VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 26 2017 - 09:53:12 CDT

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= 

-- 
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/