Hi Guys, I just upgraded to jmol 11.1.28 and would like to color by parameters taken from an external file. Could someone point me in the right direction? I can't find this in the documentation.
Thanks Sam On Apr 25, 2007, at 7:57 PM, Angel Herraez wrote: > 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 ------------------------------------------------------------------------- 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
