Egon, > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:jmol- > [EMAIL PROTECTED] On Behalf Of Egon Willighagen > Sent: Tuesday, January 15, 2008 9:21 PM > To: [email protected] > Subject: Re: [Jmol-developers] Integration of protein sequence and > 3Dstructure > > Emily, > > On Jan 15, 2008 6:20 PM, Emily Heureux <[EMAIL PROTECTED]> wrote: > > Hi. The scientists and bioinformaticians on my project would like to > know > > if there is a way to view and interact with the protein sequence and 3D > > structure in jmol, similar to how pymol works, where you can make a > > selection on the sequence and it shows up on the structure, and vice > versa. > > I have looked online, but I haven't found that or something like it yet, > if > > it exists. > > Bioclipse (http://www.bioclipse.net) might what you are looking for. A > screenshot for the plugin includes: > > http://wiki.bioclipse.net/index.php?title=Net.bioclipse.jmol > > Bioclipse allows: > > * selecting residues from a BioJava sequence viewer > * selecting strands/residues from an outline view > * full Jmol scripting support > * a Jmol script editor > > I also hacked up is a few basic Jmol script tutorials, which can be > used inline, and allow running the example code with a click on the > button. > > There is an active community of Bioclipse developer, and I am sure > they are interested in your specific needs. The Bioclipse paper was > published last year in BMC Bioinformatics > (http://www.biomedcentral.com/1471-2105/8/59/abstract). > > Egon
Thanks for the info. I should have specified, I am implementing jmol on our website, as a java applet, and it looks like bioclipse is a plugin for eclipse. Is that correct? Looks nice though...(I am in the process of installing eclipse with a perl plugin on my linux machine. It would be nice to have the bioclipse plugin for purposes other than the website.) Emily > > -- > ---- > http://chem-bla-ics.blogspot.com/ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Jmol-developers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-developers ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
