The DSSP software and database

You arrived in the historical archives of the Vriend group that worked at the EMBL late in the previous century. The new Vriend group pages (including the new DSSP pages) are at http://swift.cmbi.ru.nl/gv/.

Information

• The help document for the DSSP program.
• The DSSP article scanned in, or as PDF file.
• The license form for an academic DSSP source code.
• The license form for a commercial DSSP source code.
• A bill for commercial users.
• AFTER faxing the license form to the FAX number indicated at the form (+31 (0)24 3619395) you can extract the DSSP distribution by clicking here or from the anonymous FTP area of ftp.cmbi.ru.nl. Do a cd to pub/molbio/software and download dsspcmbi.zip . In any case, type unzip dsspcmbi.zip to unpack, then look at README.TXT. If your Unix system cannot unzip, download the .tar.gz file instead.
• Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp >messages.txt
• Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code.
• Commercial users are requested to transfer Euro 1000 to the "Stichting WHAT IF". Please transfer the money before down-loading the software.

      Stichting WHAT IF
      Euro Acc No 54 83 62 262
      ABN AMRO Bank, Thomas van Aquinostraat, Nijmegen, The Netherlands. 
      Please mention 'DSSP'.
      Optionally: 
      The SWIFT code of the bank is: ABN ANL 2 A 
      The IBAN number of the Euro account is:   NL 57 ABNA 054 83 62 262
      The VAT number is: NL003634255B02
      

• We have a version of the PDBFINDER with the secondary structure according to DSSP indicated as 1-letter code strings. Look at the example. You can download the entire file from ftp.cmbi.ru.nl/pub/molbio/data/pdbfinder2/PDBFIND2.TXT.gz.
• FTP access to the DSSP files at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp.
• If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP.
• And if all else fails, you can get the DSSP-files from 5-5-2007 here as one big tar file (compressed, but still very big!!).

'News'

In 1994, a fast algorithm for surface calculation was added to the accessibility module.
The July-1995 version has a slightly changed output format and several runtime options under unix. Over the years many people have contributed to the maintenance of DSSP. Most noticebly Michael Scharf and Rob Hooft. In 2000 maintenance was taken over by Elmar Krieger who further improved the software, and cleaned it up so that it now compiles on all kinds of machines without any trouble.

Reference

The DSSP code

• H = alpha helix
• B = residue in isolated beta-bridge
• E = extended strand, participates in beta ladder
• G = 3-helix (3/10 helix)
• I = 5 helix (pi helix)
• T = hydrogen bonded turn
• S = bend

A blank in the DSSP secondary structure determination stands for loop or irregular. Loops and irregular elements are often, very incorrectly, called "random coil" or "coil". Many programs, including the PDBFINDER, replace this blank by a C (doing undue justice to the historical artefactual naming of loops and irregular stretches) because one never knows if a blank means loop or no-output, or something-went-wrong.

Using the files

Feel free to copy over all DSSP files from our FTP site. Occasionally, we make small corrections in some files, so your mirror script should check the time stamps/file sizes. If you have problems FTPing the files (something like "argument list too long" or "too many files"), then you are using an outdated FTP client, and it's high time to swap to something more efficient like ncftp (www.ncftp.com). Most Linux distributions have it already installed. Use the command "get -r dssp" to get the entire directory.

Problems?

In case of problems, feel free to contact me via Email at "Vriend@CMBI.KUN.NL". I am neither the author of DSSP, nor the person who gets the money (...), but I will help if I can.