What is VMD?
VMD is a molecular visualization program for displaying molecular structures. It was first developed by researchers at UIUC, perhaps to visualize large biomolecules. However, it can be used to visualize normal molecules as well. Free download can be found on the VMD official website.
After opening a structure file in VMD and making all essential adjustments, the next thing before publishing it is to make a high-resolution image. One can do this in “File-Render”. There are several ways to do it.
The default rendering tool is “VMD OpenGL window”, which simply takes a snapshot of the displaying window. The resolution of the image is exactly how it looks like on the screen, which is okay-ish if you are visualizing a small molecule and you can enlarge the displaying window to make it medium-quality.
A much better one: Tachyon
The default rendering tool soon gets awkward when your molecule gets large: you screen is simply too small to enlarge the displaying window to a needed size if high-quality is desired. Another built-in rendering tool is Tachyon. Once selected, the “FILENAME” field will become “xxx.dat” and the “Render Command” field will change accordingly. Rendering using these settings generates a data file which can be furthermore refined to generate image of arbitrary resolution.
To do so, we need to first find where Tachyon is. On Mac OS, you can find it in the following path:
This command has several arguments that are relevant to making high-resolution images:
-format [image format]
-res [xres] [yres]
-aasamples [sample rate]
All of them are pretty self-explainary. My setting is something like
/Applications/VMD 1.9.3.app/Contents/vmd/tachyon_MACOSXX86 xxx.dat -aasamples 12 -format BMP -res 4096 3200 -o hr-image.bmp
This command generate a bmp image of 4096*3200 pixels, named “hr-image.bmp”.