Ligands in Coot

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Usage Tips: Navigation(Type) Ctrl-G : → recentres on “G”: go to blob“P”: go to nearest atom (or CA if the residue if theresidue is a standard AA)“L” (unlabel) the atom at the screen centre“O” jump to other NCS chain“V”: Undo symmetry view“Go To Ligand” (icon) → Jump to (next) ligand
Usage Tips: Use Keybindings(Noob → Pro)Built-in: “A”, “B”, “C”, “D” “F”, “Ctrl-Z”, “G”, “I”, “M”,“N”, “O”, “P”, “S”, “U”,“Ctrl-Z”, “”(My personal set): “Shift A”, “Shift B”, “E”, “Shift E”,“H”, “J”, “Shift J”, “K”, “Shift K”, “Shift M”, “Shift P”,“Q”, “Shift Q”, “R”, “Shift R”, “T”, “Shift T”, V”, “ShiftV”, “W”, “Shift W”, “X”, “Y”, “Shift 4”, “”,“(You can download these from the Coot Wiki)
Page 2 and 3: Model-Building Proteins andLigands
Page 4 and 5: Feature IntegrationRefinementExtern
Page 8 and 9: Using NVIDIA CardsFor antialiasing:
Page 10: Previous
Page 20 and 21: Networking...PDBe interface...Drag
Page 22 and 23: Using the API21/80
Page 24 and 25: RCrane: Semi-AutomatedBuilding of R
Page 27 and 28: Ligands Tools in Coot“What should
Page 29 and 30: 2D Ligand BuilderFree sketchSbase s
Page 31: Cocktail Examples
Page 35 and 36: Parmatisation issues...(what if the
Page 37 and 38: Ligand RepresenationBond orders (fr
Page 39 and 40: Chemical Features
Page 41 and 42: Chiral Centre InversionInverted chi
Page 43 and 44: Ligand Environment LayoutBinding po
Page 45 and 46: Ligand Enviroment LayoutConsiderati
Page 47 and 48: ”Don't overlap the ligand”
Page 49 and 50: Optimising the minimiser
Page 51 and 52: Determination of theSubstitution Co
Page 54: 58/80
Page 57 and 58:
Layout Problems
Page 59 and 60:
Layout Examples3uic
Page 61 and 62:
Layout Problems
Page 63 and 64:
Modelling CarbohydratesValidation,M
Page 65 and 66:
Carbohydrate LinksThomas Lütteke (
Page 73:
Refinement Trials(NAG-ASN example)
Page 77 and 78:
Technical Details
Page 79:
AcknowledgementsKeith WilsonEleanor
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Ligands in Coot

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