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2. CustomizetheoptionsfoundintheGeneralPreferencesdialogbasedonyourworkneeds. Theoptionsdis-
playunderthreecategories:Molecules& Structures,Import/Export,andMisc:
Molecules& Structures:
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DoubleClickToAddMolecule:LaunchesChemDrawwhenyoudouble-clickacell.
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AskBeforeAddingMolecule:Promptsamessagewhenyoudouble-clickacelltoaddamolecule.
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UseFilenameinLoadMolecule:Displaysfilenameinsteadofchemicalformulabelowthemoleculeafter
loadingthemolecule.
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AlignStructure:Specifieshowthestructureisalignedinacell.Youcanchoosetoreducethecolumnwidth,
rowheight,orboth.
Import/Export:
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ImportTable:Specifieswhethertooverwritethetableortoappendrecordstotheexistingtable.
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Automaticallygeneratestructureswhileimportingatable:Generatesstructurepicturesforeachrecord
whileimportingatableusingtheImportTablecommand.Disablingthisoptioncanspeeduptheimportpro-
cess.Onlystructureandtabledataareimportedandnopicturesaregenerated.Selectthestructurecellsand
useShowPicturetodisplaythepictures.
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AskIfRecordImportCountExceeds:Promptsamessagewhenthetablebeingimportedcontainsmore
recordsthanthecountnumberspecified.
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SDFExportVersion:SpecifiestheStructureDataFile(SDF)versionexportedbyChemDrawforExcel.SDF
FilescaneitherbeV2000orV3000.ThedefaultvalueisV2000,whichlimitsthenumberofatomsandbondsin
amolecule:V2000filesallowupto1000ofeach.V3000isasupersetofV2000,andoffersanenhancedste-
reochemistryspecification.UnlikeV2000,theV3000formatdoesnotlimitthenumberofatomsandbondsina
molecule.
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Misc:
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AskBeforeClearingCells:PromptsamessagewhenyouattempttodeletethecellcontentinaChemOffice
worksheetbyeitherpressing<Delete>or<Backspace>keys.
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CopyStructuretoMS WordAs: Letsyouselecttheformatthatyouwanttousetocopyyourstructuretoan
MS Worddocument,forexample,BitmaporOLEObject.
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SearchResults:Bydefault,thesearchresultappearsinthesameworksheetonwhichthesearchisper-
formed.TheDisplayinanewworksheetoptioncreatesanewworksheetwiththename"SearchResultsX"
(whereXis1,2.3...)anddisplaysthesearchresultsinthisnewworksheet,withoutchanginganythingintheori-
ginalworksheet.
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DefaultStyleSheet:Specifiesthestylesheetalwaysappliedtothestructureswhenstructuresareadded
usingImportTable,LoadMolecule,orbyAddMoleculecommands.Toapplyastyletoparticularmolecules,
navigatetoChemOffice>Molecule>Style.ThedefaultstylesheetisNewDocument.cds.
CombiChem
UsingCombiChem,youcanbuildvirtualcombinatoriallibrariesofstructurallyrelatedmolecules.Youcanthenscreen
yourlibrariesforvariouspropertiestodeterminewhichcompoundsyouwanttosynthesize.
CombiChemisapluginforMicrosoftExcelandisincludedwithChemDraw/Excel.IfyouarefamiliarwithExcel,you
willfindCombiChemsimpletouse.However,ifyouneedhelp,seetheExcelUser’sGuide.
GettingStarted
WhenyouinstallChemBioFinderorChemBioOffice,theCombiChemadd-inisalsoinstalled.CombiChemrequires
MicrosoftExcel2003orlater.
AssistancewithCombichem
CombichemprovidesHelpintheExcelworksheets.GotoChemOffice14>CombiChem>Help.
Bydefault,eachworksheetyoucreatealsoincludesbriefinstructionstohelpguideyou.Ifyoudonotseetheinstruc-
tions:
1. GotoChemOffice14>CombiChem>Preferences.
2. SelectAddInstructionstoEverySheet.
3. ClickOK.
Theinstructionsappearonnewworksheetsthatyoucreate.
Creatingcombinatoriallibraries
Tocreateacombinatoriallibrary,youfirstneedagenericreaction.Thisreactionresemblestherealreactionyouwill
useinthelabtosynthesizecompounds.Thegenericreactioncontainsoneormorequerystructuresthatrepresentthe
reactantsandproductsintherealreaction.Anexampleofagenericreactionisshownbelow:
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Youusethegenericreactiontosearchyourchemicaldatabaseforcompoundsthatmatchthereactantquerystruc-
tures.Onceallthematchingcompoundsarefound,CombiChemgeneratesalistofreactionsfromthecompounds
thatwerefoundinthequery.
Thegenericreactionyoucreatemustmeetthesecriteria:
Allgenericatomsinthereactant(s)mustberepresentedbyR-groups.
Solvents,catalysts,andother“real-world”elementsmustnotbeincludedinthegenericreaction.
Multi-stepgenericreactionsaresupported.
Enteringagenericreaction
Toenterthegenericreaction,youmustfirstcreateareactionworksheet:
GotoChemOffice14>CombiChem>NewReaction.Anewworksheet,named“Reactions”appearsinyourwork-
book.
YouthenaddthegenericreactiontothereactionworksheetbyeitherimportingitordrawingitinChemBioDraw.
Toimportthereaction:
1. Placeyourcursorinthecellthatcontainsthetext“Reaction-Double-clicktoedit.”
2. EitherclicktheLoadMoleculeiconontheChemOfficetoolbarorgotoChemOffice14>Molecule>Load.
3. BrowsetothefilethatcontainsthegenericreactionandclickOpen.ThereactionappearsintheReactionswork-
sheet.
TodrawthereactioninChemBioDraw:
1. Double-clickthecellthatcontainsthetext“Reaction-Double-clicktoedit.”.
2. Whenaskedwhethertoaddanewmolecule,clickYes.ChemBioDrawlaunches.
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3. InChemBioDraw,drawthegenericreaction.
4. InChemBioDraw,gotoFile>Exit.YouwillbereturnedtoExcelandthereactionwillappearintheworksheet.
Tip:Todisplayorhidethereaction,clicktheShowPictureorHidePictureicon.
Note:Donotaddmorethanonereactiontoareactiontemplate.
Creatingreactantworksheets
Thegenericreactioncontainsatleastonegenericreactant(areactantthathasoneormoreR-groupattachments).
AfteryouenterthegenericreactioninExcel,youcreateaworksheetforeachgenericreactant.CombiChemusesthe
reactantworksheet(s)tosearchyourdatabaseforstructuresthatmaybeusedinsynthesis.Inmulti-stepreactions,
CombiChemsearchesforreactantsinthefirststep;butignoresintermediatereactants.
Tocreatereactantworksheets:
1. SelecttheReactionsworksheettab.
2. GotoChemOffice14>CombiChem>Reactants>MakeReactantWorksheets.Anewworksheetisaddedfor
eachgenericreactant.
CombiChemcreatesaworksheetforeachgenericreactant(typically,eitheroneortworeactantworksheetsforthe
reactionyouentered).
Searchingforreactants
ReactantworksheetsareemptywhenCombiChemcreatesthem.Topopulateeachworksheetwithstructuresfrom
yourdatabase,youmusteitherimportthedatabaseasanSDfileoruseChemBioFindertosearchforrecords.
TosearchforreactantsinanSDfile:
1. SelectaReactantworksheettab.
2. GotoChemOffice14>CombiChem>Reactants>SearchforReactants.Adialogboxappears.
3. SelectSearchDirectlytoimportanSDfiletosearch.
Note:SDfileshavetheextension.sdf.
4. EnterthefilepathintheDatabasefieldorclickBrowsetolocatethefile.
5. ClickOK.Recordsinthefilethatmatchthegenericreactionarereturned.
TosearchforreactantsusingChemBioFinder:
1. GotoChemOffice14>CombiChem>Reactants>SearchforReactants.
2. Inthedialogbox,selectSearchinChemFinder.
3. IntheDatabasefield,enterthepathtotheChemBioFinderformtobeusedtosearchtheChemBioFinderdata-
base.
Note:ChemBioFinderformfileshavetheextension.cfxor.cfw.
4. ClickOK.ChemBioFinderlaunches.
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Afterlaunching,ChemBioFinderusestheformyouenteredtosearchitscorrespondingdatabaseforrecordsthat
matchthegenericreactant.YoucanbrowsethesearchresultsinChemBioFinderbeforeimportingthemintothe
Excelreactantworksheet.
Tip:Toomitarecordfromthesearchresults,navigatetotherecordinChemBioFinderandgotoRecord>Omit
fromListintheChemBioFindermainmenu.
5. InExcel,gotoChemOffice14>CombiChem>Reactants>ImportChemBioFinderHitlist.
Alternatively,youcancopyandpastethequerystructureintoChemBioFindertoperformasearch.
1. InExcel,selectthecellthatcontainsthegenericreactant.
2. ClicktheCopyMoleculeiconontheChemOfficetoolbar.
3. InChemBioFinder,openthedatabasetosearch.
4. Pastethegenericreactantstructureintoaqueryformandrunthesearch.
5. InthereactantworksheetinExcel,gotoChemOffice14>CombiChem>Reactants>ImportChemBioFinder
Hitlisttoimportthesearchresults.Thesearchresultsappearinthereactantworksheet(s).
Tip:UsetheShowPicture/HidePicturecommandstotogglethedisplay.
Recreatingreactantworksheets
Youcaneditthegenericreactionatanytime.However,youmustthendeleteandrecreateeachreactantworksheet.
Torecreateareactantworksheet:
1. Right-clickthereactantworksheettabandselectDelete.
2. Whenprompted,confirmthatyouwanttodeletetheworksheet.
3. GotoChemOffice14>CombiChem>Reactants>MakeReactantWorksheets.
4. GotoChemOffice14>CombiChem>Reactants>SearchforReactants.(Formoreinformation,see"Searching
forreactants"onpage214.)
Ifyoutrytocreatenewreactantworksheetsinaworkbookthatalreadycontainsreactantworksheets,youwillbe
askedwhetheryouwanttodeletetheexistingworksheets.Whenprompted,chooseoneoftheseoptions:
ClickYestoreplacetheexistingworksheet(s).Theexistingworksheetispermanentlydeleted.
ClickNo.Nonewworksheetiscreatedandthecurrentworksheet(s)arekept.
TopreservetheexistingworksheetsgotoFile>SaveAsandsavetheworkbook.Then,followthestepsaboveto
recreatethereactantworksheet(s).Whenpromptedtodeleteeachexistingworksheet,clickYes.Newreactantwork-
sheetswillbecreatedandthepreviousworkbookwillbeavailableasasavedfile.
Creatinganexperiment
Anexperimentisalibraryofproductstructuresthatiscreatedwhenthereactantsearchresultsareappliedtothegen-
ericreaction.Youcancreateorenumeratemultipleexperimentsperworkbook.
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Forexample,youcantakeallthereactantsyouimportedandenumerateanexperimentcontainingallpossiblecom-
binationsofreactants.Aftercalculatingpropertiesontheseproducts,youmightdecidethat10%oftheseproductsare
worthsynthesizinginthelab.Youcouldthencreateanexperimentwithjustthoseproductsthatthecalculationsshow
tobepromising.
The‘Use(Y/N)’columninareactantlistdetermineswhethertheassociatedreactantinthelistwillbeused(‘Y’)inthe
experimentornot(‘N’).Bydefault,Y,appears.
Note:OnlytheStructureandUse(Y/N)columnsarenecessary.OthercolumnsmayalsobeincludedbutCom-
biChemignoresthem.Youcandeletethemifyouwant.
Tocreateanewexperiment:
1. Ineachreactantlist,selectthereactantstousebytypingYintheir“Use(Y/N)”column.TypeNforthosereactants
youdonotwishtouse.
Note:Cellswithout“n”or“N”defaultto“Y”.
2. GotoChemOffice14>CombiChem>Experiments>Neworusethefloatingexperimentsform(CombiOption-
s>Experiment>New).Adialogboxappearsaskingwhetheryouwanttocreatetheexperimentwiththeselected
numberofreactants.
Note:Enumerationofaproductlibrarymaytakealongtime,especiallyiftherearemanyreactantsoryouare
usingaslowerprocessor.
CombiChem/ExcelsavesyourenumerationtoaChemFinderdatabasefile.
3. Whenprompted,savetheexperimentsfile.
Note:Whentheenumerationisdone,CombiChem/Excelimportsyourdatatoaworksheet.
Experimentworksheets
Afteryoucreatetheexperiment,severalsheetsareaddedtoyourworkbook:
ExperimentReactantsheets.Containlistsofthereactantsusedintheexperiment.ThereisoneExperimentReact-
antsheetforeachreactant.ThesesheetsarenamedExperimentn-Reactantmwherenisthedesignatesaspe-
cificexperiment(incaseyoucreatemorethanone)andmisthereactantfortheexperiment.
ExperimentProductsheet.Containsthegenericreactionandtheenumeratedproductsintheexperimentbasedon
thereactantsyoumarked‘Y’inthereactantworksheet(s).Bydefault,onlytheproductsarelisted.Tolistthecomplete
enumeratedreactions:
1. GotoChemOffice14>CombiChem>Preferences.
2. IntheCombiPreferencesdialogbox,selectShowFullReactionforeachproduct.
3. Selectareactantworksheet.
4. GotoChemOffice14>CombiChem>Experiments>New.Anewexperimentisaddedwiththefullreactions
appearingintheproductworksheet.
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Note:Wheneveryoucreateanewexperiment,existingexperimentworksheetsareretained.Ifyouwanttodelete
them,right-clickeachexperimenttabandselectDeleteorusetheexperimentsfloatingform(CombiOption-
s>Experiment>Delete).
GotoCombiOptions>Experiment>Toggletohide/unhidealltheexperimentworksheetsintheworkbook.
Configuringplates
Afteryoucreateanexperiment,youcanassignyourproductstoproductwellsandyourexperimentreactantstoreact-
antblockplates.Thisisusefulifyouaregoingtousearoboticsynthesizer.Youcanconfigureplatesofupto50rows
and50columns.
Tosetupassignments:
1. OpeneitheranExperimentReactantorExperimentProductworksheet.
2. GotoChemOffice14>CombiChem>Plates>ConfigurePlates.
TheConfigurePlatesdialogboxappears.
3. IntheConfigurationof:drop-downlist,selecteitherProductPlatesorReactantBlockPlates.
4. Enterthenumberofrowsandcolumnstoassigntotheplate.
Thenumberedbuttonsrepresentwellsintheplateyouchose.
5. Designatewhichwellsyouwanttouseascontrols,synthesizedcompounds,andleftempty.Clickawellto
changeitsdesignation.
6. Whenyouarefinished,clickApply.
Assigningplates
Thenextstepistoassignplatestoeachreactantandproduct.
Toassignthereactantsorproductstoplates:
1. SelectanExperiment-Reactantworksheet.
2. GotoChemOffice14>CombiChem>Plates>AssigntoWells.
3. Selectaproductworksheet.
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4. GotoChemOffice14>CombiChem>Plates>AssigntoWells.
Threecolumnsareaddedtothereactantorproductworksheet:WellPlate,WellRow,andWellColumn.
Tochangespecificplateassignments,editthevaluesontheworksheet.
Toremoveallplatewellassignments:
1. Selecttheworksheetwhereyouwanttoremoveassignments.
2. GotoChemOffice14>CombiChem>Plates>Removewellassignments.
Browsingplates
Afterassigningreactantsorproductstowells,youcanviewwhichonehasbeenassignedtoeachwell.
1. Selecteitherareactantorproductworksheet.
2. GotoChemOffice14>CombiChem>Plates>BrowsePlates.ThePlateBrowserdialogboxappears.
3. InthePlatescrolllist,selectorentertheplatenumbertoview.
4. Inthedialogbox,selectthewelltoview.Theworksheetscrollstothereactantorproductassignedtothewellyou
select.
Viewingrelatedstructures
Afterenumeratinganexperiment,youmayviewwhichreactantswentintoaproductorwhichproductsarosefroma
givenreactant.
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Toviewtherelatedstructures:
1. SelectarowonanExperimentReactantorExperimentProductsheet.
2. GotoChemOffice14>CombiChem>HighlightRelatedRecords.
TherelatedrecordsontheExperimentReactantandExperimentProductsheetaredisplayedincolor.
3. (Optional)Toremovethehighlightingfromallrows,gotoChemOffice14>CombiChem>Highlight>Unhighlight
All.
Settingpreferences
Combichemprovidesseveraloptionsforyoutochoosehowandwhethercertaininformationappearsoneachwork-
sheet.GotoChemOffice14>CombiChem>Preferencesandselectfromtheseoptions:
Bydefault,row1ofeachCombichemworksheetcontainsinstructions.Select/deselectthisoptiontodisplayor
removethemfromeachnewsheetyoucreate.
Bydefault,thereactionarrowandproductsappearoneachExperimentworksheet.Selectthisoptiontodisplaythe
fullreactiononeachnewExperimentsheet.
Assignrowsandcolumnsinplates.ChooseLefttoRighttoassignwellnumbersbyrow(1-1,1-2,1-3,etc.).Choose
ToptoBottomtoassignwellnumbersbycolumn(1-1,2-1,3-1,etc.).
Assignnumericoralphabeticlabelstoplatecolumns.
Assignnumericoralphabeticlabelstoplaterows.
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ChemScript
ChemScriptisthecheminformaticsSoftwareDevelopmentKit(SDK).Itcontainstheprogrammingalgorithmsthat
arecommonthroughoutPerkinElmerproducts.Asasoftwaredeveloper,youcanapplyChemScripttocreateyour
ownscriptstousewithChemBioOfficeapplications.
AllexamplescriptfilesintheChemScriptlibraryareavailableinPythonandC#/.NET.Ifyouarefamiliarwitheitherof
theselanguages,youwillfindthesescriptseasytounderstand.However,ifyouarenewtoeitherPythonorC#/.NET,
wesuggestthatyourefertotheWebsitesandbookslistedattheendofthischapter.
AlthoughChemScriptisavailableinPythonandC#/.NET,wewillusePythoninthisguidetoexplainChemScript.
Pythonisanon-proprietaryandwidelyusedprogramminglanguage.
WhyuseChemScript?
ChemScriptaddsconsiderableversatilitytohowyoumanageyourchemicaldata.UsingChemScript,youcan
modify,view,andtransferyourdatafromoneplacetoanotherusingyourowncustomrules.1
Herearejustafewcommonuses:
Saltsplittingandstripping
Identifyandremovesaltfragmentsfromadrawnstructureandregisterthepurecompound.
Canonicalcodes
Generatecanonicalcodesforasetofstructuresandusethecodestofindduplicatesinyourdata.
Fileformatconversion
Convertstructureorreactionfilesfromoneformattoanother.
Generateproperties
ExecuteStruct=NameorgeneratephysicalpropertyfeaturesfoundinChemBioDraw.
Commonscaffoldorientation
Enforcestandardorientationsofstructuresbasedontheestablishedorientationofacommonsubstructure.
2DStructureDiagramGeneration(SDG)andCleanup
Generatenew2Dstructuresfromconnectiontableswithoutcoordinatesandcleanupexisting2Dstructureusingthe
ChemBioDrawalgorithms.
1
ChemScriptletsyouconvertupto10,000datarecordsperday.Forgreatercapacity,youwillneedChemScriptUltra.Forinform-
ation,contactPerkinElmer.
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