Zusammen

If you've ever wanted to create high resolution images from protein-ligand complexes, today's stop on our continuing tour of free chemistry databases and web services may be worth your time. Polyview 3D lets you set up and render publication-quality images from protein X-ray crystal structure poses. Unlike other tools, Polyview 3D requires no installation of software and can be used more or less immediately from any computer.

From the tutorial:

By integrating the web technology with state-of-the-art software for macromolecular visualization, POLYVIEW-3D enables versatile structural and functional annotations coupled with publication quality structure rendering. In addition to static pictures, high quality animated images for electronic resources such as PowerPoint or Web-sites can be easily generated with POLYVIEW-3D as well.

Rendering starts by choosing a structure. Polyview 3D can load structures either from the Protein Data Bank or from your local hard drive. For example, I selected "1mba", (Aplysia limacina myoglobin) by entering "1mba" into the field labeled "PDB ID".

Next, choose your pose. After clicking "View by Jmol / Set orientation", a popup window appeared containing the structure which could be zoomed, panned, and rotated. After selecting the pose I wanted, I clicked the "set and close" button.

At this point, a number of visual effects can be applied, such as coloring, applying surfaces, and adding annotations. When making changes, the effects of these settings can be previewed.

When all effects have been applied, the image can be rendered. A number of formats are available including png, jpg, and tiff. Images can be as large as 1000x1000 pixels. Clicking on the "Submit" link submits a job to the server.

Rendering took less than five seconds in my tests; periodic page refreshing can be used to find out when the job is done, or an automatic message will appear every 60 seconds.

There are some technical issues to watch out for. Very long load times (>5 minutes) for the Jmol applet were observed on two different systems - one Mac and one Linux. Fortunately, after the first load, subsequent loads were nearly instantaneous.

The resolution of the images produced by Polyview 3D was quite high. The online gallery gives a good idea of what's possible.

Polyview 3D's interface can take some getting used to. For example, it really doesn't matter how you configure the Jmol view of your structure - the way it gets rendered is determined by the settings you apply after orienting. This is not a what-you-see-is-what-you-get process and can takes some trial and error to get right. Additionally, the all-in-one submission form can be difficult to navigate due to the the need to frequently scroll up and down the page to adjust settings.

Polyview 3D offers a very interesting feature that deserves more attention. When you're done creating an image, you have the option to save it to the gallery. For example, the image I created is available here. But this idea can be taken much further. For example, offer individual user accounts that store not just raster images, but all of the parameters needed to regenerate the image. Allow users to share their parameters with other users, derive entirely new images, and discover users with interests in similar structures or imaging techniques.

It's not always easy or convenient to get modeling software installed and configured on a computer. Polyview 3D makes a good choice for anyone looking for a convent way to get high-quality images of protein structures.

Kudos

• Interactive structure posing.
• High quality image output.
• Zero-installation.
• Images can be saved on server and shared with community.

Ideas for Improvement

• Reduce initial Jmol deployment time to 20 seconds or less.
• To the extent possible, use settings from Jmol to to enable better WYSIWYG experience (for example - surfaces).
• Simplify the user interface with tabs to group related rendering options.
• Expand capabilities for sharing.