VMD-L Mailing List

From: Maurício Menegatti Rigo (mauriciomr1985_at_gmail.com)
Date: Tue Aug 12 2014 - 08:31:12 CDT

Dear Norman,

thank you for your help. I'll try your tips and also learn a bit (actually
a lot) more about TCL scripting.

o/

2014-08-11 2:29 GMT-03:00 Norman Geist <norman.geist_at_uni-greifswald.de>:

> You can use the user (or user2, user3) fields in the atomic structure in
> VMD to save per frame/per atom data. Afterwards choose coloring method
> "user" (or user2, user3) within representations.
>
> Example:
>
> set [sel atomselect top "resid 1 to 10"]
> $sel frame $myframe
> $sel set user $myvalue
> $sel delete
>
> Of course you need to loop over your file. Google for "TCL line wise file
> read". You will also be interested in "VMD
> Main->Extensions->Visualization->Color Scale Bar"
>
> Norman Geist.
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> > Auftrag von Maurício Menegatti Rigo
> > Gesendet: Freitag, 8. August 2014 20:13
> > An: vmd-l_at_ks.uiuc.edu
> > Betreff: vmd-l: Tcl scripting - Coloring residues by frame along
> > trajectory
> >
> > Hi,
> >
> > I'm trying to make a script in Tcl to perform the following task over
> > my
> > "File.txt":
> >
> > ********************************************
> > File.txt
> >
> > 0 379 ARG - 476 TYR - 1.852063
> > 0 380 ALA - 476 TYR - 3.242678
> > 0 380 TYR - 621 TYR - 3.263404
> > 0 380 TYR - 476 TYR - 2.483822
> > 0 379 PHE - 412 TYR - 2.844423
> > 1 378 ARG - 476 TYR - 1.947969
> > 1 378 PHE - 412 TYR - 2.629322
> > 1 377 ARG - 414 TYR - 1.777359
> > 1 377 ARG - 667 GLY - 2.279196
>
>
> ---
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> 

-- 
M.Sc. Maurício Menegatti Rigo
Núcleo de Bioinformática do Laboratório de Imunogenética
Departamento de Genética
Instituto de Biociências
Universidade Federal do Rio Grande do Sul - Campus do Vale
Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M
CEP:91501-970 Caixa Postal 15053
Porto Alegre, RS, Brasil
Tel: +55 51 3308 9938