From: Shirley Li (li19104_at_yahoo.com)
Date: Thu Oct 06 2005 - 15:54:24 CDT
Thank Peter and JC so much for the very quick
response. That works!
Shirley
--- JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> vmdtext is just an alias that we use in the
> tutorials to streamline
> some things.
>
> While you can of course run it from the tkcon in vmd
> (source split.s),
> what you want is "vmd -dispdev text -e split.s ".
>
>
> On Oct 6, 2005, at 2:33 PM, 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.s
> > --------------------------------------------
> >
> >
> >
> > # 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
> >
> > }
> >
> > Yahoo! for Good
> > Click here to donate to the Hurricane Katrina
> relief effort.
>
__________________________________
Yahoo! Mail - PC Magazine Editors' Choice 2005
http://mail.yahoo.com
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:59 CST