Tools Index

1. Accelerators - use and define keyboard shortcuts for many operations in Chimera
2. AddH - add hydrogens
3. Adjust Torsions - rotate bonds (change dihedral angles)
4. AlignPlot - examine structural alignments of proteins from MinRMS^* (see also Minrms Plot)
5. Angles/Torsions - measure bond angles and dihedral angles
6. Benchmark - measure hardware performance on standard Chimera rendering tasks
7. Browser Configuration - configure web browsers to send Chimera data linked to web pages
8. Camera - control viewing parameters
9. Color Editor - create colors interactively
10. Color Secondary Structure - color peptides/proteins by secondary structure
11. Collaboratory: Start Session and Join Session - start and join a Chimera session shared among multiple sites
12. Command Line - command line within Chimera
13. Constrained Move - perform rotations and translations about specified axes
14. Define Attribute - assign attribute values to atoms, residues, or models
15. DelPhiController and DelPhiViewer - set up DelPhi electrostatic potential calculations and view results
16. Demos - a general mechanism for creating demonstrations in Chimera with blocks of explanatory text
17. Distances - measure distances between pairs of atoms
18. Effects - control visual effects such as depth cueing and subdivision quality
19. EnsembleMatch - match conformations from two ensembles
20. EnsembleTile - display ensemble members in a tiled arrangement
21. Export Surfaces as VRML - save surfaces generated by Multiscale Models and Volume Viewer as VRML files
22. FindHBond - find possible hydrogen bonds
23. IDLE - Python Interactive DeveLopment Environment
24. KeepSticks - display sticks only
25. Lens Inspector - create rectangular regions of alternative display within the graphics window
26. Lighting - adjust and save lighting parameters
27. MainChain - display only protein backbone atoms (N, CA, C)
28. Match -> Align - generate a sequence alignment from a structural alignment
29. MatchMaker - superimpose structures with similar sequences by first constructing a sequence alignment and then performing a least-squares fit of the aligned residue pairs
30. Minrms Plot (the Collaboratory-aware alternative to AlignPlot) - examine structural alignments of proteins from MinRMS^*
31. Model Panel - panel for convenient control of models
32. Movie - play molecular dynamics trajectories
33. MPOSE - display protein structural alignments created with MPOSE
34. MSF Viewer - view multiple sequence alignments, optionally with structures
35. Multalign Viewer - view multiple sequence alignments, optionally with structures
36. Multiscale Models - view macromolecular assemblages at high and low resolution, generate multimers from transformation matrices, and define and navigate levels of structural hierarchies
37. Nucleotides - create special nucleotide-specific displays
38. PBReader - create pseudobonds connecting arbitrary pairs of atoms
39. Per-Model Clipping - clip models individually with a plane at any angle
40. Phantom Force Feedback - use a Phantom force feedback device to trace paths within volume displays
41. PipesAndPlanks - make VRML pipes-and-planks representations of proteins
42. PseudoBond Panel - panel for convenient control of pseudobond groups
43. Rainbow - color molecule models over a range, changing the color per residue, chain, or model
44. Read MS/DMS - open a dot molecular surface in MS/DMS format
45. Render by Attribute - depict atoms, residues, and models by their attribute values (with color, etc.)
46. Reply Log - log of informational, warning, and error messages from Chimera
47. ResProp - color amino acids by category; define new categories
48. Ribbon Style Editor - change ribbon heights/widths (scalings) and cross-sections (styles)
49. Rotation - control the center of rotation
50. Scale Bar - draw a scale bar and associated label
51. Selection Inspector - examine and change the attributes of items that have been selected
52. Shininess Control - adjust shininess, brightness, and the color used for shiny highlights
53. Side View - scale the view and move clipping planes interactively
54. SimpleSession - save basic features of a Chimera session
55. Surface Area/Volume - calculate surface areas and Voronoi volumes
56. Surfnet - examine cavities and surface indentations
57. Undo Move and Redo Move - go back and forth in the history of model rotational/translational positions
58. Unit Cell - generate crystallographic unit cell contents from coordinates and transformation matrices
59. ViewDock and HearDock - view and sort docked molecules
60. Volume Path Tracer - trace paths within volume displays
61. Volume Viewer - visualize three-dimensional data sets