From: Matthew Stewart (
Date: Thu Oct 24 2013 - 18:30:51 CDT


If you are referring to a variable that you have set, in this case sel, you need to add a $ to call the variable. So, your second line should be ->

$sel writepdb test.pdb

Matthew Stewart

Dr. Matthew B. Stewart
Postdoctoral Research Fellow
Institute for Sustainability and Innovation
Werribee Campus, Victoria University
Phone: +61 3 9919 7641
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From: [] On Behalf Of Rejwan
Sent: Friday, 25 October 2013 7:49 AM
To: John Stone
Subject: vmd-l: writing PDB

I bit puzzled here. Not sure what I'm doing wrong in TK console in writepdb command.

>Main< (VMD) 10 % set sel [atomselect top "not (resname POPC)"]
>Main< (VMD) 11 % sel writepdb test.pdb
bad option "writepdb": must be clear, get, handle, or own
>Main< (VMD) 12 %


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