From: Axel Kohlmeyer (
Date: Sat Dec 08 2007 - 14:37:00 CST

On Sat, 8 Dec 2007, OZGE ENGIN wrote:

OE> Hi all,

OE> I have a problem with the new cartoon/structure mode of

whenever you have a problem with VMD, please state the version
of VMD you are using and the platform that you are running on.

OE> representation. Each time, it assigns a different secondary

what do you mean by "each time"? please describe in more detail
what you are doing and what you expect (and don't see). none of
us can see your computer screen or what you do.

OE> structural pattern to my peptide. So, I could not get a clear
OE> picture of the structure of my peptide.

OE> Why is it the case? What may be the problem?

with so little information, one can only speculate.

since computers and software are (usually) deterministic,
it is quite possible, that VMD is simply reflecting an
inconsistency in what you are doing. PEBCAC?



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.