VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Aug 25 2007 - 23:04:51 CDT

Hi,
  The main reason you get a different number of digits is that VMD
doesn't care what the original number of decimal places was, as it stores
all coordinates as 32-bit IEEE-754 floating point numbers internally,
regardless what type of file the molecule originally came from. Even the
number of decimal places in the PDB isn't particularly meaningful, as
the more interesting fact would be how good the crystallographic resolution
is, rather than the decimal precision limits of the file format itself.
In any case, VMD stores things with much higher precision than PDB formats
internally, since VMD also works with binary file formats that contain
far more precise atom coordinates etc. If you want fewer decimal places
in output for example, you can use the Tcl "format" command to emit the
atom coordinates with however many decimal places you prefer.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Aug 26, 2007 at 12:10:02AM +0100, Nuno Loureiro Ferreira wrote:
> Hi *
>
> I loaded a regular pdb (e.g. through mol pdbload).
> I wonder why a "$sel get x" command in the console gives me 10 decimal
> digits for each atom in $sel?
> A pdb commonly has only 3 digits.
> Cheers,
>
> Nuno.
> P.S. 1.8.6 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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