ProteinShader Tutorials  

Style Options

When a protein structure is first loaded from a Protein Data Bank file, ProteinShader displays it as a pen-and-ink style drawing using ribbons and tubes to represent the backbone of each polypeptide chain. Alpha-helices are drawn as tubes, while beta-strands and general loop regions are drawn as ribbons. To emphasize regions of protein secondary structure, alpha-helices and beta-strands are drawn with a larger tube radius or ribbon width than loops. The Style menu above the canvas can be used to change the cartoon to tubes only, ribbons only, a combination of ribbons and tubes, or to an atom-style display: space filling (spheres), balls and sticks (spheres and cylinders), or sticks (cylinders).

The appearance of cartoon or atom-style displays can be modified extensively with the retractable control panel on the right side of the canvas. This tutorial will use the proteins shown below to help familiarize the user with the control panel and its interchangeable modifier panels. The Saving Images section at the bottom of this page gives advice on saving an image to a file and on using the antialising control panel to improve image quality.

Saving Images

The images on the tutorial pages were saved as PNG (Portable Network Graphics, www.libpng.org/pub/png) or JPEG (Joint Photographic Experts Group, www.jpeg.org) files by using the Export Image submenu of the File menu above the canvas. For the images produced by the ProteinShader program, the PNG format usually produces the best images because it uses lossless compression. The JPEG format, which is lossy compression, generally produces files about four times smaller, although the exact difference depends a great deal on the complexity of the image. However, the JPEG images sometimes have minor artifacts such as a little splotchiness where a color is very gradually changing shade across a surface. In general, it is a good idea to save images in both PNG and JPEG formats, and then go with the smaller JPEG image only if the quality is not too much different than the PNG file.

Most of the original images for the tutorial pages were saved at a size of a little over 600 by 600 pixels, and in all cases the Antialiasing subpanel was used to smooth out any jagged edges. The maximum of jittering 16 times was used, but for most images jittering 5 or 6 times is all that is needed, and increasing the jitter beyond that does not seem to make any difference on a monitor with 72 pixels per inch resolution. When images needed to be reduced in size (such as the thumbnails further above), the free GIMP (GNU Image Reduction Program, www.gimp.org) was used, and the minimized images were saved with cubic filtering (best quality).

The Export Image submenu of the File menu also has an "Invisible Canvas PNG..." option that allows PNG files to be saved with a transparent background. An image file with a transparent background can be useful for displaying images on a web page where a particular background color is in use. If the page background color is changed, an image with a transparent background does not need to be redone to make its background match the page. For an example look at the top of this page.

The ability to save a GIF (Graphics Interchange Format, en.wikipedia.org/wiki/GIF) image has also been added to the Export Image submenu. However, for static screenshots, GIF is usually less desirable than PNG or JPEG images because GIF only supports a table of 256 colors, whereas PNG or JPEG support millions of colors. The only reason for adding GIF is that a future version of the ProteinShader program will likely use GIF to save small animations suitable for posting on a web site (PNG and JPEG do not support animations).