From: John Stone (
Date: Tue Jan 24 2006 - 10:09:12 CST

  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

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

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

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