Tools Index

1. 2D Labels - create labels with text, symbols, and arrows in 2D
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. Animation **under development, not fully functional, may change significantly** - save/restore Chimera scenes
8. Area/Volume from Web - use the StrucTools server to calculate surface areas and Voronoi volumes
9. Attribute Calculator - generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute
10. Axes/Planes/Centroids - define geometric objects (axes, planes, centroids) based on sets of atoms, perform related measurements
11. Benchmark - measure hardware performance on standard Chimera rendering tasks
12. Blast Protein - perform protein BLAST searches using a web service hosted by the UCSF RBVI
13. Browser Configuration - configure web browsers to send Chimera data linked to web pages
14. Build Structure - create and modify atomic structures
15. Cage Builder - create polyhedral cages
16. Camera - control viewing parameters
17. Change Chain IDs - reassign chain identifiers
18. Color Editor - create colors interactively
19. Color Key - create a color key for figures
20. Color Secondary Structure - color peptides/proteins by secondary structure
21. Color Zone - color surfaces to match selected atoms, split volume data by the resulting color zones
22. Command Line - enter Chimera commands
23. Constrained Move - perform rotations and translations about specified axes
24. Coulombic Surface Coloring - color molecular surfaces by Coulombic electrostatic potential
25. Crystal Contacts - identify clashes between PDB symmetry copies
26. Define Attribute - assign attribute values to atoms, residues, or models
27. DelPhiController - interface to DelPhi (obtained separately) for calculating electrostatic potential
28. Demos and Demo Editor - create and replay demonstrations in Chimera
29. Distances - measure distances between pairs of atoms
30. Dock Prep - add hydrogens, charges, etc. to prepare structures for DOCK or for other calculations
31. Effects - control visual effects such as depth cueing and silhouette edges
32. Electrostatic Surface Coloring - color surfaces using an electrostatic potential map (from any of several separate programs)
33. Ensemble Cluster - cluster members of a conformational ensemble
34. Ensemble Match - match conformations from two ensembles
35. Find Clashes/Contacts - identify clashes and/or contacts
36. FindHBond - find possible hydrogen bonds
37. Fit in Map - fit atoms into a map (volume data) or one map into another
38. Fit to Segments - fit structures into map segmentation regions
39. Flatten Icosahedron - rearrange the faces of an icosahedral virus capsid into a plane to create a paper model
40. Hide Dust - hide small disconnected bits of a surface
41. Icosahedron Surface - create a hybrid icosahedron/sphere surface
42. IDLE (Python Interactive DeveLopment Environment) - enter Python commands
43. Intersurf - generate and display interface surfaces
44. Keyboard Shortcuts - define and use keyboard shortcuts for Chimera functions
45. Lighting - adjust and save lighting parameters
46. Match -> Align - generate a sequence alignment from a structural alignment
47. MatchMaker - superimpose structures by first constructing a sequence alignment (optionally including secondary structure scoring) and then fitting the aligned residue pairs
48. MD Movie - replay and analyze molecular dynamics trajectories
49. Measure and Color Blobs - color and measure disconnected parts of a surface
50. Measure Volume and Area - measure surface area and surface-enclosed volume
51. Metal Geometry - analyze metal coordination geometry
52. Minimize Structure - energy-minimize structures
53. Minrms Plot - examine structural alignments of proteins from MinRMS (obtained separately, available as source code)
54. Model Loops - interface to Modeller (obtained separately) for generating alternative conformations of peptide segments already present in a structure; see also comparative modeling with Modeller
55. Model Panel - list and act on models
56. Morph Conformations - create a trajectory that morphs between structures
57. Morph Map - morph between two related sets of volume data
58. Movement Mouse Mode - move just part of a structure with the mouse
59. Movie Recorder - capture image frames and assemble them into a movie file
60. Multalign Viewer - view sequence alignments, optionally with structures
61. MultiFit - fit multiple structures into density using a web service hosted by the UCSF RBVI
62. Multiscale Models - view macromolecular assemblies at high and low resolution, generate multimers, and navigate structural hierarchies
63. Nucleotides - create special representations of nucleotide bases and sugars
64. Palette Editor - create and choose palettes
65. PDB/UniProt Info - retrieve PDB and UniProt annotations using a Web service provided by the RCSB PDB
66. Per-Model Clipping - clip models individually with a plane at any angle
67. PipesAndPlanks - show peptide/protein helices as "pipes" (cylinders) and strands as "planks"
68. PseudoBond Panel - list and act on pseudobond groups
69. PseudoBond Reader - create pseudobonds arbitrarily
70. Rainbow - use a range of colors, changing the color per residue, chain, or model
71. ReadStdin - allow communication with Chimera through standard input/output
72. Render by Attribute - show attribute values of atoms, residues, and models (with color, etc.)
73. Renumber Residues - reassign residue numbers
74. Reply Log - show informational, warning, and error messages from Chimera
75. ResProp - define amino acid categories
76. Ribbon Style Editor - change ribbon heights/widths (scalings) and cross-sections (styles)
77. Rotamers - view and evaluate amino acid sidechain rotamers, incorporate them into structures
78. Rotation - control the center of rotation
79. Scale Bar - draw a scale bar and associated label
80. Segment Map - partition density maps
81. Sequence - show amino acid and/or nucleic acid sequence
82. Shininess - adjust shininess and brightness
83. Side View - scale the view and move clipping planes interactively
84. Small-Angle X-Ray Profile - calculate a SAXS profile from a structure, fit with experiment
85. Solvate - solvate structures using AmberTools
86. Structure Diagram - generate 2D chemical diagrams of small molecules
87. Surface Capping - cap surfaces where they intersect a clipping plane
88. Surface Color - color surfaces by volume data values or by distance from a point, axis, or plane
89. Surface Zone - restrict the display of certain types of surfaces to a zone around selected atoms
90. Surfnet - examine cavities and surface indentations
91. Task Panel - manage jobs started by Chimera
92. Thermal Ellipsoids - show anisotropic B-factors
93. Tile Structures - arrange models in a plane
94. Transform Coordinates - transform a model by specified Euler angles and shifts
95. Undo Move and Redo Move - go back and forth in the history of model rotational/translational positions
96. Unit Cell - generate crystallographic unit cell contents from coordinates and transformation matrices
97. Values at Atom Positions - map volume data to atom positions and assign values as an attribute
98. ViewDock - view and prioritize docked molecules
99. Volume Eraser - interactively zero out parts of volume data
100. Volume Filter - smooth or transform volume data
101. Volume Mean, SD, RMS - calculate statistics for volume data
102. Volume Series - display a series of volume data sets
103. Volume Tracer - place markers and trace paths within volume displays
104. Volume Viewer - visualize volume data (3D numerical data such as electron density)
105. Write DMS - save molecular surfaces as DMS files
106. Write Prmtop - write Amber parameter/topology files using AmberTools