From: Axel Kohlmeyer (
Date: Wed Jul 02 2008 - 16:36:57 CDT

On Wed, 2 Jul 2008, Fred (Rui FENG) wrote:

RF> Hi All,

hi fred,

RF> I'm using VMD 1.8.6. I'd like to draw a circle. The circle consists of
RF> 154 atoms. Its center is ( 0, 0, 0 ), and the radius is 6,500
RF> Angstrom. The circle is in the YZ plane. The PDB file is in the
RF> attachment.
RF> I use the command "mol new test.pdb type pdb start 0 end 0 step 1
RF> autobonds off" to open the PDB file. The problem is the output is not
RF> a circle, but a line!

that is because your pdb file is not conforming
to the pdb standard and VMD honors it.

try writing the same object in, e.g. .xyz format and it works.

if you just want to draw some spheres or lines somewhere,
why not use graphics/draw commands?


RF> Do you think the size of the radius has exceeded the limitation of
RF> VMD? What's the biggest size in VMD? Or is there anything wrong in the
RF> PDB file?
RF> Thank you so much!
RF> Fred

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.