2022年wincoot简易教程 .pdf

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1、Coot TutorialCCP4 WorkshopBangaloreMarch 23, 2005Contents1Mousing22IntroductoryTutorial22.1Get the ?les. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22.2Start Coot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22.3DisplayCoordinates. . . . . . . . . . . . .

2、. . . . . . . . . . . . . . .32.4AdjustVirtualTrackball. . . . . . . . . . . . . . . . . . . . . . . . . .32.5Displaymaps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42.6Zoomin and out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42.7Recentre on DifferentAtoms. . .

3、. . . . . . . . . . . . . . . . . . . . .62.8Change the Clipping(Slab). . . . . . . . . . . . . . . . . . . . . . . .72.9Recontourthe Map. . . . . . . . . . . . . . . . . . . . . . . . . . . . .82.10 Change the Map Colour. . . . . . . . . . . . . . . . . . . . . . . . . .82.11 Select a Map. . . . .

4、. . . . . . . . . . . . . . . . . . . . . . . . . . . .83ModelBuilding83.1Rotamers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93.2More Real Space Re?nement. . . . . . . . . . . . . . . . . . . . . . . .104Blobology104.1Find Blobs. . . . . . . . . . . . . . . . . . . . . . .

5、. . . . . . . . . . .104.1.1Blob 3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .104.1.2Blob 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .114.2Make a (Pretty?)Picture. . . . . . . . . . . . . . . . . . . . . . . . . .125Extra Fun (if you have time)125.1Waters. . .

6、. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .125.2Add TerminalResidue. . . . . . . . . . . . . . . . . . . . . . . . . . .125.3MutateResidue. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .135.4DisplaySymmetryAtoms. . . . . . . . . . . . . . . . . . . . . . . . .135.5

7、Re?ne withRefmac. . . . . . . . . . . . . . . . . . . . . . . . . . . . .131名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 1 页，共 13 页 - - - - - - - - - 1MousingFirst, how do we move aroundand select things?Left-mouseDragRotate viewCtrl Left-MouseDragTranslates viewSh

8、ift Left-MouseLabel AtomRight-MouseDragZoom in and outMiddle-mouseCentre on atomScroll-wheelForwardIncrease map contourlevelScroll-wheelBackwardDecrease map contourlevel2IntroductoryTutorialIn this tutorial,we willlearn how to do the following:1. Start Coot2. Displaycoordinates3. Displaya map4. Zoom

9、in and out5. Recentre on DifferentAtoms6. Change the Clipping(Slab)7. Recontourthe Map8. Change the Map Colour9. Displayrotamersand re?ne residue2.1Get the ?lesThe files are already in the tutorials folder 2.2Start CootBefore you start coot, you need to setup the proper environment.This is currently

10、done by “ sourcing”a setup ?le. The locationof this setup ?le is systemdependent,For the LMB tutorial To then use coot, simply type (in the X11 window)% source /Users/vis/.cshrc %cootWhen you first start coot for this tutorial, you may see a message saying that there is an auto-save file and asking

11、if you want to use it. For the purpose of this tutorial, click on No to answer this question. When you ?rst start coot, it should look somethinglike Figure 1.2名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 2 页，共 13 页 - - - - - - - - - Figure1: Coot at StartupNot much

12、 to see at present.Actually,from now coot screenshots willbedisplayedwith a whitebackground,whereas you willseea black one2.3DisplayCoordinatesSo let sread in those coordinates:Select “ File”from the Coot menu-bar1Select the “ OpenCoordinates”menu itemCoot displays a Coordinates File Selection windo

13、w For the LMB tutorial, the files you need will be in: /Users/vis/tutorials/coot EitherSelect tutorial.pdbfrom the “ Files”listorType demo.pdbin the Selection: entryClick “ OK” in the CoordinatesFile Selection windowCoot displays the coordinates in the Graphics Window2.4AdjustVirtualTrackballBy defa

14、ult,Coot has a “ virtual trackball”to relate the motionof the moleculetothe motionof the mouse. Manypeople dontlike this.So you mightlike to try the following:In the Coot main menu-bar:HIDVirtualTrackballFlat(Use the “ SphericalSurface” optionto turn it back to how it is by default)1Note you can als

15、o use “Alt-F”instead of clickingon “File”3名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 3 页，共 13 页 - - - - - - - - - Figure2: Coot AfterLoadingCoordinates2.5DisplaymapsWe are at the stage wherewe are lookingat the resultsof the re?nement.There?nementprogramsstores i

16、ts data (labelledlists of structurefactoramplitudesand phases) in an “ MTZ ”?le. Let stake a look.Select “ File”from the Coot menu-barSelect “ AutoOpen MTZ” menu itemCoot displays a Dataset File SelectionwindowSelect the ?lename rnasa-1.8-allrefmac1.mtzIf you choose instead “ OpenMTZ, cif or phs.”yo

17、u willsee:Coot displays a Dataset File Selection windowSelect the ?lename rnasa-1.8-allrefmac1.mtzCoot displays a Dataset Column Label Selection windowNoticethat you have a selection of differentcolumnlabels for the “ Ampli-tudes ” and “ Phases ”,however,let suse the defaults:“ FWT ”and “ PHWT ”.Pre

18、ss “ OK” in the ColumnLabel WindowNow open the MTZ ?le and select column labels “ DELFWT ” and “ PHDELWT ”.So now we have 2 maps (whetherauto-openedor not).2.6Zoom in and outTo zoom in, click Right-mouseand drag it left-to-right2. To zoom out again, movethe mouse the oppositeway.2or up-to-down,if yo

19、u prefer that4名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 4 页，共 13 页 - - - - - - - - - Figure 3: Coot MTZ ColumnLabel Selection WindowFigure 4: Coot after readingan MTZ?le and zoomedin.5名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - -

20、第 5 页，共 13 页 - - - - - - - - - 2.7Recentre on DifferentAtomsSelect “ Draw ”from the Coot menu-barSelect “ Go To Atom.”Coot displays the Go To Atom windowSelect “1A ASP”in the residue listClick “ Apply”in the Go To AtomwindowAt your leisure, use “ NextResidue”and “ PreviousResidue”(or “ Space ”and“ S

21、hift”“ Space” inthe graphicswindow)to move along the chain.Click Middle-mouseover an atom in the graphicswindowCoot recentres on that atomCtrlLeft-mouse& Dragmoves the viewaround.If this is a too slowandjerky:Select Drawfrom Coot s menu-barSelect the “ Dragged Map.”menu itemSelect “ No” in the “ Act

22、ive Map on Dragging ” windowClick “ OK ” in the “ ActiveMap on Dragging”windowNowthe map is recontouredat the end of the drag, not at each step3.Figure 5: Coot sGo To AtomWindow.3whichlooks less good on faster computers.6名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第

23、 6 页，共 13 页 - - - - - - - - - You can displaythe contacts too, as you do this:Select “ Measures ”from the Coot menu-barSelect “ Environment Distances.”Click on the “ ShowResidue Environment?”check-buttonAlso Click “ Label Atom? ”if you wish the Catoms of the residuesto be labelled.Click “ OK ” in th

24、e EnvironmentDistances windowClick “ Apply ” in the Go To AtomwindowFigure 6: Coot showingAtomLabel and environmentdistances.You can turnoff the Environmentdistances if you like.2.8Change the Clipping(Slab)Select “ Draw ”from the Coot menu-barSelect “ Clipping. ”from the sub-menuCoot displays a Clip

25、ping windowAdjustthe slider to the clippingof your choiceClick “ OK” in the ClippingwindowAlternatively,you can use “ D” and “ F”4on the keyboard.4think:Depth of Field.7名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 7 页，共 13 页 - - - - - - - - - 2.9Recontourthe MapScr

26、oll your scroll-wheelforwardsone click5Coot recontours the map using a 0.05electron/?Ahigher contour levelScroll yourscroll-wheelforwardsand backwardsmoreclicks and see thecontourlevel changing.2.10Change the Map ColourSelect “ Edit”from the Coot menu-barSelect “ Map Colour” in the sub-menuSelect “0

27、 xxx FWT PHWT” in the sub-menuCoot displays a Map Colour Selection windowChoose a new colourby clickingon the colourwidgetsCoot changes the map colour to match the selection Click “ OK” in the Map ColourSelection window2.11Select a MapSelect a map for model building:Menubar:CalculateModel/Fit/Re?ne.

28、Coot displays the Model/Fit/Re?ne windowSelect “ Select Map.”from the Model/Fit/Re?ne windowclick OK (you want to select the map with “ .FWT PHWT ”)3ModelBuilding“ So what s wrongwith this structure?”you mightask.There are several ways to analyse structuralproblemsand some of them areavailablein Coo

29、t.ValidateExperimentalGeometryAnalysistutorial.pdbLook at the graph.There are 2 area of outstandingbadness in the A chain, around41A and 89A.Let slook at 89A ?rst - click on the block for 89A.Coot moves the view so that 89A CA is at the centre of the screen 5dontclick it down .8名师资料总结 - - -精品资料欢迎下载

30、- - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 8 页，共 13 页 - - - - - - - - - 3.1RotamersExaminethe situation.The sidechainis pointingthe wrongway. Let sFix it.Menubar:CalculateModel/Fit/Re?ne.Coot displays the Model/Fit/Re?ne windowSelect “ Rotamers”from the Model/Fit/Re?ne window.In the

31、graphicswindow,(left-mouse)clickon an atom of residue89A (theC, say)Coot displays the “Select Rotamer”windowChoose the Rotamer that most closely puts the atoms into the lumpof densityClick “ Accept”in the “ Select Rotamer” windowCoot updates the coordinates to the selected rotamerClick “ RS Re?ne Zo

32、ne ” in the Model/Fit/Re?ne window.In the graphicswindow,click on an atom of residue 89A. Click it again.Coot thinks for a while then displays the re?ned coordinates in white in thegraphics and a new “AcceptRe?nement”windowClick “ Accept”in the “ AcceptRe?nement” window.Coot updates the coordinates

33、to the re?ned coordinates. 89A now ?ts thedensity nicely.You can undo these operationsby clickingon the “ Undo” button (twice).Youcan then try again to ?t the residue to the density using “ Auto Fit Rotamer ”or “ Re ?ne Zone”on that residue and click and drag the intermediateatomsinto the density.Fi

34、gure 7: 89A now ?ts the densitynicely.9名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 9 页，共 13 页 - - - - - - - - - 3.2More Real Space Re?nementNow let shave a look at the other region of outstandingbadness:Click on the graph block for 41 A (In the Validate/Geometry a

35、nalysis) Coot moves the view so that 89A CA is at the centre of the screen Examinethe situation.Residue 41 is in a mess and not ?ttingto the density. Can you ?x it?Yes you can.The trickis to RS (Real Space) Re?ne that zone. So.You can either RS Re?ne a few residues (40, 41 and 42) or just 41. Take y

36、ourpick.Click on “ RS Re?ne Zone ” in the Model/Fit/Re?ne windowSelect a range by clickingon atoms in the graphics window(eitheratoms in40 then 42 or an atom in 41 twice)Coot displays intermediate (white) atomsClick and drag on some atoms untilthe atoms ?t nicely in the density. If youwant to move a

37、 single atom then Ctrl Left-mouse to select (just) it.4Blobology4.1Find BlobsTo be foundunder Validate(called “ Unmodelled Blobs ” ).You can use the defaultsin the subsequentpop-up.Press “ Find Blobs ” andwait a short while.You willget a new windowthat tell you that it has foundunexplanedblobs.Time

38、to ?nd out what they are.4.1.1Blob3Let sstart from Blob 3Click on “ Blob 3”Coot centres the screenon a blobExaminethe situation.We need somethingtetrahedralthere.“ Place AtomAt Pointer”on the Model/Fit/Re?ne windowCoot shows a Pointer Atom Type window“ SO4”in the new window.In the “ PointerAtomAdded

39、to Molecule:”frame, change “ NewMolecule”to “ tutorial.pdb”Click OK.10名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 10 页，共 13 页 - - - - - - - - - Examinethe situation.the orientationis not quite right.Let sRS Re?ne it (you shouldknowwhatto do by now.)( “ RSRe?ne Zon

40、e ” then click an atom in the SOtwice. Accept)The SO ?ts better now.4.1.2Blob2Click on the button Blob 2”and examine the density.Somethingis missingfromthe model.What?This proteinand has been co-crystallizedwithits ligandsubstrate.That swhatmissing:3 GMP . So let sadd it.FileGet Monomer.Type “ 3GP”i

41、n the box (Use UpperCase). Press return.Coot appears to do some thinkingfor a few seconds3GP appearsIt is generallyeasier to workwithouthydrogens,so let sdelete them“ Delete.”from the Model/Fit/Re?ne window“ Hydrogens in Residue”click on an atom in 3GPHydrogensdisappearThe 3GP is displacedfrom where

42、 we want it to be.“ Rotate/Translate Zone ” from the Model/Fit/Re?ne windowclick on an atom in 3GP twiceIntermediate(white) atoms appearDrag it or use the sliders to move the intermediatefragmentto the approxi-matelythe right place.Click “ OK” in the slider windowNowoptimizethe ?t using “ RS Re?ne Z

43、one ” like we did before.Nowmerge this ligandinto the protein:CalculateMerge Molecules.Click (activate)“ monomer-3GP.pdb”into Molecule:tutorial.pdbMerge11名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 11 页，共 13 页 - - - - - - - - - 4.2Make a (Pretty?)PictureArrangea n

44、ice viewPress F8Wait a few seconds. Unfortunately, on most of the macs weve tried, this doesnt seem to work at present .This is a far as I expect you to get.5Extra Fun (if you have time)5.1WatersFit waters to the structure“ FindWaters. ”in the Model/Fit/Re? ne window,then OK (usingthe de-faults)Wate

45、rs appearTo check the waters:Click on “ Measures”in the main menubar.Click on EnvironmentDistancesClick on the “ Show Residue Environment?”check-buttonChange the distances as you likeUse the Go To Atomwidge t to g o to the fir st w ater (probably towards theend of the list of residues in Chain “ W ”

46、)Use the Spacebar to navigateto the next residue (and Shift Spacebar to gobackwards)If you don tlike the fast sliding6you can turn it off:Click “ Draw” in the main menubarClick “ SmoothRecentering.”Click “ No”5.2Add TerminalResidueTo be foundon the Model/Fit/Re?ne dialogUse the Go To Atomwindowto go

47、 to residue 93 A. Noticethere is some densityunaccountedfor - it is the as yet unbuiltC terminusof the A chain. This is Blob 1.Add TerminalResidue and click on 93 A CA (or any atom in that residue).Coot displays intermediate (white) atomsAccept them.Now autozonere?ne them:Click on “ Re ?ne Zone”in t

48、he Model/Fit/Re?ne dialog6it snot very good for water checking12名师资料总结 - - -精品资料欢迎下载 - - - - - - - - - - - - - - - - - - 名师精心整理 - - - - - - - 第 12 页，共 13 页 - - - - - - - - - Press the “ A” key on the keyboard7While pressing A click on an atom in the new residue.Coot displays intermediate atomsAccept

49、 themDo the same for the next 2 residues (add and autozonere?ne).You should now have 3 extra ALAsat the C-terminus.Mutate them (and ?t them):Click on “ MutateMolecule.”in the “ Calculate”menu of the main menubar.The new residue numbersare 94 to 96 inclusive.Choose the sequence QTCClick on the “ Auto

50、?t the mutatedresidues” check button.Click on the “ Mutate ” button5.3MutateResidueYou can also mutateresidues individually:Use “ SimpleMutate ” on the Model/Fit/Re?ne dialog.Click on an atom in theresidue that you wish to mutate.You can choose the rotamer manuallyusing “ Rotamers ”in the Model/Fit/