From: Akiyama, Jotaro (jotaro_at_ti.com)
Date: Fri Nov 12 2004 - 02:45:10 CST

Hi

I download the latest plugin and it seems work well.
Thanks a lot!

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 12:51 PM
Subject: Re: vmd-l: Coloring by type?

>
> 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