VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 18 2008 - 11:17:44 CDT

Hi,
  When you say it doesn't work when you source the tcl script
in the console, what happens? Do you get an error, or your script
simply doesn't run?

Regarding calling STRIDE, you would do that with this command,
or a variant thereof:
  mol ssrecalc top

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Aug 17, 2008 at 04:51:56PM -0700, Yuan Feng wrote:
> Hello,
>
> I am writing a tcl script to calculate secondary sturcure for a trajectory based on dssp. I use "writepdb" to generate a pdb file for every frame, and then use "exec dssp ex.pdb ex.dssp" to call the dssp program. Then I parse the dssp file to get information. However, I find it does not work if I source the tcl script, althought it works if I enter them in the tk console. Also, it only works for one frame. Does anyone know how vmd call stride (I cannot find the scripit of "ssrecalc") so I can learn from that? 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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