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$Small-Angle X-ray Scattering SAXS vs. X-ray Diffraction SAXS vs. X ...$

Hydrogen Atoms and ChargesThe tools available in PMV are used to read coordinates in PDB and other formats, to addhydrogens, to select portions of the molecule, and to add partial charges. These functions are allaccessed through menus at the top of the PMV window. A few useful commands will be describedhere—for more information on the many other functions of PMV, please see the PMVdocumentation.File>ReadMolecule: opens a browser that allows reading of PDB coordinate files12
Edit>Delete: several options for deleting entire molecules, selected sets of atoms, or hydrogenatoms.Edit>Hydrogens>Add: options for adding all hydrogens or polar hydrogens using Babel.Edit>Charges: options for computing Gasteiger charges for arbitrary molecules using Babel.Ligand PDBQT Files – the “Ligand” MenuOnce ligand coordinates are created with hydrogen atoms and charges, they can be processed in the“Ligand” menu to create the ligand PDBQT file.Ligand>Input>QuickSetup: uses defaults to create the PDBQT file. PDB files can be readfrom the PMV viewer or from a file, and written directly to a new PDBQT file. Please note thathydrogen atoms will not be added.Ligand>Input>Open: reads coordinates from a file.Ligand>Input>Choose: chooses a molecule already read into PMV.Ligand>Input>OpenAsRigid: reads an existing PDBQT file and writes a new file with NOactive torsions.TorsionTree>ChooseRoot: manual selection of the root atom.TorsionTree>DetectRoot: automatic detection of the root that provides the smallest largestsubtree.TorsionTree>ShowRootExpansion: for molecules with several atoms in the root, displayssmall spheres to show all atoms in the root, including atoms connected to each root atom by rigidbonds.TorsionTree>ShowRootMarker: displays a sphere on the root atom.TorsionTree>ChooseTorsions: launches an interactive browser for choosing rotatablebonds. Rotatable bonds are shown in green, and non-rotatable bonds are shown in red. Bonds thatare potentially rotatable but treated as rigid, such at amide bonds and bonds that are made rigid bythe user, are shown in magenta. Rotation of rotatable bonds may be switched on and off by clickingon the bonds.TorsionTree>SetNumberOfTorsions: sets the number of rotatable bonds in the ligand byleaving the specified number of bonds as rotatable. The two options will choose the torsions thatrotate either the fewest atoms in the ligand or the most atoms in the ligand.AromaticCarbon>SetNames: clicking on atom positions will switch carbon atoms betweenaromatic and aliphatic. Aromatic carbons are shown in green. Click on the “Stop” button whenfinished.13
Page 5 and 6: Expanded Atom Types. Parameters hav
Page 7 and 8: TheoryOverview of the Free Energy F
Page 9 and 10: AutoDock Potentials. Examples of th
Page 11: Care should be taken when the PDB f
Page 15 and 16: STEP 2: Running AutoGridAutoDock re
Page 17 and 18: STEP 3: Docking with AutoDockAutoDo
Page 19 and 20: “unbound_model_extended.” This
Page 21 and 22: STEP 4: Evaluating the Results of a
Page 23 and 24: Clusterings>Recluster: Reclusters d
Page 25 and 26: Sample PDBQT fileREMARK 4 active to
Page 27 and 28: AutoGrid Grid Parameter File: GPFEx
Page 29 and 30: Atomic Parameter FileFilename: AD4.
Page 31 and 32: Grid Map FileExtension: .mapThe fir
Page 33 and 34: AutoDock Docking Parameter File: DP
Page 35 and 36: Filename for the electrostatics gri
Page 37 and 38: falls within a disallowed zone, how
Page 39 and 40: is small enough to fit into the low
Page 41 and 42: [10]This is the number of preceding
Page 43 and 44: do_global_only [50]This keyword ins
Page 45 and 46: Ring closure parameters. Comparison
Page 47 and 48: implicit limit of the docking compl
Page 49: Appendix III: AutoDock ReferencesAu

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