MAST-634  Marine Molecular Science

Visual Molecular Dyanmics:  Modeling Tutorial Project



STEP 1:  Download and install  VMD  for your own coputer.






STEP 2:  Get a protein PDB file to work with from the Protein Data Bank:

RCBShome

Enter a protein name into the "Site Search" box. For now use 'cytochrome f'.  
And then download the PDB file for  "1I6D", by clicking on the little icon with the blue "down" arrow just to the right of the PDB accession number "1I6D".




STEP 3:  Start VMD. Then click "FILE-->NewMolecule" to open the Molecule browser.  Select the 1I6D.pdb file and click LOAD. Then click "GRAPHICS-->REPRESENTATIONS" to open the visualization window and set "Coloring Method" to STRUCTURE and Drawing Method to "NEW CARTOON".



STEP 4.  Now we are going to select the heme group to display.  In 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 have.
    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.

Basically, the 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".


STEP 6:  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 MovieMaker.
    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 capture.
    4.  In Movie Settings, select ROTATE ABOUT Y-AXIS.
    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.



7. If all goes well, you should end up with something like this:


8. But . . . if you want to increase the quality of the animation, you can try different rendering protocols, different Formats (mpeg), set the trajectory step down to 1, increase the movie duration. All these things will add to the file size of the final animation and the processing time needed to generate it.


LAST STEP FOR WINDOWS MACHINES:  
      If you are using a Windows machine to do this, your only option for generating a movie file directly from VMD is to purchase and install a copy of VideoMach.  Alternatively you could just use VMD's MovieMaker to generate all the BMP files, then get a utility to convert the BMPs to GIF format, then use the free Microsoft GIF Animator to compile those frames into an animation.


But I don't want this to become an exercise in computer gymnastics. So . . . .

. . . .   Email your saved VMD state files to me and I will generate the mpeg for you.