Contents Table of Contents Introduction .. The ADF-GUI modules .. The SCM (logo) menu .. Automatic bug reports .. Environment Variables Mouse Interaction .. Rotate, Translate and Zoom .. Selecting Shared Menus .. Pop-up menus .. .. Pop-up menu on atom X .. .. .. Define X color .. .. .. Store default X color .. .. .. Hide all X atoms .. .. .. Select all X atoms .. .. Pop-up menu in empty space .. .. .. Show bonds to hidden atoms .. .. .. Hide bonds to hidden atoms .. .. .. Default atom properties .. View Menu .. .. Reset View .. .. Fly to selection .. .. Align screen .. .. Mouse as .. .. Anti-alias .. .. Molecule Resolution .. .. Show Bondtype .. .. Background ADF-GUI modules .. ADFinput .. .. Introduction .. .. Starting ADFinput .. .. Menu Commands .. .. .. File menu .. .. .. .. New .. .. .. .. Open... .. .. .. .. Import Coordinates... .. .. .. .. Export Coordinates... .. .. .. .. Save .. .. .. .. Save As... .. .. .. .. Revert... .. .. .. .. Save Picture... .. .. .. .. Default Picture Format .. .. .. .. Picture Resolution .. .. .. .. Run .. .. .. .. Preferences... .. .. .. .. Quit .. .. .. Edit menu .. .. .. .. Undo .. .. .. .. Redo .. .. .. .. Cut .. .. .. .. Copy .. .. .. .. Paste .. .. .. .. Clear .. .. .. .. Group .. .. .. .. Ungroup .. .. .. .. Set origin .. .. .. .. Bond Lengths constrained .. .. .. .. Add Bond .. .. .. .. Add Hydrogen .. .. .. .. Remove Hydrogen .. .. .. .. Fuse Atoms .. .. .. .. Select All .. .. .. .. Select Molecule .. .. .. .. Select Connected .. .. .. .. Guess Bonds .. .. .. .. Remove Bonds .. .. .. View menu .. .. .. .. Standard View commands .. .. .. .. Tip of the day .. .. .. Model menu .. .. .. Properties menu .. .. .. Details menu .. .. .. Help menu .. .. .. Pop-up menu .. .. .. .. Standard pop-up commands .. .. .. .. Delete atom(s) .. .. .. .. Connectors .. .. .. .. Change atom(s) type .. .. .. .. Add structure(s) .. .. .. .. New Fragment... .. .. .. .. Another ... Fragment .. .. .. .. Add to ... Fragment .. .. Buttons and Tools .. .. Getting and changing geometry details .. .. Keyboard shortcuts .. .. Presets and Defaults .. .. .. Use a Preset .. .. .. Revert to preset values .. .. .. Color Code .. .. .. Make your own presets .. .. .. Defaults .. .. Calculation Tasks .. .. .. Fragment Analysis .. .. .. Frequencies .. .. .. Geometry Optimization .. .. .. IRC (Intrinsic Reaction Coordinate) .. .. .. Linear Transit .. .. .. Properties Only .. .. .. Single Point .. .. .. Transition State Search .. .. Structures .. .. .. Replacing an existing atom .. .. .. Left-click in empty space .. .. .. Metal Complexes .. .. .. Dummy atoms and Multidentate ligands .. .. .. Your own structures .. .. Symmetry .. .. Molecule Editor Tricks .. .. .. Selecting .. .. .. Delete an atom .. .. .. Delete a bond .. .. .. Delete the selection .. .. .. Make a bond .. .. .. Make a bond, alternative method .. .. .. Change the bond type .. .. .. Move an atom (possibly perpendicular to the screen) .. .. .. Rotate or translate the selection .. .. Run Script .. .. Input options remarks .. .. .. Empty fields .. .. .. Coordinates .. .. .. User Input .. .. .. Protein QMMM calculations with PDB files .. ADFview .. .. Introduction .. .. Starting ADFview .. .. Menu commands .. .. .. File .. .. .. .. Open... .. .. .. .. Save Picture... .. .. .. .. Default Picture Format .. .. .. .. Picture Resolution .. .. .. .. Quit .. .. .. Add .. .. .. .. Isosurface .. .. .. .. Isosurface: Colored .. .. .. .. Isosurface: Double (+/-) .. .. .. .. Cut Plane: Colored .. .. .. .. Cut Plane: Contours .. .. .. .. Cut Plane: Contours (+/-) .. .. .. .. Spinor: spin magnetization density .. .. .. .. Add Bond .. .. .. .. Delete Bond .. .. .. Fields .. .. .. .. Calculated .. .. .. .. Interpolated .. .. .. .. Grid .. .. .. .. Sort by .. .. .. View .. .. .. .. Standard View commands .. .. .. .. Show Molecule details .. .. .. .. Show Scene Light .. .. .. .. Periodic .. .. .. .. Auto Update .. .. .. .. Update .. .. .. .. HOMO .. .. .. .. LUMO .. .. .. Help .. .. .. Pop-up menus .. .. .. .. Standard pop-up commands .. .. Compare fields from different ADF calculations .. .. Temporary Files .. ADFspectra .. .. Introduction .. .. Starting ADFspectra .. .. Zooming in or out .. .. Peak width and shape .. .. Scaling peak positions .. .. Axes menu .. .. .. Horizontal Unit .. .. .. Flip Horizontal or Vertical .. .. Save Postscript .. .. Export XY values .. .. DOS (density of states) .. .. Vibration (IR spectrum) .. .. Optical spectrum .. .. CD spectrum .. .. Raman .. ADFmovie .. .. Introduction .. .. Starting ADFmovie .. .. Buttons .. .. Input Files .. .. .. TAPE21 and logfile .. .. .. ADFmovie files .. .. Geometry Information .. .. Menu Commands .. .. .. File: Open... .. .. .. File: Save Geometry... .. .. .. File: Update Geometry in ADFinput .. .. .. File: Save Picture... .. .. .. File: Save Movie Frames... .. .. .. File: Default Picture Format .. .. .. File: Picture Resolution .. .. .. File: Quit .. .. .. View: Standard Commands .. .. .. View: Converged Geometry Only .. .. .. Pop-up: Standard Commands .. ADFlevels .. .. Introduction .. .. Starting ADFlevels .. .. ADFlevels window .. .. Stacks: Molecule, Fragment types, Fragments .. .. Mouse interaction .. .. .. Zooming .. .. .. Selecting .. .. .. Moving a stack .. .. Menu commands .. .. .. File: Open... .. .. .. File: Add... .. .. .. File: Save Postscript... .. .. .. File: Quit .. .. .. Axes:Reset Zoom .. .. .. View:Interactions .. .. .. View:Occupations .. .. .. View:Labels .. .. .. View:Fragments .. .. .. View:Fragment Types .. .. .. View:Hide Stacks .. .. .. Help .. .. Pop-up menus .. .. .. Background (white space) pop-up .. .. .. Stack pop-up .. .. .. Level pop-up .. ADFtail .. .. Introduction .. .. Starting ADFtail .. .. ADFtail window .. BOB .. .. Introduction .. .. Starting BOB .. .. BOB window .. .. .. Click on Marked Items .. .. .. Include Menu .. .. .. Other Menus

 

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