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)