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CootTutorialSoleil2008WorkshopSeptember1,2008Contents11 MousingFirst,howdowemovearoundandselectthings?Left-mouseDrag RotateviewCtrlLeft-MouseDrag TranslatesviewShiftLeft-Mouse LabelAtomRight-MouseDrag ZoominandoutMiddle-mouse CentreonatomScroll-wheelForward IncreasemapcontourlevelScroll-wheelBackward Decreasemapcontourlevel2 IntroductoryTutorialInthistutorial,wewilllearnhowtodothefollowing:1. StartCoot2. Displaycoordinates3. Displayamap4. Zoominandout5. RecentreonDifferentAtoms6. ChangetheClipping(Slab)7. RecontourtheMap8. ChangetheMapColour9. Displayrotamersandrefineresidue2.1 GetthefilesBeforewestart,let’sgetthefilesonwhichwewillbeworking:$ wget http://www.ysbl.york.ac.uk/emsley/coot/tutorial/tutorial-˜modern.pdb$ wget http://www.ysbl.york.ac.uk/emsley/coot/tutorial/rnasa-1.8-˜all refmac1.mtzorcopythemfrom/home/emsley/tutorial2.2 StartCootTousecoot,inaterminalwindow,type:$ cootWhenyoufirststartcoot,itshouldlooksomething likeFigure??.2Figure1: CootatStartupNotmuchtoseeatpresent... Actually,afterthis,cootscreenshotswillbedisplayedwithawhitebackground,whereasyouwillseeablackone3!!2.3 DisplayCoordinatesSolet’sreadinthosecoordinates:1Select “File”fromtheCootmenu-barSelectthe “Open Coordinates”menuitem[CootdisplaysaCoordinatesFileSelectionwindow]Either– Selecttutorial-modern.pdbfromthe“Files”listor– Typetutorial-modern.pdbintheSelection: entryClick ...

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CootTutorial
Soleil2008Workshop
September1,2008
Contents
11 Mousing
First,howdowemovearoundandselectthings?
Left-mouseDrag Rotateview
CtrlLeft-MouseDrag Translatesview
ShiftLeft-Mouse LabelAtom
Right-MouseDrag Zoominandout
Middle-mouse Centreonatom
Scroll-wheelForward Increasemapcontourlevel
Scroll-wheelBackward Decreasemapcontourlevel
2 IntroductoryTutorial
Inthistutorial,wewilllearnhowtodothefollowing:
1. StartCoot
2. Displaycoordinates
3. Displayamap
4. Zoominandout
5. RecentreonDifferentAtoms
6. ChangetheClipping(Slab)
7. RecontourtheMap
8. ChangetheMapColour
9. Displayrotamersandrefineresidue
2.1 Getthefiles
Beforewestart,let’sgetthefilesonwhichwewillbeworking:
$ wget http://www.ysbl.york.ac.uk/emsley/coot/tutorial/tutorial-˜
modern.pdb
$ wget http://www.ysbl.york.ac.uk/emsley/coot/tutorial/rnasa-1.8-˜
all refmac1.mtz
orcopythemfrom
/home/emsley/tutorial
2.2 StartCoot
Tousecoot,inaterminalwindow,type:
$ coot
Whenyoufirststartcoot,itshouldlooksomething likeFigure??.
2Figure1: CootatStartup
Notmuchtoseeatpresent... Actually,afterthis,cootscreenshotswillbe
displayedwithawhitebackground,whereasyouwillseeablackone
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2.3 DisplayCoordinates
Solet’sreadinthosecoordinates:
1Select “File”fromtheCootmenu-bar
Selectthe “Open Coordinates”menuitem
[CootdisplaysaCoordinatesFileSelectionwindow]
Either
– Selecttutorial-modern.pdbfromthe“Files”list
or
– Typetutorial-modern.pdbintheSelection: entry
Click “OK”intheCoordinatesFileSelectionwindow
[CootdisplaysthecoordinatesintheGraphicsWindow]
Figure2: CootAfterLoadingCoordinates
2.4 AdjustVirtualTrackball
By default, Coot has a “virtual trackball” to relate the motion of the molecule to
themotionofthemouse. Manypeopledon’tlikethis.
Soyoumightliketotrythefollowing. IntheCootmainmenu-bar:
HID Virtual Trackball Flat
1Noteyoucanalsouse“Alt-F”insteadofclickingon“File”
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(Usethe “Spherical Surface”optiontoturnitbacktohowitisbydefault)
What is the difference? “Flat” mode is like the mode used by “O”. In both
modes,draggingthemousenearthecentreofthescreencausestheviewtorotate
about the X- or Y- axis. However in spherical mode you can also rotateabout the
z-axisbydraggingthemousealonganedgeofthewindow.
2.5 Displaymaps
We are at the stage where we are looking at the results of the refinement. The
refinement programs stores its data (labelled lists of structure factor amplitudes
andphases)inan“MTZ”file. Let’stakealook...
Select “File”fromtheCootmenu-bar
Select “Auto Open MTZ” menu item [Coot displays a Dataset File Selection
window]
Selectthefilenamernasa-1.8-all refmac1.mtz
Ifyouchooseinstead“OpenMTZ,ciforphs...” youwillsee:
[CootdisplaysaDatasetFileSelectionwindow]
Selectthefilenamernasa-1.8-all refmac1.mtz
[CootdisplaysaDatasetColumnLabelSelectionwindow]
Figure3: CootMTZColumnLabelSelectionWindow
Notice that you have a selection of different column labels for the “Ampli-
tudes”and“Phases”,however,let’susethedefaults: “FWT”and“PHWT”.
Press “OK”intheColumnLabelWindow
NowopentheMTZfileandselectcolumnlabels“DELFWT”and“PHDELWT”.
Sonowwehave2maps(whetherauto-openedornot).
2.6 Zoominandout
2Tozoomin,clickRight-mouse anddragitleft-to-right . Tozoomoutagain,move
themousetheoppositeway.
2orup-to-down,ifyoupreferthat
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Figure4: CootafterreadinganMTZfileandzoomedin.
2.7 RecentreonDifferentAtoms
Select “Draw”fromtheCootmenu-bar
Select “Go To Atom. . . ”
[CootdisplaystheGoToAtomwindow]
Expandthetreeforthe“A”chain
Select1 ASPintheresiduelist
Click “Apply”intheGoToAtomwindow
Atyourleisure,use “Next Residue”and “Previous Residue”(or“Space”and
“Shift”“Space”inthegraphicswindow)tomovealongthechain.
ClickMiddle-mouseoveranatominthegraphicswindow
[Cootrecentresonthatatom]
Ctrl Left-mouse & Drag moves the view around. If this is a too slow and
jerky:
– Select DrawfromCoot’smenu-bar
– Selectthe “Dragged Map. . . ” menuitem
– Select “No”inthe“ActiveMaponDragging”window
– Click “OK”inthe“ActiveMaponDragging”window
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Figure5: Coot’sGoToAtomWindow.
3Nowthemapisrecontouredattheendofthedrag,notateachstep .
Youcandisplaythecontactstoo,asyoudothis:
– Select “Measures”fromtheCootmenu-bar
– Select “Environment Distances. . . ”
– Clickonthe “Show Residue Environment?” check-button
AlsoClick “Label Atom?” ifyou wishthe C atoms ofthe residues
tobelabelled.
– Click “OK”intheEnvironmentDistanceswindow
– Click “Apply”intheGoToAtomwindow
[You can’tchangethecolour of theEnvironmentdistances]
YoucanturnofftheEnvironmentdistancesifyoulike.
2.8 ChangetheClipping(Slab)
Select “Draw”fromtheCootmenu-bar
Select “Clipping. . . ” fromthesub-menu
[CootdisplaysaClippingwindow]
Adjusttheslidertotheclippingofyourchoice
3whichlookslessgoodonfastercomputers.
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Figure6: Cootshowing AtomLabelandenvironmentdistances.
Click “OK”intheClippingwindow
4Alternatively, you can use “D” and “F” on the keyboard, or Control Right-
mouseup/down(ControlRight-mouseleft/rightdoesz-translation).
2.9 RecontourtheMap
5Scrollyourscroll-wheelforwardsoneclick
˚[Cootrecontoursthemapusinga0.05electron/A highercontourlevel]
Scroll your scroll-wheel forwards and backwards more notches and see the
contourlevelchanging.
If you don’t have a wheel on your mouse you can use “+” and “-” on the
keyboard.
Note that the “Scroll” button in the Display Manager allows you to select
6whichmapisaffectedbythis .
2.10 ChangetheMapColour
Select “Edit”fromtheCootmenu-bar
Select “Map Colour”inthesub-menu
4think: DepthofField.
5don’tclickit down.
6bydefaultitisthelastmap,which isnotnecessarilythemapthatyouwant.
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Select “1 xxx FWT PHWT”inthesub-menu
[CootdisplaysaMapColourSelectionwindow]
Chooseanewcolourbyclickingonthecolourwidgets
[Cootchangesthemapcolourtomatchtheselection]
Click “OK”intheMapColourSelectionwindow
2.11 SelectaMap
Selectamapformodelbuilding:
Menubar: Calculate Model/Fit/Refine...
[CootdisplaystheModel/Fit/Refinewindow]
Select “Select Map. . . ” fromtheModel/Fit/Refinewindow
clickOK(youwanttoselectthemapwith“...FWTPHWT”)
3 ModelBuilding
“Sowhat’swrongwiththisstructure?” youmightask.
There are several ways to analyse structural problems and some of them are
availableinCoot.
Validate Density Fit Analysis tutorial-modern.pdb
[Cootdisplaysabargraph]
Look at the graph. The bigger and redder the bar the worse the geometry. There
are2areaofoutstandingbadnessintheAchain,around41Aand89A.
Let’slookat89Afirst-clickontheblockfor89A.
[Cootmovestheviewsothat89ACAisatthecentreofthescreen]
3.1 Rotamers
Examinethesituation...[ Thesidechainis pointingthewrongway. Let’s Fixit...]
Menubar: Calculate Model/Fit/Refine...
[CootdisplaystheModel/Fit/Refinewindow]
Select “Rotamers”fromtheModel/Fit/Refinewindow.
In the graphics window, (left-mouse) click on an atom of residue 89A (the
C ,say)
[Cootdisplaysthe“SelectRotamer”window]
ChoosetheRotamerthatmostcloselyputstheatomsintotheside-chainden-
sity
Click “Accept”inthe“SelectRotamer”window
[Cootupdatesthecoordinatestotheselectedrotamer]
Click “Real Space Refine Zone”intheModel/Fit/Refinewindow.
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Inthegraphicswindow,clickonanatomofresidue89A.Clickitagain.
[Coot displays the refined coordinates in white in the graphics and a new
“AcceptRefinement”window]
Click “Accept”inthe“AcceptRefinement”window.
[Coot updates the coordinates to the refined coordinates. 89A now fits the
densitynicely.]
OK.That’sgood.
Now,howaboutifwejustuseRealSpaceRefinementonly?
Click “Undo”twice
[Cootputsthesicechainbacktotheoriginalposition]
Click “Real Space Refine Zone”intheModel/Fit/Refinewindow.
Inthegraphicswindow,clickonanatomofresidue89A.Clickitagain.
[Coot displays the refined coordinates in white in the graphics and a new
“AcceptRefinement”window]
Now using left-mouse, click and drag on the intermediate (white) CZ atom
ofthePHE(ifyoumis-clicktheatom,theviewwillrotate).
Canyoupulltheatomaroundsothattheside-chainfitsthedensity?
[Yes, you can]
Figure7: 89Anowfitsthedensitynicely.
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