VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 24 2006 - 10:09:12 CST

Dean,
  Yes, the RCSB PDB site changed in a way that breaks the old webpdb plugin.
Can you verify that you've got the plugin update 3 installed correctly?
If you have installed the update correctly, added the .vmdrc lines to load
them, and all of the paths etc are correct, you should get a message that
looks similar to this (though not the same) when VMD starts up:

Found 21 plugins or data handlers in directory
        '/home/johns/plugins/compile/lib_SOLARIS2_64/molfile'

If you're not seeing that message at startup, then VMD isn't seeing
the plugin update.

Let me know if you need more help with this.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 24, 2006 at 08:59:08AM -0600, Dean Appling wrote:
> I have not used VMD (ver. 1.8.3 for MacOSX) since December.
> Yesterday, when I tried to load a pdb file, the structure fails to
> load and I get the following error message:
>
> ERROR) BaseMolecule: init_atoms called with invalid number of atoms: 0
> ERROR) molecule_structure: Unable to read structure for molecule 0
> Info) Using plugin webpdb for coordinates from file 1ee9
> ERROR) Some frames from file '1ee9' could not be loaded
> ERROR) because the number of atoms could not be determined. Load a
> ERROR) structure file first, then try loading this file again.
>
> I installed the latest Plugins Update 3, but I still get the same
> error message. It is as if something has changed at the RCSB PDB web
> site so that the structure files are not recognized correctly.
>
> Can anybody help?
>
> thanks,
>
> dean 

-- 
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