Protein Family Alignment Annotation Tool News

We have integrated a copy of the JMOL structural viewer into PFAAT. You try this out by launching the example:

http://pfaat.sourceforge.net/webstart/pfaat_example.jnlp

or

by launching the latest version of PFAAT (1.0.091) and performing one of the following
File->launch->Structural viewer
File ->Load Sequence from PDB file
File ->Associate Structure with Sequence

There is a bug in JAVA 1.4.2_01 and some other versions so please use JAVA 1.4.2_06 or greater.

The bug that caused the loading of alignments in the MacOS X version of Pfaat to fail has been fixed starting with version 1.0.052. We regret any inconvenience this may have caused.

Pfaat is now available via Java Webstart from the Home Page http://pfaat.sourceforge.net. Updates will be automatically reflected via this location. The new HTML documentation is still a work in progress but can be viewed at http://pfaat.sourceforge.net/pfaat-documentation.htm

Please contact dcaffrey at users.sourceforge.net for more information about Java Webstart.

Apparently the core system itself (the non 3D visualization stuff) uses some of the low level algorithm and data structure classes from the Java 3D package. We have added these 4 libraries back into the installer and the errors you see are gone and it works very well on Mac OS X 10.2.4 with jdk 1.4.1. The new installer is live and on http://pfaat.sourceforge.net/install.htm.