations.Therefore,youmayneedtoselect
thecommandmorethanonce.
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Youcanalsocleanupareaction,orabiopolymer.Formoreinformation,see"CleanUpReactions"onpage130and
"CleanUpBiopolymers"onpage106
CheckingStructures
Youcancheckthechemistryofaselectedstructure,partofastructure,orcaption(inFormulastyle)withtheCheck
Structurecommand.Thestructureischeckedusingnormalvalencesandelements,anddefinednicknames.
Tocheckthevalencesofallselectedatomsinastructure:
1. Selectastructure,partofastructure,orcaption.
2. NavigatetoStructure>CheckStructure.
Ifastructureisincorrect,amessagewindowappears,forexample:
3. Tocontinuecheckingthestructure,clickIgnore.
4. Toignoreallsubsequenterrors,clickIgnoreAll.
5. Tostopcheckingforerrors,clickStop.
CheckingCopiedStructures
Toautomaticallyperformacheckstructureanalysiseachtimeyoucopyastructurefromtheclipboard:
1. Navigateto File>Preferences.
2. FromtheGeneraltab,clickCheckStructureWhenCopyingtoClipboardorExporting.
Thischangeaffectsalldocuments.
ChemicalWarnings
ChemBioDrawcheckschemicalsyntaxasyoudraw.Ifitfindsanerrorinyourstructure,awavyredboxappears
aroundtheobject.Theboxdisplaysonthescreenonlyanddoesnotprint.
DisablingChemicalWarnings
Warningsdisplaybydefault.Todisablechemicalwarnings,navigateto View>ShowChemicalWarnings.
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Todisableerrorcheckingonaspecificobject,right-clicktheobjectanddeselectDisplayWarningsonthecontext
menu.
WhenDisplayWarningsisdisabledforanobject:
Aredboxdoesnotappeararoundtheobject.
ProblemsarereportedbytheCheckStructurecommand(NavigatetoStructure>CheckStructure).
Toviewadescriptionoftheproblem,performoneofthefollowing:
Pointatthewarningwiththemousetodisplayatooltipthatdescribestheerror.
Right-clickthewarningandselectExplainThisWarning.
SelectthestructureandnavigatetoStructure>CheckStructure.
WarningPreferences
Toselectwhichtypesofchemicalwarningstodisplay:
1. NavigatetoFile>Preferences.
2. ClicktheWarningstab.
3. SelectthetypesofwarningsandclickOK.
Thetypesofwarningsarelistedbelow:
Warning
Description
ValenceandCharge
Errors
AnObjectdrawnhasanimpropervalenceorcharge.Forexample,whenpositiveandneg-
ativechargeshavebeenassignedtothesameelement,chargeshavebeenassignedin
morethanoneway,orachargehasbeenassignedtoanickname,genericnickname,or
alternativegroupname.
UnbalancedPar-
entheses
Parenthesesarenotmatchedintonestedopen-closepairs.
InvalidIsotopes
Generatedforinvalidisotopes.Forexample,thiswarningisgeneratedforeverylabelthat
hasanumericsuperscriptimmediatelyprecedinganatomicsymbol,wherethesuper-
scriptednumberdoesnotcorrespondtoarecognizedisotope.Forexample,
24
CH
3
.
IsolatedBonds
Anunlabeledsinglebondisnotattachedtootherbonds.
AtomsNearOther
Bonds
Anatomisclosetoabondbutnotattachedtoit.
UnspecifiedStereo-
Chemistry
Anasymmetriccenteriswithoutattachedwedged,hashed,dashed,orboldbonds.
AmbiguousSte-
reochemistry
Astereocenterwheretheabsolutestereochemistrycannotbedeterminedfromthestruc-
tureasdrawn.Forexample,thiswarningwouldbegeneratedforacarbonatomattached
byboldbondstofourdifferentligands.
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