1) Find a molecule using something like molecules R Us
2) Save molecule to your disk by right clicking on the molecule
(hold down mouse button on Mac)
Choose
File, Save Molecule as
things will go smoother if you name the
molecule with small letters and no spaces and end it with
.pdb
3) Drag molecule to the Class Drop
1) Create a home page folder in First Class with File | Open | Home Page
2) Recreate in your FirstClass Home Page folder the elements found
in Tools | student
homepage
these include an index.html file
and a folder named chem222, inside the
chem222 folder is a file called
chem222.html
pay attention to capitalization (none) and spaces (none)
3) To move the two html files from tools to your Home Page folder you will need to first drag them to your desktop. They can then be dragged or uploaded to the Home Page folder.
1) copy the file chem222.html to your disk
2) open the file with Claris Home Page
3) select the plug-in ( the big square ) and open the object editor (the icon that looks like a wrench on the tool bar) [alternatively with a pc, you can right click on the plug-in and select plug-in object editor]
4)The location input box will have the address of the molecule; at
the moment it will say:
http://www.wellesley.edu/Chemistry/chem227/molecules/znfing.pdb
you will want to edit it to change
znfing.pdb to the name you gave your
protein, the rest of the address
http://www.wellesley.edu/Chemistry/chem227/molecules/
shouldn't be changed
5) Add any text you would like to the page, such as a title identifying the protein, and if you wish you can say why you choose it or something you may know about it.
6) save chem222.html to your drive
7) get rid of the old version of chem222.html in your FirstClass folder and replace it with the new version
8) check that it worked by going to
http://www.wellesley.edu/Chemistry/chem227/misc/studentspages.htm
Once you have your molecule up and running display it in a format other than wireframe (the default).
1) Open the chem222.html file for editing with Claris HomePage as above and open the object editor for the plug-in as before.
2) Towards the top of the editor is a choice called Extended, select it to open an input box called Extra HTML Attributes
4) enter in the input box: display3D= ribbons
ribbons is not the only option you can instead specify: backbone, ball&stick, cartoons, spacefill, sticks, strands or wireframe
Edit the input box as above, leave the
display3D=
whatever intact, insert a space and then
enter
color3d= structure
other color choices you can use instead
of structure include:
chain each
subunit is a different color
cpk each type of atom is a different
color C=grey. O=red N=blue etc.
group
colors change along the length of the
molecule
monochrome
shapely colored by amino acids
temperature
crystalographic motion
user
Open chem222.html for editing in
Claris. Set the blinking cursor (click) on where you want the button
to be.
change the editing mode by selecting
View, Edit HTML
Source (alternatively click the button that has
</> on it)
Add the following text: <EMBED SRC=""
WIDTH=15 HEIGHT=15 type="application/x-spt" button=push
>
Return to the original editing mode by selecting
View, Edit
Page (or the button with a fat pencil on it)
You can add commands to the buttons the same way you did to the
molecule via the Extended input box of the object editor.
Trouble shooting: the display3d and color3d commands don't seem to work with the buttons, so you will need to use script commands. It may also be necessary to add the text target = moleculename to the extended html input box where moleculename can be anyname you choose. In addition, you may also need to add name = moleculename to the extended html of the molecule.
for those who wish to move ahead on their own here is a complete list of the CHIME Embed options.