VMD-L Mailing List

From: Jim Parker (jimparker96313_at_gmail.com)
Date: Fri Aug 23 2013 - 06:02:26 CDT

An older thread

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21955.html

suggested the following code to label all atoms with their index

proc labelAtoms { molid seltext } {
    label delete Atoms $seltext
    set sel [atomselect $molid $seltext]
    set i 0
    set atomlist [$sel list]
    foreach {atom} $atomlist {
    set atomlabel [format "%d/%d" $molid $atom]
    label add Atoms $atomlabel
    label textformat Atoms $i {%i}
    incr i
  }
  $sel delete
}

It does not work as a script and throws the error

label textformat failed

The "interesting" part is that label textformat Atoms $i {%i} does work
when entered as a lone command from the TkConsole. It is also the output
of generating a logfile and using the GUI to manipulate the label.

Any suggestions on how to correct this script would be appreciated.

Cheers,

--Jim Parker

W dniu 17.05.2013 12:22, Axel Kohlmeyer pisze:
*> On Fri, May 17, 2013 at 11:17 AM, Paweł Kędzierski *
*> <pawel.kedzierski_at_pwr.wroc.pl<pawel.kedzierski_at_pwr.wroc.pl?Subject=Re:%20%20Formatting%20labels%20in%20script>>
wrote: *
*>> Dear VMD users, *
*>> It is possible to format atom labels using VMD GUI (Graphics->Labels,
tab *
*>> Properties), but I can't find in the user guide such functionality for
the *
*>> Tcl label command. *
*>> I want to automate relatively simple tasks like labeling every atom
with its *
*>> index: *
*>> *
*>> set all [atomselect $molid "all"] *
*>> foreach atom [$all list] { *
*>> label add Atoms $molid/$atom *
*>> } *
*>> $all delete *
*>> *
*>> Can I set the label format to e.g "%i" in Tcl code or via GUI only? *
*> you can always monitor Tcl commands that do the same thing as the GUI *
*> by turning on logging. *
Good idea indeed, thanks :)
*> please try something like this (untested): *
*> *
*> set all [atomselect $molid "all"] *
*> set i [llength [label list Atoms]] *
*> foreach atom [$all list] { *
*> label add Atoms "$molid/$atom" *
*> label textformat Atoms $i {%i} *
*> incr i *
*> } *
*> $all delete *
Thanks for the code. I have checked that a single atom can only have one
label so the indexes will start at 0 and they can't grow beyond the
number of atoms.
The code (possibly useful for someone else) would be then:

label delete Atoms all
set all [atomselect $molid "all"]
set i 0
foreach atom [$all list] {
    label add Atoms "$molid/$atom"
    label textformat Atoms $i {%i}
    incr i
}
$all delete

The initial deletion of all Atoms labels is there because relabeling of
an atom actually hides its label.
Thank you,
Pawel
*> *
*>> Thanks, *
*>> Pawel *
*>> *
*> *
*> *
*> -- *
*> Dr. Axel Kohlmeyer
akohlmey_at_gmail.com<akohlmey_at_gmail.com?Subject=Re:%20%20Formatting%20labels%20in%20script>
http://goo.gl/1wk0 *
*> International Centre for Theoretical Physics, Trieste. Italy. *