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Clip 2 illustrates independent movement of models, color editing, and use of an extension. The input files contain two halves of a leucine zipper and were derived from 1zik 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...
(change file type to Mol2, choose and open zika.mol2)
Command: open zikb.mol2- open the other half of the leucine zipper using the command line
Command: linewidth 2- use thicker lines
Command: scale 1.5- increase the size (multiply by 1.5)
Command: color green #0- color model 0 (containing zika.mol2) green
Command: color yellow #1- color model 1 (containing zikb.mol2) yellow
Command: color magenta #0:leu- color leucines in model 0 magenta
Command: color cyan #1:leu- color leucines in model 1 cyan
Command: surface- display rotatable solid surface
the left mouse button is used for rotation and the middle mouse button is used for translation
menu item Tools... Viewing
(the left mouse button is used to scale and move the clipping planes within the SideView)
each model can be moved independently after turning off the active status of the other; clicking the small boxes at the bottom of the window toggles between on and off
Command: reset- restore the position the molecules were in at the beginning of the session
menu item Tools... Color
(click the square next to Opacity to allow creation of transparent colors)
the sliders for red, green, blue and opacity components are adjusted to create a transparent rose (0.6 0.3 0.3 0.3), a transparent periwinkle (0.3 0.3 1.0 0.3), and an opaque pink (1.0 0.3 1.0 1.0); each color is saved into the palette by drag-and-drop
Command: color byatom- color atoms by element; note that the surface corresponding to the atoms is colored accordingly
Command: color colorpanel,s- color the surface only (not the atoms) the active colorpanel color (opaque pink)
doubleclick on rose in palette to make that the active colorpanel color
Command: color colorpanel,s- color the surface the active colorpanel color (transparent rose)
doubleclick on perwinkle in palette to make that the active colorpanel color
Command: color colorpanel,s #1- color the surface of model 1 only the active colorpanel color (transparent periwinkle)
close the Color Editor
(the left mouse button is used to scale and move the clipping planes within the SideView)
Command: ~surface- undisplay surface
menu item Extensions... Utilities... FindHBond- start the extension FindHBond; click box indicating that H-bonds not meeting stringent criteria should be colored differently; hit OK to start the calculation
Ctrl-left mouse button is used to select a single atom from the screen; Shift-Ctrl-left mouse button is used to add another single atom to the selection without deselecting the first
Command: distance selected- show a dashed line and the distance between the two selected atoms
Command: repr bs selected- change the representation of the two selected atoms to ball-and-stick
Ctrl-left mouse button click away from any atoms can be used to clear the current selection
Command: ~distance- undisplay the distance measurement
Command: close all- close all open models
Command: stop- exit from the Chimera session