Tools Index

  1. 2D Labels - create arbitrary text labels and place them in two dimensions
  2. Add Charge - assign partial charges to atoms
  3. AddH - add hydrogens
  4. Adjust Torsions - rotate bonds (change dihedral angles)
  5. Angles/Torsions - measure bond angles and dihedral angles
  6. Area/Volume from Web - use the StrucTools server to calculate surface areas and Voronoi volumes
  7. Attribute Calculator - generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute
  8. Axes - define axes and perform related measurements
  9. Benchmark - measure hardware performance on standard Chimera rendering tasks
  10. Browser Configuration - configure web browsers to send Chimera data linked to web pages
  11. Build Structure - perform simple structure-building operations
  12. Camera - control viewing parameters
  13. Color Editor - create colors interactively
  14. Color Secondary Structure - color peptides/proteins by secondary structure
  15. Color Zone - color surfaces to match selected atoms, split volume data by the resulting color zones
  16. Command Line - enter Chimera commands
  17. Constrained Move - perform rotations and translations about specified axes
  18. Crystal Contacts - identify clashes between PDB symmetry copies
  19. Define Attribute - assign attribute values to atoms, residues, or models
  20. DelPhiController - interface to DelPhi (obtained separately) for calculating electrostatic potential
  21. Demos and Demo Editor - create and replay demonstrations in Chimera
  22. Distances - measure distances between pairs of atoms
  23. Dock Prep - add hydrogens, charges, etc. to prepare structures for DOCK or for other calculations
  24. Effects - control visual effects such as depth cueing and silhouette edges
  25. Electrostatic Surface Coloring - color surfaces by electrostatic potential
  26. Ensemble Cluster - cluster members of a conformational ensemble
  27. Ensemble Match - match conformations from two ensembles
  28. Find Clashes/Contacts - identify clashes and/or contacts
  29. FindHBond - find possible hydrogen bonds
  30. Fit in Map - fit atoms into a map (volume data) or one map into another
  31. Flatten Icosahedron - rearrange the faces of an icosahedral virus capsid into a plane to create a paper model
  32. Fourier Transform - calculate the 3D Fourier transform of volume data
  33. Gaussian Filter - convolute volume data with a Gaussian function
  34. Icosahedron Surface - create a hybrid icosahedron/sphere surface
  35. IDLE (Python Interactive DeveLopment Environment) - enter Python commands
  36. Intersurf - generate and display interface surfaces
  37. Keyboard Shortcuts - define and use keyboard shortcuts for Chimera functions
  38. Lens Inspector - create rectangular regions of alternative display within the graphics window
  39. Lighting - adjust and save lighting parameters
  40. Match -> Align - generate a sequence alignment from a structural alignment
  41. MatchMaker - superimpose structures by first constructing a sequence alignment (optionally including secondary structure scoring) and then fitting the aligned residue pairs
  42. MD Movie - replay and analyze molecular dynamics trajectories
  43. Measure and Color Blobs - color and measure disconnected parts of a surface
  44. Measure Volume and Area - measure surface area and surface-enclosed volume
  45. Minimize Structure - energy-minimize structures
  46. Minrms Plot - examine structural alignments of proteins from MinRMS *
  47. Model Loops - interface to MODELLER (obtained separately) for generating alternative conformations of peptide segments already present in a structure
  48. Model Panel - list and act on models
  49. Morph Conformations - create a trajectory that morphs between structures
  50. Morph Map - morph between two related sets of volume data
  51. Movement Mouse Mode - move just part of a structure with the mouse
  52. Movie Recorder - capture image frames and assemble them into a movie file
  53. Multalign Viewer - view sequence alignments, optionally with structures
  54. Multiscale Models - view macromolecular assemblies at high and low resolution, generate multimers, and navigate structural hierarchies
  55. Nucleotides - create special representations of nucleotide bases and sugars
  56. Per-Model Clipping - clip models individually with a plane at any angle
  57. Phantom Force Feedback - use a Phantom force feedback device to trace paths in volume displays
  58. PipesAndPlanks - show peptide/protein helices as "pipes" (cylinders) and strands as "planks"
  59. PseudoBond Panel - list and act on pseudobond groups
  60. PseudoBond Reader - create pseudobonds arbitrarily
  61. Rainbow - use a range of colors, changing the color per residue, chain, or model
  62. ReadStdin - allow communication with Chimera through standard input/output
  63. Render by Attribute - show attribute values of atoms, residues, and models (with color, etc.)
  64. Reply Log - show informational, warning, and error messages from Chimera
  65. ResProp - color amino acids by category; define new categories
  66. Ribbon Style Editor - change ribbon heights/widths (scalings) and cross-sections (styles)
  67. Rotamers - view and evaluate amino acid sidechain rotamers, incorporate them into structures
  68. Rotation - control the center of rotation
  69. Scale Bar - draw a scale bar and associated label
  70. Sequence - show amino acid and/or nucleic acid sequence
  71. Shininess - adjust shininess and brightness
  72. Side View - scale the view and move clipping planes interactively
  73. Solvate - solvate structures using AmberTools
  74. Structure Diagram - generate 2D chemical diagrams of small molecules
  75. Surface Capping - cap surfaces where they intersect a clipping plane
  76. Surface Color - color surfaces by volume data values or by distance from a point, axis, or plane
  77. Surface Zone - restrict the display of certain types of surfaces to a zone around selected atoms
  78. Surfnet - examine cavities and surface indentations
  79. Tile Structures - arrange models in a plane
  80. Transform Molecule Coordinates - transform a structure by specified Euler angles and shifts
  81. Undo Move and Redo Move - go back and forth in the history of model rotational/translational positions
  82. Unit Cell - generate crystallographic unit cell contents from coordinates and transformation matrices
  83. Values at Atom Positions - map volume data to atom positions and assign values as an attribute
  84. ViewDock and HearDock - view and prioritize docked molecules output by DOCK
  85. Volume Eraser - interactively zero out parts of volume data
  86. Volume Mean, SD, RMS - calculate statistics for volume data
  87. Volume Series - display a series of volume data sets
  88. Volume Tracer - place markers and trace paths within volume displays
  89. Volume Viewer - visualize volume data (3D numerical data such as electron density)
* MinRMS is a stand-alone, nongraphical program that generates structural alignments of proteins; it is run from the system command line, not from within Chimera. MinRMS is not distributed with Chimera, but can be downloaded separately.