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
.. .. .. Atom Info: name, charges etc.
.. .. .. Geometric Info
.. .. .. Info Style
.. .. .. Atom Radius
.. .. .. Define X color
.. .. .. Store default X color
.. .. .. Hide all X atoms
.. .. .. Select all X atoms
.. .. Pop-up menu in empty space
.. .. .. Atom Info
.. .. .. Geometric Info
.. .. .. Info Style
.. .. .. 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
.. .. Molecule Ball & Sticks
.. .. Show Bondtype
.. .. Background
ADF-GUI modules
.. ADFjobs
.. .. Introduction
.. .. Starting ADFjobs
.. .. File and Job listing
.. .. .. Job elements
.. .. .. Selecting
.. .. .. Changing directories, open a job, change a job name
.. .. .. Filtering
.. .. .. Job details
.. .. .. Local files
.. .. .. Remote files
.. .. .. Change job name
.. .. Queues
.. .. Menu commands
.. .. .. File menu
.. .. .. .. New Directory
.. .. .. .. Delete Directory
.. .. .. .. Preferences
.. .. .. .. Quit
.. .. .. Edit menu
.. .. .. Job menu
.. .. .. .. Run
.. .. .. .. Kill
.. .. .. .. Transfer To Remote
.. .. .. .. Transfer From Remote
.. .. .. .. Delete
.. .. .. .. Delete Remote
.. .. .. .. Generate Test Job
.. .. .. .. Reset
.. .. .. Queue menu
.. .. .. .. New...
.. .. .. .. New From Job
.. .. .. .. Edit...
.. .. .. .. Delete
.. .. .. .. Set Default
.. .. .. .. Status
.. .. .. .. Queue name
.. .. .. Sort menu
.. .. .. Filter menu
.. .. .. Style menu
.. 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
.. .. .. 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
.. .. .. .. New
.. .. .. .. Open...
.. .. .. .. Save Picture...
.. .. .. .. Default Picture Format
.. .. .. .. Picture Resolution
.. .. .. .. Export As VRML...
.. .. .. .. Quit
.. .. .. Add
.. .. .. .. Isosurface
.. .. .. .. Isosurface: Colored
.. .. .. .. Isosurface: Double (+/-)
.. .. .. .. Cut Plane: Colored
.. .. .. .. Cut Plane: Contours
.. .. .. .. Cut Plane: Contours (+/-)
.. .. .. .. COSMO surface: Colored
.. .. .. .. Spinor: spin magnetization density
.. .. .. .. Add Bond
.. .. .. .. Delete Bond
.. .. .. Fields
.. .. .. .. Calculated
.. .. .. .. Interpolated
.. .. .. .. Grid
.. .. .. .. Sort by
.. .. .. View
.. .. .. ..
Standard View commands
.. .. .. .. Show Molecule details
.. .. .. .. Show Scene Light
.. .. .. .. Show All Geometries
.. .. .. .. Periodic
.. .. .. .. Auto Update
.. .. .. .. Update
.. .. .. .. HOMO
.. .. .. .. LUMO
.. .. .. Help
.. .. .. Pop-up menus
.. .. .. ..
Standard pop-up commands
.. .. Comparing data from several molecules
.. .. .. The current geometry
.. .. .. Comparing different 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
.. .. VCD
.. 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: Save Movie...
.. .. .. File: Default Picture Format
.. .. .. File: Picture Resolution
.. .. .. File: Save As PostScript
.. .. .. File: Save As XY
.. .. .. File: Quit
.. .. ..
View: Standard Commands
.. .. .. View: Add Graph
.. .. .. View: Delete Graph
.. .. .. View: Graph X Axes
.. .. .. View: Graph Y Axes
.. .. .. View: Loop
.. .. .. View: Converged Geometry Only
.. .. .. View: Displacement Vectors
.. .. ..
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
.. .. .. Axes: Unit
.. .. .. 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
ADFinput
Introduction
Starting ADFinput
Menu Commands
File menu
Edit menu
View menu
Model menu
Properties menu
Details menu
Help menu
Pop-up menu
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
85.10.201.17
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