VMD-L Mailing List

From: Seibold, Steve Allan (stevesei_at_ku.edu)
Date: Wed Jan 02 2019 - 15:03:47 CST

Hi Joao
Thanks for your response…The start of the script is as follows:

proc distance {seltext1 seltext2 N_d f_r_out f_d_out} {

set sel1 [atomselect top "$seltext1"]
set sel2 [atomselect top "$seltext2"]

I finally figured it out..You are correct it was a selection problem…When running the script through VMD I needed to call the “seltext1” (in my case “protein and resid 450”) instead of “sel1”
That is,
>distance “protein and resid 450” “protein and resid 471” 10 test1.dat test2.dat

It is clearly pointed out in the example, I just missed understood the script…

I was incorrectly using “sel1” and “sel2”..That is,
>distance “sel1” “sel2 “ 10 test1.dat test2.dat

Thanks again for your response…

Steve

From: João Ribeiro <jribeiro_at_ks.uiuc.edu>
Sent: Wednesday, January 2, 2019 2:47 PM
To: Seibold, Steve Allan <stevesei_at_ku.edu>
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Parsing error in TkConsole

Hi Steve,

Without knowing what "distance.tcl" has in it, it is impossible to say for sure what is the problem. I would bet that the proc distance is expecting a selection text, rather than an atom selection id. If this is not the case, please provide the content of the distance.tcl file.

Best

Joao

On Wed, Jan 2, 2019 at 1:44 PM Seibold, Steve Allan <stevesei_at_ku.edu<mailto:stevesei_at_ku.edu>> wrote:
Hello
I think this is a simple problem, but I can’t seem to fix it…

I have loaded into vmd my psf file and the accompanying dcd file.

Then, using the TkConsole,:
>set sel1 [atomselect top “protein and resid 450”]
>atomselect0
>set sel2 [atomselect top “protein and resid 471”]
>atomselect1
>source distance.tcl
>distance $sel1 $sel2 10 test-r.dat test-d.dat
Atomselect: cannot parse selection text : atomselect0
>$sel1 get resname
GLY GLY GLY GLY GLY GLY GLY GLY GLY

GLY is the first three residues of the peptide…450, 451, 452…

Can someone tell me what I am doing incorrectly?

Thanks, Steve


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……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/ta=VdKbmJQxnxqm2r3X%2BDPyS0JUlHxN4rE%2F%2FrQyIvLczfw%3D&reserved=0>
jribeiro_at_ks.uiuc.edu<mailto:jribeiro_at_ks.uiuc.edu>
+1 (217) 3005851