Ligands in Coot

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Feature IntegrationRefinementExternale.g. REFMACInternalInternalValidationExternale.g. MolProbityValidation, Model Building and Refinementshould be used together
Refinement TechniquesSingle-Atom DragOver-draggingKey-bindings:Triple RefineSingle Residue Refine with Auto-acceptRamachandran Refinement
Page 2 and 3: Model-Building Proteins andLigands
Page 6 and 7: Usage Tips: Navigation(Type) Ctrl-G
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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