From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 20 2010 - 12:42:15 CDT

Hi,
  The cionize README file is here:
http://www.ks.uiuc.edu/Research/vmd/plugins/cionize/

On unix systems, the cionize binary is part of the VMD installation,
and can be found in the directory printed when you run this command
from within your VMD installation:
  puts "$env(VMDDIR)/plugins/[vmdinfo arch]/tcl/cionize1.0"
 
Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 20, 2010 at 01:36:32PM -0400, Parisa Akhski wrote:
> Hi,
>
> Thanks for the information. Would you please let me know where I can find
> the instructions to use it on the other platforms?
>
> Thanks,
> Parisa
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Tue 7/20/2010 10:41 AM
> To: Parisa Akhski
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Cannot find "cionize plugin" in VMD
>
> Hi,
> For the short term, you will need to use the cionize tool
> on one of the other platforms, as we don't have a Windows version
> compiled at present. Let us know if you need help with this.
>
> Ultimately this functionality will become part of VMD, but if I
> end up having the time, I will look into getting a Windows version
> compiled.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jul 16, 2010 at 03:26:59PM -0400, Parisa Akhski wrote:
> > Hi everyone,
> >
> > Does anyone please know which version of VMD covers "cionize plugin"
> > (preferably on windows)? I need to neutralize a DNA molecule and I'am
> > really confused in finding it!
> >
> > Thanks a lot,
> >
> > Parisa
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078