VMD-L Mailing List

From: Teletchéa Stéphane (steletch_at_biomedicale.univ-paris5.fr)
Date: Tue Nov 18 2003 - 10:39:08 CST

Le mar 18/11/2003 à 17:05, John Stone a écrit :
> Stephane,
> I don't have time to make this change for VMD 1.8.2, however the graphing
> interface in VMD is implemented with Tcl scripting, so users can easily
> override the default behavior by defining your own graphing callbacks,
> replacing the default routines with your own.
>
> I've attached the default graphing script (vmd/scripts/vmd/graphlabels.tcl)
> for you to have a look at. Let us know what you think.

Thanks, i've looked at it, and i think it could be trivial or not.
The title is written via the $item command, line 19 of the script:

    set input "@type xy\n@ title \"$item\"\n"

And i suspect that $item contains an internal vmd variable designing the
bond, angle, ... like bond0, bond1, ...

So the trivial way of doing it is replacing bond0 by a more explicit
description like : RESNAME1(ATOMNAME1)-RESNAME1(ATOMNAME1) for a bond,
RESNAME1(ATOMNAME1)-RESNAME2(ATOMNAME2)-RESNAME3(ATOMNAME3) for an
angle,
RESNAME1(ATOMNAME1)-RESNAME2(ATOMNAME2)-RESNAME3(ATOMNAME3)-RESNAME4(ATOMNAME4) for a dihedral.

The problem may arise from changing the vmd nomenclature ($item may be
used elsewhere ?) in that case, i would define a new one like $item_name
containing the above way of numbering (or a better one, i'm really
open).

I'm ready to help, but i think i would search for :
1 - variable defining bond/angles/dihedral (as they are in the box, i
think it is quite easy to find them)
2 - define $item with them
or
2' - define $item_name with them

3 - change nothing in the script
or
3' - change like 19 of script vmd/scripts/vmd/graphlabels.tcl to

    set input "@type xy\n@ title \"$item_name\"\n"

I don't know how complicate this is, but i'll appreciate very much this
feature. I i can help more, i'm ready.

Stef

PS : If you can tell me which variables contain the atom names, etc or
where i can find them, it will be a pleasure for me to implement it. 

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