Tuesday, March 31, 2009

I just made a big commit on Jmol stuff for Bioclipse

During the last couple of weeks I have given the Jmol editor in Bioclipse some love. Today I made a big commit. It all started when I tried opening a multiple model pdb in it and started figuring out how to browse it using the outline. That was very unintuitive -- and still is, because I haven't fixed that yet... :)

What I have fixed is only the first thing that felt strange about the Jmol editor. I have been working on synchronizing selections between the outline and the Jmol editor. The Jmol outline in Bioclipse comes in two flavours depending on what is being browsed. So far I have made the one showed when looking at a small molecule synchronized with the outline. So when selecting in Jmol the corresponding atom in the outline is selected. As for the other version of the outline there I have so far only made Jmol select groups instead of atoms as default when clicked on.

In the future we probably want buttons for switching between different ways to select things in Jmol. Much more that can so far only be done using Jmol scipts can be made easily available from the Bioclipse graphical user interface.