3. Visualize the DNA + dyes using VMD

This tutorial is part of a detailed guide on making an abstract scientific illustration. You can get all the files associated with the guide here.

VMD is a freeware that can downloaded here.

1. Open VMD and go to File -> New Molecule.

2. In the Molecule File Browser dialog box press Browse and open the DNA.pdb molecule file. Then press Load.

3. Do the same with all the dye molecules and the AV, however, make sure the 'Load files for:' is set to 'New Molecule' every time  The molecules are now listed in the VMD main window.

4. Now change the molecular representations. In the VMD main, go to Graphics -> Representations.

5. The visual representations of the individual molecule files are set in the 'Graphical Representations' dialog box. Start with selecting the DNA molecule from the pop-up list. Go to the Selections-tab and double-click backbone. This will make a visual representation of the DNA backbone without bases.
Then go to the 'Draw style' tab and set:
ColorID: 12: Opaque. 'Drawing Method': NewCartoon.

6. Next make the representations of the bases and exclude those that are in the background of the final image. Press 'Create Rep'. 
In the Selected Atoms edit box type 'all not resid 17 18 19 20....' followed by all the ID's of the residues that should be removed from the plot. These were identified manually. Set the Color and Drawing Style the same as the backbone.

7. Now set the representations of the dyes. First select Cy3_DNA.pdb. Set 'Selected Atoms' to all. In the 'Draw style' tab, set 'Coloring Method' to Element, Material to Opaque and 'Drawing Method' to DynamicBonds.
Do the same for the other dyes.

Note: you navigate the VMD graphics window by pressing R for rotation, S for zoom and T for translate.

8. The AV surface is visualized using the 'VolMap Tool' in VMD. In the Main window go to Extensions -> Analysis -> VolMap Tool.

9. In the 'VolMap Tool' dialog box set 'selection' to all and select the AV-molecule from the molecule-list. In the 'Output Destination' panel select Append to molecule: New. 
Press 'Create Map'. This will create the AV surface as shown below.

In the images above, the background color was set to white in the Graphics -> Colors dialog box from the VMD main window.

Save the final VMD visualization state called VMD_session.vmd. It is loaded into VMD using File -> Load Visualization State.

Finally, prepare a POV-Ray render file before going to the next step:

10. From the VMD main window, go to File -> Render.

11. In the dialog box, select POV-Ray 3.6 and specify filename.