VMD-L Mailing List

From: Peter C. Lai (pcl_at_uab.edu)
Date: Wed Jun 06 2012 - 14:21:46 CDT

Well technically the PDB standard doesn't support hexadecimal atom numbers
either, which is why non-VMD/NAMD will not read them.

Does CAVER require the entire solvated box? (which is usually why the
atomcounts are so high). If not, does stripping irrelevant waters/lipids from
the structure keep you under the limit?

You may unfortunately ultimately be stuck splitting your structures down an
axis and running CAVER on each section, shotgun style.

Also: I've seen you on the list before, so hi from the other building!

On 2012-06-06 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
> > 

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