Tools Index

  1. 2D Labels - create arbitrary text labels and place them in two dimensions
  2. Accelerators - define and use keyboard shortcuts
  3. Add Charge - assign partial charges to atoms
  4. AddH - add hydrogens
  5. Adjust Torsions - rotate bonds (change dihedral angles)
  6. Angles/Torsions - measure bond angles and dihedral angles
  7. Area/Volume from Web - send molecular coordinates to the StrucTools server to get surface area and atomic Voronoi volume attributes
  8. Attribute Calculator - generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute
  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 certain types of surfaces to match selected atoms
  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. EnsembleMatch - match conformations from two ensembles
  27. EnsembleTile - display ensemble members in a tiled arrangement
  28. Find Clashes/Contacts - identify clashes and/or contacts
  29. FindHBond - find possible hydrogen bonds
  30. Fit Map in Map - locally optimize the overlap of two density maps
  31. Fit Model in Map - locally optimize the fit of a structure within a density map
  32. Flatten Icosahedron - rearrange the faces of an icosahedral virus capsid into a plane to create a paper model
  33. Fourier Transform - calculate the 3D Fourier transform of volume data
  34. Gaussian Filter - convolute volume data with a Gaussian function
  35. Icosahedron Surface - create a hybrid icosahedron/sphere surface
  36. IDLE (Python Interactive DeveLopment Environment) - enter Python commands
  37. Intersurf - generate and display interface surfaces
  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 Volume and Area - measure surface areas and surface-enclosed volumes
  44. Minimize Structure - energy-minimize structures
  45. Minrms Plot - examine structural alignments of proteins from MinRMS *
  46. Model Loops - interface to MODELLER (obtained separately) for generating alternative conformations of peptide segments already present in a structure
  47. Model Panel - list and act on models
  48. Morph Conformations - create a trajectory that morphs between structures
  49. Morph Map - morph between two related sets of volume data
  50. Movement Mouse Mode - move just part of a structure with the mouse
  51. Movie Recorder - capture image frames and assemble them into a movie file
  52. Multalign Viewer - view sequence alignments, optionally with structures
  53. Multiscale Models - view macromolecular assemblies at high and low resolution, generate multimers, and navigate structural hierarchies
  54. Nucleotides - create special representations of nucleotide bases and sugars
  55. Per-Model Clipping - clip models individually with a plane at any angle
  56. Phantom Force Feedback - use a Phantom force feedback device to trace paths in volume displays
  57. Pick Surface Pieces - color and measure disconnected parts of a contour surface
  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 - depict atoms, residues, and models by their attribute values (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 sequences of molecule models
  71. Shininess - adjust shininess and brightness
  72. Side View - scale the view and move clipping planes interactively
  73. Split Volume by Color Zone - split volume data into multiple sets according to color zones
  74. Surface Capping - cap surfaces where they intersect a clipping plane
  75. Surface Color - color surfaces according to volume data or geometry (distance from a point, axis, or plane)
  76. Surface Zone - restrict the display of certain types of surfaces to a zone around selected atoms
  77. Surfnet - examine cavities and surface indentations
  78. Transform Molecule Coordinates - transform a structure by specified Euler angles and shifts
  79. Undo Move and Redo Move - go back and forth in the history of model rotational/translational positions
  80. Unit Cell - generate crystallographic unit cell contents from coordinates and transformation matrices
  81. Values at Atom Positions - map volume data to atom positions and assign values as an attribute
  82. ViewDock and HearDock - view and prioritize docked molecules output by DOCK
  83. Volume Eraser - interactively zero out parts of volume data
  84. Volume Mean, SD, RMS - calculate statistics for volume data
  85. Volume Path Tracer - trace paths within volume displays
  86. Volume Series - display a series of volume data sets
  87. 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.