VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 06 2012 - 12:07:11 CDT

Bryan,
  Assuming your atom counts aren't too terribly huge, VMD should be
writing the atom indices in hexadecimal, which can be parsed using any
typical computer language. The PDB writer is doing this:

  if (index < 100000) {
    sprintf(indexbuf, "%5d", index);
  } else if (index < 1048576) {
    sprintf(indexbuf, "%05x", index);
  } else {
    sprintf(indexbuf, "*****");
  }

Cheers,
  John Stone
   vmd_at_ks.uiuc.edu

On Wed, Jun 06, 2012 at 09:47:44AM -0500, Bryan Roessler wrote:
> Hi John,
> Yes, I'm trying to write out pdb files. I know that VMD is adhering to the
> PDB standard, I was hoping there was a way to easily override it. I'm
> guessing I'll need to save chunks of the pdb and add a numerical prefix
> before each atom number before recombining them? I'm currently unaware of
> any language that can parse alphanumeric characters...
> Thanks,
> Bryan
>
> On Tue, Jun 5, 2012 at 1:05 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Above 99999 you can't write a legal PDB file without playing tricks.
> I assume you are trying to write PDB files yes? Other file formats
> don't
> have this issue.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Tue, Jun 05, 2012 at 12:07:15PM -0500, Bryan Roessler wrote:
> > Hello,
> > Is there a method to force VMD to save atom numbers numerically
> instead of
> > alphanumerically above atom number 99999? Several programs (notably
> CAVER)
> > have problems storing alphanumeric labels into int fields.
> > Thanks,
> > Bryan
>
> --
> NIH Resource 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/ Fax: 217-244-6078 

-- 
NIH Resource 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/       Fax: 217-244-6078