非常好的pymol教程

PYMOLTUTORIALPARTOFBIOCHEMISTRY712ANDBIOCHEMISTRY660UNIVERSITYOFWISCONSIN-MADISONMAJORPROFESSOR:AnnPalmenbergInstituteforMolecularVirology&[e-mail]:Dr.Jean-YvesSgroBiologyNewMedia&BiotechnologyCenters,&[e-mail]/ANSWSERSSECT[e-mail]11/2006BIOCHEMISTRY660/712–FALL2006J.Y.SGROL02–page1L02:DESKTOPMOLECULARGRAPHICSIII:PyMolCONTENTSPyMol-ExerciseA:DownloadaPDBfromtherepositoryPyMol-ExerciseB:OpenPyMolandloadaPDBfilePyMol-ExerciseC:PyMolinterfacePyMol-ExerciseD:ActionpresetmenusPyMol-ExerciseE:UsefulcommandstoanalyzestructureandcreateimagesPyMol-ExerciseF:AsimpleanimationwithinPyMol,andforPowerPointPyMol-ExerciseG:HarnessingthepowerofPyMol:introducingscriptsPyMol-ExerciseH:Selectcommand,parameters,scripting,andsubsets.=========================================FromtheprefaceoftheUser’sguide:“PyMOLwascreatedinanefficientbuthighlypragmaticmanner,withheavyemphasisondeliveringpowerfulfeaturestoendusers.Expediencyhasalmostalwaystakenprecedenceoverelegance,andadherencetoestablishedsoftwaredevelopmentpracticesisinconsistent.PyMOLisaboutgettingthejobdonenow,asfastaspossible,bywhatevermeanswereavailable.”PyMolisamultiplatformmoleculargraphicssoftwarewithmanyadvancedfeaturessuchasrenderedcartoonribbonsandsurfaces,internalraytracingandmovietoolsandisfastbecomingthenew“standard”inmoleculargraphics.ThePyMolwebsiteislocatedat=========================================Note:withintheexercises,Boldtextshowswhatactionsaretakenbytheuser:typingtextorclickingthemouse.=========================================PyMol-ExerciseA:DownloadaPDBfromtherepositoryReminder:StructureshaveaPDBIDcodemadeof4lettersandnumbers.PDBfilescontaincoordinatespertinenttothecrystallographicarrangementofthemoleculeswithinthecrystal.Thebiologicalfunctionalentitycanbeeitheramultimerofthedepositedstructure,orjustoneofmultiplecopieswithinthefile.Inthefollowingexamplewewilldownloadonefunctionalbiologicalsubunit,inthiscaseamonomer.1)OpenawebbrowsersuchasSafariorFirefox.2)Pointyourwebbrowserto)IntheSearchboxenterthefollowingID:2biwandclickSEARCHbuttonBIOCHEMISTRY660/712–FALL2006J.Y.SGROL02–page24)OntheleftcolumnclickDownloadFilestoshowsubmenus5)ClickthefirstoptionBiologicalUnitCoordinates2Note:DONOTUSEBiologicalUnitCoordinates16)Thefileissavedonthedesktopas2BIW.pdb2Youcannowcloseyourbrowser,orhideit(Command-H).=========================================PyMol-ExerciseB:OpenPyMolandloadaPDBfilePyMolorMacPyMolshouldbelocatedwithintheApplicationsClassesattheBNMCcomputer.Yourinstructormaygiveyouadifferentlocationifnecessary.1)double-clickonthePyMolicontolaunchthesoftware.Note:SomeversionsofPyMolhavethetopandbottompanelsinseparatewindows,butofferthesameinterface.2)TypethenextcommandsafterPyMOLwithinthetoplinecommand:PyMOLcddesktopNotetheechoonthetextareaabovePyMOLpwdthiswillecho/Users/BNMC/Desktoporasimilarpath.OnaWindowssystemthepathwouldbeginwithC:\PyMOLload2BIW.pdb2PyMOLload2BIW.pdb2HEADEROXIDOREDUCTASE19-JAN-05XXXXBIOCHEMISTRY660/712–FALL2006J.Y.SGROL02–page3Thiswillloadthestructureandechoinformationinthetextpanelasreproducedtotheright.Note:filenameiscasesensitiveTITLECRYSTALSTRUCTUREOFAPOCAROTENOIDCLEAVAGEOXYGENASEFROMTITLE2SYNECHOCYSTIS,NATIVEENZYMECOMPNDAPOCAROTENOID-CLEAVINGOXYGENASEObjectMolecule:Readsecondarystructureassignments.ObjectMolecule:Readcrystalsymmetryinformation.Symmetry:Found4symmetryoperators.CmdLoad:2BIW.pdb2loadedas2BIW.pdb2.Note:whynotusetheFileOpenmenusequence?Goodquestion…Youcanactuallytrythatoptionanditmightworkonyourcurrentsystem.HoweveryouwilllikelyfindthatwhenyougettotheOpenformthefilesyouwanttoopenarelistedingrayandthereforecannotbeopened.Theeasyfixistosimplyrenamethefilefrom*.pdb1or*.pdb2tosimply*.pdbbeforeyoutrytoopenit.=========================================PyMol-ExerciseC:PyMolinterfaceThisexercisecontinuesonthepreviousexercisewhere2BIW.pdb2wasloadedwithinthePyMolsoftware.Yourscreenshouldbesimilartothisimagewithouttheextramarkings.TheViewerandInternalGUIarethepartswewillusemost.Thedefaultsizeoftheimageinthevieweris640x480pixels.ThemenubarmightbeattachedtotheexternalGUIinsystemsotherthanMac.BydefaultPyMolwilldisplaythemolecule(s)containedwithinthePDBfileasawireframe.Thiscyanobacteriummoleculeisacarotenoidoxygenaseandcontainsacarotenoidligand.1)Mousecontrolofthe3DrepresentationThe3Dmoleculeisrepresentedwithinavirtual3Dworld.TheflatsurfaceofthescreenrepresentstheXandYaxeswhiletheZ,depthaxisisperpendiculartothescreen.BIOCHEMISTRY660/712–FALL2006J.Y.SGROL02–page4PyMolisoptimizedfora3-buttonmousebutmostbasicfunctionscanstillbeachievedbyaone-buttonmouse,inparticulartherotationsaroundX,Y,andZ.RotationaroundtheXorYaxis:(left)clickanddrag.RotationaroundtheZaxis:(left)clickonthetopleftorrightcorner.Translate(movesideways)XorY:clickmiddlebuttonanddrag.Zoom(movealongZaxis):clickrightbuttonanddragupordown.2)ChangingthedefaultmousesettingsBy