VMD-L Mailing List

From: Andrew M. Simms (amsimms_at_u.washington.edu)
Date: Fri Apr 16 2010 - 18:18:16 CDT

Perfect--that works! Thanks!

--Andrew

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Friday, April 16, 2010 4:10 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)

Andrew,
  Try this:
vmd_mol_urlload http://some.url/somewhere/my.pdb c:temp.pdb
mol new c:temp.pdb waitfor all
file delete temp.pdb

Let me know if that works for you or not.

Cheers,
  John

On Fri, Apr 16, 2010 at 03:48:11PM -0700, Andrew M. Simms wrote:
> 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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ 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
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078