From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 10 2015 - 01:55:52 CDT

Hi,
  If I understand you correctly, it seems that you're using a Tcl script
from one of the tutorials? Normally you would run the Tcl script inside
of VMD, e.g. by running a command such as:
  source script.tcl

I don't know which specific script you're using nor what it says so
I can't comment on your other questions related to "workdir" etc.
If you provide the URL where you got the script from that might be
helpful.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Mar 21, 2015 at 03:06:42PM -0700, Akshata Rudrapatna wrote:
> Hello:
> I am currently trying to merge sixty copies of the cowpea mosaic virus
> capsid molecule into one large solvated molecule (like the one provided
> for the satellite tobacco mosaic virus tutorial). I found the
> MergeMultiFramesPDB Tcl file, but I had a few questions regarding it.
> 1) Do I need to download Tcl itself separately from NAMD and then
> implement this code?
> 2) Where do I program the code? Do I just use the TkConsole?
> 3) Where in the code do I need to provide file paths? Is "workdir" a part
> of the code or a reference to providing the file path to the work
> directory?
> I have already tried to use the TkConsole to utilize the code but it has
> not worked and does not yield any new files.
> Any help is greatly appreciated.
> Thanks,
> Akshata Rudrapatna

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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