VMD-L Mailing List

From: O'Reilly Science Art (oreillyscienceart_at_gmail.com)
Date: Thu Oct 05 2017 - 17:20:24 CDT

Bingo! Thank you so much!!
Mary

On Thu, Oct 5, 2017 at 2:49 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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
> > Ā
> >
> > 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
> > Ā
> >
> > 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:Ā ā**startup.commandā**
> > canā**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/
> 

-- 
Mary O'Reilly, Ph.D.
*Owner, O'Reilly Science Art, LLC*
*www.oreillyscienceart.com <http://www.oreillyscienceart.com>*