I.
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Introduction
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| Rotate | Left Click |
| Scale | Shift + Left Click |
| Translate | Ctrl + Right Click |
| Measure Distance | Double click on 1st atom + double click on 2nd atom |
| Measure Angle | Double click on 1st atom + single click on 2nd atom + double click on 3rd atom |
| Measure Dihedral Angle | Same as above, but single click on 3rd atom + double click on 4th atom |
| Menu | Right Click |
Note: To change the measurement units, right click for menu, then select Measurements.
The first step to altering a molecule is to select the atoms in which changes
are to take place.
Clicking any of the preset atom groups under "Select" will highlight them
in a yellow glow.
This effect can be turned off by unchecking the "Selection Halos" box.
All atoms are selected by default. If you want to see the molecule without
halos, select "None."
A selection can be hidden from the screen with "Hide" and shown with "Show."
Note that halos still appear even after the atoms are hidden (unless the effect
is disabled).
To zoom in on the molecule, click on any of the zoom buttons, or use mouse
controls (Shift + Left Click).
"Center View" returns the scale to 100% and centers the molecule.
"Clear Measure" clears the measurement lines, angles, and
labels (see Mouse Controls).
"Reset All" returns the molecule to the original state (100% zoom,
centered, show all, wireframe bonds).
Allows for the searching of specific amino acids within the selected atoms.
Specifies the space each atom occupies. Default is "Off."
Specifies the bond thickness. Default is "Wireframe 0."
"van der Waals" draws a dotted representation of 100% Spacefill.
"Solvent-Accessible" only draws dots for exposed surfaces.
"Contours" shows convex points in yellow, concave points in red, and
saddle points in blue.
In order to see secondary structures, either "Mainchain" or "All"
must be selected.
It is possible that the molecule you are viewing does not have any secondary
structures.
The color of these structures may be chosen below.
Colors the selected atoms.
"None" returns the atoms to their original colors (O = red, N = blue, S =
yellow...etc).
It also colors any selected secondary structures gray.
"Color White" colors the selected atoms white.
"Color by Structure" gives alpha helices, beta sheets, turns, and loops
different colors.
"Color by Amino" colors the atoms by their amino acid membership.
"Color by Shape" differentially colors nucleotides as well as protein
residues.
For more information regarding colors, see
http://jmol.sourceforge.net/jscolors/
"Auto Spin" spins the molecule.
"Amino Acid Labels" gives a label to every selected atom.
"Show Hydrogens" allows display of hydrogen in the entire molecule,
regardless of what was selected.
"Hydrogen Bonds" shows hydrogen bonds (only in selected
portion).
"Disulfide Bonds" shows disulfide bonds (only in selected
portion).
"Ligand" shows the ligand by itself.
The rest of the first preset row displays ligand and mainchain under different
representations.
"Ligand Surface" shows the solvent-accessible surface for the ligand
inside the protein.
"Mainchain Surface" shows the solvent-accessible surface for the protein
mainchain with bound ligand.
"Sidechain Surface" shows the solvent-accessible surface for the protein
sidechain with bound ligand.
"Protein Surface" shows the solvent-accessible surface for the entire
protein with bound ligand.
"All Surfaces" shows the solvent-accessible surface for the protein
mainchain and bound ligand w/ surface.
"All Amino Acids" shows all the amino acids in the molecule.
Note: The mainchain, sidechain, protein, and all surfaces
presets are time intensive.
Jmol will not respond to input and may appear to freeze until calculations are
complete.
