VMD-L Mailing List

From: Zhuyi Xue (alfred532008_at_gmail.com)
Date: Tue Feb 21 2012 - 21:24:14 CST

Hi, there,

If my input is a gro file, which just contains atom coordinates (I mean
no secondary structure information). When I do Newcartoon representation
and there comes out to be alpha helix and beta sheets. I am wondering
how vmd calculates those secondary structures. Whether it follows the
same way dssp does or only based on dihedral angles (those areas that
belong to a particular secondary structure shown in Ramachandran map)?
Pymol can also assign secondary structures, but the result sometimes
differ from that of vmd, I am not sure how pymol does the calculation,
either.

Thank you for any explanation or suggestion in advance.

Regards,
Zhuyi