VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue May 22 2007 - 11:59:35 CDT

You may also find the VMD tutorial helpful, at least to see some ways
various commands are used:

http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html

Especially the sections "Tcl Scripting Basics and Tk Console" and "An
Example Tcl Script: Calculating the RMSD of a Trajectory".

On May 22, 2007, at 4:32 AM, Petrica GASCA wrote:

> Hello,
>
> I am still in the learning phase of VMD, and I am not clear at all
> what does it mean a script like you sent. I searched through the
> manuals to find some relevant information, but there isn't.
>
> How exactly can I introduce scripts in VMD? Can I save them as
> files (where?), and call them by the file name, or do I have to
> type each line in the console (which? vmd or tk?) ?
>
> I would really appreciate a tutorial on the scripting possibilities
> of VMD, or a few basic informations at least.
>
> Thank you for the help.
>
>
>
> On 5/11/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> If I understand your question correctly, you wish to display the
> text labels
> for all atoms?
>
> If so, you can use a simple script like this one, to add labels
> for any selection you like:
>
> proc label_atoms { molid seltext } {
> set sel [atomselect $molid $seltext]
> set atomlist [$sel list]
> foreach {atom} $atomlist {
> set atomlabel [format "%d/%d" $molid $atom]
> label add Atoms $atomlabel
> }
> $sel delete
> }
>
> You'd call this with something like:
> set molid [molinfo top]
> label_atoms $molid "name CA"
>
> If you want to draw your own text labels for each of the atoms
> (rather than using the built-in labeling feature) you can also
> devise a script that does this, for example:
>
> proc show_partial_charge { selection } {
> set sel [atomselect top $selection]
> foreach q [$sel get charge] pos [$sel get {x y z}] {
> set qstr [format %4.3f $q]
> graphics 0 text $pos $qstr
> }
> }
>
> You'd call this with something like:
> show_partial_charge "residue 0"
>
> You can of course modify this to do anything you like.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, May 11, 2007 at 01:49:10PM +0200, Petrica GASCA wrote:
> > Hello,
> >
> > I am a new user of VMD and I am trying to get used to it on a
> Linux machine.
> > What is really important for my work is to see atom numbers (the
> index field
> > from the Labels window).
> >
> > Is there any possibility to show them as atom labels the same way
> that we
> > can see the name of the atom when we select them manually?
> >
> > Thanks in advance.
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>