VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 09 2013 - 10:35:21 CDT

Hi,
  In your note below there are several statements that are somewhat
unclear. What is it that you're trying to export to STL, a surface mesh,
or something else? You haven't really explained in what way the .stl files
you're generating "don't match" the originals. If you would like more
assistance, you will either need to provide much more detail, or you may
need to post your input and output files somewhere so that we can inspect them.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 08, 2013 at 05:06:29PM +0000, Nandigana, Vishal Venkata Raghave wrote:
> 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 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/