Tools

[List Alphabetically]

[Full-Page Index]

General Controls
Command Line
Model Panel
PseudoBond Panel
Keyboard Shortcuts
Task Panel
IDLE

Viewing Controls
Side View
Camera
Effects
Lighting
Shininess

Depiction
Color Secondary Structure
Rainbow
PipesAndPlanks
Nucleotides
Render by Attribute
2D Labels
Color Actions
Ribbon Style Editor
Surface Capping
Per-Model Clipping
Color Zone
PseudoBond Reader
Color Key

Structure Analysis
FindHBond
Find Clashes/Contacts
Distances
Angles/Torsions
Metal Geometry
Axes/Planes/Centroids
Thermal Ellipsoids
Render by Attribute
Define Attribute
Attribute Calculator
ResProp

Structure Comparison
MatchMaker
Match -> Align
Morph Conformations
RR Distance Maps
Ensemble Cluster
Ensemble Match
Tile Structures
Minrms Plot

Sequence
Sequence
PDB/UniProt Info
Multalign Viewer
Match -> Align
Blast Protein
Align Chain Sequences

Surface/Binding Analysis
FindHBond
Find Clashes/Contacts
Electrostatic Surface Coloring
Coulombic Surface Coloring
APBS
Surface Capping
Surface Zone
ViewDock
Dock Prep
AutoDock Vina
Measure Volume and Area
Area/Volume from Web
Measure and Color Blobs
Intersurf
Surfnet
DelPhiController

Structure Editing
AddH
Add Charge
Dock Prep
PDB2PQR
Rotamers
Adjust Torsions
Build Structure
Model/Refine Loops
Movement Mouse Mode
Minimize Structure
Add Ions
Solvate
Write DMS
Change Chain IDs
Renumber Residues

Amber
Add Ions
Solvate
Write Prmtop

MD/Ensemble Analysis
MD Movie
Ensemble Cluster
Ensemble Match
Tile Structures
Molecular Dynamics Simulation

Higher-Order Structure
Multiscale Models
Unit Cell
Crystal Contacts
Small-Angle X-Ray Profile
Scale Bar
Icosahedron Surface
Flatten Icosahedron
Cage Builder

Volume Data
Volume Viewer
Fit in Map
Surface Color
Color Zone
Morph Map
Volume Tracer
Volume Filter
Hide Dust
Segment Map
Fit to Segments
MultiFit
Volume Eraser
Measure Volume and Area
Measure and Color Blobs
Volume Mean, SD, RMS
Values at Atom Positions
Volume Series
Volume Menu on Menubar

Demos
Demo Editor

Movement
Rotation
Undo Move
Redo Move
Movement Mouse Mode
Constrained Move
Transform Coordinates

Utilities
Reply Log
2D Labels
Notepad
Movie Recorder
Color Key
Animation
Structure Diagram
Browser Configuration
Benchmark
Color Editor
Palette Editor
ReadStdin
RESTServer