Dear all, Thanks for all your answers.
> I am interested to know more about your project for visualizing > pockets (and cavities). Do you have a publication or something online now? Here: http://www.biomedcentral.com/1471-2105/10/168 Fpocket is a new, open source, geometric based pocket detection algorithm written in C. Currently, the results vizualisation is made using VMD or pymol. We would like to create a new GUI and use JMol to integrate the vizualisation into the GUI. > What do you think about Jmol's built in pocket visualization capbilities? I'm open to anything, but the vizualisation should be specific to fpocket output: several so-called alpha spheres having a defined radius (PQR format). In the example you gave, I see that the pocket is actually represented by the lingand binding to it. We want the same kind of representation, but using alpha spheres with defined radius instead of lingand. > Are you talking about integrating Jmol into a java application as opposed to > a web application? Yes indeed. > If so the way I accomplish that is to create a class for housing jmol that > is an extension of JPanel <snip> That's what I've done so far. I can vizualise any PDB file and execute rasmol command line, but I'm missing the popup menu that allow the user to customize the view, and more importantly make selections. I'm currently looking at JmolPopup panel, but I think I have to catch mouse event on the jmol viewer as a right click does not trigger any popup right now. Of course any help or tips is still welcome :) ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
