From: Josh Vermaas (
Date: Tue May 07 2013 - 17:26:52 CDT

Oh. That isn't so bad then. VMD can write stl files too, it just isn't a
feature that gets highlighted very often (although they will be missing
normals). After you rescale the positions and radii, you can render the
VMD window (File->Render) using STL, and the resulting file will contain
all the triangles used to draw what is shown on the screen, and be
normalized to nanometers in real space.

On 05/07/2013 04:39 PM, Nandigana, Vishal Venkata Raghave wrote:
> Hi Joshua,
> Thanks for your reply. I was trying to convert my pdb file into .stl file using UCSF chimera software. The resulting .stl file, would be imported in my solver which was normalized in nm units. I would make note of your suggestions.
> Thanks.
> Regards,
> Vishal
> ________________________________________
> From: Vermaas, Joshua V
> Sent: Tuesday, May 07, 2013 3:09 PM
> To: Nandigana, Vishal Venkata Raghave
> Cc:
> Subject: Re: vmd-l: convert pdb file from angstorm to nm units
> 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
> ( 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