| DS ViewerPro |
DS ViewerPro helps you understand molecular structure, communicate chemical information, and produce more effective reports and presentations. It brings high quality molecular visualization to affordable desktop computers. Computational chemists, experimentalists, researchers, educators, and students can use one tool to visualize and communicate chemical information.
DS ViewerPro allows you to rotate, translate, scale, and label 3D graphical models of molecules, macromolecules, and crystals. You can view these models in a wide variety of informative graphical representations. You control the model display type, surface representation, labeling, color scheme, lighting, and other details of the molecule's representation and environment. With the appropriate hardware installed on your computer, molecules can also be visualized in stereo.
DS ViewerPro has a full complement of molecular sketching tools and commands. You can sketch with the sketch, ring, and chain tools, add hydrogens, modify bond and atom types, cut and paste atoms or groups of atoms or models, and add a variety of labels and monitors, among other things.
The most commonly used file formats are available to you with DS ViewerPro; you can open PDB, MOL, CSD, MOL2, SMI, and XYZ formatted files, plus a wide variety of Accelrys formats.
DS ViewerPro's MSV files contain not only molecular and atomic information, but also such information as display styles, the current rotation, and labels, which are not generally supported in the usual text file formats.
You can choose to have DS ViewerPro automatically add hydrogens, clean a model's conformation, identify aromatic bonds, convert 2D models to 3D, calculate charges, or identify secondary structure when opening PDB files.
With DS ViewerPro you can export a variety of graphic and file formats to be used with other scientific applications or publishing packages. You can also place active images in other OLE-compliant software applications such as Microsoft Word, Excel, or PowerPoint. These embedded images can then be edited from within the target application. For instance, you can embed a molecule in a report in Microsoft Word and your colleagues can rotate the molecule to suit their own viewing needs.
An animation can be created by opening a file containing multiple molecules, for example, an MDL SD file containing multiple molecules, or an XYZ file containing multiple molecules.
Internet/intranet
You can use DS ViewerPro as a helper application for Web browsers, so you can use the World Wide Web and your browser to transfer and view chemical information across the Internet or an intranet.
Using this book
This book introduces you to Accelrys DS ViewerPro. To discover more about a specific topic, read the corresponding section:
All of the features and commands in DS ViewerPro are described in the online help. Access help from the Help menu.
DS ViewerPro provides you with a great deal of flexibility
in displaying and sharing chemical information. The following scenarios demonstrate
some of the features that DS ViewerPro offers.
What can I do with DS ViewerPro?
If you would like to try some of these tasks, see the Quick Start lessons in Chapter 3.
Presentation graphics
Imagine Sam, sitting at his computer and needing to prepare
a talk about his company's proposed toxic contamination abatement program. He
has a familiar problem: a presentation with lots of technical content -- but it
needs to be jazzed up. Sam doesn't want to use any gimmicky clip-art. He decides
to include actual graphics of the chemicals discussed in the presentation. After
checking with the project technical staff, he uses DS ViewerPro to load a model
of their problem molecule, dioxin, from a site on the Internet. Since molecular
graphics will provide most of the punch in his presentation, he constructs a colorful
graphic of dioxin's structure. To help illustrate the high point of his presentation,
he e-mails his molecule to the environmental engineer, who uses the DS ViewerPro
to add a sketch of the catalyst that will help clean up dioxin-contaminated sites.
He is able to add labels and details to show the role this second molecule fits
into the proposed abatement plan. After receiving the new file from the engineer,
Sam pastes the customized image into his PowerPoint presentation.
Even though Sam's chemistry knowledge is minimal, he can
solve his presentation problems by using DS ViewerPro as a chemically-aware
graphics tool. When Sam meets with executives to brief them on the plan and
his presentation, he not only has a topical and visually appealing presentation,
he can actually demonstrate specific points about the molecules in his graphic
by rotating, zooming, and displaying informative labels from within his PowerPoint
file. When his report is electronically distributed, his readers can interact
with the model in the report.
Classroom instruction
Our second scenario brings us to a chemistry classroom,
where the teacher assigns the students to sketch several molecules in their lab
copies of DS ViewerPro, starting from the 2D structural formulas in the textbook.
Anne builds her molecule atom by atom, automatically cleaning the structure and
adding hydrogens. Although Anne draws in two dimensions, her drawing is interactively
converted to 3D representation. Once at home, Anne retrieves her molecules from
school over the Internet and finishes adding labels and distance monitors using
her home copy of DS ViewerPro, which she downloaded from the Accelrys web site.
When she is unsure of a step, she uses DS ViewerPro's File / Send
command to e-mail the molecular display to her classmate, who simply double-clicks
the file to open it in her own copy of DS ViewerPro. In this way she can compare
multiple versions of the molecules using DS ViewerPro's tiled windows. At the
next class, Anne's teacher loads Anne's DS ViewerPro file into the classroom PC
and projects it onto the classroom screen with an attached projector.
The teacher goes on to demonstrate concepts the class has been discussing, including bumps, hydrogen bonding, the effects on conformation of substituting atoms or changing bond types, and more. This teacher is engaging her class with a vivid demonstration of the ideas expounded in their textbook.
Anne's success with molecule building and her interest in chemistry lead her to create a Science Fair poster that extends her classwork, a poster that incorporates clear and effective graphics printed from DS ViewerPro. When the Science Fair posters were published on the Web, Anne had no problem meeting the requirement for GIF or JPEG image formats to display her molecules within the Web pages.
Corporate information sharing
Mirabile Company's medicinal chemists are working hard to find molecules that could fit into a receptor site that appears to have a role in cancer resistance. The expert modelers conduct detailed searches of the huge databases for candidate molecules, but when it is time to share their results, the process traditionally hits a bump. Not only is it difficult for the computational chemists, bench chemists, and other technical staff to easily share this sophisticated chemical information, but they also have trouble communicating their findings to the collaborators, managers, and executives who must make decisions based on this highly technical data. DS ViewerPro serves as a lingua franca for all these information consumers -- with their molecular candidates transported via DS ViewerPro, the information can circulate conveniently among all of the technical staff at the same time that it is available to the management, public relations, information systems, and communications groups for their own specialized needs. Each group works with the information at the level and within the computing environment that is comfortable for them.
Increasing the accessibility of key molecular information in these ways gives a technological enterprise an advantage over competitors who are still struggling with incompatible file formats, who are limited to expensive software and workstations, who crash into data distribution dead-ends. Acquiring corporate information should be like turning on a water faucet, not like rolling a boulder uphill.
Importing chemical information into DS ViewerPro
DS ViewerPro reads standard files from many sources, including the Brookhaven Protein Data Bank. Molecules drawn in 2D structure sketching packages such as ChemDraw and ISIS/Draw are automatically converted to 3D models with the correct stereochemistry when you open them in DS ViewerPro. DS ViewerPro can also view models exported from molecular modeling packages such as Cerius2 and Insight II, among others.
Placing DS ViewerPro's output in other programs
DS ViewerPro interacts with other applications, enabling you to display molecules within documents from word processors, spreadsheets, or presentation packages. The image of the molecule is placed as a picture, either by inserting it as an object or by pasting it from the clipboard. The power of DS ViewerPro lies in its ability to interact with and modify these molecular images while they are embedded within the other application. Just double-click on the image to activate DS ViewerPro. The molecule can then be modified, rotated, labeled, or given a new display style. Any changes made are applied to the embedded image.
This functionality means that you can distribute a report containing 3D chemical information as a standard word processor document. Any recipient with a DS ViewerPro can extract and view that information and explore the structure from within the report.
You can make use of the hardcopy options of productivity applications to output your molecular graphics, as well as printing direct from DS ViewerPro to color or gray-scale printers.
DS ViewerPro will also export a picture of your molecular model as a GIF, JPEG, PNG, or bitmap image file. These standard formats are used to display pictures within Web pages. The DS ViewerPro can also export a picture as VRML. VRML output allows users who do not have the DS ViewerPro to see and manipulate a 3D image of your molecule through their web browser. (Visit http://www.web3d.org/vrml/vrml.htm to learn more about or download VRML browsers.)
But you can do more than send a picture through the Web -- you can transfer all of the chemical data associated with your model. To do this, you simply send it as an e-mail enclosure, or link to it from a Web page. You can even e-mail molecules directly by clicking a button in the DS ViewerPro user interface. All of the chemical information-- such as charges, annotations, and group definitions -- is preserved. Any other DS ViewerPro user can open the file and retrieve and visualize the data.
DS ViewerPro is a fully supported product. Accelrys provides support using several channels.
Customer support
For 30 days after the initial purchase, free telephone, fax, and e-mail support are provided. Accelrys Scientific Support can be contacted by e-mail or by telephone:
If you would like more information about molecular visualization, molecular modeling, computational chemistry, or communicating chemical information over the Web, Accelrys provides several resources: