VMD-L Mailing List

From: Akiyama, Jotaro (jotaro_at_ti.com)
Date: Thu Nov 11 2004 - 18:56:02 CST

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