Tools Index

  1. 2D Labels - place text and symbols in the display
  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. Area/Volume from Web - use the StrucTools server to calculate surface areas and Voronoi volumes
  8. Attribute Calculator - generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute
  9. Axes/Planes - define geometric objects (axes, planes) based on sets of atoms, perform related measurements
  10. Benchmark - measure hardware performance on standard Chimera rendering tasks
  11. Blast Protein - perform protein BLAST searches using a web service hosted by the UCSF RBVI
  12. Browser Configuration - configure web browsers to send Chimera data linked to web pages
  13. Build Structure - generate atomic structures "from scratch" or modify existing molecules
  14. Camera - control viewing parameters
  15. Color Editor - create colors interactively
  16. Color Key - create a color key for figures
  17. Color Secondary Structure - color peptides/proteins by secondary structure
  18. Color Zone - color surfaces to match selected atoms, split volume data by the resulting color zones
  19. Command Line - enter Chimera commands
  20. Constrained Move - perform rotations and translations about specified axes
  21. Coulombic Surface Coloring - color molecular surfaces by Coulombic electrostatic potential
  22. Crystal Contacts - identify clashes between PDB symmetry copies
  23. Define Attribute - assign attribute values to atoms, residues, or models
  24. DelPhiController - interface to DelPhi (obtained separately) for calculating electrostatic potential
  25. Demos and Demo Editor - create and replay demonstrations in Chimera
  26. Distances - measure distances between pairs of atoms
  27. Dock Prep - add hydrogens, charges, etc. to prepare structures for DOCK or for other calculations
  28. Effects - control visual effects such as depth cueing and silhouette edges
  29. Electrostatic Surface Coloring - color surfaces using an electrostatic potential map (from any of several separate programs)
  30. Ensemble Cluster - cluster members of a conformational ensemble
  31. Ensemble Match - match conformations from two ensembles
  32. Find Clashes/Contacts - identify clashes and/or contacts
  33. FindHBond - find possible hydrogen bonds
  34. Fit in Map - fit atoms into a map (volume data) or one map into another
  35. Flatten Icosahedron - rearrange the faces of an icosahedral virus capsid into a plane to create a paper model
  36. Hide Dust - hide small disconnected bits of a surface
  37. Icosahedron Surface - create a hybrid icosahedron/sphere surface
  38. IDLE (Python Interactive DeveLopment Environment) - enter Python commands
  39. Intersurf - generate and display interface surfaces
  40. Keyboard Shortcuts - define and use keyboard shortcuts for Chimera functions
  41. Lighting - adjust and save lighting parameters
  42. Match -> Align - generate a sequence alignment from a structural alignment
  43. MatchMaker - superimpose structures by first constructing a sequence alignment (optionally including secondary structure scoring) and then fitting the aligned residue pairs
  44. MD Movie - replay and analyze molecular dynamics trajectories
  45. Measure and Color Blobs - color and measure disconnected parts of a surface
  46. Measure Volume and Area - measure surface area and surface-enclosed volume
  47. Minimize Structure - energy-minimize structures
  48. Minrms Plot - examine structural alignments of proteins from MinRMS (obtained separately, available as source code)
  49. Model Loops - interface to MODELLER (obtained separately) for generating alternative conformations of peptide segments already present in a structure
  50. Model Panel - list and act on models
  51. Morph Conformations - create a trajectory that morphs between structures
  52. Morph Map - morph between two related sets of volume data
  53. Movement Mouse Mode - move just part of a structure with the mouse
  54. Movie Recorder - capture image frames and assemble them into a movie file
  55. Multalign Viewer - view sequence alignments, optionally with structures
  56. Multiscale Models - view macromolecular assemblies at high and low resolution, generate multimers, and navigate structural hierarchies
  57. Nucleotides - create special representations of nucleotide bases and sugars
  58. Per-Model Clipping - clip models individually with a plane at any angle
  59. Phantom Force Feedback - use a Phantom force feedback device to trace paths in volume displays
  60. PipesAndPlanks - show peptide/protein helices as "pipes" (cylinders) and strands as "planks"
  61. PseudoBond Panel - list and act on pseudobond groups
  62. PseudoBond Reader - create pseudobonds arbitrarily
  63. Rainbow - use a range of colors, changing the color per residue, chain, or model
  64. ReadStdin - allow communication with Chimera through standard input/output
  65. Render by Attribute - show attribute values of atoms, residues, and models (with color, etc.)
  66. Reply Log - show informational, warning, and error messages from Chimera
  67. ResProp - color amino acids by category; define new categories
  68. Ribbon Style Editor - change ribbon heights/widths (scalings) and cross-sections (styles)
  69. Rotamers - view and evaluate amino acid sidechain rotamers, incorporate them into structures
  70. Rotation - control the center of rotation
  71. Scale Bar - draw a scale bar and associated label
  72. Sequence - show amino acid and/or nucleic acid sequence
  73. Shininess - adjust shininess and brightness
  74. Side View - scale the view and move clipping planes interactively
  75. Solvate - solvate structures using AmberTools
  76. Structure Diagram - generate 2D chemical diagrams of small molecules
  77. Surface Capping - cap surfaces where they intersect a clipping plane
  78. Surface Color - color surfaces by volume data values or by distance from a point, axis, or plane
  79. Surface Zone - restrict the display of certain types of surfaces to a zone around selected atoms
  80. Surfnet - examine cavities and surface indentations
  81. Task Panel - manage jobs started by Chimera
  82. Thermal Ellipsoids - show anisotropic B-factors
  83. Tile Structures - arrange models in a plane
  84. Transform Molecule Coordinates - transform a structure by specified Euler angles and shifts
  85. Undo Move and Redo Move - go back and forth in the history of model rotational/translational positions
  86. Unit Cell - generate crystallographic unit cell contents from coordinates and transformation matrices
  87. Values at Atom Positions - map volume data to atom positions and assign values as an attribute
  88. ViewDock - view and prioritize docked molecules output by DOCK
  89. Volume Eraser - interactively zero out parts of volume data
  90. Volume Filter - smooth or transform volume data
  91. Volume Mean, SD, RMS - calculate statistics for volume data
  92. Volume Series - display a series of volume data sets
  93. Volume Tracer - place markers and trace paths within volume displays
  94. Volume Viewer - visualize volume data (3D numerical data such as electron density)
  95. Write DMS - save molecular surfaces as DMS files
  96. Write Prmtop - write Amber parameter/topology files using AmberTools