Dear Vincent, I am interested to know more about your project for visualizing pockets (and cavities). Do you have a publication or something online now?
What do you think about Jmol's built in pocket visualization capbilities? Here is an example. Click on "View 2". http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo/ch_view2/chapter.htm I am thinking of adding cavity and pocket visualization in a new version of FirstGlance in Jmol. -Eric At 10/4/09, you wrote: >Hi, > >I'm planing to integrate JMol to my application to view PDB files and >ligand pockets. Basically, my pockets will be represented by several >spheres placed in the structure (input as PQR format), and atoms next >to those speres, and I want the user to be able to select and extract >pocket interactively. > >Anyway, I'm currently using a small code snippet taken from the >biojava documentation. It makes use of the JmolSimpleViewer class. > >So currently, I'm able to display a pdb file in the viewer and execute >some rasmol-like queries. > >My question would be: is there any way to get the Jmol popup menu that >one get when right clicking on the desktop version of Jmol ? > >And more generally, what is the best and most recent place to learn >how to integrate Jmol into an application? I'm currently using >Biojava's examples, and I've checked the Jmol wiki here: >http://wiki.jmol.org/index.php?title=Applications_Embedding_Jmol > >but currently I haven't found the way to do what I want to do. > >Thanks in advance! >Vincent > > >------------------------------------------------------------------------------ >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 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://Martz.MolviZ.Org Top Five 3D MolVis Technologies http://Top5.MolviZ.Org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.molviz.org Workshops: http://workshops.molviz.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://list.molviz.org Protein Explorer - 3D Visualization: http://proteinexplorer.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------------ 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
