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Highqualityimagingforpublication.

Chimera

IntroductiontoProteinStructureBioinformatics2007
VincentZoete02/23/2007

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Table of Contents
PresentationofChimera.......................................................................................................................3
Exercise1.............................................................................................................................................4
LoadingastructureintoChimera....................................................................................................4
Moving/zooming............................................................................................................................5
Ribbonrepresentation......................................................................................................................5
Coloringthesecondarystructureelements.TheModelPanel........................................................6
Changingbondsandatomsdisplay.Selections...............................................................................7
Selectionsusingtheselectmenu.................................................................................................7
Changingbonddisplayandcolor................................................................................................8
Selectionsusingthecommandline.............................................................................................9
Changingribbonattributes............................................................................................................11
Calculatingandshowinghydrogenbonds.....................................................................................11
Showingtheligandsurface............................................................................................................12
Labelresidues................................................................................................................................13
Savingimage..................................................................................................................................13
Savingthesessionstatus................................................................................................................14
Closingthesession.QuittingChimera..........................................................................................14
Restoringaprevioussession..........................................................................................................14
Exercise2...........................................................................................................................................15
Loadingthemacromolecularstructure..........................................................................................15
Showingthemolecularsurfaceoftheprotein...............................................................................15
Changethesurfacecolor...............................................................................................................16
Changingbondsandatomsdisplay...............................................................................................16
Clippingtheprotein.......................................................................................................................16
Surfacecapping.............................................................................................................................18
Exercise3...........................................................................................................................................19
Openaprevioussession.................................................................................................................19
Usingthesideview........................................................................................................................19
ChangingtheLighting...................................................................................................................20
Goingfurther......................................................................................................................................21

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Presentation of Chimera
This introductorycourseabouthighquality imaging forpublication will makeuse of the free
program Chimera. The official website of chimera can be found at the following address:
http://www.cgl.ucsf.edu/chimera
HereisabriefdescriptionofChimeraanditsfeaturestakenfromthewebsite:
UCSFChimeraisahighlyextensible,interactivemolecularvisualization
andanalysissystem.Chimeracanreadmolecularstructuresandassociated
datainalargenumberofformats,displaythestructuresinavarietyof
representations,andgeneratehighqualityimagesandanimationssuitable
forpublicationandpresentation.Inaddition,Chimeraprovidestoolsto:
show density maps and analyze microscopy data; utilize symmetry
information for the display of higherorder structures; display multiple
sequencealignments,withcrosstalkbetweenthesequencesandstructures;
andenableanalysisofmoleculardynamicstrajectoriesanddockingresults.
Chimeraisdistributedwithfulldocumentationandanumberoftutorials,andcanbedownloaded
freeofchargeforacademic,government,nonprofit,andpersonaluse.Chimeraisavailablefor
several platforms, including Windows, MacOS X, and Linux. For more information, see the
Chimera web site. Chimera is developed and supported by the Resource for Biocomputing,
Visualization,andInformaticsandisfundedbytheNIHNationalCenterforResearchResources
(grantP41RR01081).
Theprogramcanbedownloadedatthefollowingaddress:
http://www.cgl.ucsf.edu/chimera/download.html
Whenusingchimera,oneshouldcitethisreference:
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and
Ferrin,T.E."UCSFChimeraAVisualizationSystemforExploratoryResearchandAnalysis."J.
Comput.Chem.25(13):16051612(2004).

ThefollowingexerciseswillbeusedastutorialstointroducesomebasiccommandsofChimera.
TheHIV1 proteaseincomplexwiththeA77003inhibitor(1HVIinPDB)willbeusedasan
example.Youarehighlyencouragedtotestthedifferentoptionsthatyouwillencounterinthe
differentmenus.
Generally,scientificjournalsrequireEPSorTIFFimages,witha300dotsperinchresolutionor
higher,andwithRGBcolors.YouwillseehowtoobtainsuchimagesusingChimera.

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Exercise 1
Loading a structure into Chimera
TwomethodscanbeusedtoloadastructureintoChimera.
1)Ifthestructurefileispresentintheuser'scomputer,choosethemenuitemFile/Open.Then
select1HVI.pdbandclickOpen.

Under Unix or Mac OSX, the structure (for instance 1HVI.pdb) can also be loaded using the
followingcommand:
>chimera1HVI.pdb

2)Thestructuremightalsobefetchedfromadatabase,whenavailable.Choosethemenuitem
File/FetchbyID.ChoosethePDBdatabankandtypethePDBcode1HVI.ThenclickFetch

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Oncethestructurehasbeenloaded,allmacromolecule'sbondsshouldshouldappearinthewire
representation,whichisChimera'sdefault.

Moving / zooming
The macromolecule can be rotated by clicking the left button and dragging the cursor over
Chimera's window. The translation is obtained similarly, but using the central mouse button.
Finally,onecanzoominandoutusingthemouserightbutton.

Rotate:pressleftbuttonanddrag
Translate:presscentralbuttonanddrag
Zoom:pressrightbuttonanddrag

Ribbon representation
The secondary structure elements can be shown using the ribbon representation. This can be
accessedthroughtheActions/Ribbonsubmenu.
OneconvenientfeatureofChimeraisitsabilitytodetachsubmenussothatonecanusethem
severaltimeswithouttheneedtogoagainthroughthedifferentmenus.Forinstance,choosethe
Actions/Ribbonmenuitem,andclickonthedottedlineatthetopofthissubmenu.Thesub
menuwillbedetachedandfreelymovable.

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Theribbonrepresentationofthesecondarystructureelementscanbeswitchedonbychoosing
showintheRibbonmenu.Threevariantsareavailable:flat,edgedandrounded.You
cantrythemallbyclickingthecorrespondingmenuitem.Selecttherepresentationyouprefer.

Coloring the secondary structure elements. The


Model Panel
Theribboncanbecoloredaccordingtothesecondarystructureelement,i.e.strand,helixorloop.
OpentheModelPanelbychoosingtheFavorites/ModelPanelmenuitem.IntheModelPanel,
choose color bySS...ThiswillopentheColorSecondaryStructurewindow.Checkthe
Helix,StrandandOtherboxes.Foreachone,itispossibletomodifythedefaultcolorby
clickingonthecorrespondingcoloredsquaretoopentheColorEditorwindowandchangethe
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RGDcursorspositions.ClickontheApplybuttonoftheColorSecondaryStructurewindow
toapplythecoloring.

Youcantryseveralcolorcombinationsandkeeptheoneyouprefer.Finally,youcanclosethe
Ribbon,ColorSecondaryStructureandColorEditorwindowsbyclickingtheClose
button,orthetoprightXicon.

Changing bonds and atoms display. Selections


Theobjectiveofthispartistodisplayonlytheligand,theactivesitewatermoleculeandresidues
25and50oftheHIV1protease.Otherresidueswillbehiddentoclarifythefigure.Thiswill
requiretoselectpartsofthestructureandapplythemdifferentrepresentationschemes.
There are three ways of selecting atoms with Chimera: using the Select menu, using the
CommandLine,andusingthemousetoselectatomsfromthescreen.Thelatterwillbedescribed
later.

Selections using the select menu


Open the Select menuand detached it byclickingon the upper dottedline. Verify that the
SelectionModeisreplace.Otherwise,chooseit.
ThefirstfourmenuitemsallowtoselectpartofthestructureaccordingtotheChain(protein
chains,ligand,water),theChemistry(chemicalnatureoftheatomsorfunctionalgroups),the
Residue(residuenameortype)andtheStructure(backbone,sidechains,secondarystructure,
etc...).Youcantrytoselectdifferentpartsofthecomplex.Forinstance,youcanselecttheligand
bychoosingtheSelect/Chain/hetmenuitem.Youwillseethattheselectedpartsofthestructures
aresurroundedbygreenthinlines.
NotethatthisHIV1proteaseinhibitorisalsodefinedbyitsligandnatureoritsresiduename
(i.e., A77). Therefore, it can be selected also by Select/Structure/ligand or
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Select/Residue/A77.

Youcantryselectingdifferentpartsofthecomplex:thewatermolecule,chainsAorBofthe
protein,theaspartateresidues,thestrands,etc...
Itispossibletoappendaselectionwithanewone.Forinstance,toselectalltheprotein,youcan
choose the menu items Select/Selection Mode/append, then Select/Chain/A and
Select/Chain/B.
Finally,youcanclearallselectionsusingSelect/ClearSelection.

Changing bond display and color


SelectthereplacemodeforselectionsusingSelect/SelectionMode/replace andselectthe
ligand.
OpentheActions/AtomsBondsmenuanddetachitbyclickingontheupperdottedline.Choose
successivelythestick,ballandstick,sphereandwiremenuitemsandseehowtheligand
isdisplayedineachcase.Finally,choosetheballandstickrepresentation.

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OpentheActions/Colormenuanddetacheditbyclickingontheupperdottedline.Youcan
eventuallyclosesomeotherwindowstosavespaceonthescreen.Checktheatoms/bondsboxso
thatthecolorchangingwillbeappliedonlytoatomsandbonds.Then,youcanselectacolorfrom
theleftcolumnthatwillbeusedforallligandatoms.Anotherpossibilityistocolorallatoms
accordingtotheiratomtypes.Thisisobtainedbyclickingbyelement.

Similarly,selectthewatermolecule,displayitinballandstickandcoloritaccordingtotheatom
types.

Selections using the command line


ClosetheSelectwindowusingtheupperrightXicon.Openthecommandlinebychoosing
Favorites/Commandline.AlineprecededbyCommandwillappearonthelowerpartofthe
principalwindow.Thislinecanbeusedtotypeandexecutecommandsrelativetoselectionand
display,forinstance.Toexecuteacommand,oneneedstotypeitinthecommandlineandpress
Return.Theunionandintersectionselectionkeywordsarenoted|and&,respectively.The
negationsymbolis~.
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Adetaileddescriptionofthedifferentselectionpossibilitiesusingthecommandlineareprovidedin
thequickreferenceguide.Hereisalimitedlistshowingsomepossibleselectionsbasedonour
particularstructurethatyoucouldtry:
select:selecteverything.
select:.A:selectchainAoftheprotein.
select:.A,.B:selectchainsAandBoftheprotein.
selectligand:selecttheligand.
select:A77:selecttheresiduenamedA77.Anotherwaytoselecttheligand.
select:HOH:selecttheresiduenamedHOH,i.e.theactivesitewatermoleculeinourcase.
select:HOH|ligand:selectboththewatermoleculeandtheligand.
select:25:selectallresiduesthatarenumbered25inthePDB.Oneinbothchains.
select:25@CA:selectatomCofresidues25.
select:25.A:selectresidue25ofchainA.
select:25,50:selectallresiduesthatarenumbered25and50inthePDB.
selectstrand:selectstrands.

Selectalltheproteinbytypingselect:.A,.Binthecommandline,andhidetheatomsandbonds
usingAction/Atomsbonds/hide.

Selectresidues25and50bytypingselect:25,50inthecommandline,andshowtheminball
and stick representation, colored according to the atom type: Action/Atoms Bonds/show,
Action/AtomsBonds/ballandstick,Actions/Colors/byelement.

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Changing ribbon attributes


Ascanbeseen,thebackboneatomsoftheproteinresiduesarenotshown,whilethebondlengths
betweenthebackbone(displayedasaribbon)andCatomsareartificiallytoolong.Thisisdueto
thedefaultbehaviorofChimerathathidesbackboneatomswhenribbonsaredisplayed.Thiscanbe
modified by changing some attributes of the structure. From the Model Panel, open the
attributeswindow,andchoosethefalsevalueforribbonhidesbackboneatoms.

Calculating and showing hydrogen bonds


Chimera can calculate and display the hydrogen bonds between selected atoms. To show the
hydrogenbondnetworkbetweentheligand,theactivesitewatermoleculeandtheIle50backbone
atoms,thefollowingsequenceofactionscanbeused.Selecttheactivesitewatermolecule(using
the command line or the Select menu). Open the Tools/Structure Analysis/FindHBond
window.ChecktheOnlyfindHbondswithbox,sothatitwillcalculateonlyhydrogenbonds
involvingtheactivesitewatermolecule.Finally,clickontheApplybutton.
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YoucanchangethehydrogenbondcolorandlinewidthfromtheHBondParameterswindow,
andclickApplytoapplythem.

Showing the ligand surface


Selecttheligand.Then,opentheSurfacewindowusingAction/Surface.Clickshow.You
cantrymodifyingthesurfacerepresentationtomeshanddot.Then,gobacktothesolid
representation.
The surface quality may be increased by changing the corresponding attribute. In the Model
Panelwindow,selecttheMSMSligandsurfaceintheleftlist.Thenclickattributesandchange
thevertexdensityattributeto10.PressEntertoapplythechange.

Thissurfacegivesagoodideaofthevolumeoccupiedbytheligand.However,italsohidesthe
molecule. To correct this, it can be made transparent. In the Surface window, click on
transparencyandselect80%.

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Label residues
SelectatomsCofresidues25bytypingselect:25@CBinthecommandline.Openanddetach
theLabelwindowbychoosingtheActions/Labelmenuitem.IntheLabelwindow,choose
residue/name+specifier.Youcantryothertypesoflabeling.Eventually,youcanchangethe
labelcolorusingtheColorwindow,checkingresiduelabelsandchoosingacolor.

Saving image
ClearallselectionsusingSelect/ClearSelection.Chooseanorientationandzoomthatprovidesa
satisfyingpointofview.Then,selecttheFile/SaveImagemenuitem.Inthenewwindow,click
onImageSetupandchooseanimageresolutionof300pixelsperunit.ClickSaveinthis
Preferenceswindow.IntheSaveImagewindow,selectMaintaincurrentaspectratio,
andenteranImagewidthof6inches.ClickSaveAs.Waitwhiletheimageiscalculated.
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Selecttheformatofthefilethatwillbesaved.ScientificjournalsgenerallyacceptTIFFandEPS
files.SelectTIFFinthiscase.Finally,chooseandFilenameandclickSave.

ImagesaresavedasRGBfigures.

Saving the session status


TheChimerasession(theactualrepresentation)canbesavedforfutureuseormodifications.This
canbemadeusingtheFile/SaveSessionAs...menu.SelectafilenameandclickSave.The
savedfileisactuallyapythonscriptandwillhavethe.pyextension.

Closing the session. Quitting Chimera


ThesessioncanbeclosedusingtheFile/CloseSessionmenuitem.OnecanquitChimerawith
File/Quit.

Restoring a previous session


ApreviouslysavedsessioncanberestoredusingtheFile/RestoreSessionmenuitem.Selectthe
file(witha.pyor.pycextension)andclickOpen.

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Exercise 2
Loading the macromolecular structure
Loadthe1HVI.pdbstructurefileintoChimerausingoneofthetwomethodsseeninexercise1.

Showing the molecular surface of the protein


First,hidethebondsandatomsoftheproteinchainsandkeeponlytheligandandactivesitewater
moleculevisible.Todoso,selectthetwoproteinchains,forexamplebytypingSelect:.A,.Bin
thecommandline.ThenopenanddetachtheAction/AtomsBondsmenuandchoosethehide
menuitem.

Besurethattheproteinisstillselected.Ifnecessary,orincaseofdoubt,selectitagainasdescribed
above. Then, open and detach the Action/Surface menu, and choose show. Open the
Favorites/Model panel menu, select the MSMS main surface in the left list, then click
attributesandchangethevertexdensityto10.Ifyourcomputeristooslow,itmightbe
necessarytoreducethevertexdensityto5.

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Change the surface color


Besurethattheproteinisstillselected.OpenanddetachtheActions/Colorsmenu.Checkthe
surfacesbox,andclickonthecoloryouwouldliketoapplytotheproteinsurface.Thefollowing
imagehasbeenobtainedusingthecornflowerbluecolor.

Changing bonds and atoms display


Selecttheligandandwatermolecules,thendisplaytheminballandstickrepresentation,colored
accordingtotheatomtype.

Clipping the protein


Itispossibletocuttheproteinsurfaceintogetabetterviewoftheligandbindingmodeinsidethe
bindingsite.Todoso,openanddetachtheTools/Depictionmenu.ThenchoosethePermodel
Clipping menu item. In Model, select the MSMS main surface and check the Enable
clippingbox.Rotatethestructuretogetabetterviewoftheclippingeffect.
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Itispossibletomanipulatetheclippingpositionusingthemouse.ChecktheAdjustclippingwith
mousebox.Aclick/dragofthemousecentralbuttonwillcontrolthetranslationoftheclipping
plane.Aclick/dragofthemouserightbuttonwillmodifyitsorientation.Notethatthiscancelany
possibilityofproteintranslationorzoomusingthemouse.Youcangetbacktothedefaultbehavior
ofthemousebyuncheckingtheAdjustclippingwithmousebox.
Youcanselectanddisplayresidues25and50oftheHIV1proteasebytypingselect:25,50in
thecommandline,andthendisplaytheminthestickrepresentation.Thenchangethepositionand
orientationoftheclippingplanetohaveagoodviewoftheinteractionsbetweentheseresiduesand
theligand.

Youcanalsogetagoodviewoftheshapeofaburiedbindingsiteusingtheslabmode.InthePer
ModelClippingmenu,checktheUseslabmodewiththicknessandchoose6forthethickness.
This creates aproteinslabthatyoucan manipulateusingthemousebycheckingtheAdjust
clippingwithmousebox.

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UnchecktheUseslabmodewiththicknessbox.

Surface capping
Aclippedsurfacemaybecapped.Todoso,choosetheSurfaceCappingmenuiteminthe
Depictionwindow.IntheSurfaceCappingwindow,checktheCapsurfaceatclipplanes
box.YoucanchangethecolorofthecappingplanebycheckingtheUsecapcolorboxand
choosethecolorbyclickingthecoloredsquarenexttoit.

Thiscappingcanalsobeappliedwiththeslabmode.
Saveanimageasdescribedinthepreviousexercise,thensavethesessionandcloseit.

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Exercise 3
Open a previous session
Openthefinalstateofexercise2usingtheFile/RestoreSessionmenu.Removingallclippingand
capping,andchangethebackgroundcolortoblackifnecessary.

Using the side view


OpentheViewingmenubychoosingtheFavorites/Sideviewmenuitem.TheSideView
taboftheViewingwindowshouldbeactive.Otherwise,clickontheSideViewtab.Youwill
seeareducedviewofthestructureappearingintheViewingwindow.Theverticallinesshows
theclippingplanesthatdefinetheregionofspacedisplayedonthescreen.Thesquaregivesthe
viewer'seyeposition.Theredlinesshowthefieldofvision.
ClickingtheViewAllbuttonadjuststhescaleandclippingplanepositionssothattheviewwill
includeeverythingthatisdisplayed.Itispossibletomovethepositionoftheviewer'seyeand
clippingplanesusingthemouse.

Ifyoudrawtherearclippingplaneclosertotheprotein,youwillseetheeffectofthedepthcueing,
whichcausesregionsfartherfromtheviewertobeshaded.Thedepthcueingparameterscanbe
changedintheEffectstaboftheViewingwindow.

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Changing the Lighting


Itmightbeusefultochangethelighting(intensityanddirection)togetabetterviewofthesystem.
Select the Lighting tab in the Viewing window. This tab displays the light sources and
parameters.Thekeylightisthedominantbrightersourceoflight.Thefilllightgivesasecondary
source.Thesolidarrowsintherightviewallowtomanipulatethelightingdirectionswiththe
mouse.Youcantrydifferentlightingdirectionstoseetheireffect.

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Going further
TheseexercisesgiveonlyaverylimitedoverviewofwhatChimeraisable.Youcanfindadetailed
documentation,aswellassometutorials,atthefollowingaddress:
http://www.cgl.ucsf.edu/chimera/docindex.html
Here are someexamples of images producedusing Chimerathat were takenfrom theofficial
Website.
Slicedpotassiumchannel

ParameciumBursariaChlorellaVirus

DNAandNetropsin

BluetongueVirusandViralRNA

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