I have not blogged for about a week now, and been too busy with other things, like finishing my PhD articles/manuscript, my new job at the CUBIC where I continued the work on proper protein support in Bioclipse using the CDK and Jmol:
The latter involves getting the CdkJmolAdapter, the interface between the CDK and Jmol, updated for changes since the Jmol as 3D viewer for CDK article in CDK News, the open access journal for CDK related projects.
The screenshot is not showing the actual status: the CdkJmolAdapter does not propagate all information to Jmol correctly; as you can see in the screenshot in the BioPolymerTree and Property views, the CDK now reads the structure information from the PDB file, and I verified that Jmol really extracts this using the StructureIterator, but the secundairy structure does not show up yet. I believe the problem is in the AtomIterator: issueing the 'select protein' script, selects zero atoms.
The above screenshot is using a workaround, and was made by using Jmol's own IO instead of the CdkJmolAdapter. But I'm very close and think I will be able to fix this soon.