VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Oct 06 2005 - 14:43:15 CDT

Dear Shirley,
vmdtext is a shortcut on our systems to the command
vmd -dispdev text

If you run
vmd -dispdev text -e split.s
it should work.
Peter

Shirley Li wrote:

> 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
>
>
>
>
>
> -------------------------------------------------------------------------------------------------
>
> # 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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