MOE Tutorail.docx
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MOE Tutorail.docx
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MOETutorail
MOETour
MOEMOEWindow
SESequenceEditor
DBVDatabaseViewer
CLICommandLineInterface
MOE|RHSRightHandSideButtonBar(MOEWindow)
MOE|PopupPopupMenufromaRightClickintheMOEWindow
MOE|FooterFooterArea(MOEWindow)
Thistutorialassumesthatyouareusingathree-buttonmouse.FormoreinformationonusingthemouseinMOE,clickMOE|Help|MouseorseeUsingtheMouse.
BuildingaSmallMolecule
Whenfirststarted,MOEalwaysdisplaysitsmainwindow,theMOEWindow,inwhichmolecularsystemsarerenderedandmanipulated.
SmallmoleculescanbebuiltusingtheMoleculeBuilder.Inthisexercise,wewillbuildamoleculeofaspirin,aspicturedbelow:
1,OpentheMoleculeBuilder:
MOE|Edit|Build|Molecule
2,Createanaromaticringbypressingthebenzenebutton,locatedontherightoftheMoleculeBuilder
3,CenterthemolecularsystemintheMOEWindowbyclickingMOE|RHS|Center
4,Cleartheatomselectionbyleft-clickingintheblankspaceofthe3Dwindow.Renderthemoleculeascylindersbyclickingontheappropriatebuttonin:
MOE|Popup|Atoms
5,Toaddacarboxylgroup,selectoneofthebenzenehydrogensbyclickingtheleftmousebuttononit.Substituteitwithacarboxylgroupbyclickingon-CO2intheBuilder
6,Toaddahydroxylgroup,selectthehydrogenatomorthotothecarboxylgroup
7,IntheBuilder,clickonOintheElementbuttons.Toacetylatethehydroxylgroup,selectthehydroxylhydrogenatomintheMOEWindowandclickonthe-C=OsubstituentbuttonintheBuilder,followedbytheCelementbutton.Youhavenowcompletedtheaspirinmolecule.
Wecouldalsohavebuilttheaspirinmoleculebytyping:
O(C(=O)C)c1c(C(=O)O)cccc1
intheSMILESStringtextfieldoftheMoleculeBuilderandthenpressingtheSMILESbutton(thesmileyface).
8,PresstheCenterbuttontocenterthemolecularsystemintheMOEWindow:
MOE|RHS|Center
9,RotatethemoleculebydraggingthemiddlemousebuttonintheMOEWindow.YoucanalsorotatethemoleculeusingtheMOE|RHStrackball
Whenrotatingthemoleculeinthewindow,thecenterofrotationisthecenterofmassoftheentiremolecularsystem.Whenzoomedinclosetoanatom,however,youmayprefertolocalizemovementbyforcingrotationabouttheatom.Todoso,placethemousecursorovertheatomandclickthemiddlebutton.Toregainthedefaultsetting,simplyclickthemiddlemousebuttonintheMOEWindowawayfromanyatoms
10,Topanthemolecule,pressShiftanddragthemiddlemousebutton.Topanthemoleculewiththetrackball(MOE|RHS|Trackball),activatepanningmodebyclickinginthegraysquareatthebottomleftofthetrackball(thesquareislabeled"R"wheninrotationmodeand"T"whenintranslationmode)
11,Tozoominorout,pressCtrlanddragthemiddlemousebutton.Alternatively,ifyourmouseisequippedwithascrollwheel,itcanalsobeusedtocontrolzooming.Anotheralternativeisusingthewheelbelowthetrackball
12,ThecurrentforcefieldsettingisshownontheleftoftheMOEFooter:
Tochangetheforcefield,clickthebuttonshowingtheforcefieldname,oruseMOE|Window|PotentialSetup.
InthePotentialSetuppanel,ensuretheMMFF94xforcefieldisactivebyselectingitintheLoad...pulldownmenu.Closethepanel.
13,MinimizetheenergyofthemolecularsystembychoosingMOE|RHS|MinimizeorbyclickingMinimizeintheBuilder.
1,Savetheacetylsalicylicacidmoleculeyouhavejustbuilt:
MOE|File|Save...
Double-clickonthedirectoryinwhichtosavethemoleculefile.Next,enteraspirininthetextfieldandsavewitha.moeextension(theMOEfileextension)byclickingSave.
TipForquickaccesstoMOEdirectories,clickonthearrowinthetextfield.Thisopenstheshortcutlistofrecentdirectorypaths.
2,Now,youwillloadthenewlysavedmoleculebackintoMOE.However,beforedoingso,youmustfirstclearthedatacurrentlyinMOE:
MOE|File|CloseorMOE|RHS|Close
3,LoadthemoleculebackintoMOE:
MOE|File|Open
IntheOpenpanel,selectaspirin.moefromthelistoffilesandpressOK.
IfafterloadingthemoleculefilenoatomsareshownintheMOEwindow,itmaybethatthemoleculeisnotvisiblewiththecurrentviewingparameters.Tochangetheviewsothatthemoleculeisfullyvisible,chooseMOE|RHS|Center.
SavingaMoleculeinaDatabase
WhenbuildingmoleculesinMOE,itisconvenienttosaveandretrievemolecularfragmentstoandfromadatabase.BelowisashortexampleonhowtocreateadatabaseandcopytheaspirinmoleculefromMOEtothedatabase.
1,Tocreateamoleculardatabase,choose:
MOE|File|New|Database
A,IntheNewDatabasepanel,selectthedirectoryinwhichthenewdatabasewillbesaved.
B,InthePathtextfield,enteraspirin.mdb.
C,PressOK.ThenewdatabaseappearsinaMOEDatabaseViewer.Thedatabasecontainsasinglefieldcalledmol,whichisoftypemolecule.
2,Createasecondfieldinthedatabase,whichwillcontainthemoleculenames,byselecting:
DBV|Edit|New|Field...
ThecommandlineintheDatabaseViewerchangestoaprompt.ChoosecharintheNewFieldTypeoptionmenutocreateatextfield.Next,enterMoleculeNameintheNametextboxandpressOK.AnewfieldcalledMoleculeNameiscreatedinthedatabase.
3,Tocopytheaspirinmoleculefromthecurrentsystemtothedatabase,choose:
DBV|Edit|New|Entry...
IntheAddEntrypanel,selectMode:
SystemandtypeaspirinintheMoleculeNametextfield.PressOK.Bothfieldsnowcontaininformationinthedatabase.
4,IntheDatabaseViewer,togetabetterviewofthemoleculeinthedatabase,positionthecursoroverthecellinthefirstfield(calledmol),presstheleftmousebuttonanddragdown(andslightlytotheright)untilyouclearlyseethemoleculardrawing.Youcanrotatethedrawingbydraggingthemiddlemousebuttonoverit.
5,OnlytheheavyatomsaredisplayedintheDatabaseViewer.Todisplayhydrogenatoms,choose:
DBV|Display|Molecule|Hydrogens
RenderingtheMolecule
TheRendermenuallowsyoutochangethevisualdisplaymodeofthecurrentmolecule.TheprimaryrenderingcontrolsarefoundinMOE|Render|Atoms,whichcanalsobeopenedusingMOE|Popup|Atoms.
ThedefaultrenderingmodeisLinemode,whichisalsogivesthefastestdisplay.Inbuildingtheaspirinmolecule,youpreviouslyusedtheRendermenutochangetoStickmode.Threeothermodesare:
BallandLine,BallandStick,andSpaceFilling.ThereisevenaNone(nobonds)mode.Takeamomentnowtotryeachrenderingmode.
Notethatifyouhaveanyselectedatoms,thechosenrenderingwillaffectonlythoseatoms.Thefollowingstepswillshowyouhowtorenderdifferentpartsofasystemindistinctmodes:
1,TosettheentiremoleculeinStickmode,makesurenoatomsareselectedanduseMOE|Render|Atoms.
2,Toselectallthebenzenecarbons,opentheAtomSelectorwithMOE|Selection|AtomSelector.IntheSMILEStextfield,typeatoindicatearomaticatomsandpressAll.Thiswillperformasubstructuresearchandselectallatomswithinthematchingstrings.
3,ChoosetheappropriatebuttoninMOE|Render|Atomstodisplaytheatomnucleiofonlytheringcarbonsassmallspheres.
Therenderingoptionsallowatomstobelabeledandcoloredaccordingtochargeandelementtype.YoumaywishtotakeamomentnowtoexperimentwiththevariousLabelandColorbuttonsintheMOE|Render|Atomspanel.
Individuallyselectedatoms,hydrogens,residuesandsidechainsmaybeshownorhiddenusingtheMOE|RHS|HideandMOE|RHS|Showsubmenus.TheBackbone,SidechainandAlloptionsareusefulwhenstudyingproteins.Youwillhaveanopportunitytoexperimentwiththesecommandslaterwhenweviewaprotein.Fornow,hidethehydrogensontheaspirinmoleculewithMOE|RHS|Hide|Hydrogens.Tomaketheatomsvisibleagain,useMOE|RHS|Show|All.HydrogenatomdisplaycanalsobetoggledusingtheMOE|RHS|Hydrogensbutton;clickingthiscyclesthroughdisplayingall,polaronly,ornohydrogenatoms.
TheRendermenuisalsousedforsettingtheviewpointfromwhichthemoleculeisobserved.MOE|Render|CenterisequivalenttoMOE|RHS|Center.Theseoperateonselectedatomsoronallatomsifnoneareselected,andadjusttheviewsothatallatomsinquestioncanbeseenandarecenteredintheMainWindow.TheviewcanalsobesetusingtheMOE|Footer|TrackballPopup|Viewmenu,whichallowstheusertosaveandloadparticularviewingangles.
TodemonstratetheuseofMOE|RHS|Centeronselectedatoms,webeginbyselectingafewatomsintheaspirinmolecule:
1,Holdshiftandselectalltheoxygenatoms.
2,SelectMOE|RHS|Center.IntheMOEwindow,theviewisnowzoomedinonthepartofthemoleculecontainingtheselectedatoms.
SelectingAtoms
Tochangethepropertiesofamoleculeormanipulateasubsetofitsatoms,youmustfirstindicatewhichatomsaretobemanipulatedbycreatinganatomselectionset.Selectedatomsareidentifiedbyachangeincoloranda(small)spheredependingonthecurrentrenderingmodeoftheatomselected.
Usethemousetomanuallyselectatoms:
1,Makeaselectionsetconsistingofasingleatombyclickingtheleftmousebuttononanyatom.Thiswillcauseallotherselectedatomstobecomeunselected.
2,Selecttheatomsthatformabondbyclickingonthebondthatlinksthem.
3,SelectallatomsofaresiduebypressingdowntheCtrlkeywhileclickingtheleftmousebuttononanatom.Inthecaseoftheaspirinmolecule,allatomsbelongtothesameresidue,hence,allatomsareselected.Hiddenatomsarealsoselected.
4,Addasingleat
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