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Clip 3 illustrates protein secondary structure ribbons, amino acid categories, and a few complex atom specifications. The input file contains galactose/glucose-binding protein complexed with glucose (2gbp 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.
Command: open 2gbp.pdb- open the input file
Command: chain @ca- simplify the display to an alpha-carbon trace of the protein
Command: linewidth 2- use thicker lines
Command: scale 2.2- increase the size (multiply by 2.2)
Command: colordef pink 1 .5 .7- define a new color named pink, with red, green, and blue components of 1.0, 0.5, and 0.7, respectively
Command: color pink- color the model using the new color
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: display :glc- display the glucose molecule bound to the protein
Command: color cyan :glc- color the glucose residue cyan
Command: repr cpk :glc- change the representation of glucose to CPK
Command: resrepr ribbon- display a flat secondary structure ribbon
Command: ~display @ca- undisplay the alpha-carbons
Command: resrepr sharp- display a thick ribbon with a rectangular cross-section
Command: resrepr smooth- display a thick ribbon with an ellipsoid cross-section
Command: resrepr none- undisplay the ribbon
menu item Extensions... Utilities... MainChain- display only protein backbone atoms (N, CA, C)
Command: display :glc- display the glucose molecule bound to the protein
menu item Select... Amino acid categories... Hydrophobic- select hydrophobic amino acids
Command: color white sel- color the selection white (sel, selected, or picked can be used in the command line to indicate selected atoms and bonds)
menu item Select... Amino acid categories... Negative- select negatively charged amino acids
Command: color red sel- color the selection red
menu item Select... Amino acid categories... Positive- select positively charged amino acids
Command: color blue sel- color the selection blue
*Note that the amino acid categories are easily customizable; assignments to existing categories may be changed, and new categories can be created.
menu item Select... Clear Selection- deselect the current selection
Command: color yellow :glc z<5 & @/color=red- color any red residues within 5 angstroms of the glucose yellow
Command: display @/color=yellow- display all atoms of the yellow residues
Command: repr bs @/color=yellow- change the representation of the yellow residues to ball-and-stick
menu item Tools... Viewing
(the left mouse button is used to scale and move the clipping planes within the SideView)
Ctrl-left mouse button is used to select a single atom from the screen
Command: label selected- label the selected atoms
Ctrl-left mouse button click away from any atoms can be used to clear the current selection
Command: stop- exit from Chimera (it is not necessary to close models first)