VMD-L Mailing List

From: Shirley Li (li19104_at_yahoo.com)
Date: Thu Oct 06 2005 - 14:37:50 CDT

Dear all,

 

I have a question about VMD scripting.

 

I have created the script file using a text editor such as "vi", and save it, such as the one attached below. How can I execute it? I tried "vmdtext -e split.s" but got a error message "vmdtext: command not found". Do I need to lounch VMD in order to run this script?

 

Your help/information will be greatly appreciated.

 

Shirley

 

 

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# Split a file containing protein and water into separate segments.
# Creates files named myfile_water.pdb, myfile_frag0.pdb, myfile_frag1.pdb,...
# Requires VMD.
mol load pdb myfile.pdb
set water [atomselect top water]
$water writepdb myfile_water.pdb
set protein [atomselect top protein]
set chains [lsort -unique [$protein get pfrag]]
foreach chain $chains {
set sel [atomselect top "pfrag $chain"]
$sel writepdb myfile_frag${chain}.pdb

                
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