[Biojava-l] structure alignment display

[Andreas Prlic]

Hi Daniel,

> I was wondering if I need to build from trunk to do this;

No. There are several alternatives available for accessing the code.
Are you using Maven? There is a public Maven repository at
http://www.biojava.org/download/maven/ from which you could get the
latest "snapshot" builds/releases.

Alternatively there is also a compiled and bundled version of the
structure alignment tools (for command line execution) available at
http://source.rcsb.org/download.jsp which is usually not too far
behind the latest trunk.


the commit
> messages imply that there might have been some problems with some of the
> methods in StructureAlignmentDisplay and DisplayAFP at the time of the
> release.

There was an issue at some point causing problems with the display of
flexible and circular permutated alignments, but I don't remember if
that was also the case in the release.

 If it isn't necessary to build the libraries for that reason, I
> was planning on copying the code from
> DisplayAFP.createArtificialStructure(), as that method wasn't present at the
> time of the release.

If you are using Jmol, I recommend using
StructureAlignmentDisplay.display(). If you want to export to another
viewer, use DisplayAFP.createArtificialStructure()  and then
structure.toPDB().  You are right, that method is more recent, so try
to get one of the builds as described above.

Your comments suggest that we should tag another stable BioJava
release soon. I guess a good time will be shortly after Google summer
of code is over (in 2 weeks)...

Andreas