Re: [Jmol-users] Translation with mouse and labeling of nodes (atoms)

[Frieda R. <fr...@ns...>]

Hi Joe,

To select multiple atoms by number:
select (atomno=1, atomno=3, atomno=89)

Frieda

On Aug 17, 2007, at 2:27 PM, Joe Ivanic - Contractor & Foreign  
National/bioanalysis wrote:

> 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: jmo...@li... [mailto:jmol-users- 
> bo...@li...] On Behalf Of Rolf Huehne  
> <rh...@fl...>
> Sent: Tuesday, August 07, 2007 1:42 PM
> To: jmo...@li...
> 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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