If you’ve been reading in order, then you know that I keep throwing this “publication-quality images” phrase around. Well, what do you know, the “Generating Images” section will actually tell you how to make these images! Amazing. Once you’ve gotten the the screen to look how you want the image you wanted created to look, follow File → Render in the main menu. This brings up the File Render Controls menu (see the image below).

The File Render Controls window. The first option is 'Render the current scene using:' with Tachyon, internal, in-memory rendering selected. The next choice is 'Filename', and the name given is my-delightful-protein-system.tga. Next to this box is a Browse button. Finally, the 'Render command' is shown. This is usr slash bin slash open space percent s. The button next to it is 'Restore Default.' The 'Start Rendering' button is at the bottom.
The Render screen for image generation.

The first dropdown, Render the current scene using:, selects the image-quality type. If you’re just doing something super quick that’s kind of irrelevant, then it’s fine to save the file with the default Snapshot (VMD OpenGL window). If you’re going to want to use the image for a presentation, poster, or publication, however, then you’ll want to select Tachyon (internal, in-memory rendering). For a juxtaposition of these, see the next to figures. (We’ll get to why the colors are different at the end of this section.)

The protein is blue, yellow, and pink. The image is grainy.
Image generated with Snapshot (VMD OpenGL window).
The protein is mostly blue with some yellow and with flecks of pink. It appears to be of a high quality.
Image generated with Tachyon (internal, in-memory rendering).

The second dropdown is where you select the save location and the filename. For these images, keep the .tga extension; you can convert the .tga using Gimp or the UNIX convert command later. The final box shouldn’t be something you have to mess with at all, as it is the default option. Once you’re ready, hit Start Rendering.

Woohoo! You’ve saved a picture! Enjoy remaking it 73 more times because it wasn’t good yet. Oh, and a quick note: If you’re coloring specific sections of a protein (like with resid 1 to 23 and resid 95 to 293), then you will need to make sure that you don’t also have just protein selected; it’d need to be like protein not resid 1 to 23 and not resid 95 to 293. The reason why is because VMD cannot handle the layering in image creation, and your picture will look terrible (just revisit the images above).

Saving a High-Quality Image with Transparency

You can also save higher-quality images in VMD (with transparency!) using POVRay. It needs to be installed separately.

The ray-tracers work well with the AO-type and diffuse materials. Select POV-Ray in the render window. The number version (likely 3.6) is the earliest version you can use. For the render command, you need the +UA option to make it transparent. The image renders using the width and height of the on-screen window. Because you want a higher quality image, you can add a 0 after the height and width. It will take a bit more time (almost a full minute for a 450 residue protein), but it looks much better than 300 DPI.

When you specify the file command, you may wish to leave off the .pov extension. That way, when it renders, the final image file isn’t named like .pov.tga.

  • For TGA output: povray +W%w0 +H%h0 -I%s -O%s.tga +X +A +FT +UA
  • For PNG output: povray +W%w0 +H%h0 -I%s -O%s.png +X +A +FN +UA