VMD-L Mailing List

From: Nandigana, Vishal Venkata Raghave (nandiga1_at_illinois.edu)
Date: Wed May 08 2013 - 12:06:29 CDT

Hi Josh,

I had performed the steps you had suggested and was able to rescale the coordinates and converted the rescaled .pdb file to .stl file using vmd. However, the .stl file I had generated from chimera software (before rescaling DNA coordinates) gives a much better replicate of the DNA structure compared to the .stl file generated from vmd (after rescaling DNA coordinates). I would however like to point that the .stl file generated from Chimera software after rescaling DNA coordinates looked weird with the bonds not be scaled properly. I am not able to attach the files due to the limit in the file size while replying to this message. Please let me know if we can generate a complete replicate of DNA using vmd in .stl format.

Thanks

Regards,
Vishal
________________________________________
From: Vermaas, Joshua V
Sent: Tuesday, May 07, 2013 3:09 PM
To: Nandigana, Vishal Venkata Raghave
Cc: vmd-l_at_ks.uiuc.edu
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
(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