Tools Index

1. 2D Labels - create arbitrary text labels and place them in two dimensions
2. Accelerators - use and define keyboard shortcuts for many operations in Chimera
3. AddH - add hydrogens
4. Adjust Torsions - rotate bonds (change dihedral angles)
5. Angles/Torsions - measure bond angles and dihedral angles
6. Attribute Calculator - generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute
7. Benchmark - measure hardware performance on standard Chimera rendering tasks
8. Browser Configuration - configure web browsers to send Chimera data linked to web pages
9. Camera - control viewing parameters
10. Collaboratory: Start Session and Join Session - start and join a Chimera session shared among multiple sites
11. Color Editor - create colors interactively
12. Color Secondary Structure - color peptides/proteins by secondary structure
13. Color Zone - color patches of surfaces from Volume Viewer and Multiscale Models near selected atoms
14. Command Line - command line within Chimera
15. Constrained Move - perform rotations and translations about specified axes
16. Define Attribute - assign attribute values to atoms, residues, or models
17. DelPhiController - set up DelPhi electrostatic potential calculations
18. Demos and Demo Editor - a general mechanism for creating and replaying demonstrations in Chimera
19. Distances - measure distances between pairs of atoms
20. Dock Prep - prepare structures as input to the DOCK suite of programs
21. Effects - control visual effects such as depth cueing and subdivision quality
22. EnsembleMatch - match conformations from two ensembles
23. EnsembleTile - display ensemble members in a tiled arrangement
24. FindHBond - find possible hydrogen bonds
25. Fit Models in Maps - locally optimize the fit of a structure within a density map
26. Icosahedron Surface - create a hybrid icosahedron/sphere surface
27. IDLE - Python Interactive DeveLopment Environment
28. Intersurf - generate and display interface surfaces
29. Lens Inspector - create rectangular regions of alternative display within the graphics window
30. Lighting - adjust and save lighting parameters
31. MainChain - display only protein backbone atoms (N, CA, C)
32. Match -> Align - generate a sequence alignment from a structural alignment
33. MatchMaker - superimpose structures with similar sequences by first constructing a sequence alignment and then performing a least-squares fit of the aligned residue pairs
34. MD Movie - play and analyze molecular dynamics trajectories
35. Measure Volume - measure the volume enclosed in a surface
36. Minrms Plot - examine structural alignments of proteins from MinRMS^*
37. Model Panel - panel for many operations on models
38. Movie Recorder - capture image frames and assemble them into a movie file
39. MPOSE - display protein structural alignments created with MPOSE
40. Multalign Viewer - view sequence alignments, optionally with structures
41. Multiscale Models - view macromolecular assemblages at high and low resolution, generate multimers from transformation matrices, and define and navigate levels of structural hierarchies
42. Nucleotides - create special nucleotide-specific displays
43. Per-Model Clipping - clip models individually with a plane at any angle
44. Phantom Force Feedback - use a Phantom force feedback device to trace paths within volume displays
45. PipesAndPlanks - make VRML pipes-and-planks representations of proteins
46. PseudoBond Panel - panel for many operations on pseudobond groups
47. PseudoBond Reader - create pseudobonds connecting arbitrary pairs of atoms
48. Rainbow - color molecule models over a range, changing the color per residue, chain, or model
49. Render by Attribute - depict atoms, residues, and models by their attribute values (with color, etc.)
50. Reply Log - log of informational, warning, and error messages from Chimera
51. ResProp - color amino acids by category; define new categories
52. Ribbon Style Editor - change ribbon heights/widths (scalings) and cross-sections (styles)
53. Rotation - control the center of rotation
54. Scale Bar - draw a scale bar and associated label
55. Sequence - show sequences of molecule models
56. Set Bond Length - change bond lengths
57. Shininess Control - adjust shininess, brightness, and the color used for shiny highlights
58. Side View - scale the view and move clipping planes interactively
59. Surface Area/Volume - calculate surface areas and Voronoi volumes
60. Surface Capping - cap surfaces where they intersect a clipping plane
61. Surface Color - color surfaces according to volume data or geometry (distance from a point, axis, or plane)
62. Surface Zone - restrict the display of surfaces from Volume Viewer and Multiscale Models to a zone around selected atoms
63. Surfnet - examine cavities and surface indentations
64. Undo Move and Redo Move - go back and forth in the history of model rotational/translational positions
65. Unit Cell - generate crystallographic unit cell contents from coordinates and transformation matrices
66. Values at Atom Positions - map volume data to atom positions and assign values as an attribute
67. ViewDock and HearDock - view and sort docked molecules
68. Volume Eraser - interactively zero out parts of volume data
69. Volume Path Tracer - trace paths within volume displays
70. Volume Viewer - visualize three-dimensional data sets