VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jan 16 2008 - 12:26:08 CST

On Wed, 16 Jan 2008, Sergey Mkrtchyan wrote:

SM> Hey guys!
SM>
SM> All I want to do is simply visualize the polymer chain, say I have 100
SM> monomers with x, y, z for each and I want to give a radius of 1 to each of
SM> them. I don't really care what type they are, I just need a "spheres at the
SM> corrdinates".
SM>
SM> I tried PDB format something like this...
SM>
SM> ATOM 1 N UNK 1 47.92091 65.22737 21.88935
SM> ATOM 2 N UNK 2 48.78523 65.71315 21.75909
SM> ATOM 3 N UNK 3 49.62076 65.48353 21.25993
SM> ATOM 4 N UNK 4 50.13233 64.65174 21.47537
SM>
SM> ... but it does not display that properly.

please explain "not properly".
from the looks of it, my first guess is that your
"pdb" file is not according to the PDB standard.
please note, that .pdb is not "some columns" but
is formatted fortran with specific columns for
specific information and VMD honors that.

cheers,
   axel.

SM>
SM> Isn't there a way to do this? I've done tonns of google-ing, nothing really
SM> helpful.
SM>
SM> Thanks a lot.
SM>
SM> Sergey
SM> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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If you make something idiot-proof, the universe creates a better idiot.