VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Sat Aug 16 2014 - 03:49:18 CDT

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On Aug 16, 2014, at 3:40 AM, Ashar Malik <asharjm_at_gmail.com> wrote:

> You sent me this. I am not renaming anything.
>
>
> On Sat, Aug 16, 2014 at 8:36 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
> Ashar, this thread is not related to your problem... unless you are trying to change labels in VMD while creating a psf file.
>
> Maxim
>
>
> On Aug 16, 2014, at 3:24 AM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> I am not sure how this applies to my problem. Can you explain a bit please.
>>
>>
>> On Sat, Aug 16, 2014 at 7:48 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>> Here is a recipe that you can use to cook up the labels to your liking:
>>
>> ###
>> set labelsToCook [llength [label list Atoms]]
>>
>> for {set label 0} {$label < $labelsToCook} {incr label} {
>> label textformat Atoms $label {%i}
>> }
>> ###
>>
>> Maxim
>>
>>
>> On Aug 15, 2014, at 4:46 PM, Andrew DeYoung <adeyoung_at_andrew.cmu.edu> wrote:
>>
>> > Hi,
>> >
>> > In an archived message on this mailing list (
>> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/9356.html ), there is
>> > a recipe by John Stone for labeling all atoms of a molecule:
>> >
>> > 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
>> > }
>> >
>> > which John Stone explains can be called with:
>> >
>> > set molid [molinfo top]
>> > label_atoms $molid "name CA"
>> >
>> > When I use this recipe, the labels appear to be the residue and atom names.
>> > How can I modify the above recipe so that the atom indices (e.g., 0, 1, 2,
>> > ..) -- which, according to "Selections" in the "Graphical Representations"
>> > window, are referred to by "index" -- are displayed instead?
>> >
>> > Thank you very much for your time!
>> >
>> > Andrew DeYoung
>> > Carnegie Mellon University
>>
>>
>>
>>
>>
>> --
>> Best,
>> /A
>
>
>
>
> --
> Best,
> /A