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StructureEditorWindow
ToopentheStructureEditorwindow:
clicktheStructureEditorbuttononthemaintoolbar.
orchoosetheTools|StructureEditormenuitem.
oropenastructurebychoosingtheFile|Open|StructuremenuitemandStructureEditorwillstartautomatically.
OnlyoneStructureEditorwindowcanbeopenedatanyonetimeintheprogram.IfyouclicktheStructureEditorbutton,oryouchoosetheTools|StructureEditormenu,andtheStructureEditorisalreadyopened,thiswindowbecomesactive.
TobegindrawingachemicalstructureinStructureEditor,clickoneofthebuttonsontheverticalbar.Everytimeyouclickoneofthesebuttonstheshapeofthecursorwillchangetovisuallyrepresenttheengageddrawingmode.Theverticalbuttons,incontrasttothehorizontalbuttons,arenotrepresentedinthemenu.Ifthefunctionofabuttonisnotapparentfromitsappearance,simplypointthecursoratthisbuttonusingthemouseandahintwillbedisplayed.Werecommendtryingoutallthevariousfeaturesonateststructure.
ReducedSizeofStructureEditorWindow
WhenyoureducethesizeoftheStructureEditorwindowthebuttonarrayonyourdesktopchanges.ThereducedStructureEditorwindowismorecompact,butretainsallthebuttonsonthebuttonbars.Asmallerwindowmayproveadvantageousifyourprogramdesktopisfilledwithothermodules.
RestoringDefaults
IntheStructureEditor'sdefaultstateallbuttonsareswitchedoffandnoatomorbondisselected.TheplainarrowcursorindicatesthattheStructureEditorisindefaultstate.Torestorethedefaultstateoftheeditor,chooseanyofthesemethods:
ClicktheDefaultmodebuttonintheupperleftcornerintheStructureEditorwindow.
Presstherightmousebottom.
Switchofftheactivatedbuttonanddeselectallatoms.
OpeningandSavingStructures
Toopenorsaveastructure:
ClickontheOpenStructureorSaveStructurebuttonintheStructureEditorwindow.
ChoosetheFile|Open|StructureortheFile|Save|Structuremenuitem.
Ifyouareopeningafilewhichcontainsmorethenonestructure(*.sdffile),onlythefirststructureinthefilewillbeloadedintoStructureeditor.
MassFrontierisa32-bitapplication,soyoucanuselongnamestosavestructures.Youcanevensavestructuresbytheiractualnames(e.g.1-Amino-2-hydroxyindane.mol).
StructureDataFormats
StructureEditorsupportstwokindsofstructureformats:MDLMOL-files(SDF-files),withthe*.mol(*.sdf)extension,andHighChemMCSformat(MaximalCompressedStructure),withthe*.mcsextension.TheseformatsarealsosupportedintheDatabaseManagermodule.
Templates
arestoredinMCS-format,usingtheextension*.tml.
OneofMassFrontier'sparticularlyusefulfeaturesistheabilitytorestrictasearchbyasetofstructuralconstraints,thesocalled
"Good-Bad"
list.Forexample,youcaninstructtheprogramtoconductalibrarysearchcomparinganunknownspectrumonlywiththespectraofketons.Thisfeatureprovidesanendlessrangeofpossibilitiestotargetyoursearchresultswith.The“Good-Bad”structuresarestoredinthedirectory..\Constraints,andthestructuresaresavedinMSC-format(*.mcs).TheprogramautomaticallyretrievesallMCS-structuresfrom..\Constraintsdirectoryandputsthemina“Good-Bad”listboxintheConstraintsdialogbox.
StructureLayout
MassFrontierisalayoutpowerhouse.Forstructures,aswellasforotherobjects,youcanchangealmostanythingthatitispossibletochange.Everylayoutsettingchangealsoaffectsprintingand
copying
intoClipboard,exceptbackgroundcolor,whichaffectsonlyscreendisplayintheMassFrontierprogram.Thevariouslayoutitemsallowyoutotailorthegraphicstoyourindividualreportorpublicationneeds.
ToopenStructureLayoutdialogwindow,
ClickontheStructureLayoutbuttonintheStructureEditorwindow.
ChoosetheOptions|StructureLayoutmenuitem.
Bydefaultthesymbolsforhydrogenatomsattachedtocarbonatomsarenotdisplayed(examplea).IfyouwishtodisplaythemselectShowCarbonSymbols(exampleb)intheStructureLayoutdialogbox.
HydrogenatomsareonlydisplayedforcarbonsiftheShowCarbonSymbolscheckboxisclicked.Otherwisecorrespondinghydrogensaredisplayedforheteroatomsonly.
Note:
Ifyoudrawnonisotopicexplicithydrogenatoms(examplec)theseareremovedintheFragments&Mechanismswindow,astheycanmakethemechanismnetworkunclear,especiallyforcomplexhydrogenrearrangementsteps.Asubstructuresearchignoresthenumberandpositionsofhydrogenatoms.
ThestructurelayoutsettingsapplytoallstructuresinMassFrontiersimultaneously.Thismeansthatifyouchangeastructurelayoutitem,allstructuresinthe
StructureEditor
,
DatabaseManager
,
Fragments&Mechanisms
,
FragmentationLibrary
,and
FragmentsComparator
modulesareaffected.
Note:
Ifyoudonothaveacolorprinterandareprintinginblackandwhite,andyouhavesetbrightcolorsforbondsoratoms,thelinesandfontsmayappearindistinct.Toavoidthisproblem,specifydarkercolorsforallstructuralitems,includingspectra,chromatograms,andmechanisms.
StructureTextNote
StructureEditoroffersthepossibilityoflabelingastructureordisplayingatextnoteonthescreenorontheprintout.
Toenteratextnote:
ClickontheTextbuttonintheStructureEditorwindow.
Clickanywhereinthedrawingareatoplacethetext.
Typethedesiredtext.
ConfirmthetextbyclickingoutsidethetextareaorpressanybuttoninStructureEditor..
Itispossibletocreateupto127separatetextnotes.Ifyouwanttochangethefont,color,size,orbackgroundofthetextnotesyoucandothisinthe
StructureLayout
dialogwindowintheTexttab.
Note:
Textnotesarenotassociatedwithstructures.Asaresult
Open
,
Save
,
Copy
,and
Paste
actionsapplytostructure(s)only.Whentheseactionsareappliedthetextnotesareignoredevenifastructureisselectedtogetherwithatext.Additionallystructurehandlingroutinessuchas
resizing
,
rotating
,or
mirroring
canbeperformedonlyonstructures.
Templates
WhenyouclicktheTemplatesbuttonintheStructureEditorwindow,theTemplatedialogwindowappears.MassFrontiercomeswithmorethen200predefinedtemplates.ToinsertatemplatestructureintoStructureEditor:
Selectagroupoftemplatesinthedirectorylistbox.Youcandothisusingthearrowkeysonthekeyboardorclickingtheappropriatenameofthegroup.
Clickanyatomorbond,dependingonwhetheryouwanttoattachthetemplatetoanatomorabondofastructureinStructureEditor.
TheTemplatedialogwindowwillthendisappearandyoucanplaceorattachthechosentemplate.
Switchoffthetemplatebuttonorrestorethe
defaultstate
oftheEditor.
MassFrontiermakesiteasyforyoutocreateyourowngroupoftemplatesoraddastructuretoanexistinggroup.Thetemplatesareorganizedbydirectory.Thetemplaterootdirectoryis..\Templates.Everygroupoftemplatesisstoredinaseparatesubdirectoryofthetemplaterootdirectory.Subdirectoriesarenamedaftercompoundgroups(e.g.Steroids).Thefileswithineachsubdirectoryarenamedafteractualstructuresusingtheextension
*.tml
(e.g.Cholesterol.tml).WhenyousaveastructurefortemplatepurposesselectTemplate(*.tml)formatintheSaveasTypescrollboxintheSaveStructuredialogbox.
Tobuildyourowntemplates,followthesesteps:
Drawatemplatestructure.
ClickontheSaveStructurebuttonintheStructureEditorwindoworchoosetheFile|Save|Structuremenuitem.
SelectTemplate(*.tml)formatintheFilesoftype:comboboxintheSaveStructuredialogwindow.
Createorselectasubdirectoryinthedirectory..\HighChem\MassFrontier4.0\Templatesforyournewtemplate.
TypenameofyournewtemplatestructureandclickOK.
SelectingAtomsandBonds
AnymodificationthatyoumaketoastructureappliesonlytotheselectedatomsorbondsInaddition,whena
(Sub)Structure
searchisinitiated,theprogramautomaticallyusestheselected(sub)structureinStructure.Beforeyouselectoneormoreatomsyoushouldrestorethe
defaultstate
oftheeditor.Toselectagroupofatomsthatarenexttoeachother:
Holddownthemousebuttonanddragarectanglearoundtheatomsyouwanttoselect.
TheusualWindowsconventionforselectingmultipleitemsapplies.Toselectatomsatdifferentlocations,youshouldusethekeyboardSHIFTkey.Youcanselectagroupofatomsthatarenotadjacentinoneoftwoways:
Clicktheatomsyouwanttoselect,whileholdingdowntheSHIFTkey.
Orholddownthemousebuttonanddragarectanglearoundtheatomsyouwanttoselect,whileholdingdowntheSHIFTkey.
Ifyouwanttoselectalloftheatomsandbondsinthestructure:
ClicktheSelectAllbuttonintheStructureEditorwindoworchoosetheStructure|SelectAllmenuitem.
OrdoubleclickanywhereinthedrawareawithinStructureEditor,exceptonatomsandbonds.
StructureEditorofferstwoselectionmodes:RectangleSelectionandLassoSelection.Tochoosetheselectionmodethatfitsyourneeds:
ClickwiththerightmousebuttonontheDefaultModebuttonandchoosetheappropriateselectionmodefromthepopupmenu.
OrclickwiththerightmousebuttonanywhereinthedrawareawithinStructureEditor,andclicktheRectangleorLassoSelectionmenuitemonthepop-upmenuthatwillappearinthedrawarea.
AtomProperties
Tochangethechargestateorisotopeofanatom,ortochangetheelemententirely,usetheAtomPropertiesdialogbox.
ToopentheAtomPropertieswindow,useoneofthefollowingmethods:
SelecttheAtomPropertiesbuttonintheStructureEditorwindowandthenclicktheatomyouwanttochange.
Or
restoredefaults
,andthendouble-clickontheatomyouwanttochange.
IntheAtomPropertiesdialogwindow,youcanmakethechangesbyclickingtheappropriateelementbutton,chargeandradicalcheckbox,ornucleonnumbereditbox.
Note:
AllchangescarriedoutintheAtomPropertiesdialogwindowwillonlyaffectasingleatom.
Ifyouwishtochangeanelementthathasasinglecharactersymbol,i.e.C,H,N,O,B,F,K,P,S,I,V,W,Y,UandR;afastermethodisavailable:
Selectalltheatomsthatyouwanttochangeandpresstheappropriatekeyonthekeyboard.Alltheselectedatomswillbetransformedintotheelementyouhavechosen.
Chlorine(Cl)orbromine(Br)atomscanbesetinasimilarmanner:
SelectalltheatomsthatyouwanttochangeandpresseithertheC(forchlorine)keyorB(forbromine)keyonthekeyboard,whileholdingdowntheSHIFTkey.
Itispossibletousea
substituent
insteadofaspecificelement.Thesymbol”R”representsasubstituent.Asubstituentcanbewithorwithoutindex.
Substructuresearch
and
fragmentsgeneration
algorithmsconsidersubstituentswithidenticalindexesasequalandsubstituentswithdifferentindexesasnotequal.Whensearchingstructureswithsubstituents,pleasenotethe
searchrules
thatapply.
BondProperties
BondPropertiesincludebondmultiplicity,bondstyleandbondcolor.
Tochangethemultiplicityofabond,
Clickthe,or,orbuttonintheStructureEditorwindowandthenclickthebondyouwanttochange.
Tochangethecolororopticalorientationofabond,usetheBondPropertiesdialogwindow.
ToopentheBondPropertieswindow:
ClicktheBondPropertiesbuttoninStructureEditorandthenclickthebondyouwanttochange.TheBondPropertiesdialogwindowwillthenappear.
Or
restoredefaults
,andthendouble-clickonthebondyouwanttochange.TheBondPropertiesdialogwindowwillthenappear.
MassFrontierautomaticallyrecognizesaromaticbondsinanappropriatesix-memberedringorinpolyaromaticstructures.However,ifunusualsemiaromaticoraromaticresonancestructuresarerequired,thearomaticbondcanbeforcedtoselectedbond(s)bycheckingtheForceAromaticitycheckbox.
CopyingStructure
MassFrontiersupportsextensiveuseoftheWindowsClipboardfortheexchangeofstructuralinformationbetweenmodules.Inaddition,copyandpastefunctionsmaybeusedinsideStructureeditor.Todrawlargerstructuresefficiently,werecommendedtakingadvantageofthecopyandpastefunctions.
TocopyastructureorpartofastructureintotheClipboard:
Selectthestructureorpartofstructure
youwanttocopy.
ClicktheCopybuttonintheStructureEditororchooseCopyfromtheEditmenu.
Note:
Onlythe
selectedatomsandtheirassociatedbonds
willbecopied!
Inadditiontostructureexchangebetweenmodules,MassFrontierallowsstructureexporttootherprogramsthatdealwithstructuralinformation.Whenyoucopyastructure,MassFrontierautomaticallycopiestwodifferentformatsintoclipboard:structuralinformationin
MOLformat
andgraphicsinWindowsMetafileFormat(wmf).IfyoupasteastructureintothestructureeditingsoftwaretheMOLformatwillbeused.Ifyoupastethestructureintoanytexteditor,spreadsheetoranyotherprogramthatworkswithgraphics,thegraphicalinformationwillbeused.Alltheseactionsoccurautomaticallysotheuserneednotworrywhichformatisused.
StructureExchangeviaCopy&Pastecommands.
PastingStructure
Ifyouhavecopiedastructureorfragmentanywhereintheprogramorinathirdpartystructuredrawingtool,youcanpasteittoStructureEditor.Ifnecessary,thestructurecanbechangedorcorrectedandthenreturnedtowhereitoriginated.Thisisespeciallyusefulforstructureelucidation.Forexample,youcancopyastructurefromthe
DatabaseManager
window,pasteittoStructureEditor,makeappropriatechanges,andthenmoveitbacktoDatabaseManager.Ifthespectrumandthestructuralproposalarenotconsistent,theprocesscanberepeated.
TopasteastructuretoStructureEditor:
ClickthePastebuttonintheStructureEditor.
OrchoosethePasteitemfromtheEditmenu.
IfyouhavecopiedastructureorfragmentinaprogramotherthanMassFrontier,youcanonlypastethisstructureiftheexternalstructuredrawingsoftwaresupports
MOLformat
andthisformatisactivated.ThemajorityofstructuredrawingtoolssupportMOLformatandusuallyhavethisformatactivatedbydefault.IfyoupasteastructurefromanexternalsourceitmaysometimesappearlargerinMassFrontierthanintheoriginalsoftware.Ifthisshouldhappen,youcansimplymakethestructuresmallerusingthe
Resize
tool.
StructureExchangeviaCopy&Pastecommands.
MovingStructure
TomoveastructureintheStructureEditor:
Selecttheatomsorbonds
youwishtomove.
Pointthemousecursoratanyselectedatomorbond.
Holddownthemousebuttonanddragtheselectedstructuretothenewlocation.
Releasethemousebuttontodroptheselectedstructureatthenewlocation.
ResizingStructure
ToresizeastructureintheStructureEditor:
Selectthestructure/orpartofstructure
youwishtoresize.
ClicktheResizebutton,orselecttheStructure|Resizemenuitem.
Dragoneofthesmallrectanglesonthestructureedgeuntilthenewsizeisachieved.
Releasethemousebutton.
Note:
Ifyoudragoneofthediagonalrectanglestheaspectratiowillbekeptconstantduringstructureresizing.
RotatingStructure
TheRotateStructureoptionallowsyoutotwistastructureinanydirection.Thecenterofrotation,indicatedbyasmallcirclewithacrossinthemiddle,canbemovedtoanylocation.
TorotateastructureintheStructureEditor:
Selectthestructure/orpartofstructure
youwanttorotate.
ClicktheRotatebutton,orselecttheStructure|Rotateitem.
Movethecenterofrotationtothedesiredpositionbydraggingthecirclewithacross.
Draganyofthesmallrectanglesonthestructureedgetoachievethenewangularposition.
CleaningStructure
TheCleanfunctionallowsyoutoachieveaprofessionallooktoyourstructures.Incontrasttoothercommercialstructuredrawingprograms,withMassFrontieryoucanevencleanupanindividualpartofastructure.Forexample,youcanrestrictcleaningtocertain
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