VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 05 2017 - 13:49:28 CDT

Hi,
  The RCSB PDB changed the structure of their web-based download mechanisms
earlier this summer. This change breaks the ability all of all versions of
VMD that pre-date the change from being able to download directly from
the RCSB web site. The test versions of VMD 1.9.4 that are posted on
the web site have been updated to accomodate the new RCSB web site
structure, and you should be able to use the new test versions and
access web-downloaded PDB structures as before.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 05, 2017 at 02:43:16PM -0400, O'Reilly Science Art wrote:
> I use the Molecule File Browser window, and enter the pdb accession code
> (4 digit) after Filename. For Determine File Type I've tried both
> "Automatically" and "Web PDB Download", so they are coming from the
> databank.
> On Thu, Oct 5, 2017 at 2:37 PM, Belkin, Maxim <[1]mbelkin_at_illinois.edu>
> wrote:
>
> The problem you're having should not be VMD version-specific, so it
> would better to solve it for the latest version of VMD.
> How do you (attempt to) load molecules? Do you use VMD's GUI or command
> line? Are molecules in local PDB files or from the PDB Databank?
> Maxim
> Â
>
> On Oct 5, 2017, at 13:25, O'Reilly Science Art
> <[2]oreillyscienceart_at_gmail.com> wrote:
> Thanks so much, that did allow me to open it, but both versions are
> still unable to load molecules. I am running MacOSX version 10.11.6 if
> that helps at all.
> Thanks!
> Mary
> On Thu, Oct 5, 2017 at 2:09 PM, Belkin, Maxim
> <[3]mbelkin_at_illinois.edu> wrote:
>
> Try moving VMD to /Applications folder and launch it from there.
> Maxim
> Â
>
> On Oct 5, 2017, at 13:07, O'Reilly Science Art
> <[4]oreillyscienceart_at_gmail.com> wrote:
> Hi,
> I recently downloaded VMD 1.9.3 for MacOSX and I am unable to
> import pdb structures. I just got an error message that says it is
> unable to load.
> And now I'm getting this error message:Â â**startup.commandâ**
> canâ**t be opened because Sandbox is not allowed to open documents
> in Terminal.
> I tried going back to 1.9.2 and got the same results.
> Any suggestions?
> Thanks!
> Mary
> --
> Mary O'Reilly, Ph.D
>
> --
> Mary O'Reilly, Ph.D.
> Owner, O'Reilly Science Art, LLC
> [5]www.oreillyscienceart.com
>
> References
>
> Visible links
> 1. mailto:mbelkin_at_illinois.edu
> 2. mailto:oreillyscienceart_at_gmail.com
> 3. mailto:mbelkin_at_illinois.edu
> 4. mailto:oreillyscienceart_at_gmail.com
> 5. http://www.oreillyscienceart.com/ 

-- 
NIH Center 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/