Advanced display options: viewportsdisplay.pdf · A.‐F. Miller 2010 1 Advanced display 1 Advanced...

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Advanced display options: viewports Wegetcomplementaryinformationfromthedifferentspectrawecollect.Whenputtingthistogetheritisextremelyhelpfultobeabletoworkwiththedifferentspectraatonce,simultaneously.Varian's"Viewports"allowthis.

Preliminaries.

Loadeachofthespectratobecomparedintoworkspacesandmakesurethatthechemicalshiftaxesofeachareproperlyreferenced.

Youcanmix1Dsand2Dsbutinordertohavethemoverlaidorstacked,youwillneedthemtohaveatleastonscaleincommon.(Eg.allhaveone1Hchemicalshiftaxis.)

SettingupViewports.Joinoneoftheworkspacesthatcontainoneoftheexperimentstobecompared.InmycaseIhaveTOCSYinworkspace4,NOESYinworkspace1,ROESYinworkspace2andDQCOSYinworkspace5.

Pulldownthe'Edit'menuandselect'Viewports'(fourthformthebottom)(Page2[1]).Inthepanelthatopens,choosetheeye‐ballbuttonnextto'4'tosimultaneouslyviewfourexperiments.Close.

Intheleft‐handpanel,enterthenumbersoftheworkspacesthatcorrespondtoeachoftheexperimentsyouwanttoview[2].Atthistimeyoucanalsoelecttocolour‐code[3}.Ifyes,thenyoucanchooseacolourforeachexperiment[4].(Allcontourswillhavethesamecolour,exceptthattwocolourswillbeallocatedforexperimentswherebothpositiveandnegativecontourshavesignificance.)Notethatyoumayhaveto'activate'aviewportinordertobeabletoalterthechoiceofworkspaceitwilldisplayetc.Inordertodothisyouwillhavetodrawtheslidertotheright[5],andthiswillrevealacolumnofeye‐balls,whichallowyoutochoosewhichONEviewportyouaremodifying.Theotherwaytodecidewhichviewportistheactiveone,istoclickonthebaronthetopofthewindowdisplayingthatworkspace[6].Whenanworkspaceisactive,youcanmanipulatethespectruminitjustasyouareusedtodoinginsingle‐displaymode,usingthetoolsintheverticalpanel[7],orthehorizontalbar[8].

Choosewhetheryouwanttheviewportsside‐by‐sideoroneabovetheother[9]

Usethecheckboxestoflexiblyalterwhichofthepossibleviewportsareactuallydisplayed[10].

Selecttheviewportsyouwanttohaveonthesamescale,usingthecheckboxes.Clickon'Overlayviewports'[11].

Page3showsthatyounowhavetheoptionto'StackSpectra'[1].Whatthismeansisthatthesoftwarewilllinethemupaccordingtotheirchemicalshiftaxes.WhenyouselectXandYoffsetsof0[2],thenthesamechemicalshiftwillappearinexactly

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thesameplaceinthetwospectra:theaxeswillbesuperimposedandmadetomatchoneanother.Thiswillbeaccomplishedevenifyoucollectedthedatausingdifferentswortof,solongasbothhave1Hchemicalshiftaxes.Ifbotharecorrectlyreferenced,youshouldseethepeaksoverlapperfectlywherethisisexpected(mineisclosetoperfect)[3].(Ifyouhaveacollectionofspectraofdifferenttypes,suchasa1H1DandaCOSY,youwillseean'AlignSpectra'buttoninsteadof'StackSpectra'.Thisallowsyoutolineupyourbeautiful1Dalongtheedgeofyour2D.)

Activatethe'SynchronizeAxes'option[4]soyoucanzoominononespectrumandhavetheotheronezoomaswell.Anythingdonetoonespectrum'saxeswillbedoneforalltheotherspectratoo.Similarly,youwillprobablywantto'SynchronizeCursor'(above[4]).

Atthispoint,Iliketoreverttoaside‐by‐sidedisplay[1].InPage4youseethatIhaveloadedallfourworkspacesandselectedthemall.Eachhasaname(whichyoucanchange[2]),andthenameappearsinitstitlebar[3].Mysynchronizedcursor[4]movesthesamewayinallfourwindows,regardlessofwhichoneistheactiveone[5](bluetitlebarinsteadofgrey).Thus,IcanmovetoapeakinthyTOCSYanddeterminewhetheritispresentintheCOSY.InthisexampleIamlookingataspinsystemrevealedbytheTOCSYandlearningfromtheCOSYthatonlyoneofthepeaksisastrongcandidateforasinglestep.Inordertomakemorespaceavailablefordata,Ioftengoto'Fields'andturnthemoff(loosesdisplayofcranddelta[6]).

Youcanalterthenumberandspacingofcontours,forwhicheverviewportisactive[7].Dothisforeachspectruminturntogetthemalldisplayingthedesiredstrengths(orsignificance)ofsignals.

Youcanusetheprintscreentoobtaindigitalfiguresofyourdisplay,asforsinglespectra.Selectedthe'2D'tab[8]toswitchleft‐handpanels.

Page5thenshowsthatIusedEdit>Displaytoconverttoawhitebackgroundandblackaxes.Thenandnearthebottomchoosetosaveasafile[1](insteadofprinting)andthenactivatethe'PrintScreen'[2]toenterafiledirectoryandname,specifyoutputtypeetcandSAVE.

ThefigureproducedisshownonPage6.TogetthefigureonPage7,Iexploitedthesynchronizedzoom.WithoneworkspaceactiveIusedthecursorsasusualtodelineateaspectralregionofinterestandthenusedthemagnifyingglassicontozoomin.Allfourspectrawerezoomedidentically.AzoomedoverlayfigureisonPage8.Makingfiguresthiswayisextremelyconvenient.

Theotherhugeconvenienceisthepossibilityofselectingonerowinonespectrumandhavingacompanioncursormovetotheidenticalpositioninotherspectra.ThisenormouslyfacilitatestheinterpretationofHSQCandCIGAR(forexample).YoucanplacethecrosshairsonapeakinanHSQCandthiswillrevealinthecompanionCIGARwhichother13Cchemicalshiftsarecoupledremotelytothechosen1H,and

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similarlywhichother1Hchemicalshiftsarecoupledremotelytothechosen13C.(SeethenotesonHMBC‐CIGAR.)

Settingupinset

First,displaytheentirespectrumtosuityourpurpose(Page9).

Ontheleft‐handside,choosetheFrametab[1].Clickontheaddinsetbutton[2]tocreateasecondframeinsideyour(full)defaultframe.Usingtheleftmousebutton,placethecursorattheleftedgeofthespectralwindowyouwanttodisplayinthenewframe.Holdtheleftmousebuttondownwhiledraggingtotherightuntilyouhaveselectedthespectralregiontobedisplayedinthenewframe[3].Withoutreleasingthemousebutton,nowdragitverticallydown,toindicatetheverticalheightyournewframeshouldhave[4].(Thismotionislikewritingacapital'L'butwiththeorderinwhichtheverticalandthehorizontallegsareexecutedreversed.)Nowreleasethemousebutton.Yournewframecanbemovedtothedesiredpositionbydraggingitbyoneofitsedges,anditcanberesizedbydraggingonitscorners.Ifyouhaveseveralframes,youcanactivateonebyclickinginit(theframenowdisplaysaborder).

Insideanactiveframe,youcanzoomandpanusingtheappropriatetoolsfromtheviewportpanel(left‐handside).

Theresultingspectracanbeprintedviathe1Dpanel(left‐handside)whichgivesyouaccesstothePrintscreen(Page10).

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Viewports:co-analysis of multiple

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