I am having trouble selecting groups of atoms which may not occur within
an expression. For example, atom numbers = {1,3,89}. The reason I want
to do this is to set the bonds between just these atoms to have a
certain colour.
Any help will much appreciated.
Joe
---
Dr. Joe Ivanic - Contractor, Foreign National
Scientist
Biotechnology HPC Software Applications Institute
ATTN: MCMR-ZB-T (Joe Ivanic)
Building 363, Miller Drive
Ft. Detrick, MD 21702-5012
Voice: (301) 619 1976
Fax: (301) 619 1983
________________________________
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Rolf
Huehne <[EMAIL PROTECTED]>
Sent: Tuesday, August 07, 2007 1:42 PM
To: [email protected]
Subject: Re: [Jmol-users] Translation with mouse and labeling of nodes
(atoms)
Joe Ivanic - Contractor & Foreign National/bioanalysis wrote:
> Hi,
>
> I am a quantum chemistry theory and program developer (mainly GAMESS),
> plenty of experience with Fortran and C, but none really with Java. My
> questions may be very simple but I have to ask them.
>
> Jmol is fantastic for visualizing almost everything. However, I still
> have not found a way to translate a molecule with the mouse. There are
> the move, moveto, and translate Jmol commands, however, being able to
> move the molecule sideways with the mouse, rather than only rotation
and
> zoom, helps to accurately focus in on very specific parts of a system.
> Is there a way to translate with the mouse?
The mouse manual for Jmol can be found in the Jmol Wiki at
"http://wiki.jmol.org/index.php/MouseManual";.
>
> The above question is asked mainly because I am also using Jmol to
> visualize very large networks. So I trick Jmol (with a .gpr file) into
> thinking I have lots of atoms (difference for each type of node) and
> then specify their connections (with bonds). This has proven very
> useful. Being able to translate, though, would make network
> visualization and "navigation" that much better. Being able to select
a
> node (atom) with the mouse, or script, and then recentering the
network
> (molecule) about this node would also be extremely useful, very
similar
> to the free translation.
You can center around the currently selected atoms (nodes) by using this
command:
center selected;
Or center around a specific atom by this one:
center atomno=10;
A detailed description can be found in the Jmol scripting manual at
"http://chemapps.stolaf.edu/jmol/docs/";.
>
> My last query is about the labeling of the nodes (atoms). There is the
> script command "label" which can do this very efficiently. However,
> being able to have the pointer on top of a node (or atom) and then
> automatically include showing of the label (not the atom, e.g. H, Li,
> rather a string label) would be nice. I'm not sure how to do this
within
> Jmol. It seems to have the flexiblity to have an "atom name" shown,
> rather than an "atom label" but I am not able to figure out just how
to
> accomplish this. Certainly not within the .gpr format anyway. Typing
an
> atom label (node label) into the script window, with the relevant
> command, and this being highlighted would also be extremely useful. I
> guess I am asking if we can input other types of nodes, rather than
just
> atoms, into Jmol.
>
I guess what you mean is something that is called "hover" in Jmol: a
label that appears if the mouse rests a while on top of an atom (node).
You can activate this and determine what is shown (but only globally,
not individually) by the following command:
hover "Node=%a"
This would display the text "Node=" plus the individual atom name of the
atom. The command is described also in the Jmol scripting manual at
"http://chemapps.stolaf.edu/jmol/docs/?ver=11.2#hover";. It accepts the
same label definitions as the label command
("http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.2#label";).
Regards,
Rolf
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