VMD-L Mailing List

From: Heidenreich, Joseph David (joheiden_at_imail.iu.edu)
Date: Thu Jul 02 2009 - 14:17:25 CDT

I have created a script to color the atoms in the way I was asking about by utilizing the user field. I'd be happy to send it to anyone if they run into the same issue in the future.

________________________________________
From: Axel Kohlmeyer [akohlmey_at_cmm.chem.upenn.edu]
Sent: Wednesday, July 01, 2009 9:12 AM
To: Pawel Kedzierski
Cc: Heidenreich, Joseph David; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Coloring atoms by a general scalar

On Wed, 2009-07-01 at 11:27 +0200, Pawel Kedzierski wrote:
> On Tue, Jun 30, 2009 at 05:19:29PM +0000, Heidenreich, Joseph David wrote:
> > this, is there a way I could complete this in one swoop by merging the
> > XYZ file and the scalars I have into one file (I'm assuming a
> > different format than XYZ). And if so, could I be pointed toward a
> > direction that shows the standards and syntax of said file format?
>
> You may save your molecule(s) in PDB format and paste your scalars,
> possibly scaled (due to width constraint) in the beta field of every
> atom, then color by beta in VMD.

pawel,

beta is a "once per molecule" field so this doesn't work for
trajectories. in general "abusing" the beta field like this
is not a very good idea. many people screw up the format and
the format restrictions of the field cuts off a lot of accuracy.

people have historically done this, but it is more of a crutch
than a solution. once we have expanded the molfile API and some
more portable and flexible file formats, this will hopefully
all be a thing of the past.

cheers,
   axel.

>
> PDB file format is described here:
> http://www.wwpdb.org/docs.html
>
> however you only need to know the format of ATOM lines.
>
> > Thanks for the time,
> >
> > Joe Heidenreich
>
> HTH,
> Pawel Kedzierski 

--
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
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