From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Feb 13 2014 - 03:28:18 CST

As far as I know, the PDB format holds 2 columns that could be used for that, called "Beta" and "Occupancy". Otherwise you can set any value you want for those columns and for multiple user defined values from the TCL interface. So you could also read those information afterwards to you structure from any file and format you want. Afterwards you can use Coloring Method->Beta for instance to visualize.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: Arham Amouie [mailto:erham65t_at_yahoo.com]
> Gesendet: Donnerstag, 13. Februar 2014 09:51
> An: Norman Geist
> Cc: VMD Mailing List
> Betreff: Re: AW: vmd-l: Simplest file format that includes atom color?
>
> I mean coloring by some physical quantity, like velocity, speed,
> potential energy, etc.
>
> Thanks
> Arham Amouei
>
> --------------------------------------------
> On Thu, 2/13/14, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
>
> Subject: AW: vmd-l: Simplest file format that includes atom color?
> To: "'Arham Amouie'" <erham65t_at_yahoo.com>
> Cc: "VMD Mailing List" <vmd-l_at_ks.uiuc.edu>
> Date: Thursday, February 13, 2014, 9:50 AM
>
>
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> Hi Arham,
>
>
>
> I suppose with „each atom can
> have its particular color“ you
> mean coloring by element? If so, the xyz format does already
> allow to mention
> the element of the atoms in the 1st column, see
> http://en.wikipedia.org/wiki/XYZ_file_format, and VMD should use
> it. Otherwise please explain more detailed.
>
>
>
>
>
> Norman Geist.
>
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> Von:
> owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu]
> Im Auftrag von Arham
> Amouie
>
> Gesendet: Mittwoch, 12. Februar 2014 20:29
>
> An: vmd-l_at_ks.uiuc.edu
>
> Betreff: vmd-l: Simplest file format that includes
> atom color?
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> Hello
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> I've
> written a MD code for EAM potentials. The typical number of
> atoms is of the order of 1 million. This code saves the
> positions in xyz files
> and I use VMD for visualization. Now, I'm going to
> change the output, so that each
> atom can have its particular color. I used csv format of
> ParaView for this
> reason, but ParaView doesn't work fast for me. What is
> the easiest solution in
> VMD?
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> Thanks in
> advance
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> Arham
> Amouei
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