Marine Molecular Science
Visual Molecular Dyanmics: Modeling Tutorial Project
Download and install VMD
for your own coputer.
Get a protein PDB file to work with from the Protein Data Bank:
a protein name into the "Site Search" box. For now use 'cytochrome
download the PDB file for "1I6D", by clicking on the little
with the blue "down" arrow just to the right of the PDB accession
3: Start VMD. Then click "FILE-->NewMolecule" to open
Molecule browser. Select the 1I6D.pdb file and click LOAD.
click "GRAPHICS-->REPRESENTATIONS" to open the visualization
and set "Coloring Method" to STRUCTURE and Drawing Method to "NEW
4. Now we are going to select the heme group to display.
VMD, there are 3 variables you have to define for a display: a) what
atoms to display, how they should be drawn, and what color they should
1. click "Create Rep". This will make a copy of the current
representation command. You will now edit that copy.
2. In the Selected Atoms text box type "resname HEC" and hit enter.
3. Then change Coloring Method to "NAME" and Drawing Method to
"Licorice". Clicking the Bond Radius selector will make the
licorice stick drawing thicker or thiner.
Step 5. Now
we are going to select the Iron atom in the heme group.
1. Click Create Rep, and now you have another display command entry
that you will edit.
2. In the VMD MAIN window open the MOUSE menu and then check the
"Query" circle. Move the mouse into the DISPLAY window and click on the
green atom at the center of the heme group. The command/terminal window
will output the atom info for what you clicked on.
Fe atom is number 1,455 in the file, it is assigned to the residue name
HEC, the HEC has a residue ID of 101, and is grouped into Chain A. All
this information can be used to select and display different levels of
organization within a protein file.
3. In the Selected Atoms text box type "name FE", enter, then change
the Drawing Method to "VMD" and then adjust the Sphere Resolution to 20.
4. Go back to the MOUSE menu and de-select the Query option.
5. From the VMD Main window open the
FILE menu and select "Save State" to generate a file with all the
visualization steps saved. Put it in the same folder as the PDB file.
You can always return to this view by selecting "Load State".
Make Movie. . . . .
(Note: If you are using a Windows machine GO TO THE NEXT STEP)
For Linux, Unix, OS X . . . .
1. From the VMD Main window, open the
EXTENSIONS menu, then open the VISUALIZATIONS menu, then select
2. In Format, select the simplest output: animated GIF (In MS-Windows Version just use the default selection).
3. In Renderer, select the simplest/fastest option, screen
4. In Movie Settings, select ROTATE ABOUT
5. For Screen input then change Rotation angle = 360, Step =
2, duration = 20, and
click make movie. The final movie file will be located in the working
directory specified in the first line of the window.
6. Change the working directory to something
appropriate for your computer. All the temporary screen shot files will
be written to this location.
If all goes well, you should end up with something like this: