VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 21 2010 - 16:22:05 CDT

Hi Parisa,
  If you let me know which unix platform you're using, I can
provide you a pre-compiled binary.

Cheers,
  John

On Wed, Jul 21, 2010 at 02:31:39PM -0400, Parisa Akhski wrote:
> Hi John,
>
> By compiling the plugin tree for cionize, do you mean:
> "package require cionize"
> "cionize"
>
> If yes, after typing "cionize" it says that the command is invalid.
> If not, would you please let me know how I can compile it?
>
> Thanks,
>
> Parisa
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Tue 7/20/2010 3:09 PM
> To: Parisa Akhski
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Cannot find "cionize plugin" in VMD
>
> Hi,
> Actually, I gave the wrong info for the location of the binaries
> in an installation. They were not being copied into the final
> distribution in the previous VMD revs. I have changed this for
> the new version of VMD, but for VMD 1.8.7 one would get cionize
> by compiling the plugin tree, or I can provide executables on request.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Jul 20, 2010 at 12:42:15PM -0500, John Stone wrote:
> > 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
>
> --
> 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