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 <[EMAIL PROTECTED]> 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.
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