Helper Applications for Biochemical Browsing

Web Browser Helper ("Client-side") Applications

Capable graphical Web browser programs, such as Netscape Navigator (e.g. versions 1.1N-2.0), can be configured to automatically launch programs that can interact with information that is being downloaded. An example is chemical structures that conform to MIME standards. The helper programs must be available on the user's PC, i.e. client-side, and not on the server that one is connected to.

For example, protein crystal structure 3-D coordinates are resident at the Brookhaven National Laboratory (PDB, or Protein Data Bank) and all released entries can be searched (e.g. by protein name) and browsed on the PDB server. Such coordinate entries file names end with *.pdb or *.ent. If a user had Roger Sayle's RasMol program downloaded on his or her PC, then one can configure Netscape to automatically launch the RasMol program to view and manipulate the coordinates as soon as one clicks on the name of the file. This contrasts with servers such as Molecules R Us (NIH) or Swiss-3D ExPASy server (in Geneva) that generate a static picture of a protein at the remote server site and then downloads the graphic of the structure. This does not allow one to manipulate the view in real-time, so if an alternate view is desired the process must be repeated and a new request is made.

Directions to configure Web browsers to launch helper applications are available in the "Help" facilities of these browsers. To configure the programs, one accesses the "Options" in the top menu bar and chooses "Helper Applications." Remember to first obtain and load the program on your PC before asking the Web Browser to launch it!

Recommended Helper Applications

• RasMol

  Roger Sayle's fantastic shareware program is availabe for multiple platforms (PC, Mac, UNIX). It puts commercial PC programs to shame with its incredible speed and ability to handle very large structures and to select substructures to view or display. It allows visualization of PDB protein and nucleic acid structures in a variety of highly useful ways (stick, ball-and-stick, space-filling, ribbons). Most importantly, it allows color display coding according to properties such as different chains, different secondary structures, or even temperature factors if available. It also allows selection by residue number or type or solvent or nucleic acid. The program is NOT designed to build or change the structures. It can recognize PDB files as well as some others such as Sybyl Mol files, and it can save scripts to allow particular views. The PC Windows version (v 2.5, 2.6 beta) appears to have problems printing (expects only postscript) but can output GIF and other bitmap images, as well as Kinemagefiles for viewing with the Richardson MAGE program.

  In addition to interacting with PDB viewers or server front ends, such as SCOP (Structural Classification of Proteins), it can be used for small biomolecule servers such as KLOTHO.

  RasMol and an On-Line Manual, plus a new RasMol Home Page.

  ---

• Kinemages

  Protein Science journal issues contain associated files delivered on diskettes with each issue that contain views of molecules prepared by the authors of the articles. These kinemage *.kin files are viewed by a program called Mage, developed by David Richardson at Duke University, that is freely available for different platforms. All published kinemage files are available on-line at the Protein Science Server. Web browsers can be configured to recognize this chemical MIME type and to launch the MAGE 3.3 program when *.kin files are clicked on during browsing. It is notable that an authoring program (PREKIN) is also made available free that permits anyone to design different views of protein sections if the 3-D coordinates are available, e.g. if downloaded from a source such as the Protein Data Bank at Brookhaven.

  Protein Science, Kinemages and how to configure your Web browser

  ---

• MathCAD

  A browser for MathCAD, a powerful data analysis program, has been made available by the developer (MathSoft, Inc.). Its configuration is a little different, as the browser program allows regular browsing of the Web, as well as of MathCAD documents posted on-line.

  Mathbrowser

  ---

• ISIS/Draw

  A superb complete chemical structure drawing program has also recently been made available for creating chemical structures and for viewing them. Associated manuals are in postscript or HTML formats.

  ISIS/Draw chemical structure drawing from MDL

  ---

• ChemWeb

  SoftShell has created a free but partially disabled (shame!) Web version of ChemWindow and ChemIntosh called ChemWeb. ChemWeb is identical to the standard versions of ChemWindow and ChemIntosh except for a few important changes. It is designed for electronic publishing only. It cannot be used to copy and paste graphics to other documents or print to paper. It saves files only in the GIF format, a image format that is supported by nearly all web document browsers. The GIF files saved by ChemWeb can also be opened and edited by ChemWeb. This makes it possible for Internet users around the world to download the GIF structure files and use them on their own computers. Using ChemWeb, you can draw structures, save them as GIF files, and add them to HTML documents. Later, another user can download the GIF files with their Web browser, open the GIF in ChemWeb, and edit them just as they would any other ChemWindow or ChemIntosh file. ChemDraw and ISIS/Draw users can also use ChemWeb to convert their structure drawing files into the GIF format for electronic publishing.
  Note: it is possible to imbed a compressed version of the actual ChemWindow document within the GIF (GIF supports this). This is what ChemWeb does. The connection table is effectively embedded within the GIF. This means that when a user (ChemWeb, ChemWindow, ChemIntosh) is viewing a ChemWeb GIF, the GIF can be easily saved to disk and opened in ChemWeb with the ENTIRE document being restored.

  ChemWeb. (You must register as a ChemWeb user with SoftShell)

---

Other Useful Helper Applications

• Acrobat Reader for viewing formatted documents (*.pdf) with graphics on multiple platforms, available free from Adobe. For an example, see the weekly KUMC Topics newsletter and the KUMC Faculty Report. It will become a "plug-in" for Netscape 2.0.
• Microsoft Word Viewer for viewing Web *.DOC documents created with Microsoft Word for Windows 6.0. This free and downloadable program is a "helper Applications" designed to work with Netscape and other viewers and is launched automatically when a *.doc document is found. More complete information, including downloading, is available from the KUMC Information Technology Network Home Page.
• LView or LViewPro for manipulating or converting various bitmap graphics files, such as JPEG, JFIF, GIF and BMP.
• MPEG and QuickTime players for viewing video motion files.