VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_vitae.cmm.upenn.edu)
Date: Wed Nov 23 2005 - 11:31:57 CST

On Tue, 22 Nov 2005, andrea spitaleri wrote:

andrea,

please have a look at the mailing list archives.
VMD does not (yet) honor CONECT records.

the workarounds are:
- you set the SS bond manually (e.g. from
  a selection or using the mouse)
- you add a 'Dynamic Bonds' representation with
  a large enough cutoff for only SS-bridges
- you (build and) load a .psf file.
  check out the autopsf plugin.

axel.

AS> Hi all,
AS> I have a file.pdb with CONECT flag at the end giving the S-S connection
AS> atom numbers. While in pymol or insight I can see the S-S bond,
AS> in vmd it doesn't appear at all. I am wondering if it is a problem of
AS> cutoff since the dist is quite large (0.25nm).
AS> Any help??
AS>
AS> Regards,
AS> Andrea
AS> 

-- 
=======================================================================
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
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.