Hello, Vincent Your sphere objects may be rendered as atoms or as drawn objects. Other objects are most likely done as drawn objects. For that, rather than changing the source code, I would vote for converting the input file so it can be used as a script with 'draw' commands.
> 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? Jmol reads PQR files, but I'm not sure waht exactly is your 'last column', to which field it corresponds and how Jmol maps it. There is some doc in the Wiki, File Formats http://wiki.jmol.org/index.php?title=File_formats/Coordinates#PQR > 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. Yes, Jmol reads a DX format as isosurfaces. Not sure if it is the same format you have. Again, check the doc in the Wiki and ask again if needed. http://wiki.jmol.org/index.php?title=File_formats/Surfaces#Open_DX > 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 ? As I said, I'd go with the 'draw' command. It is most flexible for that. ------------------------------------------------------------------------------ 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
