From: Maxim Belkin (
Date: Tue Feb 11 2014 - 09:31:47 CST

Hi Boris,

Are you trying to add that PDB to some other molecule that has been already loaded?
“Incorrect number of atoms” means that VMD expects that PDB to have certain number of atoms. Try this in your console:

mol new 1oxy waitfor 1

It should work.


On Feb 10, 2014, at 9:16 PM, Boris Steipe <> wrote:

> VMD can't read 1OXY from PDB Web download, local file or even after I edit it to contain only the ATOM records.
> Error message:
> ERROR) Error reading optional structure information from coordinate file 1oxy
> ERROR) Will ignore structure information in this file.
> Info) Using plugin webpdb for coordinates from file 1oxy
> ERROR) Incorrect number of atoms (5006) in
> ERROR) coordinate file 1oxy
> Info) Finished with coordinate file 1oxy.
> This contains no information that I could use to troubleshoot :-(
> Chimera works fine for the file, this mail is just FYI.
> Kind regards,
> B.