Molecular visualisation tools have become very popular in various fields of life science research and development, as they have broadened our understanding of biomolecules, their spatial conformations and atomic arrangements, as well as their physiological and pathological roles. Many organisations are constantly updating these tools to keep up to date with the latest developments in such fields as molecular biology, genomics and proteomics.
DS ViewrPro 5.0 is a release from Accelrys which combines the functionality of numerous tools into one easy-to-use package. It can be used to view molecular structures from several popular file formats, produce high quality molecular images for web publishing and printing, sketch 3D molecular models, and integrate saved work with other bioinformatics/chemoinformatics tools and system applications. Each of these functions offers a variety of options, which makes DS ViewerPro 5.0 a very powerful and practical tool, and even fun to use.
DS ViewerPro 5.0 has a fairly simple and easy to follow user interface with a familiar look-&-feel of Windows-based programs. It contains a top toolbar for molecular display and alteration options and a side toolbar for rotation, sketching and annotation of molecules.
Users can customise these toolbars by adding, removing or rearranging tool buttons. This simple interface provides a larger area for viewing molecules and for stacking several opened windows in a manageable approach, with a useful feature of automatically resizing the viewed molecules according to their resized windows. This is certainly useful for smaller computer displays.
DS ViewerPro (MSV) Files
MSV is the standard file format written by DS ViewerPro with the ability to save the current display styles of the viewed molecules, as well as their atomic and molecular data, their current rotation, annotations and labels. This provides greater advantages over the usual text file formats when saving your work.
Furthermore, since DS ViewerPro is OLE (Object Linking and Embedding) compliant, MSV file contents can be embedded, displayed, and edited within other OLE compliant applications. We tested this feature with WordPad 5.1, Microsoft Works 6.0 applications and Microsoft Office XP applications by simply dragging and dropping MSV files into the application’s window. When double clicking the displayed molecules, the standard tools of DS ViewerPro 5.0 are loaded within the application to edit or even sketch molecules. This feature is quite handy for presentations and producing reports on the analysed molecules. If the contents of the embedded MSV files are modified within DS ViewerPro itself, it is possible to automatically update the embedded contents inserted within other applications by using the Update command in the File menu. So there is no need for re-embedding the MSV files into the selected applications.
One of the key features of DS ViewerPro 5.0 is its multi-file support capability. Users can import files of several popular formats (See InfoBox), such as PDB (Brookhaven Protein Data Bank) and MOL (Molecular Design, Ltd. [MDL]) and export the viewed and sketched molecular models into many file formats (See InfoBox), which are importable by other bioinformatics and chemoinformatics tools. However, there are restrictions related to exporting the viewed molecules into certain file formats. For example, MOL files are suited best for smaller molecules whereas PDB files are suitable for DNA and protein molecules. So you need to be aware of the specific conditions associated with each file format before exporting your molecular models and related data.
Another strong feature of DS ViewerPro 5.0 is its ability to export high resolution image files, including Bitmap (BMP), JPEG (JPG) and GIF files, of the viewed and sketched molecules. Even though the image files do not contain any molecular information they can be used for publication purposes. But a word of warning, creating high-resolution images requires a substantial amount of memory.
Viewing Molecular Structures
As with most molecular viewing tools, with DSViewerPro 5.0 users can select, rotate, zoom, move, and annotate molecular structures. Nevertheless, DS Viewer offers advanced options with each of these functions which present more detailed information on the analysed molecules. In this review we will only cover a few selected examples of these tools.
DS ViewerPro 5.0 contains a number of options for selecting molecular objects, other than just using the mouse pointer, which is not very practical when viewing complex molecules. The Select tool, from the Edit menu, is one approach to selecting specific objects and regions within molecules. This tool opens a dialog box which contains object selection options. It is possible to select and unselect objects based on individual or a combination of properties including Type, such as atoms, amino acid chains and bonds, Element, Object Name, Object ID, Radius, and Group, such as hydrophobic regions, side chains or acidic regions. Moreover, it is possible to group multiple objects using the Group command in the Edit menu, which can then be treated as a single object. The specified group name is registered in the MSV file of the viewed molecule and listed within the selection tools.
Another extremely useful selection tool is the molecular hierarchy window, which displays the hierarchal arrangements of molecular components, such as side chains, residues, atoms and bonds, within the viewed molecule. The hierarchy consists of rows of separate and distinct molecules, groups or residues, as well as their subcomponents. Each of these objects is represented by its name or type, and when selected, its corresponding location within the loaded molecule is highlighted.
Furthermore, this tool can be used in conjunction with the molecular data window tool, which contains tabulated data of the viewed molecule in a spreadsheet-like presentation, providing details of all of the elements associated with the loaded molecule. This information can be used with the selection tool described above for future selections and search queries. Users may sort the tabulated data by objects name or ID, rearrange columns order, and export the information to spreadsheet applications such as Excel for further data manipulations.
It might seem that most of these tools are only necessary for analysing complex molecules. Indeed they are very precise, efficient and timesaving when used with complex structures, based on our tests with the molecular model of haemoglobin. But the most important feature of these tools is that they are quite informative and reasonably straightforward to use. Thus, they can be used for analysing and understanding the chemical and biochemical properties of simple molecules as well as complex macromolecules.
DS ViewerPro 5.0 offers advanced editing features for loaded molecules. Apart from just changing display styles, rotations and colouration schemes, it is possible to actually modify the properties of the loaded molecules, as well as the data within the molecular data window, which automatically updates the 3D structure of the molecule. Furthermore, Users can add or remove atoms, modify bond orders and atomic charge, modify van der Waals radii of the selected elements, add text annotations and notes, and even apply the sketch tools (see below) to alter the loaded molecules. All of these modifications are saved in the MSV files and can be used to further analyse the molecules of interest.
Sketching Molecular Models
Sketching molecular structures using DS ViewerPro 5.0 was impressively easy. We decided to put it to the test and sketch a fairly simple molecule, such as adenine. The aim of the test was to see how long it would take us to sketch the molecule, identify its individual elements, change the colour of individual elements, change some visual properties of the molecule, identify the electronic potentials of each element using visual effects, and finally produce an “Ultra” high resolution image for printing.
Although it may seem that completing all of these tasks would take a considerable amount of time, it took us a mere 32 minutes, which included running through different display types, colouration schemes and visualisation options, to produce the final figure from our DS ViewerPro 5.0 Sketching Quick Guide. The key feature of sketching molecules with DS ViewerPro 5.0 is that each element is automatically displayed as a 3D object. So there is no need to worry about converting 2D sketches to 3D models. Likewise, there is no need to worry about figuring out the spatial conformation of your sketched molecules as DS ViewerPro automatically positions and resizes elements individually as you define them. This can also be achieved by using the “Clean Molecule” tool.
Other advantages of using DS ViewerPro 5.0 as a molecular sketching program is the ability to utilise the visualisation tools described above on the sketched molecules. This does not only aid users to produce high quality images, but also to understand the molecular and chemical properties of their sketched molecules. Click here for our quick guide on sketching simple molecules with DS ViewerPro 5.0.
DS ViewerPro 5.0 is an excellent and impressive tool that can be applied for different analytical purposes. It can be used to accurately and effectively manipulate and analyse molecular models from several file formats and you can sketch your own molecular structures quite efficiently. Both aspects are extremely useful for understanding the properties of the investigated molecules. The one drawback of DS ViewerPro 5.0, however, is that it is only available for Windows-based platforms. This means that non-Windows users simply do not have access to DS ViewerPro 5.0, which for some professionals it can be seen as breaking the rules of Bioinformatics in terms of platform independency. This principle has made technologies such as Java (www.java.sun.com) and tools such as the RasMol-derivative Protein Explorer (www.umass.edu/microbio/rasmol) very popular amongst scientists, bioinformaticians and computational biology developers.
When asked, Accelrys stated that from their past releases of DS ViewerPro they received a higher demand for Windows versions more than any other operating system.
One possible way around this, however, is to use Windows emulators, such as VirtualPC from Microsoft (www.microsoft.com/uk/mac/virtualpc.mspx) for MacOS and WINE (www.winehq.com) for Linux systems. But reliability and performance issues are usually associated with the use of emulators. We tested DS ViewerPro 5.0 on these emulators and the general performance was reduced quite significantly, especially when working with larger molecules. Some users might find this slow performance acceptable but that is a big “might”!
Another issue with DS ViewerPro 5.0 that some users might find as a drawback is the price. Many bioinformaticians like using tools that are freely available on the Internet, not only for the fact that they are free, but also due to the fact that a number of these tools are actually quite powerful and efficient, and are available for more than one operating system. For this reason some users might think a bit hard before coughing up over £500 (or £230 pounds for academics) to purchase a tool, as apposed to downloading a free one. Although this might seem a difficult decision to make, the most important question to ask one’s self when choosing any tool is “What can this tool do for my work and how efficiently can it do it?”
Well, let’s put this way, if you need a tool just to quickly have a look at a structure of a molecule and identify few chemical properties, for example, then you might have to think twice before investing. But if you need to analyse molecular structures in a more comprehensive, advanced and detailed approach, and produce publications of your work, then DS ViewerPro 5.0 is surely worth the investment.