Bioinformatics Advance Access originally published online on January 3, 2007
Bioinformatics 2007 23(3):383-384; doi:10.1093/bioinformatics/btl603
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SChiSM2: creating interactive web page annotations of molecular structure models using Jmol
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
 |
ABSTRACT |
|---|
 TOP ABSTRACT 1 INTRODUCTION2 IMPLEMENTATION3 APPLICATIONSREFERENCES |
|---|
Summary: SChiSM2 is a web server-based program for creating web pages that include interactive molecular graphics using the freely-available applet, Jmol, for illustration. The program works with Internet Explorer and Firefox on Windows, Safari and Firefox on Mac OSX and Firefox on Linux.
Availability: The program can be accessed at the following address: http://ci.vbi.vt.edu/cammer/schism2.html
Contact: cammer{at}vbi.vt.edu
|
1 INTRODUCTION |
|---|
|
TOPABSTRACT1 INTRODUCTION2 IMPLEMENTATION3 APPLICATIONSREFERENCES |
|---|
Molecular graphics in web publications enhance the communication of scientific results and education. Most often, molecular graphics are simply presented as several static images that accompany text. Interactive molecular graphics, in contrast, allow the reader to explore views beyond those views preset by the author, and allow the reader to focus on the structure as seems most appropriate, in order to understand the science communicated by the illustrations.
Some of the most commonly used tools for displaying interactive graphics on the web have been based on the widely used molecular graphics program, Rasmol (Sayle and Milner-White, 1995). One such program, the browser plug-in Chime, was designed to enable viewing of molecular structures in web pages. Chime use today is limited to only a few browsers, so Chime has, for many authors, been superseded by the applet Jmol (jmol.sourceforge.net, Herráez, 2006). Jmol allows an author to create web pages that link to any structure accessible publicly through the web, and Jmol pages are viewable on the three major platforms: Windows (IE and Firefox), Mac OS (Safari and Firefox), and Linux (Firefox). Jmol-enabled pages can be used to create websites and annotate/curate databases, are useful as supplemental information for journal articles, and can serve as electronic notebook pages. Jmol-based documents are especially useful in classroom settings where the use of interactive demonstrations can aid in understanding the lecturer's presentations.
Creating web pages that include Jmol graphics usually requires knowledge of HTML, and understanding of either the Jmol JavaScript library or JavaScript scripting techniques. To simplify and facilitate creation of Jmol pages, a server-based web program, SChiSM2, has been developed. SChiSM2 replaces the program SChiSM (Cammer, 2000), which was designed to facilitate creation of Chime-enabled pages. SChiSM2 allows easy creation of web pages for annotating molecular structures. SChiSM2 eliminates the need for programming. Instead, the program allows the author to focus on content creation using Rasmol/Jmol scripts, rather than having to write and re-write HTML pages. As a major improvement over the original SChiSM, SChiSM2 also provides a scratch area where a web page author can develop and test Rasmol/Jmol scripts prior to making the page. This functionality greatly facilitates and speeds page development.
As noted above, SChiSM2-created pages can be viewed on the three major platforms, using popular browsers. This versatility allows an author to reach a broad community of scientists, students, and others interested in molecular structure.
|
2 IMPLEMENTATION |
|---|
|
TOPABSTRACT1 INTRODUCTION2 IMPLEMENTATION3 APPLICATIONSREFERENCES |
|---|
SChiSM2 is written in Perl and runs on a web server accessible using a browser (Fig. 1). The SChiSM2 interface provides two options for choosing a structure file to display in the page. First, the web page author can provide the URL of a structure on the web. This allows an author to use either her/his own structure, or one at a site elsewhere on the web. Alternatively, the author may provide the four-character identifier for a structure stored in the Protein Data Bank (PDB; Berman et al., 2000). SChiSM2 automatically creates a link to the structure in the output page. When a PDB structure identifier is used, the author can choose to provide the reader a link to NCBI's structure page in order to enrich the annotation for the protein structure in the SChiSM2 page. Another useful feature is that SChiSM2 can be used with structures located on private networks without ever exposing the structures to the external web.
|
The interface includes spaces for the author to add 10 Rasmol/Jmol scripts and text to accompany these scripts, as well as a space to add a page title and an introduction. For each script/text pair, a ‘show’ button is created which executes the script on the output page, and the text label appears beside it. As an option, the author can add a link, which will allow the reader to view the scripts used for making the page. This can be very useful in educational use of SChiSM2-created pages, especially when teaching how to create Rasmol/Jmol scripts. This ‘view scripts’ link is entirely contained by the created page and does not require maintaining an external page link once the page is made.
SChiSM2 allows the author to set the size of the molecular display on the output page in pixels of height and width. These settings let the author determine how much of the page is taken by the display. The author also can set the color of the molecular display background, as well as the page color. In order to facilitate color selection using HTML-safe colors, an interactive color pallet is provided. To use the pallet, the author simply clicks on the color link in order to add the color to the spaces for either display color or page color. The default colors are black for the display and gray for the background. Both the display and page can be set to the same color if desired, thus creating a seamless background to display the molecular structure.
Six different page styles can be created using this version of SChiSM2. For these styles previews are provided through image links on the SChiSM2 interface. Since page creation is very quick, an author can easily test all of these styles to determine which will be most appropriate for the demonstration. Fast page creation also enables an author to iteratively test the completed page many times by using the browser navigation buttons. In the future more page styles can be added to those already provided, if the author community desires.
While SChiSM2 is designed to eliminate the need for HTML and JavaScript scripting, the program can be useful for programmers as well. SChiSM2 pages can be used as templates to populate a database of structure annotations. SChiSM2 also can reduce repetitive HTML and JavaScript programming and re-testing during page development, enabling a programmer to focus on content. In addition, bioinformaticians interested in developing Jmol-enabled pages can use SChiSM2 as a learning tool.
To facilitate using the program, a guide has been written that covers the major areas of SChiSM2 use. The guide addresses how to use Jmol, as well as how to use the scripting scratch pad to develop and test Rasmol/Jmol scripts. SChiSM2 will undergo continual development to improve upon its features and the author would appreciate user comments.
|
3 APPLICATIONS |
|---|
|
TOPABSTRACT1 INTRODUCTION2 IMPLEMENTATION3 APPLICATIONSREFERENCES |
|---|
At the Virginia Bioinformatics Institute (VBI) we are using SChiSM2 to develop web page annotations of protein structures in our NSF-funded CI-TEAM Cyberinfrastructure Demonstration project, and for the Proteomics Data Center subcontract of the NIAID-funded Resource Center for Biodefense Proteomics Research. SChiSM2 also will be a tool used during development of protein structure annotations in our NIAID-funded PATRIC (Pathoystems Resource Integration Center) project. We also use SChiSM2 to educate current and future scientists about protein structure.
|
Acknowledgments |
|---|
The author appreciates comments from Joseph Gabbard regarding usability, and Tim Driscoll for his comments and suggestions. Support was provided in part by NSF-0537461, awarded to Oswald Crasta (PI), NIAID-HHSN266200400061C, and by VBI. I would like to thank the reviewers for their comments and suggestions.
Conflict of Interest: none declared.
|
FOOTNOTES |
|---|
Associate Editor: Anna Tramontano
Received on October 10, 2006; revised on October 27, 2006; accepted on November 20, 2006
|
REFERENCES |
|---|
|
TOPABSTRACT1 INTRODUCTION2 IMPLEMENTATION3 APPLICATIONSREFERENCES |
|---|
Berman, H.M., et al. (2000) The Protein Data Bank. Nucleic Acids Res, . 28, 235–242
Cammer, S.A. (2000) SChiSM: Creating interactive web page annotations of molecular structure models using Chime. Bioinformatics, 16, 658–659
Herráez, A. (2006) Biomolecules in the Computer: Jmol to the rescue. Biochem. Educ, . 34, 255–261[ISI].
Sayle, R. and Milner-White, B.J. (1995) Rasmol: biomolecular graphics for all. Trends Biochem. Sci, . 20, 374[CrossRef][ISI][Medline].
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. Zhang, O. Crasta, S. Cammer, R. Will, R. Kenyon, D. Sullivan, Q. Yu, W. Sun, R. Jha, D. Liu, et al. An emerging cyberinfrastructure for biodefense pathogen and pathogen host data Nucleic Acids Res., January 11, 2008; 36(suppl_1): D884 - D891. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||