5.1.6
Tube
Tube draws a spline curve that goes through all the “Carbon-alpha” (CA) atoms in the molecule.
The spline curve is drawn as a series of cylinders.
5.1.7
Trace
Trace draws cylinders connecting the “Carbon-alpha” (CA) atoms in the molecule. This is similar
to Tube, except the atoms are directly connected by cylinders, not by a smooth spline.
5.2
Coloring Methods
JMV implements a variety of ways to color the molecule. To change the coloring method, select
“Color by” from the “View menu”, and select one of the choices. The choices are:
Style
Description
Name
Each atom type is assigned a different color. These colors are:
Carbon: Cyan
Hydrogen: White
Oxygen: Red
Nitrogen: Blue
Sulfur: Yellow
Phosphorus: Tan
Zinc: Silver
Other: Green
Index
The pdb file assigns each atom a unique index identifier. In the Index color scheme, JMV
creates a color gradient that creates a smooth color transition going through each atom, in
order of their index numbers.
Resname
In the pdb file, each atom belongs to a certain residue.The Resname color scheme assigns a
color to each Residue Name (based on the gradient), and colors each residue with the given
color.
Chain
In the pdb file, each atom belongs to a certain Chain. The Chain color scheme assigns a
color to each Chain (based on the gradient), and colors each chain with the given color.
Segment
In the pdb file, each atom belongs to a certain Segment. The Segment color scheme assigns
a color to each Segment (based on the gradient), and colors each segment with the given
color.
Structure
Certain series of atoms may have a “structure” associated with them. If these structures
are written n the pdb file, JMV can color the molecule by structure. The structures and
their colors are:
No structure specified: White
Helix: Red
Turn: Green
Sheet: Blue
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