VMD-L Mailing List

From: Steven(Yuhang) Wang (ywang148_at_illinois.edu)
Date: Wed Jul 26 2017 - 20:50:37 CDT

Dear John,

The current VMD 1.9.4 only have installer for Mac and Linux. Is there
going to be a windows installer soon? One thing I noticed is that after
failing to download a pdb file on Windows 8.1, VMD 1.9.3 won't show the
menu bar the second time I open it. I had to uninstall and reinstall to
fix it.

Steven Wang

On 7/26/2017 9:53 AM, John Stone wrote:
> Hi,
> This issue is caused by the recent (significant) changes that were made
> to the structure of the RCSB PDB web site, that have relocated the PDB files
> and changed the way that they are downloaded. This affects all of the
> previously released versions of VMD prior to the latest VMD 1.9.4 test versions.
>
> The VMD 1.9.4a7 test version that is currently posted on the VMD
> download page was updated to adapt to the new PDB web site structure,
> and it works for me when I use both the old "mol pdbload WXYZ" and newer
> "mol new WXYZ" commands for a given PDB accession code, WXYZ.
>
> If you have a case that doesn't work with VMD 1.9.4a7, please let us know.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Wed, Jul 26, 2017 at 04:40:14AM +0000, Mike McCallum wrote:
>> Hi there,
>> Iâ**m not quite sure when this happened, but I am unable to get â**mol
>> pdbloadâ** to work. I tried this with 1.9.2, 1.9.3 and 1.9.4a versions on
>> OS X, new and old versions of the OS. Iâ**m running a class right now
>> and Iâ**m asking the students to do this, so help is much appreciated.
>> Here is the startup info + error.
>> â**
>> Info) VMD for MACOSXX86, version 1.9.3 (November 30, 2016)
>> Info) [1]http://www.ks.uiuc.edu/Research/vmd/
>> Info) Email questions and bug reports to [2]vmd_at_ks.uiuc.edu
>> Info) Please include this reference in published work using VMD:
>> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
>> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
>> Info) -------------------------------------------------------------
>> Info) Multithreading available, 8 CPUs detected.
>> Info) OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
>> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
>> Info) Full GLSL rendering mode is available.
>> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture
>> (8)
>> Info) Dynamically loaded 2 plugins in directory:
>> Info) /Applications/VMD 1.9.3.app/Contents/vmd/plugins/MACOSXX86/molfile
>> vmd > The PDB is supported by RCSB, the NSF, US PHS, NIH, NCRP, NIGMS,
>> NLM,
>> and US DoE, who are not liable for the data. PDB files shall not be
>> sold. See [3]ftp://ftp.rcsb.org/advisory.doc for full details.
>> Info) Using plugin webpdb for structure file 1anv
>> ERROR) BaseMolecule: init_atoms called with invalid number of atoms: 0
>> ERROR) molecule_structure: Unable to read structure for molecule 0
>> ERROR) molecule_structure: severe error indicated by plugin aborting
>> loading of molecule 0
>> Info) Using plugin webpdb for structure file 1sse
>> ERROR) BaseMolecule: init_atoms called with invalid number of atoms: 0
>> ERROR) molecule_structure: Unable to read structure for molecule 1
>> ERROR) molecule_structure: severe error indicated by plugin aborting
>> loading of molecule 1
>> --
>>
>> Cheers
>> Mike
>> --
>> C. Michael McCallum
>> Professor
>> Department of Chemistry, UOP
>> mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209)
>> 946-2607 fax
>>
>> References
>>
>> Visible links
>> 1. http://www.ks.uiuc.edu/Research/vmd/
>> 2. mailto:vmd_at_ks.uiuc.edu
>> 3. https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.rcsb.org_advisory.doc&d=DwMGaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=f0N5v4NY00lzag1jzuVkui7_420G9K7DR41QSpC55bU&m=rWWR9Az2MVsLhO_SXXIc2q-87aWJLXgWKZh3iS4aSww&s=THZnqm0QkLreWUIzWfNNHup7T3ZCORN2OPOYRoy7n7U&e=