VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 24 2004 - 13:26:50 CST

Joe,
  Can you email me a gzipped copy of one of the PDB files that gives you
trouble on your mac? I suspect that what's going on is that your PDB files
contain carriage returns in addition to line feeds, and it may be confusing
VMD's PDB parser. If you send me one of the troublesome files, I will know
for sure. Be sure to gzip the file before you send it so that your mail
program doesn't alter the file...

  John

On Wed, Nov 24, 2004 at 11:34:47AM -0700, bozell, joe wrote:
> I have been using an older version of Chem3D (version 5.0) to generate PDB
> files for visualization. All files so far open and can be manipulated in
> both RasMol and Protein Explorer. However, when these files are loaded into
> VMD, only a small fraction of the atoms, and none of the bonds show up. One
> file contains 920 atoms, and only 13 show up in VMD. Another contains about
> 90 atoms, and only 1 or 2 show up. A third file (444 atoms) shows up
> correctly in VMD, however, the text version of its PDB file does not appear
> to be different than the ones that fail.
>
> I¹m using the latest version of VMD on a PowerBook G4, OS 10.3.6.
>
> Any hints would be greatly appreciated.
>
> Joe Bozell
> National Renewable Energy Laboratory 

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