Hello Ajay > http://wiki.jmol.org:81/index.php/AtomSets
As I wrote most of the page you cite, I'll try to answer first. (although that info is collected from other places, not invented or written by me) > I'm curious as to how jmol goes about classifying hetero atoms into various > atom sets as defined > here. First, we must make sure there is no misunderstanding. Do you refer to atoms belonging to PDB HETERO groups, in HETATM records? (in organic chemistry, heteroatoms are non-carbon atoms) > If someone could please provide a reference to the code that would be > spectacular. As I understand it, the code can be disperse, but I know for sure that many of these are defined in JmolConstants.java http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/viewer/JmolConstants.java?vie w=markup For more technical terms, you need help from the programmers, for that maybe Bob and most likely Miguel --but they will read your post for sure and answer when they can--. > As far as the application, I want to be able to parse any given pdb file with > a jmol script and > classify them based on > predefined atom sets for the user to select and then modify. I don`t understand exactly what you mean. The predefined sets already "classify" somehow. Are you interested in just HETATMs? Not sure Jmol will make much of a distinction between HETATMS and ATOMS. Wait..., the pop-up menu has a "select all HETATM", so there must be a way... Aha! I had forgotten: "select hetero" So, maybe you can do things like "select hetero and nucleic" But you need to explain better what you want. ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
