VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jun 02 2009 - 09:22:43 CDT
- Next message: John Stone: "Re: APBS error : Cannot read output file"
- Previous message: Axel Kohlmeyer: "Re: Memory Problem with tcl/tk script..."
- In reply to: Thomas Evangelidis: "adding atoms to empty molecules"
- Next in thread: Thomas Evangelidis: "Re: adding atoms to empty molecules"
- Reply: Thomas Evangelidis: "Re: adding atoms to empty molecules"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
On Mon, 2009-06-01 at 21:47 +0300, Thomas Evangelidis wrote:
> Dear VMD users,
dear tom,
> is there a neat way to add atoms to empty molecules generated with mol
> new atoms [natoms] command?
just have a look at the scripts in the topotools plugins.
you can now write molecule reader plugins entirely from script.
all you need to do is to:
set mol [mol new atom ####]
animate dup $mol
then "fill" the atoms with properties (name, type, mass,
charge, resid, rename, ...)
and finally do a:
mol reanalyze $mol
and you should be at the same point as when you read in
the molecule via mol new.
cheers,
axel.
> thanks,
> Tom
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
- Next message: John Stone: "Re: APBS error : Cannot read output file"
- Previous message: Axel Kohlmeyer: "Re: Memory Problem with tcl/tk script..."
- In reply to: Thomas Evangelidis: "adding atoms to empty molecules"
- Next in thread: Thomas Evangelidis: "Re: adding atoms to empty molecules"
- Reply: Thomas Evangelidis: "Re: adding atoms to empty molecules"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]