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1. TodisplaytheQuerytools,navigatetoView>OtherToolbars>QueryTools,orclicktheQueryToolsicononthe
MainToolpalette.
2. OntheQuerytoolspalette,clickthetoolfortheflagyouwanttouse.
3. Clicknexttothestructuretowhichyouwanttoassigntheflag.
3DProperties
3Dqueriesareusefulinpharmacophoresearchingwhenlookingfora3Drelationshipamongatomsandbonds,(for
exampleinaseriesofpotentialreceptorligands).Tocreatea3Dquery,youaddgeometries(lines,planes,andsoon)
andconstraints(specifiedasranges)toaquerystructure.Forexample,youcanspecifythattwoatomsmustbe
between4and5Åapart,orthattwoplanesmustbeseparatedby80-100degrees.
Toassign3Dpropertiestoastructure:
1. Selectthestructureorsubstructure.
Note:Becausesome3Dpropertiesspecifyanorder,useSHIFT+Clicktoselectthemintheorderyouwant.
2. NavigatetoStructure>Add3DPropertyandselectanoptionfromthetablebelow.
Note:Inthetable,pointsmaybeatoms,centroids,orpoints.Linesmaybelinesornormals.
Angle.Definesanangleconstraintbetweenthreepoints(inorder).Indicatedasarange.
Dihedral.Definesadihedral(torsional)angleconstraintamongfourpoints(inorder),betweentwolines,ortwo
planes.Indicatedasarange.
Distance.Definesadistanceconstraintbetweentwopoints,apointandaline,orapointandaplane.Indicatedasa
range,inangstroms.
Line.Definesthebest-fitlinefortheselectedpoints.
Plane.Definesthebest-fitplanefortheselectedpoints,orforapointandaline.
ExclusionSphere.Definesanexclusionspherearoundapoint.Ifmorethanonepointisselected,theexclusion
sphereisaroundthefirstselectedpoint,andthesubsequentpointsareallowedwithintheexclusionspherewhenthe
queryisevaluated.Indicatedasarange,inangstroms,beginningat0.
Normal.Definesthenormalfromadefinedplaneinthedirectionofapoint.
Point.Definesapointpositionedataspecifieddistancefromafirstpointinthedirectionofasecondpoint(inorder),
orinthedirectionofthenormal.
Centroid.Definesapointpositionedattheaveragepositionofallotherpointsselected.
Note:
Allconstraintvaluescanbeeditedwiththetexttool.Onlyexclusionspheresshowthechange.
Whenyoucreateapoint,adialogappearswhereyouspecifythedistancefromthefirstselectedpointtothecal-
culatedpoint.ThedistancemaybeanabsolutevalueinÅorapercentageofthedistancebetweentheselected
points.
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Negativevaluesindicatethatthecalculatedpointisfurtherfromthesecondpointthanthefirstpointis,rather
thanbetweenthem.
Geometryandconstraintobjectsupdatewhenyouchangethestructure;theycannotbemovedindependently.
TheymaybeusedwithCDX,MOL,SKC,andTGFfiles(fullread-writecompatibility);theyarenotcompatible
withotherformats.
Theycan,however,besavedinprint-onlyformatssuchasTIFF.
ExportCompatibility
Becausequerypropertiesareusefulonlyinachemicaldatabase,youmusttransferyourstructuresfrom
ChemBioDrawintoyoursearchsystem.Notallfileformatssupportthesamequerypropertiesandnotallchemical
databasessupportthesamefileformats.Consultthedocumentationforyourdatabaseforwhichfileformatsaresup-
ported.
ThefollowingtableliststhequerypropertiesthatChemBioDrawwritestoSKC,TGF,andClipboardfileformats.The
CDXformatretainsallqueryproperties.
.
ExportedQueryProperties
ISIS™
Mol
Rxn
AtomProperties
Substituents
Unspecified
X
X
X
FreeSites
b
b
b
Upto
a
a
a
Exactly
X
c
X
c
X
c
ImplicitHydrogens
Notallowed
X
X
X
Allowed
X
X
X
RingBondCount
Any
X
X
X
Noringbonds
X
X
X
Asdrawn
X
X
X
Simplering
X
X
X
Fusion
X
X
X
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ExportedQueryProperties
ISIS™
Mol
Rxn
Spiroorhigher
X
X
X
Unsaturation
Unspecified
X
X
X
Mustbeabsent
Mustbepresent
X
X
X
ReactionChange
Maybeanything
X
X
Mustbeasspecified
X
X
ReactionStereo
Any
X
X
Inversion
X
X
Retention
X
X
Translation
Equal
Broad
Any
Narrow
AbnormalValence
NotAllowed
X
X
X
Allowed
X
X
X
BondProperties
BondType
Single
X
X
X
Dashed
X
d
X
Hashed
d
d
d
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ExportedQueryProperties
ISIS™
Mol
Rxn
WedgedHashed
X
X
X
Bold
X
e
e
Wedged
X
X
X
Wavy
X
X
X
HollowWedged
e
e
e
Dative
f
f
f
Double
X
g
X
X
DoubleEither
X
X
X
DoubleBold
h
h
h
Aromatic
X
X
X
Tautomeric
i
i
i
Triple
X
X
X
Quadruple
l
l
l
Any
X
X
X
S/D
X
X
X
D/A
X
X
X
S/A
X
X
X
Topology
Unspecified
X
X
X
Ring
X
X
X
Chain
X
X
X
ReactionCenter
Unspecified
X
X
Center
X
X
Make/Break
X
X
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ExportedQueryProperties
ISIS™
Mol
Rxn
Change
X
X
Make&Change
X
X
NotCenter
X
X
OtherQueryAttributes
GenericNicknames
X
j
X
j
X
j
ElementLists
X
ko
X
ko
X
ko
ElementNotLists
X
k
X
k
X
k
AlternativeGroups
X
X
m
AnonymousAlternative
Groups
n
n
LinkNodes
p
p
p
Bracketproperties
X
X
X
Atom-Atommapping
X
X
VariableAttachmentPos-
itions
3Dqueryproperties
a—Convertedtotheappropriatenumberofexactsubstituents.
b—Freesitescountsofzerotranslatedto“Substitutionasdrawn”;allotherfreesitesvalueswrittenassubstitution
countsequaltothetotalcurrentvalence,plusthefreesitesvalue.
c—Substituentcountsofgreaterthan5aretranslatedto“6ormore”.
d—Convertedtowedgedhashed.
e—Convertedtowedged.
f—Convertedtoasingle,withapositivechargeappliedtothatatomatthebaseofthedativebondandanegative
chargeappliedtotheatomatthepointofthedativebond.
g—InterpretedbyISIS™asunspecifiedcis/transstereochemistry.
h—Convertedtodouble.
i—Convertedtoaromatic.
j—OnlyM,X,Q,A;otherswrittenasaliases.
k—Truncatedtothefirst5elements.
l—Convertedtosingle.
m—AnRGfilewillbecreatedautomatically.
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n—Convertedtonon-anonymousalternativegroups.
o—Listsofgreaterthan5elementsconvertedtoalternativegroups.
p—Thelowendoftherepeatrangeisalwaystreatedas1.
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Sharing Information
Manyofthesystemcommandsyoucommonlyusetotransfercontentfromoneplacetoanothercanalsobeusedin
ChemBioDraw:
Copy/paste
Importandexportcontentfiles
Whenyouusetheclipboard,theobjectsyoucopycanbeedited.
TheClipboard
Youcanusetheclipboardtotransferpart,orall,informationwithinanactivedocumentwindowbetweenapplications
onthesamecomputeroronanetwork.Usethestandardcopy-and-pasteorcut-and-pastetoolstotransferinformation
toanyapplicationthatsupportsthesetools.Theinformationistransferredasadrawingobject.Double-clicktheobject
toedititinChemBioDraw.
YoucanalsousetheCopyAstooltotranslateaselectedstructuretoaSMILES,SLN,orInChI™string.
IftheClipboardcontainsstructuresandyoupasteintoanotherChemBioDrawdocument,thepastedinformationis
scaledtothesettingsinthenewdocument.Formoreinformation,see"Autoscaling"onpage270.
TextLineNotation
Usetextlinenotation1toexpandalineoftextintothestructurethatitrepresents.Severalsoftwarepackagesuse
SMILESstringstoenterandstorechemicalstructureinformation.
IfyouselectareactionandusetheCopyAsSMILEScommand,aSMIRKSstringiscopiedtotheclipboard.Ifyou
usethePasteSpecialSMILEScommandwhenaSMIRKSstringisontheclipboard,areactionispastedintoyour
document.
CreatingSMILESStrings
TocreatetheSMILESstringforastructure:
1. Selectthestructure.
2. NavigatetoEdit>CopyAs>SMILES.
TheSMILESstringistransferredtotheClipboard.
TodisplaytheSMILESstring,pastethestringinadocumentwindow.
WhentheSMILESstringisontheClipboard,youcantransferittoanotherapplicationthatcaninterpretSMILES
strings.
IfyoucopymorethanonestructurefromChemBioDrawtotheClipboard,theSMILESstringareseparatedbya
period.
1
ASMILESstringisalineoftextthatrepresentsthestructureofamolecule.ASMIRKSstringdescribeschemicalreac-
tionsintext.
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SMILESsupportsanalternatenotationforaromaticstructuresusinglowercaseletters.ChemBioDrawgeneratesthis
typeofSMILESstringforanystructuredrawnwithexplicitaromaticbonds.
PastingSMILES
TopasteaSMILESstringasastructure:
1. SelecttheSMILESstringinthesourcefileandpressCTRL+C.
2. FromChemBioDraw,navigatetoEdit>PasteSpecial>SMILES.
CreatingSLNStrings
YoucancopyastructuretotheClipboardasanSLNstringforexporttootherapplications.
TocopyastructureasanSLNstring:
1. Selectastructure.
2. NavigatetoEdit>CopyAs>SLN.
TheStructureiscopiedtotheclipboardasanSLNString.
CreatingInChI™Strings
ChemBioDrawsupportsIUPACInternationalChemicalIdentifier(InChI™)
l.
TocopystructuresasInChI™stringstootherdocuments:
1. Selectthestructure.
2. NavigatetoEdit>CopyAs>InChI.
YoucancopyonlylegitimateInChI™structures.IfyouattempttocopyastructurethattheInChIprotocoldoesnot
support,awarninginformsyouthatthestructureisnotsupported.
CreatingInChIKeyStrings
ChemBioDrawsupportsStandardInchIKey,availableinInChI1.02.AnInChIKeystringisacondenseddigitalrep-
resentationofanInChIstring.AllInChiKeystringsarethesamelengthwhereasInChIstringsarenot.Thisstandard
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makesInChIKeystringsusefulforWebsearchinganddatabaseindexing.
TocopyastructureasanInChIKeystringtootherdocuments:
1. Selectthestructure.
2. NavigatetoEdit>CopyAs>InChIKey.
FormoreinformationonInChI™andInChIKey,seewww.iupac.org/inchi/.
CreatingCDXMLorMOLText
TocreatetheCDXML textorMOLtextforastructure:
1. SelectthestructureyouwanttocreatetheCDXML orMOLtextfor.
2. NavigatetoEdit>CopyAs>CDXMLTextorMOLText.
TheCDXML textorMOLtextistransferredtotheclipboard.
PastingCDXML orMOLText
TopasteanddisplaytheCDXMLtextorMOLtextfromtheclipboardtothedocumentwindow:
3. NavigatetoEdit>PasteSpecial>CDXMLTextorMOLText.
ScrapandClippingFiles
YoucanusescrapfilestocopypartsofadrawingtootherapplicationsaftersavingthefileinChemBioDraw.
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Tocreateascraporclippingfile:
1. Selectanobjectinadocument.
2. Dragtheselectionoutofthedocumentwindowontothedesktop.Thefileappearsonthedesktop.
Toviewthefilecontents,double-clickitsicon.Tousecontentsinadocument,dragthefileintoanopenwindowofan
applicationthatsupportsdrag-and-drop.
TransferringObjects
ThissectionexplainsbehaviorsofcertainfeaturesinChemBioDrawwhenyoutransferobjectsusingtheclipboard,or
draganddropfromonedocumenttoanother.
Autoscaling.Objectsthatyoutransferarescaledtomatchthesettingsofthedestinationdocument.
Bonds.Whenyoucopyormoveastructuretoanotherdocument,thestructureadoptsthenewdocument’sfixed-
lengthvalue,butretainsitsscalingfactor.
Forexample,assumethefixedlengthissetto1.0cminasourcedocument.Abenzeneringisresizedto200%.The
bondlengthisthen2.0cm.Inthedestinationdocument,assumethefixedLengthsetto1.7cm.Whenthebenzene
ringispastedintothedestinationdocument,thebondsarescaledbyafactorto200%toafinalbondlengthof3.4cm.
AtomLabels.Atomlabelsarescaledthesamewayasbonds.Forexample,inthesourcedocument,assumethe
atomlabelfontsizeissetto16points.Oneortwoatomlabelsinthesourcedocumentareresizedto8points,aratio
of8:16orascalefactorof0.5.Assumethatthedestinationdocumenthasanatomlabelfontsizesetto14points.If
youpastetheatomlabelintothedestinationdocument,thefontsizeisscaledbyafactorof0.5togiveafinalatom
labelfontsizeof7points.
Captions.ChemBioDrawautoscalescaptionsusingtheratioofthefixedlengthinthedestinationdocumenttothe
fixedlengthinthesourcedocumenttimesthecaptionfontsize.Thefontsizeofthecaptioncanbeanysizeandisnot
relatedtothesettingintheSettingsdialog.Thisensuresthatcaptionsarealwaysinproportiontothebondswith
whichtheyarepasted.
Forexample,ifthesourcedocumenthasafixedlengthof1.0cmandthedestinationdocumenthasafixedlengthof
2.0cm,andthecaptionyouarepastingis12points,thentheresultingcaptionsizeafterautoscalingis(2.0cm/1.0
cm)x12points=24points.
Non-bondObjectsandColor.Thedocumentsettingsdonotaffectallobjects.Objectssuchasarrowsandboxes,
arescaledtomaintainthesameproportionstobondsthatwereinthesourcedocument.
Exceptfortheforegroundandbackgroundcolor,thecolorspresentintheselectiontobepastedareaddedtothedes-
tinationdocument’sColorpaletteiftheyarenotalready(upto20totalcolors).Thebackgroundcolorinthedestination
documentremains,andallobjectscoloredusingtheforegroundcolorarechangedtomatchtheforegroundcolorinthe
destinationdocument.
PastingtoanEmptyDocument.IfyoupasteaChemBioDrawdrawingintoanemptydocumentthathasdifferent
settings,theChangeSettingsdialogappears.
Tochangethesettingsinthedestinationdocumenttomatchthesettingsinthesourcedocument,clickChangeSet-
tings.
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