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Contents
- .vmdrc
- Using text commands
- .vmdsensors
- Configuring input devices
- .vmdrc
- .vmdrc and vmd.rc Files
- vmd.rc
- .vmdrc and vmd.rc Files
- .mailcap
- Setting up your .mailcap
- -webhelper
- Setting up your .mailcap
- .vmdrc
- Hot Keys
- ACTC
- Copyright and Disclaimer Notices
- AMBER
- files
- Loading A Molecule
| Reading Trajectory Frames
- analysis
- Sequence Zooming
- angles
- Label categories
- animate
- command
- Tcl Text Commands
| Tcl Text Commands
- form
- Main Form Animation Controls
- Python module
- animate
- animation
- A Quick Animation
- appending
- Reading Trajectory Frames
- delete
- Deleting Trajectory Frames
| animate
| animate
- goto end
- animate
- goto start
- animate
- hot keys
- Hot Keys
- jump
- Jumping to Specific Frames
| animate
- movie
- Making a Movie
- play
- animate
- read
- Reading Trajectory Frames
| animate
- smoothing
- Smoothing Tab
- speed
- Animation Speed
| animate
- step
- Animation Speed
- style
- animate
- loop
- Looping Styles
- once
- Looping Styles
- rock
- Looping Styles
- timesteps
- Reading Trajectory Frames
- write
- Saving Trajectory Frames
| animate
- animationduplicate frame
- animate
- antialiasing
- Display Menu
| display
- atom
- changing properties
- Using the atomselect command
- coordinates
- rotate
| scale
| translate
- changing
- Comparing Two Structures
| Using the atomselect command
- min and max
- Coordinate min and max
- info
- atomselect
| Using the atomselect command
- name lists
- Selections Tab
| Selections Tab
- picking
- Comparing Two Structures
- selection
- Viewing a molecule: Myoglobin
| An Introduction to Atom
| Molecular Drawing Methods
| Selection Methods
| atomselect
| Using the atomselect command
- changing properties
- An atom selection example
- comparison
- Comparison selections
- default
- mol
- examples
- An Introduction to Atom
| Selection Methods
- keywords
- Selections Tab
| Selection Methods
| Definition of Keywords and
| Definition of Keywords and
- logic
- Short Circuiting
- macros
- Selections Tab
| atomselect
| Atom selections in Python
- math functions
- Definition of Keywords and
- modes
- Selection Methods
- Python
- Atom selections in Python
- macros
- Atom selections in Python
- quoting
- Quoting with Single Quotes
- regular expression
- Double Quotes and Regular
- same
- within and same
- sequence
- sequence
- Tcl
- macros
- atomselect
- text
- Using the atomselect command
- update
- Finding waters near a
- within
- within and same
- atoms
- distance between
- Comparing Two Structures
- plotting
- Plotting a label's value
- atomselect
- command
- Tcl Text Commands
| animate
| Molecular Analysis
| Using the atomselect command
- axes
- Display Menu
- command
- Tcl Text Commands
| atomselect
- Python module
- axes
- Babel
- Babel interface
- backface culling
- Display Menu
- batch mode
- VMD Command-Line Options
- beta values
- Root mean square deviation
- BioCoRE
- For information on our
- BMRT
- Higher Quality Rendering
- bonds
- add or remove
- Mouse Modes
- determining
- What happens when a
- label
- Label categories
| Label categories
- representation
- Rendering methods
| Bonds
- resolution
- Bonds
- unusual
- What happens when a
- callbacks
- Python
- Python callbacks
- Tcl
- Tcl callbacks
- cartoon representation
- Rendering methods
| Cartoon
- center of mass
- Using the atomselect command
- CHARMM
- files
- Loading A Molecule
| Reading Trajectory Frames
- chemical2vmd
- Setting up your .mailcap
- clipping planes
- Display Menu
- codes
- secondary structure
- Sequence information
- color
- access definitions
- colorinfo
- assignment
- Comparing Two Structures
- background
- Color Form
- category
- Color Form
| Color categories
| Color categories
| Coloring by color categories
| colorinfo
| Coloring Trick - Override
- command
- Coloring Methods
| Tcl Text Commands
| axes
- form
- Comparing Two Structures
| Color Form
| Coloring Methods
| Color categories
| Coloring by color categories
- id
- Draw Style Tab
| Coloring Methods
- in user-defined graphics
- graphics
- index
- colorinfo
- map
- Color Form
- material properties
- graphics
| graphics
- names
- Coloring Methods
| colorinfo
- properties
- colorinfo
- Python module
- color
- redefinition
- Changing the RGB Value
| Creating a set of
- revert to default
- Revert all RGB values
- scale
- Color Scale
| Color scale
| Color scale
| color
| Changing the color scale
- changing
- Color Scale
- color map
- Color categories
- colorinfo
- command
- Tcl Text Commands
| colorinfo
- coloring
- by category
- Coloring by color categories
- by color scale
- Color scale
| Color scale
- by property
- Coloring Trick - Override
- methods
- Viewing a molecule: Myoglobin
| Graphics Form
| Molecular Drawing Methods
| Coloring Methods
| Coloring Methods
| Coloring Methods
| mol
| mol
| Coloring Trick - Override
- Command line options
- VMD Command-Line Options
- contact residues
- Finding contact residues
- copyright
- Copyright and Disclaimer Notices
- CPK
- Rendering methods
| CPK
- culling
- display
- debug
- command
- Tcl Text Commands
- depth cue
- display
- depth cueing
- Display Menu
- display
- command
- Tcl Text Commands
| colorinfo
- device
- VMD Command-Line Options
- form
- Display Menu
- Python module
- display
- update
- display
| Using the molinfo command
| Creating a set of
| Revert all RGB values
- distance between atoms
- Comparing Two Structures
- dotted van der Waals representation
- Rendering methods
| Dotted
- draw
- command
- draw
- extensions
- draw
- drawing
- method
- Viewing a molecule: Myoglobin
| Graphics Form
- drawn
- Main Form Molecule List
- dynamic bonds
- DynamicBonds
- dynamicbonds representation
- DynamicBonds
- echo
- command
- Tcl Text Commands
| draw
- environment variables
- Environment Variables
- DISPLAY
- Environment Variables
- MSMSSERVER
- MSMS
- SURF_BIN
- Surf
- TCL_LIBRARY
- Core Script Files
- VMDBABELBIN
- Babel interface
| Environment Variables
- VMDCAVEMEM
- Environment Variables
- VMDDIR
- Environment Variables
- VMDFILECHOOSER
- Environment Variables
- VMDGDISPLAY
- Environment Variables
- VMDHTMLVIEWER
- Environment Variables
- VMDIMAGEVIEWER
- Environment Variables
- VMDSCRDIST
- Environment Variables
- VMDSCRHEIGHT
- Environment Variables
- VMDSCRPOS
- Environment Variables
- VMDSCRSIZE
- Environment Variables
- VMDTMPDIR
- Environment Variables
- exit
- command
- Tcl Text Commands
- eye separation
- Stereo Parameters
| display
- file
- load
- Viewing a molecule: Myoglobin
- file types
- input
- Loading A Molecule
| Reading Trajectory Frames
- output
- Saving Trajectory Frames
- files
- output
- Rendering an Image
- read
- animate
- reading
- Viewing a molecule: Myoglobin
| A Quick Animation
| Loading A Molecule
| Molecule File Browser Form
| Reading Trajectory Frames
| mol
- startup
- Hot Keys
| VMD Command-Line Options
| Startup Files
| .vmdrc and vmd.rc Files
- writing
- Saving Trajectory Frames
| animate
- fit
- RMSD
- RMS and scripting
| RMSD Computation
- focal length
- Stereo Parameters
| display
- form
- animate
- A Quick Animation
| Main Form Animation Controls
- color
- Comparing Two Structures
| Color Form
| Coloring Methods
| Color categories
| Coloring by color categories
- display
- Display Menu
- files
- Viewing a molecule: Myoglobin
- graphics
- Viewing a molecule: Myoglobin
| An Introduction to Atom
| Graphics Form
- hot keys
- Hot Keys
- label
- Labels Form
- main
- Main Form
- material
- Material Form
- molecule file browser
- Molecule File Browser Form
- mouse
- Mouse Form
- RamaPlot
- RamaPlot
- render
- Rendering an Image
| Render Form
- sequence
- Sequence Form
- sim
- Simulation Form
- tool
- Tool Form
- forms
- menu
- frame
- delete
- Deleting Trajectory Frames
| animate
- duplicate
- animate
- write
- animate
- frames
- Main Form Molecule List
- frames per second indicator
- Display Menu
- geometric center
- Using the atomselect command
- gopython
- command
- Using the Python interpreter
- graphics
- command
- graphics
- delete
- graphics
- form
- Graphics Form
- loading
- graphics
- primitives
- graphics
- Python module
- graphics
- replace
- graphics
- user-defined
- draw
- Gromacs
- files
- Loading A Molecule
| Reading Trajectory Frames
- gyration, radius of
- Radius of gyration
- hbonds representation
- Rendering methods
| HBonds
- help
- Help
- command
- Tcl Text Commands
| graphics
- topics
- help
- highlight
- Selecting residues from the
- hot keys
- Hot Keys
| user
- animation control
- Hot Keys
- customizing
- Hot Keys
- menu control
- Hot Keys
- mouse control
- Hot Keys
- rotation and scaling
- Hot Keys
- hydrogen bonds
- HBonds
| measure
- image
- lighting controls
- Mouse Modes
| Display Menu
- ray tracing considerations
- Caveats
- shading and material properties
- Material Form
- imd
- Interactive Molecular Dynamics
- command
- Tcl Text Commands
| help
- Python module
- imd
- requirements
- Simulation Form
- Interactive Molecular Dynamics
- Interactive Molecular Dynamics
- isosurface
- representation
- Rendering methods
| Isosurface
- JMV
- For information on our
- joystick
- using
- Using the Joystick in
- label
- command
- Tcl Text Commands
| imd
- Python module
- label
- labels
- Comparing Two Structures
- categories
- Label categories
| label
- delete
- Modifying or deleting a
- form
- Labels Form
- hide
- Modifying or deleting a
- picking with mouse
- Pick Mode
- plotting
- Plotting a label's value
- show
- Modifying or deleting a
- text
- draw
- licorice representation
- Rendering methods
| Licorice
- light
- command
- Tcl Text Commands
| label
- controlling with mouse
- Mouse Modes
- toggle
- Display Menu
- lines representation
- Rendering methods
| Lines
- logfile
- command
- Tcl Text Commands
| logfile
- logging tcl commands
- echo
| logfile
- mass
- center of
- Using the atomselect command
- of residue atoms
- Tcl callbacks
- total
- Total mass of a
- material
- changing
- mol
- command
- Tcl Text Commands
| logfile
- methods
- Graphics Form
- Python module
- material
- material properties
- graphics
| graphics
- matrix routine
- Matrix routines
- trans
- Matrix routines
- transaxis
- Matrix routines
- transidentity
- Matrix routines
- transmult
- Matrix routines
- transoffset
- Matrix routines
- transtranspose
- Matrix routines
- transvec
- Matrix routines
- transvecinv
- Matrix routines
- MDTools
- For information on our
- measure
- command
- Tcl Text Commands
| material
| Analysis scripts
| Coordinate min and max
- menu
- command
- Tcl Text Commands
| measure
- molecular surface
- Rendering methods
| Surf
| MSMS
- molecule
- active
- Main Form Molecule List
| Main Form Animation Controls
- analysis
- Analysis scripts
- best-fit alignment
- Computing the Alignment
- command
- Tcl Text Commands
| menu
| mol
- data
- molinfo
- deleting
- Deleting a Molecule
- drawn
- Main Form Molecule List
- fixed
- Comparing Two Structures
| Main Form Molecule List
- graphics
- graphics
- id
- mol
- index
- mol
- info
- Molecular Analysis
- list
- Main Form Molecule List
- loading
- Viewing a molecule: Myoglobin
| A Quick Animation
| graphics
| Root mean square deviation
- Python module
- molecule
- status
- Main Form Molecule List
| mol
- changing
- Changing the Molecule's Status
| mol
| Using the molinfo command
- top
- Main Form Molecule List
| Jumping to Specific Frames
| molinfo
- translation
- Comparing Two Structures
- molinfo
- command
- molecule
| Molecular Analysis
- keywords
- molinfo
- molrep
- Python module
- molrep
- mouse
- add or remove bonds
- Mouse Modes
- callback
- mouse
- command
- Tcl Text Commands
| molinfo
- modes
- Viewing a molecule: Myoglobin
| Comparing Two Structures
| Mouse Modes
| Hot Keys
| mouse
- mouse mode
- Mouse mode
- move
- Object menus
- atom
- Object menus
- fragment
- Object menus
- highlighted rep
- Object menus
- molecule
- Object menus
- residue
- Object menus
- object menus
- Object menus
- pick information
- Pick information
- rocking
- mouse
- using
- Using the Mouse in
- movies
- Making a Movie
- MSMS
- representation
- Rendering methods
| MSMS
- NAMD
- For information on our
- files
- Loading A Molecule
| Reading Trajectory Frames
- orthographic view
- Display Menu
| Perspective/Orthographic views
- output
- format
- Rendering an Image
- PCRE
- Copyright and Disclaimer Notices
- perspective view
- Display Menu
| Perspective/Orthographic views
- picking
- angles
- Pick Mode
| Pick Mode
- atoms
- Comparing Two Structures
| Pick Mode
| Pick Mode
- bonds
- Comparing Two Structures
| Pick Mode
| Pick Mode
- center
- Pick Mode
- dihedrals
- Pick Mode
| Pick Mode
- distances
- Comparing Two Structures
- hot keys
- Hot Keys
- modes
- Comparing Two Structures
| Pick Mode
- move atom
- Pick Mode
- move fragment
- Pick Mode
- move highlighted rep
- Pick Mode
- move molecule
- Pick Mode
- move residue
- Pick Mode
- query
- Pick Mode
- text command
- mouse
- play
- command
- Using text commands
| Tcl Text Commands
| mouse
| VMD Command-Line Options
- plot
- geometry monitors
- Plotting a label's value
- points
- representation
- Rendering methods
| Points
- postscript
- Higher Quality Rendering
| One Step Printing
- Pov-Ray
- Higher Quality Rendering
- Python
- Copyright and Disclaimer Notices
- environment variables
- Python modules within VMD
- interface
- Python Text Interface
- libraries
- Python modules within VMD
- Numeric
- Python modules within VMD
| vmdnumpy
- startup
- VMD Command-Line Options
- Tkinter
- Python modules within VMD
| Using Tkinter menus in
- version
- Python Text Interface
- quit
- Main Form
- command
- echo
| play
- quoting
- Quoting with Single Quotes
- Radiance
- Higher Quality Rendering
- radius
- of gyration
- Radius of gyration
- Ramachandran plot
- RamaPlot
- raster image creation
- Scene Export and Rendering
- Raster3D
- Raster3D file format
| Higher Quality Rendering
| One Step Printing
| Making Stereo Images
| render
- RayShade
- Higher Quality Rendering
- regular expression
- Double Quotes and Regular
| Double Quotes and Regular
- X-PLOR conversion
- Double Quotes and Regular
- remote
- connection
- imd
- detaching
- IMD Using the Sim
- killing
- IMD Using the Sim
- modifiable parameters
- IMD Using the Sim
- options
- imd
- simulation control
- imd
- render
- command
- Tcl Text Commands
| quit
- form
- Rendering an Image
| Render Form
- Python module
- render
- rendering
- Rendering an Image
| Render Form
| Scene Export and Rendering
- caveats
- Caveats
- exec command
- render
- in background process
- Render Form
- method
- Higher Quality Rendering
| render
- stereo
- Making Stereo Images
- Renderman
- Higher Quality Rendering
- representation
- Molecular Drawing Methods
| mol
- add new
- Adding a rep.
- adding
- Adding a rep.
- auto-update
- Rep auto-update.
- changing
- An Introduction to Atom
| Changing a rep.
| mol
- deleting
- Deleting a rep.
| Deleting a rep.
- examples
- Some Nice Represenations
- hiding
- Hiding a rep.
- off
- Off
- style
- Viewing a molecule: Myoglobin
| Graphics Form
| Molecular Drawing Methods
| Rendering methods
| mol
- user defined clipping planes
- mol
- reset view
- Display Menu
| display
- restore
- viewpoint
- Using the molinfo command
- vmd state
- Saving your work
- ribbon representation
- Rendering methods
| Ribbon
- RMS
- Fit
- RMS Fit and Alignment
- RMS:Alignment
- RMS Fit and Alignment
- RMSD
- Root mean square deviation
| RMS and scripting
| RMSD Computation
| A simulation example script
- rock
- Looping Styles
- command
- Tcl Text Commands
| render
- rotate
- command
- Tcl Text Commands
| rock
- side chain
- Using the atomselect command
- rotation
- continuous
- Mouse Modes
- hot keys
- Hot Keys
- stop
- Mouse Modes
- transformation matrix
- Matrix routines
| Matrix routines
- using mouse
- Mouse Modes
- save
- configuration
- Saving your work
- viewpoint
- Using the molinfo command
- vmd state
- Saving your work
| Saving and Restoring Molecule
- scale
- command
- Tcl Text Commands
| rotate
- scaling
- using mouse
- Mouse Modes
- screen parameters
- Display Menu
- scripts
- play
- Using text commands
- source
- Using text commands
- secondary structure codes
- Sequence information
- selection
- Viewing a molecule: Myoglobin
| An Introduction to Atom
| Graphics Form
| Molecular Drawing Methods
| atomselect
| mol
| Using the atomselect command
- comparison
- Comparison selections
- keywords
- Selections Tab
| Selection Methods
| Definition of Keywords and
- boolean
- Boolean Keywords
- logic
- Short Circuiting
- math functions
- Definition of Keywords and
- modes
- Selection Methods
- text
- Using the atomselect command
- sensor configuration file
- Configuring input devices
- sensors
- Configuring input devices
- sequence
- Sequence information
- caveats
- Caveats
- dna
- Caveats
- form
- Sequence Form
- zooming
- Sequence Zooming
- short circuit logic
- Short Circuiting
| within and same
- sleep
- command
- Tcl Text Commands
| wait
- solvent accessible surface
- Rendering methods
| Solvent
- solvent representation
- Rendering methods
| Solvent
- source
- command
- Using text commands
- spaceball
- driver
- Spaceball Driver
- MacOS X
- Spaceball Driver
- Unix
- Spaceball Driver
- Windows
- Spaceball Driver
- modes
- Using the Spaceball in
- using
- Using the Spaceball in
- stage
- Display Menu
- command
- Tcl Text Commands
| scale
- startup files
- Hot Keys
| VMD Command-Line Options
| Startup Files
| .vmdrc and vmd.rc Files
- stereo
- mode
- Stereoscopic Modes
- cross-eyed
- Side-By-Side and Cross-Eyed Stereo
- CrystalEyes
- CrystalEyes Stereo
- DTI side-by-side
- DTI Side-by-side Stereo
- scanline interleaved
- Scanline Interleaved Stereo
| Anaglyph Stereo
- side-by-side
- Side-By-Side and Cross-Eyed Stereo
- off
- Monoscopic Modes
- parameters
- Display Menu
| Stereo Parameters
| display
| display
- problems
- Problems with stereo on
- stop rotation
- Display Menu
- stride
- Copyright and Disclaimer Notices
- Structural Biology Software Database
- For information on our
- surf
- Copyright and Disclaimer Notices
- representation
- Rendering methods
| Surf
- surface
- molecular
- Rendering methods
| Solvent
- solvent accessible
- Rendering methods
| Solvent
- Tachyon
- Copyright and Disclaimer Notices
| Higher Quality Rendering
| render
- Tcl
- Tcl/Tk
- tcl commands
- Tcl Text Commands
- text
- displayed
- graphics
- Tk
- Tcl/Tk
- tool
- CAVE
- Configuring input devices
- command
- Tcl Text Commands
| stage
- form
- Tool Form
- FreeVR
- Configuring input devices
- Spaceball
- Configuring input devices
- VRPN
- Configuring input devices
- tools
- Using Tools
- topology files
- Loading A Molecule
- trace representation
- Rendering methods
| Trace
- trajectory
- files
- Loading A Molecule
- read
- Reading Trajectory Frames
- smoothing
- Smoothing Tab
- write
- Saving Trajectory Frames
- trans
- Python module
- trans
- transformation matrix
- Matrix routines
- align
- Matrix routines
- centering
- Matrix routines
- identity
- Matrix routines
- offset
- Matrix routines
| Matrix routines
- rotation
- Matrix routines
| Matrix routines
- translate
- command
- Tcl Text Commands
| tool
- translation
- change atom coordinates
- Using the atomselect command
- transformation matrix
- Matrix routines
- using mouse
- Mouse Modes
- transparency
- Draw Style Tab
- tube representation
- Rendering methods
| Tube
- universal sensor locator
- Configuring input devices
- url_get
- Copyright and Disclaimer Notices
- user
- command
- Tcl Text Commands
| translate
- user interfaces
- python
- Python Text Interface
- text
- Tcl Text Interface
- USL
- Configuring input devices
- van der Waals representation
- Rendering methods
| VDW
- variables
- env
- Environment Variables
| Core Script Files
- M_PI
- Misc. functions and values
- trace
- Tcl callbacks
- vector command
- coordtrans
- Multiplying vectors and matrices
- vecadd
- Vectors
- veccross
- Vectors
- vecdist
- Vectors
- vecdot
- Vectors
- vecinvert
- Vectors
- veclength
- Vectors
- veclength2
- Vectors
- vecnorm
- Vectors
- vecscale
- Vectors
- vecsub
- Vectors
- vectrans
- Multiplying vectors and matrices
- veczero
- Vectors
- vector routines
- Vectors and Matrices
- view
- Molecular Drawing Methods
| mol
- viewing modes
- changing
- Viewing Modes
- VMD
- as MIME helper application
- MIME types
- command line options
- VMD Command-Line Options
- compile options
- vmdinfo
- copyright
- Copyright and Disclaimer Notices
- customizing
- Hot Keys
| Customizing VMD Sessions
- vmd.rc
- Using text commands
- vmdinfo
- command
- Tcl Text Commands
| user
- volumeslice
- representation
- Rendering methods
| VolumeSlice
- volumetric data
- Rendering methods
| VolumeSlice
| Isosurface
- VRML
- Higher Quality Rendering
- wait
- command
- Tcl Text Commands
| vmdinfo
- wireframe
- Lines
- XPLOR
- files
- Loading A Molecule
| Reading Trajectory Frames
vmd@ks.uiuc.edu