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Clip 1 illustrates basic model manipulation, different molecular representations, and selection of chemical groups. The input file contains DNA complexed with netropsin (6bna in the Protein Data Bank). At the beginning of the clip, Chimera has already been started. The user actions and commands shown in the clip are described below.
menu item Session... Import Model...
(choose and open 6bna.pdb)
Command: linewidth 2- use thicker lines
Command: scale 2- double the size
Command: color byatom- color atoms by element
the left mouse button is used for rotation (x,y-rotation in the central region of the window, z-rotation in the periphery) and the middle mouse button is used for translation
Command: roll y 1- rotate continuously around the y-axis
Command: color yellow :nt- color netropsin yellow
Command: repr stick :nt- change netropsin from default wireframe representation into sticks
Command: repr bs :nt- change netropsin into a ball-and-stick representation
Command: repr cpk :nt- change netropsin into a CPK representation
Command: repr stick- change everything to a stick representation
Command: ~display :.water- undisplay water molecules
Command: freeze- halt the continuous rotation
menu item Select... Chemical groups... phosphate- example of selection from the menu
Command: repr cpk selected- change selected atoms (phosphates) into a CPK representation
Ctrl-left mouse button is used to select a single atom from the screen
Command: label selected- label the previously selected atom
Ctrl-left mouse button is used to select all the atoms in a region of the screen
Command: savepos pos1- save the current position to return to later
Command: window selected; thick 7- center the display on the selected atoms; increase the thickness of the displayed slice by 5 angstroms
menu item Select... Clear Selection- deselect the current selection
Command: reset pos1- restore the previously saved position
Command: repr stick- change everything to a stick representation
Command: ~label- remove any labels
menu item Tools... Viewing
(the left mouse button is used to scale and move the clipping planes in the SideView)
Command: color blue :a- color the nucleotides different colors
Command: color magenta :t
Command: color green :g
Command: color cyan :c
Command: surface- display a rotatable solid surface for the main part of the model
(the left mouse button is used to move the clipping planes in the SideView)
Command: ~surface- undisplay the surface
Command: surface ligand- display a rotatable solid surface for the ligand part of the model (netropsin)
Command: msms repr mesh- change surface representation from solid to mesh
Command: close 0- close the model
menu item Session... Exit- exit from the Chimera session