VMD-L Mailing List

From: Bryan Roessler (roessler_at_uab.edu)
Date: Wed Jun 06 2012 - 09:47:44 CDT

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
>