VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 16 2010 - 18:22:20 CDT

Andrew,
  I'm out of the office until Monday, but when I return I'll figure
out what's going on with the standard command there...

Cheers,
  John

On Fri, Apr 16, 2010 at 04:18:16PM -0700, Andrew M. Simms wrote:
> 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 

-- 
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