Dear JMol users, I'm trying to represent ligand pocket in JMol. For this purposes, I've two pocket representation as input: PQR file that contains a set of so-called alpha spheres having a defined radis, and DX file format used by DataExplorer (see http://www.cs.wpi.edu/research/DataExplorer/tutorial/data.html), that defines a discrete grid, and that can be read by pymol, and much more efficiently in term of representation by VMD.
I've two questions here: 1. I'm trying to render the alpha spheres volumes defined in the last column of the PQR format, color it according to the residue name, and make it sligntly transparent, but so far I haven't find the way to do so. Is it possible? 2. Does JMol can read DX format? This second way to represent pockets is related to electron density map, and is represented by this format. 3. In a more general way, if I want to add to a given model a custom object, say a sphere with a given radius for example, and if I want to render it (volume, transparency, surface, custom color), to link it with other objects with a distance criteria, to select neighbor atoms... what would be the best way to do so ? Or the best place to learn it actually ? (if any, I'm prepared to go through the source code!) That's it, thanks in advance! Vincent. ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) 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/devconference _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
