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