SecondGlance Help

Introduction

SecondGlance is a simple desktop application to generate cartoons of protein secondary structures from DSSP files. The general appearance is similar to the 'Wirplot' diagrams of Roman Laskowski, but with less detail.

Using SecondGlance

1. Select 'LoadFile' from the File menu, and navigate to a DSSP file in your filespace. You will receive feedback in the text area that the file has loaded.
2. Click the 'List' button and a text listing of the secondary structure regions of the protein will be displayed in the text area. This may be printed or saved as a text file, if required, using the 'Print' or 'Save' options from the File menu.
3. Click the 'Graph' button, which should now be active. A graphic window containing the secondary structure cartoon should appear.
4. The cartoon graphic may be printed or saved as a .png file using the appropriate buttons in the graphic window.
5. Quit or load a new file by selecting the appropriate option from the File menu.

Obtaining DSSP files

DSSP files are generated from Protein Databank (PDB) files using Kabat and Sander's DSSP program. DSSP files are available from EBI, via FTP (ftp.ebi.ac.uk/pub/databases/dssp) or from the website search facility (http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz). The DSSP program can be obtained from http://swift.cmbi.kun.nl/gv/dssp/.
N.B. Where DSSP files contain data for more than one subunit, only the first is displayed. To display data for other subunits you should generate separate files using a text editor.

Acknowledgements

David P. Leader wrote SecondGlance (originally as a Perl script) to generate secondary structure diagrams for the Motivated Proteins web application. He subsequently adapted it as a Java teaching exercise for the Glasgow University Bioinformatics M.Res. course, and this has been tidied up a little for general distribution. Contact him at d.leader@bio.gla.ac.uk to report bugs or request new features.