Please give me feedback:
1. Get Rasmol.
download the program and install it.
2. You need to get the PDB file of the molecule you want to view. Go to Molecules R US
This site is worth exploring, it has a lot more than PDB files. You can even configure Netscape to open a file directly in RasMol, plus get a couple of other useful viewers. But for the moment, let's find the file for FN7-10.
3. Enter "fibronectin" in the search. This brings up a dozen files with a brief description. Some are bits of fibronectin, others are FN-III domains from other proteins. The file for FN7-10 is 1fnf. Download it and have it saved as a text file.
4. Start RasMol and Open the file 1fnf. The molecule is displayed.
A. Under Display you can choose several options - wireframe is the default, showing all the atoms as sticks. Probably better for initial view and orientation is Ribbons or Spacefill. Also go to Options and get rid of Hetero and Hydrogen atoms.
B. Rotating and moving the molecule:
C. Do you want to find out what a particular atom is? Get "Command line" under windows. Make this screen smaller and move it to the bottom of the main screen, so a couple of lines are below it. Click on the main screen to bring it to the front (can you still see a couple of command lines?). Now, to identify any atom, click on it. You will see it identified on the command line (e.g., rotate the molecule until you can see a large flat plate sticking out of domain 10. This should be the RGD loop. Click on this loop and you should be able to identify the atoms in arg 1493 gly asp).
D. Select and color. Choose spacefill, and then give each domain a separate color. Type
E. If you now want to change the display of the whole molecule (to ribbons, wireframe) you first need to type "select all."
F. You can color specific amino acids, e.g., all charged residues.
G. Some structures come with multiple subunits, labeled A, B, C... You can select each subunit, but it's not the obvious way.
H. Note that with the UCB version you can load up to four molecules at once. They will all be at the same scale. Select one by clicking on it, or in the Molecules Window. (Check out the Molecules window, it has some goodies.) To determine the distance between two atoms, select the distance icon in the Molecules window, then go back to your molecule and click on one and then the other atom. The distance will be displayed on the main screen but may be hard to read. It is also given in the Command line.
I. You can save the sample as a PICT file or other format. First it is helpful to get rid of the black background, it looks ugly on a printout.
Type the command line> set background white
Then go to the Export window, save as PICT or other. Open the file in Photoshop. The image has pretty poor contrast, which you can improve enormously by Image/Adjust/Contrast. Best effect is to adjust contrast to +60-70% (you can achieve similar effect by adjusting levels - you might want to experiment). If you save as a PICT file you can then use Canvas to add labels; labels in Canvas can be moved around and changed much more easily than in Photoshop. Hint: chose the font Helvetica, not Geneva, so sizes and spacing are the same on the screen and print.
J. You can also save the RasMol data to return to a particular view. Let's say you have laboriously colored certain amino acids, and precisely oriented the view (unfortunately it doesn't seem to work with more than one molecule). You can save this view to return to later.
Type the command line >save script filename
This will save a "script" file with all information RasMol needs to duplicate the view. The file will be in the RasMol folder. To return to this view, first open the PDB file for the molecule, then
Type the command line >script filename