ChemBioDraw14.0UserGuide
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TableofContents
RecentAdditions
vi
Chapter1:Introduction
1
AboutthisGuide
1
Chapter2:GettingStarted
4
AboutChemBioDrawTutorials
4
ChemBioDrawUserInterface
4
Toolbars
5
Documents
6
Chapter3:PageLayout
10
TheDrawingArea
10
TheDocumentType
10
Printing
12
SavingPageSetupSettings
13
35mmSlideBoundaryGuides
13
ViewingDrawings
14
Tables
16
Chapter4:PreferencesandSettings
20
SettingPreferences
20
CustomizingToolbars
23
DocumentandObjectSettings
23
CustomizingHotkeys
33
WorkingwithColor
35
DocumentSettings
38
Chapter5:ShortcutsandHotkeys
44
AtomKeys
44
BondHotkeys
45
FunctionHotkeys
46
ChemBioDraw14.0
©Copyright1998-2014CambridgeSoftCorporation,asubsidiaryofPerkinElmer,Inc.Allrightsreserved.
i
VB.NET TIFF: Rotate TIFF Page by Using RaterEdge .NET TIFF
specific formats are: JPEG, PNG, GIF, BMP, PDF, Word (Docx Save the rotated page(s) to new a TIFF Multiple image formats support for saving rotated TIFF page(
pdf reverse page order online; rotate individual pages in pdf reader
VB.NET Image: Image Rotator SDK; .NET Document Image Rotation
VB.NET image rotator control SDK allows developers to save rotated image as are dedicated to provide powerful & profession imaging controls, PDF document, tiff
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Shortcuts
47
Nicknames
50
Chapter6:BasicDrawings
52
Bonds
52
Atoms
57
Captions
58
DrawingRings
67
Chains
69
Objects
71
CleanUpStructure
88
CheckingStructures
89
ChemicalWarnings
89
Chapter7:BioDraw(Ultrafeatureonly)
92
BioDrawTemplates
92
CustomizableObjects
95
Chapter8:DrawingBiopolymers
101
BiopolymerEditor
102
ProtectingGroups
103
PastingSequences
104
ExpandingSequences
106
ContractingLabels
106
ModifyingSequenceResidues
107
MergingSidechainswithResidue
107
HybridBiopolymers
110
IUPACCodes
111
DisulfideBridges
115
LactamBridges
116
Chapter9:AdvancedDrawingTechniques
118
ColoringObjects
118
ChemBioDraw14.0
©Copyright1998-2014CambridgeSoftCorporation,asubsidiaryofPerkinElmer,Inc.Allrightsreserved.
ii
C# TIFF: How to Rotate TIFF Using C# Code in .NET Imaging
VB.NET How-to, VB.NET PDF, VB.NET Word, VB Tiff page, like sorting and saving the rotated Tiff page 0); page.Rotate(RotateOder.Clockwise90); doc.Save(@"C:\rotate
rotate pdf page few degrees; rotate pages in pdf expert
How to C#: Rotate Image according to Specified angle
VB.NET How-to, VB.NET PDF, VB.NET Word, VB.NET Excel, VB.NET PowerPoint, VB.NET Tiff, VB.NET Imaging, VB.NET OCR, VB.NET Twain, VB Save the rotated image to
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Labels
119
AttachmentPoints
122
AtomNumbering
124
StructurePerspective
125
MassFragmentation
126
DrawingReactions
127
StoichiometryGrid
133
Templates
136
DefiningNicknames
138
ChemScript
141
Chapter10:Struct=Name(UltraFeature)
143
Struct>Name
143
Name>Struct
147
Chapter11:ChemistryFeatures
149
StructureAnalysis
149
ChemBioFinderhotlink
150
Stereochemistry
151
ChemicalAnnotations
154
ChemicalProperties
158
3DViewing
165
TLC
168
ChemNMR(UltraFeature)
173
Chapter12:ChemDraw/ExcelandCombiChem
180
SettingUpChemDraw/Excel
180
Importingtables
180
Importinghitlists
181
Exportingtables
181
SynchronizingTables
182
Addingstructures
183
ChemBioDraw14.0
©Copyright1998-2014CambridgeSoftCorporation,asubsidiaryofPerkinElmer,Inc.Allrightsreserved.
iii
VB.NET Imaging - Data Matrix Plug-in SDK Control
Generated Data Matrix barcode image can be freely rotated, resized and code page.AddImage(image, New PointF(100F, 100F)) docx.Save("C:\\Sample_Barcode.pdf").
rotate all pages in pdf preview; rotate one page in pdf reader
C# HTML5 Viewer: Load, View, Convert, Annotate and Edit OpenOffice
documents, CSV file and Text file are allowed to be rotated. PowerPoint (.ppt, .pptx) on webpage, Convert CSV to PDF file online Users can save annotations to
how to rotate all pages in pdf in preview; how to rotate all pages in pdf
Searching
184
R-Groupanalysis
185
WorkingwithStructures
186
ChemDraw/ExcelFunctions
188
ChemicalProperties
202
GeneralPreferences
210
CombiChem
212
Chapter13:ChemScript
220
WhyuseChemScript?
220
HowChemScriptworks
221
GettingStarted
221
EditingScripts
222
IntroducingtheChemScriptAPI
223
Tutorials
224
UsefulReferences
227
Chapter14:QueryStructures
228
SearchLimitations
228
GenericLabels
228
AtomProperties
231
BondProperties
239
ElementLists
242
Polymers
243
LinkNodes
247
AlternativeGroups
248
AnonymousAlternativeGroups
254
ExpandGenericStructures
255
Atom-to-AtomMapping
257
StereochemicalSymbols
260
3DProperties
261
ChemBioDraw14.0
©Copyright1998-2014CambridgeSoftCorporation,asubsidiaryofPerkinElmer,Inc.Allrightsreserved.
iv
VB.NET Word: VB.NET Code to Rotate Word Page Within .NET Imaging
Here, we can recommend you VB.NET PDF page rotating tutorial and multi any original quality during or after the Word page rotating; Save the rotated Word page
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VB.NET Image: How to Process & Edit Image Using VB.NET Image
permanently? A 2: This VB.NET image editor control SDK allows developers process target image file and save edited image as new file.
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ExportCompatibility
262
Chapter15:SharingInformation
267
TheClipboard
267
TransferringObjects
270
EmbeddingObjects
271
Exporting
271
Importing
272
TransferringAcrossPlatforms
276
Chapter16:ChemicalInterpretation
277
DatabaseConventions
277
Chapter17:PropertyCalculations
290
Chapter18:ChemBioDrawWebResources
293
RegisteringOnline
293
User’sGuide
293
TechnicalSupport
293
QueryingSciFinder®withChemBioDraw(UltraFeature)
295
Chapter19:Tutorials
298
Tutorial1:DrawingaStructure
298
Tutorial2:Drawingrings
299
Tutorial3:Fischerprojections
301
Tutorial4:PerspectiveDrawings
304
Tutorial5:Newmanprojections
308
Tutorial6:Stereochemistry
311
Tutorial7:Templates
314
ChemBioDraw14.0
©Copyright1998-2014CambridgeSoftCorporation,asubsidiaryofPerkinElmer,Inc.Allrightsreserved.
v
RecentAdditions
Windows8.1,MicrosoftOffice2013,andMacOSX10.9.x.
ChemDrawstrivestobeavitalandpreferredtoolforillustratingchemicalandbiologicalconcepts.Compatibilitywith
thelatestoperatingsystemsandtoolsisanessentialpartofthat.HavingtheChemDrawActive-Xcontrolfunctional
withthelatestbrowsersonbothWindowsandMacplatformsispartofthisprocess,aswell.
ChemDrawtoSciFinderInterface.
SendChemDrawstructureandreactionqueriesdirectlytoSciFindertofindusefulinformationrelevanttoyourcom-
pound/reaction.Formoreinformation,see"QueryingSciFinder®withChemBioDraw(UltraFeature)"onpage295.
BiopolymerBuilderEnhancements.
Singleandmultiletteraminoacids-Letsyoucreatesingleletteraminoacidsandnucleotideseitherbyenteringthe
correspondingIUPACcode,orbyusingtheBiopolymertoolbar.TheBiopolymerEditorletsyoucreatethreeletter,
ornon-standardaminoacids,byenteringtheresiduename.
ToggleAminoAcidStyleAA1<->AA3command-Letsyouchangetheaminoacidrepresentationfromsingleto
multi-letter,andviceversa.Formoreinformation,see"DrawingBiopolymers"onpage101.
L-andD-aminoacids-LetsyoucreatestandardL-orD-aminoacidsbyenteringtherelevantIUPACcode.
ToggleL-andD-aminoacids-The‘ToggleAminoAcidStereoL<->D’commandletsyouchangetheste-
reochemistryofaminoacidsfromLtoDandviceversa.
Protectinggroups-LetsyouaddprotectinggroupssuchasTrtandFmoctoaminoacidscontainingadditionalNH
2
orOHgroups(Arg,Aad).Youcanalsoexpandandcontracttheprotectedresidues.Formoreinformation,see"Pro-
tectingGroups"onpage103.
ChemBioDraw14.0
©Copyright1998-2014CambridgeSoftCorporation,asubsidiaryofPerkinElmer,Inc.Allrights
reserved.
vi
Cyclicandbranchedpeptides-Letsyoucreatecyclicpeptidesbybondingtogethertheterminalresiduesinapep-
tidesequence.Aloopedbondindicatesthatthepeptideiscyclic.Youcancreatebranchedpeptidesusingthe
sequencebuilderandbondtools.Formoreinformation,see"Cyclic,Crosslinked,andBranchedPeptides"onpage
113.
Lactambridges-Letsyouformlactambridgesbetweenresidueswithavailableaminoandcarboxylicacidleaving
groups,suchasLys-AspandLys-Glu.Formoreinformation,see"LactamBridges"onpage116.
Mergingsequences-Letsyoumergemultiplesequencesintoonesequencebybondingtogethertheirterminal
residues.
Hybridbiopolymers-Letsyoucreatehybrid(alsocalled'chimeric')biopolymerscontainingpeptide,nucleotide,and
linkerresidues,usingtheBiopolymertoolbar.Formoreinformation,see"HybridBiopolymers"onpage110.
Pastingsequences-LetsyoupastesequencesintheFASTAformat.Youcanalsocopyatextstringdescribinga
biopolymerasaseriesofsingleormultiletterresidues,withvalidseparators(space,tab,dash),andpasteitasa
sequence.ThetextstringcanbegeneratedwithinoroutsideofChemBioDraw.See"PastingSequences"onpage
104.
Displayingexpandedresidues-Expandedresiduescanappearineitherlinearmodeorzigzagmode.
Expandingandcontractinglabels-Letsyouexpandtheentiresequence,oranypartofit.Thesequenceisauto-
maticallycleanedfollowingexpansion.
Whenyoucontractasequence,theCleanUpBiopolymercommandcleansandre-arrangesthesequence,so
thattheresiduesarealignedandwrapped.
Numberingresidues-Letsyoudisplayresiduenumbersaboveanyresidue.Formoreinformation,see"Numbering
Residues"onpage110.
Hide/Showterminiandbonds-Letsyouhidebondsandterminiwithoutaffectingtheunderlyingchemistry.
NicknameEnhancements.
InChemBioDraw14.0,manynewresidues,forexample,non-standardaminoacids,non-standardnucleotides,linkers
havebeenaddedtothenicknamelibrary.Definingnicknamesismucheasierandmoreflexiblenow.Formoreinform-
ationonnicknames,see"DefiningNicknames"onpage138.
Struct>NameEnhancements.
Struct>NameinChemBioDraw14.0isenhancedtosupportmanyhomopolymers,copolymers,andalternatingpoly-
mers,andstoichiometryspecifiedasbracketproperties,includingfractionalstoichiometry.Formoreinformation,see
"Struct>Name"onpage143.
ElectronPushing.
ChemBioDraw14.0introducestheElectronPushingtoolforillustratingelectrontransfer.Formoreinformation,see
"ElectronandRadicalPushing"onpage132.
ChemBioDraw14.0
©Copyright1998-2014CambridgeSoftCorporation,asubsidiaryofPerkinElmer,Inc.Allrightsreserved.
vii
GelElectrophoresisTool.
Gelelectrophoresisseparatesmoleculesusinganelectricfieldappliedtoagelmatrix.Thegelelectrophoresistoolin
ChemBioDraw14.0worksmuchliketheTLCtoolandletsyoueasilydrawandmarkbandsbasedonweightordis-
tance.Formoreinformation,see"TLC"onpage168.
TLCPlateEnhancements.
Letsyoucopyanddragspotsbetweenlanes.Formoreinformation,see"TLC"onpage168.
PolymerBeadEnhancements.
Letsyoure-sizepolymerbeads.Formoreinformationonpolymerbeadsandotherattachmentpoints,see"Attach-
mentPoints"onpage122.
NewToolbars.
ChemBioDraw14.0introducesseveralnewtoolbars,including,Structure,Curves,Windows,andBiopolymertool-
bars.YouaccessthesetoolbarsfromtheViewmenu.
ColorbyElement.
Letsyoucoloratomlabelsusingcolorsassociatedwiththeiratomicsymbols,asshownintheexamplebelow.
Formoreinformation,see"ColorbyElement"onpage36.
NewPropertyPredictions.
IncorporatesnewcalculationsfromMolecularNetworksforpredictingpKa,LogSandLogP.See"PropertyPre-
dictionsinChemBioDraw"onpage158.
JPEG/JPGfileexport.
LetsyouexportfilesoftypeJPEG.
CopyAs/PasteSpecialCDXML andMOLfilesastext.
LetsyousaveCDXML andMOLfilestotheclipboardastextandthenpasteinotherapplicationsastext.See"Creat-
ingCDXMLorMOLText"onpage269.
ChemBioDraw14.0
©Copyright1998-2014CambridgeSoftCorporation,asubsidiaryofPerkinElmer,Inc.Allrights
reserved.
viii
CopyStructuretoMS WordfromChemDraw/Excel.
LetsyoucopystructuresfromChemDraw/ExcelworksheetstoMicrosoft WordthroughasettingintheGeneralPrefer-
encesdialog.See"GeneralPreferences"onpage210.
ChemBioDraw14.0
©Copyright1998-2014CambridgeSoftCorporation,asubsidiaryofPerkinElmer,Inc.Allrightsreserved.
ix
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