VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 24 2006 - 11:13:39 CST

Dean,
  the instructions are on the web page for update 3:
http://www.ks.uiuc.edu/Research/vmd/plugins/183update3/

If you don't already have a .vmdrc file, you'll want to copy
create one containing (at a minimum) the command:
  menu main on

After that, follow the update 3 instructions adding the other
necessary line(s) and you should be good to go. Start up VMD
again and you should see messages indicating new plugins have loaded.

  John

On Tue, Jan 24, 2006 at 10:44:33AM -0600, Dean Appling wrote:
> John: I guess I do not have the plugins loaded correctly - I did not
> get the startup message. I did not realize I had to add any .vmdrc
> lines to get the plugins to load - how do I do that?
>
> I am running VMD 1.8.3 on a MacOS 10.4.4
>
> thanks for your help,
>
> dean appling
>
> On Jan 24, 2006, at 10:09 AM, John Stone wrote:
>
> >
> >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 

-- 
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