VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Sun Dec 15 2002 - 23:07:05 CST

Hi,

The atom names written by VMD are the same as the file they came from; VMD
does not rename atoms in any way (though the psfgen module has the potential
to do this). The last (numeric) column is indeed the temperature factor;
for historical reasons VMD calls it "beta". Thus the Beta coloring method
will color according to the values in this column.

VMD generally adheres to the RCSB PDB format; here's a link to a formal
description:
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html

Hope this helps,
Justin

On Fri, Dec 13, 2002 at 06:23:17PM -0800, Ioana Cozmuta wrote:
> Hi,
>
> Just a simple question: what format is VMD writing the pdb files, it seems
> to me that hydrogens have Brokhaven names. Also the last column contains
> the temperature factor?
>
> Thank you,
> Ioana
>
>
> ****************************************************************************
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-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys