When you click on any of the molecules listed below, a black window
containing the molecule will appear in your browser. You should be able to see and
rotate your molecule by placing the mouse cursor in the black window and using the
commands given below:
Hold down the left mouse button and move the mouse around to rotate
the molecule
Hold down both the shift key and the left mouse button, then move the
mouse up to zoom out or down to zoom = in
Hold down both the control button and the right mouse button, then
move the mouse to translate the molecule on the xy axes
In addition, you can change the rendering of the molecule by moving
the mouse cursor within the area of the molecule. Click and hold the right mouse
button, and a new menu will appear that will allow additional manipulation of the
molecule. Experiment with these commands.
More Sophisticated Ways to
Change the Display
right click on the actual molecule, and a new selection of commands
will pop up. You can then select an appropriate command with a click of the left mouse
button. A check will apear by command indicating that you have selected it. The important
options are shown below along with a brief comment in red about the use of some of them.
File
Save Molecule As - it would
seem like you could save a rendering of your molecule this way but it doesn't seem to work
for me.
Edit
Copy Chime Script - This
might be useful if you went to someones else's Chime page (several are referenced below)
and see something particularly interesting for which you would like to use the commands.
You could then copy the Chime script and paste it into your page1.html document from the
HTML editor of Front Page and see if it works for you. It's worth a try, but if you are
trying to copy a bunch of Java code, I don't think it will work.
Rotation
Display - Can't do
much more than what's available with buttons from the command window.
Wire
Stick
Ball
Space Fill
Van der Waals Radii
Backbone
Ribbon
Strands
Cartoon
Options
Display Hydrogens - Very
useful since X-Ray structures don't have hydrogens since they don't have enough electrons
to diffract x-rays. However, by placing them in, H bonds make more sense since they will
come from a H on a N or O, and not from an N or O to a N or O.
Display Hydrogen Bonds
Display Disulfide Bridges - Useful
to see how many and where the disulfides are
Dot Surface
Van der Waals
Conally Surface - This is
the water-accessible surface of the molecule, as we encountered in Quanta/Charmm.
Labels
Sprout Hydrogens - same as
display H's above, I think.
Stereo Display - Believe it
or not, you can see these images in 3D if you can cross you eyes. This command splits the
image into two which if viewed with crossed eyes, or flayed eye, will result in the
appearance of a 3D image.
Color -allows you
to color code by something other than the originary red for O, blue for N, white for H,
etc, CPK color system.
Monochrome
CPK
Amino Acid
Shapely
Group
Chain
Temperature
Structure
Select - This is
the most imporant of all these commands because it allows you to select only certain parts
of the display for showing. You will have to experiment on your own with this, but just
looking at the commands allows you to see the possibilities. Notice that you can select
all, invert a selection (i.e. show everything you didn't select), or hide a selection.
Select All
Mouse Click Action
Highlight Selection - this
must be clicked to see the results of your selection process
Invert Selection
Hide
Hide Selected
Hide Not Selected
Change Color
(to a whole series of possilbe colors)
Modify Selection Mode
Replace Selection
Add to Selection
Add common to Selection
Subtract from Selection
Chain
A
B
Residue
(alll the amino acids in a file are listed)
Atom
(select different atoms - alpha C, H, O's etc)
Hydrogen
Nonhydrogen
Hetero
Hetero
Solvent
Nonsolvent
Water
Ions - this should be great
for displaying a bound ion
Ligand - this should be
great for displaying a bound ligand
Protein
Protein
Amino
Large
Medium
Small
Alpha Carbon
Backbone
Bonded
Buried
Helix
Sheet
Side Chain
Surface
Turn
Acidic - great to show
areas of localized charge density
Acyclic
Aliphatic
Aromatic
Basic - great to show areas
of localized charge density
Charged
Cyclic
Cystine (disulfide bond)
Hydrophobic - great to show
areas of localized hydrophobicity
Neutral
Polar
Nucleic Acid
Nucleic
DNA
Bacbone
AT
CG
Purine
Pyrimidine
Display List
Create Molecular Surface - This
takes a while to generate, and doesn't offer a significant advantage over van der Waals or
Conolly surfaces.
Color
Electrostatic Potential - Should
be great to show how differences between regions of net postive charge and regions of net
negative charge give rise to a net electrostatic potential
Lipophilic Potential - Should
be great to show how differences between regions of net high hydropathy and regions of net
low hydropathy give rise to net hydrophobic moment