Bob,

thanks, that helps a lot.  Now its time to get coding :)


ajay

On 4/26/07, Bob Hanson <hansonr@stolaf.edu > wrote:
Ajay,

When a PDB file is read, Jmol looks for the "HET" and "HETNAM" records
as well as "HETATM". It catalogs the data found in those records
and uses that for building the pop-up menu on the fly. So actual hetero
groups are not defined as static terms in JmolConstants.java. (It would be
a Looooooong list.) We just read the ones that are pertinent to the
molecule at hand. Each time a model is read, this list is flushed.

The actual definition of "hetero" itself is simply "those atoms that are
in HETATM records",  nothing more than that.

Bob Hanson



Ajay wrote:

> Hi Angel,
>
> Thanks for the link, that explains most if not all of the groups that
> i'm interested in classifying. as know i know i can classify them by
> group_id.
>
> However, the link to the JmolConstants.java code does not take into
> account hetero atom sets.
>
> The following is a snippet of code from JmolConstants.java
>
> 2424     //    "@hetero", handled specially
>
> I'd like to know how hetero molecules and "non solvents" are handled.
>
> Thanks for all your help
>
> ajay
>
>
> On 4/25/07, *Angel Herraez* <angel.herraez@uah.es
> <mailto:angel.herraez@uah.es>> wrote:
>
>     Hello Ajay
>
>     > http://wiki.jmol.org:81/index.php/AtomSets
>     <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.
>
>
>
>
>
>
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