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. Collaboratory: Start Session and Join Session - start and join a Chimera session shared among multiple sites
  14. Color Editor - create colors interactively
  15. Color Secondary Structure - color peptides/proteins by secondary structure
  16. Color Zone - color certain types of surfaces to match selected atoms
  17. Command Line - enter Chimera commands
  18. Constrained Move - perform rotations and translations about specified axes
  19. Define Attribute - assign attribute values to atoms, residues, or models
  20. DelPhiController - calculate electrostatic potential maps with DelPhi (obtained separately)
  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. EnsembleMatch - match conformations from two ensembles
  26. EnsembleTile - display ensemble members in a tiled arrangement
  27. Find Clashes/Contacts - identify clashes and/or contacts
  28. FindHBond - find possible hydrogen bonds
  29. Fit Models in Maps - locally optimize the fit of a structure within a density map
  30. Icosahedron Surface - create a hybrid icosahedron/sphere surface
  31. IDLE (Python Interactive DeveLopment Environment) - enter Python commands
  32. Intersurf - generate and display interface surfaces
  33. Lens Inspector - create rectangular regions of alternative display within the graphics window
  34. Lighting - adjust and save lighting parameters
  35. Match -> Align - generate a sequence alignment from a structural alignment
  36. MatchMaker - superimpose structures by first constructing a sequence alignment (optionally including secondary structure scoring) and then fitting the aligned residue pairs
  37. MD Movie - replay and analyze molecular dynamics trajectories
  38. Measure Volume and Area - measure surface areas and surface-enclosed volumes
  39. Minimize Structure - energy-minimize structures
  40. Minrms Plot - examine structural alignments of proteins from MinRMS *
  41. Model Loops - interface to MODELLER (obtained separately) for generating alternative conformations of peptide segments already present in a structure
  42. Model Panel - list and act on models
  43. Morph Conformations - create a trajectory that morphs between two or more conformations of a structure
  44. Movie Recorder - capture image frames and assemble them into a movie file
  45. Multalign Viewer - view sequence alignments, optionally with structures
  46. Multiscale Models - view macromolecular assemblies at high and low resolution, generate multimers, and navigate structural hierarchies
  47. Nucleotides - create special representations of nucleotide bases and sugars
  48. Per-Model Clipping - clip models individually with a plane at any angle
  49. Phantom Force Feedback - use a Phantom force feedback device to trace paths in volume displays
  50. PipesAndPlanks - show peptide/protein helices as "pipes" (cylinders) and strands as "planks"
  51. PseudoBond Panel - list and act on pseudobond groups
  52. PseudoBond Reader - create pseudobonds arbitrarily
  53. Rainbow - color molecule models over a range, changing the color per residue, chain, or model
  54. ReadStdin - allow communication with Chimera through standard input/output
  55. Render by Attribute - depict atoms, residues, and models by their attribute values (with color, etc.)
  56. Reply Log - show informational, warning, and error messages from Chimera
  57. ResProp - color amino acids by category; define new categories
  58. Ribbon Style Editor - change ribbon heights/widths (scalings) and cross-sections (styles)
  59. Rotation - control the center of rotation
  60. Scale Bar - draw a scale bar and associated label
  61. Sequence - show sequences of molecule models
  62. Set Bond Length - change bond lengths
  63. Shininess Control - adjust shininess and brightness
  64. Side View - scale the view and move clipping planes interactively
  65. Surface Capping - cap surfaces where they intersect a clipping plane
  66. Surface Color - color surfaces according to volume data or geometry (distance from a point, axis, or plane)
  67. Surface Zone - restrict the display of certain types of surfaces to a zone around selected atoms
  68. Surfnet - examine cavities and surface indentations
  69. Undo Move and Redo Move - go back and forth in the history of model rotational/translational positions
  70. Unit Cell - generate crystallographic unit cell contents from coordinates and transformation matrices
  71. Values at Atom Positions - map volume data to atom positions and assign values as an attribute
  72. ViewDock and HearDock - view and prioritize docked molecules output by DOCK
  73. Volume Eraser - interactively zero out parts of volume data
  74. Volume Path Tracer - trace paths within volume displays
  75. Volume Viewer - visualize three-dimensional numerical data sets (for example, electron density maps)
* 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.