Making Molecular Images

Here are some tips on making nice images from some of your molecular simulations.

First learn about Image Quality!

Jmol

This is a nice open-source program that I use frequently. You can get the program here. Once you have the program working follow these steps.

1. Load the coordinates of the system (usually a .xyz file). Click File then Open.
2. Change the background color to white. Black is not a good background color for a good looking image! Right-click the model and choose Color then Background. Pick White.
3. Rotate, zoom, and move the image around as needed to get what you want. I also turn off Perspective Depth since it distorts your image. Choose Display then unclick Perspective Depth. You can also move to pre-defined views by clicking View then one of the options.
4. You can choose File then Export/Export Image, but these images may not be the best quality. There are two ways to get high-quality images discussed below.
   • Click File/Export/Render in Pov-Ray which will create a .pov file. This file can be used in povray to make truly beautiful images. Povray essentially takes a bunch of commands (like draw circle, cylinder, etc.) in the .pov file and draws pictures. See here for some amazing pictures. With the .pov file you created in Jmol you can make some high-resolution images. You'll have to pick the resolution of the drawn (or rendered picture in povray language) in povray and it can be tricky, but can create great stuff.
   • An easier way is to click File/Console in Jmol. This will open up a box where you can type commands. The following command will create a png image named test.png in the folder of Jmol with resolution 3200 by 2000, or 3200 pixels in width and 2000 pixels in height.

write image 3200 2000 "test.png"

Editing an Image

Sometimes you may need to edit an image to add or delete details. See for example the bottom image on Deskins Tips on Tables and Charts where a label has been added. Or you may wish to combine several images together. You'll need some image editing software to do this.

1. First learn about layers. They will make editing an image so much easier. Basically the layers are like pieces of transparent paper stacked on top of each other and whatever is written or shown on the layers will be shown as long as it isn't covered by a more top layer. For instance, the bottom layer may be a picture of a molecule. The second layer may be some text. The third layer may be some arrows or boxes. All of these combined will make a final image with arrow or boxes on top of text which is on top of the picture.

2. Use good software. The default "paint" program in Windows can edit images, but it really is too simple for good image editing. Adobe Photoshop is a professional program for editing/creating images, but can be complicated and does take time to learn. Gimp is a free Photoshop clone. I like Paint.net which is easier than Photoshop or Gimp.