VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 11 2004 - 21:51:00 CST

Hi,
  Just FYI, even if you downloaded VMD 10 days ago, that version still has
the plugins from 2003 in it. To get the latest version of the XYZ plugin,
you've got to download new plugins from the plugin page:
  http://www.ks.uiuc.edu/Research/vmd/plugins/

To see what atom names are being assigned, use the "selections"
tab from the Main->Graphics->Representations window, and select
the "name" item from the keyword list to see the range of atom names
displayed in the "value" list. If your XYZ plugin is interpreting
the atom indices right you'll see the names that are being assigned there.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 12, 2004 at 09:56:02AM +0900, Akiyama, Jotaro wrote:
> Hi
>
> Thank you for your information.
> But I still have problem.
> I think my XYZ plugin is a newest version since I download VMD very recently
> (aroud 10days ago).
> I did as you said, but all atoms became same color.
> In that process, the only "H" in "name" was workable.
>
> I should explain about my system in more detail.
> The system I'm working on is Al-Ni alloys system
> In my result XYZ file, Al is named as atom type number 1 and Ni type 2.
> Should I change the atom type to correct periodic element number?
>
> Thanks
> Akiyama
>
> ----- Original Message -----
> From: "John Stone" <johns_at_ks.uiuc.edu>
> To: "Akiyama, Jotaro" <jotaro_at_ti.com>
> Cc: <vmd-l_at_ks.uiuc.edu>
> Sent: Friday, November 12, 2004 1:57 AM
> Subject: Re: vmd-l: Coloring by type?
>
>
> >
> > Hi,
> > This is somewhat tricky, as the method depends on whether you're
> > using a version of the XYZ plugin that converts the periodic element
> > numbers into atom name strings or not. Assuming you are (the newest
> > versions do), then you can specify a "name" atom selections and
> > draw the specifically colored atoms with with their own representations,
> > which works with any version of VMD. If you're using an old XYZ plugin,
> > the "names" might actually be the integer element numbers.
> >
> > If you don't want to manually set the color but rather want the specific
> > atoms to get a specific color by default, you can set them in the color
> > window (Main->Graphics->Colors). Highlight "Name", then the atom name
> > of interest, then the color you want to assign it.
> >
> > If that still isn't what you're looking for, let me know.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Mon, Nov 08, 2004 at 06:06:34PM +0900, Akiyama, Jotaro wrote:
> > > Hi all VMD users.
> > >
> > > I have trouble in coloring atoms.
> > > I have two atom types which are named by integer as .xyz formal file.
> > > Can I color the each atom type by number?
> > >
> > > The format is as below.
> > > (Assuming two atoms of atom type 1 and two atoms of atom type 2
> > > and I would like to color type 1 red and type 2 blue.)
> > >
> > > atom type number x y z
> > > for example
> > > 1 x y z
> > > 1 x y z
> > > 2 x y z
> > > 2 x y z
> > >
> > >
> > > For sure, I use windows version on windows 2000.
> > >
> > >
> > > Thanks.
> > >
> > > Akiyama
> > --
> > 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