VMD-L Mailing List

From: Andrew M. Simms (amsimms_at_u.washington.edu)
Date: Fri Apr 16 2010 - 17:48:11 CDT

Thanks, John. However, I do need that flexibility. I have web code that
generates PDBs from a database. When it wasn't working I thought I'd check
with a generic URL from PDB.org. I have used my URLs successfully with JMol
and Chimera, but we have VMD users who'd like to use them as well.

--Andrew

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Friday, April 16, 2010 3:00 PM
To: Andrew M. Simms
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: mol urlload -- this doesn't seem to work in Windows (it
does seem to work from Linux)

Hi,
  If you're just loading PDB files from the main RCSB site, all
you have to do is to specify the four character accession code
and VMD will automaticallly load them, e.g.:
  mol new 1enh

If you need to load an arbitrary file type from an arbitrary URL,
there are also ways to do that, but unless you need that flexibility,
the method I show above is the best way to go for getting PDB structures,
it supercedes the old "mol urlload" mechanism.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 16, 2010 at 09:30:09AM -0700, Andrew M. Simms wrote:
> Hello all,
>
> I've been trying to get the urlload command to work from Windows:
>
> vmd > mol urlload pdb
http://www.pdb.org/pdb/download/downloadFile.dofileFormat=pdb&compression=NO
&structureId=1ENH
>
> but I get:
>
> couldn't open "C:UsersmsimmsAppDataLocalTemp???urlload": no such file or
directoryvmd_mol_urllload failed.
>
> Is there another way to get vmd to load PDB files from a URL?
>
> Thanks,
>
> --Andrew
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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