POLYVIEW-3D Tutorial

Part 6. Image settings

The following group of options deals with the image rendering, including the program (RasMol vs. PyMol) employed to generate the requested image, and the type of request, such as static image or animation. Additionally, one can specify the image size, background color, and zoom of the structure view. We also describe here the Preview option, which allows one to quickly refine image settings, before requesting some time-consuming renderings, such as animations.

Type of request

The Type of request option defines the type of image to be generated. Single slides represent a snapshot of the structure at a given projection. Static images are initially generated in the PNG format, and can be automatically converted to the TIFF format with a pre-specified DPI resolution. On the other hand, the animated images are produced in the GIF format of a size specified in the General image settings section. Each submission to the POLYVIEW-3D server opens a separate window for further processing of the resulting images.

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).

Single slide request
(Default option)
Animation request
(Rocking effect)
Click on respective image to see options used for its rendering.

Rendering program

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).

PyMol rendering
(Default option)
RasMol rendering
Click on respective image to see options used for its rendering.

Stereo view

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.

Still image Animation
Click on respective image to see options used for its rendering.

General image settings

This group of settings can be used to specify the image size, its background color, and the scaling of the structure. Images are always generated with the same horizontal and vertical dimensions, with their size defined in pixels. In case of the animation requests, the image size option affects the size of animated GIF only, whereas all static slides used as frames for animation are available for download in the largest available size (1000x1000 pixels). NOTE: If the option High-Def slides is checked, then frames are generated using the 2000x2000 pixel size.

Background color may be set up using the mouse over interactive color grid, which can be open by clicking on the Pick color hyperlink. To cancel the color selection, simply click outside the area of the color grid. The default background color, which may be changed easily as well, is set to white.

Furthermore, the zoom option may be used to bring a structural element of interest to a closer view, e.g., to show in detail a ligand binding site. This option works best in conjunction with the Center of view setting, included within the Overall structure view settings. Value of the scaling can be specified in the text field, selected from the pre-defined list, or set using the same Jmol-based utility as described in previous sections.

Images shown below are of the same protein used as an example for ligand rendering (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 Find pockets by CASTp from the Protein structure annotation field set.

Image size 300px, white background
(Default option)
Image size 150px, sky blue background
Zoom 100%
(Default option)
Zoom 175%
Click on respective image to see options used for its rendering.

Image preview

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 Preview option that can be used to quickly generate a scaled-down version of the final image. In case of animation requests, the Preview option generates the first frame only, reducing significantly the time needed for adjustment and tuning of the rendering.

Last modified: Thu Feb 9 13:29:24 EST 2012

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