VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 10 2002 - 18:02:39 CST

Dear Mihaly,
  When you load multiple PDB files, be sure that you set the
molecule file brower "Load files for" chooser to "New Molecule",
when you are loading PDB files of different structures.

If you don't tell it you want it in a new molecule, VMD assumes that
you want to use the Nth PDB file as a coordinate file, loading it into a
new timestep on the existing molecule.

This is one area where VMD 1.8 differs substantially from previous versions.

Let us know if you have any other questions.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Dec 10, 2002 at 05:59:19PM -0600, owner-vmd-l_at_ks.uiuc.edu wrote:
> Date: Tue, 10 Dec 2002 18:59:09 -0500
> From: Mihaly Mezei <mezei_at_inka.mssm.edu>
> X-X-Sender: mezei_at_fulcrum.physbio.mssm.edu
> To: vmd-l_at_ks.uiuc.edu
> Subject: PDB files in VMD1.8
> Message-ID: <Pine.SGI.4.44.0212101857210.5021525-100000_at_fulcrum.physbio.mssm.edu>
> MIME-Version: 1.0
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> Sender: Mihaly Mezei <mezei_at_physbio.mssm.edu>
>
> Greetings,
>
> I just downloaded VMB1.8 (Windows) and started experimenting with it. I
> have two PDB files. VMD has no problem loading either of them. Howvever,
> if I altready loaded one of them trying to load the second gives me the error
>
> ERROR) Error reading optional structure information from coordinate file
> D:/mezei/pdb/mmz_3.pdb
> ERROR) Will ignore structure information in this file.
> ERROR) Incorrect number of atoms (2319) in
> ERROR) coordinate file D:/mezei/pdb/mmz_3.pdb
> Info) Finished with coordinate file D:/mezei/pdb/mmz_3.pdb.
>
> This happens either if I chose explicitly pdb format or ask for automatic
> detection.
>
> Pls, answer to me directly to the address mezei_at_inka.mssm.edu, as I am not
> yet a subscriber to the list.
>
> Regards,
> Mihaly Mezei,
>
> Dept. of Physiology & Biophysics, Mount Sinai School of Medicine
> Voice: (212) 241-2186 Fax: (212) 860-3369|
> WWW (MSSM home): http://
> adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01
> WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei 

-- 
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