Zoom and Rotate
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| Figure 1: View of staggered ethane ( ethane-staggered-3-21G.log) to practice zooming and rotating. To make live click on the image. |
To zoom the image in Jmol put the mouse cursor over the Jmol image then hold down the shift key and the left mouse button while dragging down to zoom in or up to zoom out. For some mice the scroll wheel also works. Fixed zoom levels are also accessible in the pull-down menus of the application (Display > Zoom > XXX%) and the pop-up menu in both the application and the web applet (Right mouse button, control-click on one button mice, > Zoom > XXX%). You can try this in an open Jmol application or by clicking the link in figure 1 to convert it to a live Jmol display.
To rotate the image in Jmol put the mouse cursor over the Jmol image then hold down the left mouse button while dragging the cursor around. You can try this in an open Jmol application or by clicking the link in figure 1 to convert it to a live Jmol display.
Spinning
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| Figure 1: View of staggered ethane ( ethane-staggered-3-21G.log) to practice setting up spinning. To make live click on the image. |
To startspinning the molecule using the default spin settings use the pop-up menu in both the application and the applet (Right mouse button, control-click on one button mice, > Spin > On). You can try this in an open Jmol application or by clicking the link in figure 2 to convert it to a live Jmol display.
To stop the spinning of the molecule use the pop-up menu again (Right mouse button, control-click on one button mice, > Spin > Off). You can try this in an open Jmol application or by clicking the link in figure 2 to convert it to a live Jmol display.
To have spinning about axes other than Y select the rate (degrees per step) for rotation about the X or Z axis. Use the pop-up menu (Right mouse button > Spin > Set X (Y or Z) Rate > XX). The default Y rate is 30 and 0 for X and Z rates. The axes are screen axes: Y is up-down, X is left-right, Z is in-out of the screen. You can try this in an open Jmol application or by clicking the link in figure 2 to convert it to a live Jmol display.Atom and Bond Size
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| Figure 3: View of staggered ethane ( ethane-staggered-3-21G.log) to practice changing atom and bond size. To make live click on the image. |
To change the atom size use the pull-down menus of the application or the pop-up menu in the application and the applet. Fixed percentages of the van der Waals radius are available. Pull-down menu (Display > Atom > XXX%). Pop-up menu (Right mouse button, control click on one button mice, > Style > Atoms > XXX %). You can try this in an open Jmol application or by clicking the link in figure 3 to convert it to a live Jmol display.
To change the bond size use the pull-down menus of the application or the pop-up menu in the application and the applet. Pull-down menu (Display > Bond > XXX). Pop-up menu (Right mouse button > Style > Bonds > XXX). You can also quickly select some common combinations of atom size and bond from the pop-up menu (Right mouse button > Style > Scheme > XXX). The options are: CPK spacefill; Ball and Stick; Sticks; Wireframe. Wireframe is also available in the pull-down display menu in the Bond submenu. You can try this in an open Jmol application or by clicking the link in figure 3 to convert it to a live Jmol display.
Making and Displaying Measurements
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| Figure 4: View of staggered ethane ( ethane-staggered-3-21G.log) to practice making measurements on. To make live click on the image. C-H bond lengths 0.108 nm, H–C–H angle 108.1 degrees, H–C–C–H dihedral angle 60.0 degrees. |
To measure bond lengths double click on the first atom. The cursor will convert to a "+". Move the cursor to the second atom. Double click on the second atom. The distance between the atoms will be shown. Using the pop-up menu you can choose between units of nm, angstroms and pm (Right mouse button, control-click on one button mice > Measurement > XXX). You can also display all the bond lengths at once using the command line. The command is: "measure allconnected (*)(*)" See Using Commands in the Script Window.
To measure bond angles double click on the first atom. The cursor will convert to a "+". Move the cursor to the second atom. Click ONCE only on the second atom. Move to the third atom and double click on it. The angle made by these three atoms will be displayed.
To measure dihedral angles (the angle between two bonds on atoms separated by one bond, or more generally the angle between two planes defined by four selected atoms) double click on the first atom. The cursor will convert to a "+". Move to the second atom and click once. Move to the third atom and click once. Move to the fourth atom and double click. This will display the angle made by the plane defined by atoms 1, 2 & 3 and the plane defined by atoms 2, 3 & 4.
Cartoon Views of Biomolecules
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Figure 5:
DNA & LAC repressor binding region (1lcd.pdb
from the protein
data bank )
to practice cartoon rendering on. To make live click on the image. |
To make cartoon views of biomolecules use the pop-up menu. There are a large number of options.
First, select the part of the structure you want to work with. Use the pop-up menu (Right mouse button, control-click on one button mice, > Select > choose among the options.)
Second select the desired representation. Use the pop-up menu (Right mouse button > Style > Scheme or Structure > XXX).
Some things to try with the model in Figure 5:
- Render the DNA as a violet cartoon:
- select DNA (Right mouse button > Select > Nucleic > All).
- Render as cartoon (Right mouse button > Style > Scheme > Cartoon).
- Make the cartoon violet (Right mouse button > Color > Structure > Cartoon > Violet).
- Render the protein as space filling with the polar groups in red.
- select the protein (Right mouse button > Select > Protein > All).
- Render as spacefilling (Right mouse button > Style > Scheme > CPK spacefill).
- Make the whole protein cyan (Right mouse button > Color > Atom > Cyan).
- Make the polar residues red (Right mouse button > Select > Protein > Polar Residues). Then (Right mouse button > Color > Atom > Red).
- Render the protein as a cartoon.
- select the protein (Right mouse button > Select > Protein > All).
- Render as cartoon (Right mouse button > Style > Scheme > Cartoon).