Tools Index
-
2D Labels
- create labels with text,
symbols,
and arrows in 2D
- Add Charge
- assign partial charges to atoms
- AddH
- add hydrogens
- Add Ions
- add monatomic counterions using
AmberTools
- Adjust Torsions
- rotate bonds (change dihedral angles)
- Align Chain Sequences
- generate a multiple sequence alignment (MSA) of structure chains using a
Clustal Omega
or MUSCLE
web service hosted by the
UCSF
RBVI
- Angles/Torsions
- measure bond angles and dihedral angles
- Animation
(under development)
- save/restore Chimera scenes,
arrange them into a timeline, play/record animation
-
APBS
- interface to electrostatics calculations with
APBS
(Adaptive Poisson-Boltzmann Solver)
-
Area/Volume from Web
- use the StrucTools server
to calculate surface areas and Voronoi volumes
- Attribute Calculator
- generate new numerical
attributes from existing ones; calculate totals or averages of a given
numerical attribute
- AutoDock Vina
- interface to single-ligand docking with
AutoDock Vina
- Axes/Planes/Centroids
- define geometric objects (axes, planes, centroids) based on sets of atoms,
perform related measurements
- Benchmark
- measure hardware performance on standard Chimera rendering tasks
- Blast Protein
- perform protein BLAST searches using a web service hosted by the
UCSF
RBVI
-
Browser Configuration
- configure web browsers to send Chimera
data
linked to web pages
- Build Structure
- create and modify atomic structures
- Cage Builder
- create polyhedral cages
- Camera
- control viewing parameters
- Change Chain IDs
- reassign chain identifiers
- Color Editor
- create colors interactively
-
Color Key
- create a color key for figures
-
Color Secondary Structure
- color peptides/proteins by secondary structure
- Color Zone
- color surfaces to match selected atoms,
split volume data by the resulting color zones
- Command Line
- enter Chimera commands
-
Constrained Move
- perform rotations and translations about specified axes
- Coulombic
Surface Coloring
- color molecular surfaces
by Coulombic electrostatic potential
-
Crystal Contacts
- identify clashes between PDB symmetry copies
- Define Attribute
- assign
attribute values to atoms, residues, or models
-
DelPhiController
- interface to
DelPhi
(obtained separately) for calculating electrostatic potential
- Demos and
Demo Editor
- create and replay demonstrations in Chimera
- Distances
- measure distances between pairs of atoms
- Dock Prep
- add hydrogens, charges, etc. to prepare structures for
DOCK
or for other calculations
- Effects
- control visual effects such as depth cueing, shadows, and silhouettes
- Electrostatic Surface Coloring
- color surfaces using an
electrostatic potential map
(from any of several separate programs)
-
Ensemble Cluster
- cluster members of a conformational ensemble
-
Ensemble Match
- match conformations from two ensembles
- Find
Clashes/Contacts
- identify clashes and/or contacts
-
FindHBond
- find possible hydrogen bonds
- Fit in Map
- fit atoms into a map (volume data) or one map into another
- Fit
to Segments
- fit structures into map segmentation regions
- Flatten
Icosahedron
- rearrange the faces of an icosahedral virus capsid into a plane
to create a paper model
- Hide
Dust
- hide small disconnected bits of a surface
-
Icosahedron Surface
- create a hybrid icosahedron/sphere surface
- IDLE
(Python Interactive DeveLopment Environment)
- enter Python commands
- Intersurf
- generate and display interface surfaces
- Keyboard Shortcuts
- define and use keyboard shortcuts for Chimera functions
- Lighting
- adjust and save lighting parameters
-
Match -> Align
- generate a multiple sequence alignment (MSA) from a structural alignment
-
MatchMaker
- superimpose structures by first constructing a sequence alignment
(optionally including secondary structure scoring) and then
fitting the aligned residue pairs
-
MD Movie
- replay and analyze molecular dynamics trajectories
-
Measure and Color Blobs
- color and measure disconnected parts of a surface
-
Measure Volume and Area
- measure surface area and surface-enclosed volume
-
Metal Geometry
- analyze metal coordination geometry
-
Minimize Structure
- energy-minimize structures
-
Minrms Plot
- examine structural alignments of proteins from
MinRMS (obtained separately,
available as source code)
- Model/Refine Loops
- interface to
Modeller
for building missing peptide segments or generating alternative conformations
of peptide segments already present in a structure
- Model Panel
- list and act on models
- Morph
Conformations
- create a trajectory that morphs between structures
- Morph
Map
- morph between two related sets of volume data
- Movement
Mouse Mode
- move just part of a structure with the mouse
-
Movie Recorder
- capture image frames and assemble them into a movie file
- Multalign Viewer
- view sequences, optionally with associated structures; analyze conservation;
view UniProt feature
annotations;
interface to
Modeller
- MultiFit
- fit multiple structures into density using a web service hosted by the
UCSF
RBVI
-
Multiscale Models
- view macromolecular assemblies at high and low resolution,
generate multimers, and navigate structural hierarchies
- Notepad
- add user notes (text) that can be saved along with
sessions
-
Nucleotides
- create special representations of nucleotide bases and sugars
- Palette Editor
- create and choose palettes
-
PDB2PQR
- interface to structure cleanup and charge/radius assignment with
PDB2PQR
-
PDB/UniProt Info
- retrieve PDB and UniProt
annotations using a web service provided by the
RCSB PDB
-
Per-Model Clipping
- clip models individually with a plane at any angle
-
PipesAndPlanks
- show protein helices as “pipes,” strands as “planks”
- PseudoBond Panel
- list and act on pseudobond groups
-
PseudoBond Reader
- create pseudobonds arbitrarily
-
Rainbow
- use a range of colors, changing the color per residue, chain, or model
-
ReadStdin
- allow communication with Chimera through standard input/output
-
Render by Attribute
- show
attribute values of atoms, residues, and models (with color, etc.)
- Renumber Residues
- reassign residue numbers
- Reply Log
- show informational, warning, and error messages from Chimera
- ResProp
- define amino acid categories
-
RESTServer
- allow communication with Chimera through REST interface
-
Ribbon Style Editor
- change ribbon heights/widths (scalings) and cross-sections (styles)
- Rotamers
- view and evaluate amino acid sidechain rotamers,
incorporate them into structures
- Rotation
- control the center of rotation
- Scale Bar
- draw a scale bar and associated label
- Segment Map
- partition density maps
- Sequence
- show amino acid and/or nucleic acid sequence
- Shininess
- adjust shininess and brightness
- Side View
- scale the view and move clipping planes interactively
- Small-Angle
X-Ray Profile
- calculate a SAXS profile from a structure, fit with experiment
- Solvate
- solvate structures using
AmberTools
- Structure Diagram
- generate 2D chemical diagrams of small molecules
- Surface Capping
- cap surfaces where they intersect a clipping plane
- Surface Color
- color surfaces by volume data values or by distance
from a point, axis, or plane
- Surface Zone
- restrict the display of
certain types
of surfaces to a zone around selected atoms
- Surfnet
- examine cavities and surface indentations
- Task Panel
- manage jobs started by Chimera
- Thermal
Ellipsoids
- show anisotropic B-factors
-
Tile Structures
- arrange models in a plane
- Transform
Coordinates
- transform a model by specified Euler angles and shifts
- Undo Move
and Redo Move
- go back and forth in the history of model rotational/translational positions
-
Unit Cell
- generate crystallographic unit cell contents from coordinates
and transformation matrices
- Values at Atom Positions
- map volume data to atom positions and assign values as an
attribute
- ViewDock
- view and prioritize docked molecules
-
Volume Eraser
- interactively zero out parts of volume data
- Volume
Filter
- smooth or transform volume data
- Volume
Mean, SD, RMS
- calculate statistics for volume data
-
Volume Series
- display a series of volume data sets
- Volume Tracer
- place markers and trace paths within volume displays
- Volume Viewer
- visualize volume data
(3D numerical data such as electron density)
- Write DMS
- save molecular surfaces
as DMS files
- Write
Prmtop
- write Amber
parameter/topology files using
AmberTools