From: Egon Willighagen <e.willighagen@sc...> - 2006-04-26 05:42:28
as I've reported before, I am embedding Jmol into Bioclipse , and currently
fixing the CDK-Jmol interface (the CdkJmolAdapter). The secondary structure
is again propagated to Jmol, now that the adapter implements the
StructureIterator. However, the secondary structure is not shown yet; which,
I think, has to do with the fact the my AtomIterator is not fully compatible
yet... 'select protein' selects 0 atoms for any PDB file.
Which AtomIterator field need to be setup correctly to have Jmol detect atoms
as protein atoms?
Radboud University Nijmegen
From: Egon Willighagen <ewilligh@un...> - 2006-04-26 21:12:56
On Wednesday 26 April 2006 07:42, Egon Willighagen wrote:
> Which AtomIterator field need to be setup correctly to have Jmol detect
> atoms as protein atoms?
The important field turned out to be the group3 field.
A screenshot of the state of Bioclipse today is at:
I think I mentioned it before, but will do it again to make sure :), it has a
built in script editor with code completion and syntax highlighting. The
screenshot shows a file browser on the left, the console below the Jmol
window and enzyme properties on the right. It currently has no
AtomSetChooser, but that might follow soon.
Binaries can be downloaded form bioclipse.sf.net, and the source is available
from SVN, and easiest run from Eclipse.