Escolar Documentos
Profissional Documentos
Cultura Documentos
Chimera
IntroductiontoProteinStructureBioinformatics2007
VincentZoete02/23/2007
1/21
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
2/21
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.
3/21
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
4/21
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.
5/21
Theribbonrepresentationofthesecondarystructureelementscanbeswitchedonbychoosing
showintheRibbonmenu.Threevariantsareavailable:flat,edgedandrounded.You
cantrythemallbyclickingthecorrespondingmenuitem.Selecttherepresentationyouprefer.
RGDcursorspositions.ClickontheApplybuttonoftheColorSecondaryStructurewindow
toapplythecoloring.
Youcantryseveralcolorcombinationsandkeeptheoneyouprefer.Finally,youcanclosethe
Ribbon,ColorSecondaryStructureandColorEditorwindowsbyclickingtheClose
button,orthetoprightXicon.
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.
8/21
OpentheActions/Colormenuanddetacheditbyclickingontheupperdottedline.Youcan
eventuallyclosesomeotherwindowstosavespaceonthescreen.Checktheatoms/bondsboxso
thatthecolorchangingwillbeappliedonlytoatomsandbonds.Then,youcanselectacolorfrom
theleftcolumnthatwillbeusedforallligandatoms.Anotherpossibilityistocolorallatoms
accordingtotheiratomtypes.Thisisobtainedbyclickingbyelement.
Similarly,selectthewatermolecule,displayitinballandstickandcoloritaccordingtotheatom
types.
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.
10/21
YoucanchangethehydrogenbondcolorandlinewidthfromtheHBondParameterswindow,
andclickApplytoapplythem.
Thissurfacegivesagoodideaofthevolumeoccupiedbytheligand.However,italsohidesthe
molecule. To correct this, it can be made transparent. In the Surface window, click on
transparencyandselect80%.
12/21
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.
13/21
Selecttheformatofthefilethatwillbesaved.ScientificjournalsgenerallyacceptTIFFandEPS
files.SelectTIFFinthiscase.Finally,chooseandFilenameandclickSave.
ImagesaresavedasRGBfigures.
14/21
Exercise 2
Loading the macromolecular structure
Loadthe1HVI.pdbstructurefileintoChimerausingoneofthetwomethodsseeninexercise1.
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.
15/21
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.
17/21
UnchecktheUseslabmodewiththicknessbox.
Surface capping
Aclippedsurfacemaybecapped.Todoso,choosetheSurfaceCappingmenuiteminthe
Depictionwindow.IntheSurfaceCappingwindow,checktheCapsurfaceatclipplanes
box.YoucanchangethecolorofthecappingplanebycheckingtheUsecapcolorboxand
choosethecolorbyclickingthecoloredsquarenexttoit.
Thiscappingcanalsobeappliedwiththeslabmode.
Saveanimageasdescribedinthepreviousexercise,thensavethesessionandcloseit.
18/21
Exercise 3
Open a previous session
Openthefinalstateofexercise2usingtheFile/RestoreSessionmenu.Removingallclippingand
capping,andchangethebackgroundcolortoblackifnecessary.
Ifyoudrawtherearclippingplaneclosertotheprotein,youwillseetheeffectofthedepthcueing,
whichcausesregionsfartherfromtheviewertobeshaded.Thedepthcueingparameterscanbe
changedintheEffectstaboftheViewingwindow.
19/21
20/21
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
21/21