tutorial

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 ...