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. Camera - control viewing parameters
  8. Color Editor - create colors interactively
  9. Collaboratory: Start Session and Join Session - start and join a Chimera session shared among multiple sites
  10. Command Line - command line within Chimera
  11. DelPhiController and DelPhiViewer - set up DelPhi electrostatic potential calculations and view results
  12. Distances - measure distances between pairs of atoms
  13. Effects - control depth cueing and subdivision quality
  14. EnsembleMatch - match conformations from two ensembles
  15. EnsembleTile - display ensemble members in a tiled arrangement
  16. FindHBond - find possible hydrogen bonds
  17. IDLE - Python Interactive DeveLopment Environment
  18. KeepSticks - display sticks only
  19. Lens Inspector - create rectangular regions of alternative display within the graphics window
  20. MainChain - display only protein backbone atoms (N, CA, C)
  21. MinRMS - create structural alignments of proteins
  22. Minrms Plot (the Collaboratory-aware alternative to AlignPlot) - examine structural alignments of proteins from MinRMS
  23. Model Panel - panel for convenient control of models
  24. Movie - play molecular dynamics trajectories from AMBER
  25. MPOSE - display protein structural alignments created with MPOSE
  26. MSF Viewer - view multiple sequence alignments, optionally with structures
  27. Multalign Viewer - view multiple sequence alignments, optionally with structures
  28. PBReader - create pseudobonds connecting arbitrary pairs of atoms
  29. Phantom Force Feedback - use a Phantom force feedback device to trace paths within volume displays
  30. PipesAndPlanks - make VRML pipes-and-planks representations of proteins
  31. PseudoBond Panel - panel for convenient control of pseudobond groups
  32. Reply Log - log of informational, warning, and error messages from Chimera
  33. ResProp - color amino acids by category; define new categories
  34. Ribbon Style Editor - change the cross-section (shape) of secondary structure ribbon representations
  35. Rotation - control the center of rotation
  36. Scale Bar - draw a scale bar and associated label
  37. Selection Inspector - examine and change the properties of items that have been selected
  38. Side View - scale the view and move clipping planes interactively
  39. SimpleSession - save basic features of a Chimera session
  40. Surfnet - examine cavities and surface indentations
  41. ViewDock and HearDock - view and sort docked molecules
  42. Volume Path Tracer - trace paths within volume displays
  43. Volume Viewer - visualize three-dimensional data sets