VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue May 07 2013 - 15:09:09 CDT

Hi Vishal,

You could, but then it would cease to be a pdb file. The pdb file format
specification explicitly expects the units to be in Angstroms
(http://www.wwpdb.org/documentation/format33/sect9.html#ATOM). If you
don't particularly care about how the structure looks in VMD, you can of
course rescale the coordinates yourself using the tkConsole, and then
write the result out to pdb.

set all [atomselect top all]
foreach dimm [list x y z radius] {
$all set $dimm [vecscale 0.1 [$all get $dimm]]
}
$all writepdb nowinnm.pdb

Again, since the pdb format assumes the units to be angstroms, all the
analysis programs I know of assume that the x, y, and z fields of pdb
files are in angstroms, so make sure you don't unwittingly make a
mistake if you choose to do the conversion.

-Josh Vermaas

On 05/07/2013 01:55 PM, Nandigana, Vishal Venkata Raghave wrote:
> Hi All,
>
> I am relatively new to VMD. I would like to know if it is possible to convert the units of a pdb file from Angstorm to nanometer.
>
> Thanks
>
> Regards,
> Vishal