Sam, Not sure exactly what you want to do, but I colour atoms using partial charge - to do this you need to read your molecules in a cml file with the property in the charge tag e.g.
<molecule title="molecule" xmlns="http://www.xml-cml.org/schema/cml2/core"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://www.xml-cml.org/schema/cml2/core cmlAll.xsd"> <atomArray> <atom id="105" elementType="H" x3="-3.5000" y3="-9.5000" z3="-1.5000"><scalar dictRef="jmol:charge">0.509</scalar></atom> .... Once you've loaded this file into Jmol, you can issue the 'color partialcharge' command. http://jmol.sourceforge.net/jscolors/#Charge Obviously the field can actually contain whatever property you want, scaled to fit between -1 and 1. This approach obviously has the disadvantage that you need to create a cml file with an artificial field in it. There might be a better way using the data command http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.1#data and/or some of the new functions for manipulating jmol variables http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.1#functions but I have yet to research this fully. Please let me know how you get on! Dave On Wed, 25 Apr 2007 19:50:23 -0400, "Samuel Flores" <[EMAIL PROTECTED]> said: > 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 -- Dave Evans [EMAIL PROTECTED] http://www.davidaevans.org ------------------------------------------------------------------------- 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
