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. Add Ions - add monatomic counterions using AmberTools
  5. Adjust Torsions - rotate bonds (change dihedral angles)
  6. Angles/Torsions - measure bond angles and dihedral angles
  7. Area/Volume from Web - use the StrucTools server to calculate surface areas and Voronoi volumes
  8. Attribute Calculator - generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute
  9. Axes - define axes and perform related measurements
  10. Benchmark - measure hardware performance on standard Chimera rendering tasks
  11. Browser Configuration - configure web browsers to send Chimera data linked to web pages
  12. Build Structure - generate atomic structures "from scratch" or modify existing molecules
  13. Camera - control viewing parameters
  14. Color Editor - create colors interactively
  15. Color Key - create a color key for figures
  16. Color Secondary Structure - color peptides/proteins by secondary structure
  17. Color Zone - color surfaces to match selected atoms, split volume data by the resulting color zones
  18. Command Line - enter Chimera commands
  19. Constrained Move - perform rotations and translations about specified axes
  20. Crystal Contacts - identify clashes between PDB symmetry copies
  21. Define Attribute - assign attribute values to atoms, residues, or models
  22. DelPhiController - interface to DelPhi (obtained separately) for calculating electrostatic potential
  23. Demos and Demo Editor - create and replay demonstrations in Chimera
  24. Distances - measure distances between pairs of atoms
  25. Dock Prep - add hydrogens, charges, etc. to prepare structures for DOCK or for other calculations
  26. Effects - control visual effects such as depth cueing and silhouette edges
  27. Electrostatic Surface Coloring - color surfaces by electrostatic potential
  28. Ensemble Cluster - cluster members of a conformational ensemble
  29. Ensemble Match - match conformations from two ensembles
  30. Find Clashes/Contacts - identify clashes and/or contacts
  31. FindHBond - find possible hydrogen bonds
  32. Fit in Map - fit atoms into a map (volume data) or one map into another
  33. Flatten Icosahedron - rearrange the faces of an icosahedral virus capsid into a plane to create a paper model
  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. Keyboard Shortcuts - define and use keyboard shortcuts for Chimera functions
  39. Lens Inspector - create rectangular regions of alternative display within the graphics window
  40. Lighting - adjust and save lighting parameters
  41. Match -> Align - generate a sequence alignment from a structural alignment
  42. MatchMaker - superimpose structures by first constructing a sequence alignment (optionally including secondary structure scoring) and then fitting the aligned residue pairs
  43. MD Movie - replay and analyze molecular dynamics trajectories
  44. Measure and Color Blobs - color and measure disconnected parts of a surface
  45. Measure Volume and Area - measure surface area and surface-enclosed volume
  46. Minimize Structure - energy-minimize structures
  47. Minrms Plot - examine structural alignments of proteins from MinRMS *
  48. Model Loops - interface to MODELLER (obtained separately) for generating alternative conformations of peptide segments already present in a structure
  49. Model Panel - list and act on models
  50. Morph Conformations - create a trajectory that morphs between structures
  51. Morph Map - morph between two related sets of volume data
  52. Movement Mouse Mode - move just part of a structure with the mouse
  53. Movie Recorder - capture image frames and assemble them into a movie file
  54. Multalign Viewer - view sequence alignments, optionally with structures
  55. Multiscale Models - view macromolecular assemblies at high and low resolution, generate multimers, and navigate structural hierarchies
  56. Nucleotides - create special representations of nucleotide bases and sugars
  57. Per-Model Clipping - clip models individually with a plane at any angle
  58. Phantom Force Feedback - use a Phantom force feedback device to trace paths in volume displays
  59. PipesAndPlanks - show peptide/protein helices as "pipes" (cylinders) and strands as "planks"
  60. PseudoBond Panel - list and act on pseudobond groups
  61. PseudoBond Reader - create pseudobonds arbitrarily
  62. Rainbow - use a range of colors, changing the color per residue, chain, or model
  63. ReadStdin - allow communication with Chimera through standard input/output
  64. Render by Attribute - show attribute values of atoms, residues, and models (with color, etc.)
  65. Reply Log - show informational, warning, and error messages from Chimera
  66. ResProp - color amino acids by category; define new categories
  67. Ribbon Style Editor - change ribbon heights/widths (scalings) and cross-sections (styles)
  68. Rotamers - view and evaluate amino acid sidechain rotamers, incorporate them into structures
  69. Rotation - control the center of rotation
  70. Scale Bar - draw a scale bar and associated label
  71. Sequence - show amino acid and/or nucleic acid sequence
  72. Shininess - adjust shininess and brightness
  73. Side View - scale the view and move clipping planes interactively
  74. Solvate - solvate structures using AmberTools
  75. Structure Diagram - generate 2D chemical diagrams of small molecules
  76. Surface Capping - cap surfaces where they intersect a clipping plane
  77. Surface Color - color surfaces by volume data values or by distance from a point, axis, or plane
  78. Surface Zone - restrict the display of certain types of surfaces to a zone around selected atoms
  79. Surfnet - examine cavities and surface indentations
  80. Tile Structures - arrange models in a plane
  81. Transform Molecule Coordinates - transform a structure by specified Euler angles and shifts
  82. Undo Move and Redo Move - go back and forth in the history of model rotational/translational positions
  83. Unit Cell - generate crystallographic unit cell contents from coordinates and transformation matrices
  84. Values at Atom Positions - map volume data to atom positions and assign values as an attribute
  85. ViewDock and HearDock - view and prioritize docked molecules output by DOCK
  86. Volume Eraser - interactively zero out parts of volume data
  87. Volume Mean, SD, RMS - calculate statistics for volume data
  88. Volume Series - display a series of volume data sets
  89. Volume Tracer - place markers and trace paths within volume displays
  90. Volume Viewer - visualize volume data (3D numerical data such as electron density)
  91. Write DMS - save molecular surfaces as DMS files
  92. Write Prmtop - write Amber parameter/topology files using AmberTools
* 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.