Tools Index

  1. 2D Labels - create labels with text, symbols, and arrows in 2D
  2. Add Charge - assign partial charges to atoms
  3. AddH - add hydrogens
  4. Add Ions - add monatomic counterions using AmberTools
  5. Adjust Torsions - rotate bonds (change dihedral angles)
  6. 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
  7. Angles/Torsions - measure bond angles and dihedral angles
  8. Animation - save/restore Chimera scenes, arrange them into a timeline, play/record animation
  9. APBS - interface to electrostatics calculations with APBS (Adaptive Poisson-Boltzmann Solver)
  10. Area/Volume from Web - use the StrucTools server to calculate surface areas and Voronoi volumes
  11. Attribute Calculator - generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute
  12. AutoDock Vina - interface to single-ligand docking with AutoDock Vina
  13. Axes/Planes/Centroids - define geometric objects (axes, planes, centroids) based on sets of atoms, perform related measurements
  14. Benchmark - measure hardware performance on standard Chimera rendering tasks
  15. Blast Protein - perform protein BLAST searches using a web service hosted by the UCSF RBVI
  16. Browser Configuration - configure web browsers to send Chimera data linked to web pages
  17. Build Structure - create and modify atomic structures
  18. Cage Builder - create polyhedral cages
  19. Camera - control viewing parameters
  20. Change Chain IDs - reassign chain identifiers
  21. Color Actions - set coloring targets, choose from longer list of colors, etc.
  22. Color Editor - create colors interactively
  23. Color Key - create a color key for figures
  24. Color Secondary Structure - color peptides/proteins by secondary structure
  25. Color Zone - color surfaces to match selected atoms, split volume data by the resulting color zones
  26. Command Line - enter Chimera commands
  27. Constrained Move - perform rotations and translations about specified axes
  28. Coulombic Surface Coloring - color molecular surfaces by Coulombic electrostatic potential
  29. Crystal Contacts - identify clashes between PDB symmetry copies
  30. Define Attribute - assign attribute values to atoms, residues, or models
  31. DelPhiController - interface to DelPhi (obtained separately) for calculating electrostatic potential
  32. Demos and Demo Editor - create and replay demonstrations in Chimera
  33. Distances - measure distances between pairs of atoms
  34. Dock Prep - add hydrogens, charges, etc. to prepare structures for DOCK or for other calculations
  35. Effects - control visual effects such as depth cueing, shadows, and silhouettes
  36. Electrostatic Surface Coloring - color surfaces using an electrostatic potential map (from any of several separate programs)
  37. Ensemble Cluster - cluster members of a conformational ensemble
  38. Ensemble Match - match conformations from two ensembles
  39. Find Clashes/Contacts - identify clashes and/or contacts
  40. FindHBond - find possible hydrogen bonds
  41. Fit in Map - fit atoms into a map (volume data) or one map into another
  42. Fit to Segments - fit structures into map segmentation regions
  43. Flatten Icosahedron - rearrange the faces of an icosahedral virus capsid into a plane to create a paper model
  44. Hide Dust - hide small disconnected bits of a surface
  45. Icosahedron Surface - create a hybrid icosahedron/sphere surface
  46. IDLE (Python Interactive DeveLopment Environment) - enter Python commands
  47. Intersurf - generate and display interface surfaces
  48. Keyboard Shortcuts - define and use keyboard shortcuts for Chimera functions
  49. Lighting - adjust and save lighting parameters
  50. Match -> Align - generate a multiple sequence alignment (MSA) from a structural alignment
  51. MatchMaker - superimpose structures by first constructing a sequence alignment (optionally including secondary structure scoring) and then fitting the aligned residue pairs
  52. MD Movie - replay and analyze molecular dynamics trajectories
  53. Measure and Color Blobs - color and measure disconnected parts of a surface
  54. Measure Volume and Area - measure surface area and surface-enclosed volume
  55. Metal Geometry - analyze metal coordination geometry
  56. Minimize Structure - energy-minimize structures
  57. Minrms Plot - examine structural alignments of proteins from MinRMS (obtained separately, available as source code)
  58. Model Panel - list and act on models
  59. Model/Refine Loops - interface to Modeller for building missing peptide segments or generating alternative conformations of peptide segments already present in a structure
  60. Molecular Dynamics Simulation - set up and run molecular dynamics
  61. Morph Conformations - create a trajectory that morphs between structures
  62. Morph Map - morph between two related sets of volume data
  63. Movement Mouse Mode - move just part of a structure with the mouse
  64. Movie Recorder - capture image frames and assemble them into a movie file
  65. Multalign Viewer - view sequences, optionally with associated structures; analyze conservation; view UniProt feature annotations; interface to Modeller
  66. MultiFit - fit multiple structures into density using a web service hosted by the UCSF RBVI
  67. Multiscale Models - view macromolecular assemblies at high and low resolution, generate multimers, and navigate structural hierarchies
  68. Notepad - add user notes (text) that can be saved along with sessions
  69. Nucleotides - create special representations of nucleotide bases and sugars
  70. Palette Editor - create and choose palettes
  71. PDB2PQR - interface to structure cleanup and charge/radius assignment with PDB2PQR
  72. PDB/UniProt Info - retrieve PDB and UniProt annotations using a web service provided by the RCSB PDB
  73. Per-Model Clipping - clip models individually with a plane at any angle
  74. PipesAndPlanks - show protein helices as “pipes,” strands as “planks”
  75. PseudoBond Panel - list and act on pseudobond groups
  76. PseudoBond Reader - create pseudobonds arbitrarily
  77. Rainbow - use a range of colors, changing the color per residue, chain, or model
  78. ReadStdin - allow communication with Chimera through standard input/output
  79. Render by Attribute - show attribute values of atoms, residues, and models (with color, etc.)
  80. Renumber Residues - reassign residue numbers
  81. Reply Log - show informational, warning, and error messages from Chimera
  82. ResProp - define amino acid categories
  83. RESTServer - allow communication with Chimera through REST interface
  84. Ribbon Style Editor - change ribbon heights/widths (scalings) and cross-sections (styles)
  85. Rotamers - view and evaluate amino acid sidechain rotamers, incorporate them into structures
  86. Rotation - control the center of rotation
  87. RR Distance Maps - generate a protein contact map color-coded by distance (and/or standard deviation, if comparing multiple structures)
  88. Scale Bar - draw a scale bar and associated label
  89. Segment Map - partition density maps
  90. Sequence - show amino acid and/or nucleic acid sequence
  91. Shininess - adjust shininess and brightness
  92. Side View - scale the view and move clipping planes interactively
  93. Small-Angle X-Ray Profile - calculate a SAXS profile from a structure, fit with experiment
  94. Solvate - solvate structures using AmberTools
  95. Structure Diagram - generate 2D chemical diagrams of small molecules
  96. Surface Capping - cap surfaces where they intersect a clipping plane
  97. Surface Color - color surfaces by volume data values or by distance from a point, axis, or plane
  98. Surface Zone - restrict the display of certain types of surfaces to a zone around selected atoms
  99. Surfnet - examine cavities and surface indentations
  100. Task Panel - manage jobs started by Chimera
  101. Thermal Ellipsoids - show anisotropic B-factors
  102. Tile Structures - arrange models in a plane
  103. Transform Coordinates - transform a model by specified Euler angles and shifts
  104. Undo Move and Redo Move - go back and forth in the history of model rotational/translational positions
  105. Unit Cell - generate crystallographic unit cell contents from coordinates and transformation matrices
  106. Values at Atom Positions - map volume data to atom positions and assign values as an attribute
  107. ViewDock - view and prioritize docked molecules
  108. Volume Eraser - interactively zero out parts of volume data
  109. Volume Filter - smooth or transform volume data
  110. Volume Mean, SD, RMS - calculate statistics for volume data
  111. Volume Series - display a series of volume data sets
  112. Volume Tracer - place markers and trace paths within volume displays
  113. Volume Viewer - visualize volume data (3D numerical data such as electron density)
  114. Write DMS - save molecular surfaces as DMS files
  115. Write Prmtop - write Amber parameter/topology files using AmberTools