Part 6. Image settings
The following group of options deals with the image rendering,
including the program
Type of request
Animated pictures are accompanied with static slides that were used as frames for the animation. These slides are available for download both in PNG and TIFF formats of fixed size (the maximum available size is 1000x1000 pixels). Obviously, due to the nature of multi-frame animations, time required to produce animations is significantly longer than for the single slide requests. The file size and time needed to generate all frames for animation depends on the angle increment, range of the rotation angle, and the number of axes to be used for rotation (see Animation settings for details). Below, we demonstrate some options for the static slide rendering and animation requests with the rocking effect, using the same protein as in ligands rendering section (PDB id 1n9l).
Currently, POLYVIEW-3D utilizes two rendering programs, namely PyMol and RasMol. The latter is commonly used for its fast and reliable basic rendering. On the other hand, PyMol, although slower in some cases, offers a much wider array of rendering options, and can be used to produce truly impressive images, appropriate for papers, electronic presentations (e.g., PowerPoint slides) and other documents. For example, PyMol features smooth surface rendering, which can be optionally set up to be semi-transparent.
Using a protein/DNA complex as an example (PDB id 1k6o), we show the differences in rendering between these two programs with the same set of parameters. We would like to point out that, unfortunately, some options, such as the text labels that could be assigned to selected amino acid residues, are not available with PyMol rendering at present (RasMol, or post-processing of the images with graphics editors, can be used in this context as an alternative).
This option invokes the rendering of a macromolecular structure in the anaglyph stereo view mode. Red-blue or red-cyan 3D glasses are required to view the image in order to perceive the effect. It allows one to see a 3D structure in details even within a still image towards the better understanding of structural organization of a molecule. The option might be useful for educational purposes as well.
General image settings
This group of settings can be used to specify the
Background color may be set up using
the mouse over interactive color grid, which can be open
by clicking on the
Images shown below are of the same protein used as an example for
(PDB id 1n9l) in the
Overall structure view
section. First two images demonstrate the use of the size
and background color settings, whereas the last two
illustrate the use of the zooming option. The list of
residues located at the ligand binding site, and rendered
as blue sticks, was obtained using the option
Some complex renderings, with multiple settings to be tuned, may
require multiple submissions for the same query protein,
which can lead to a tedious trial and error process. In
particular, animation requests usually take much time to
process, which makes it difficult to refine them. To
facilitate this process, POLYVIEW-3D provides the
Last modified: Thu Feb 9 13:29:24 EST 2012