VMD-L Mailing List

From: Akemi Matsuno-Yagi (ayagi_at_scripps.edu)
Date: Tue Jun 09 2009 - 13:01:09 CDT

Hi,

I have a problem that is similar to what was reported earlier:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/13173.html

In my case, it is a pdb file I created using molecular modeling
software. It contains 2 protein subunits. Each one displays
without any problem. However, when the two files are combined
into one pdb, vmd cannot create the bonds all the way through. I
understand this has to do with the distance-based bond search
heuristic vmd employs.

Could someone please confirm that my pdb file is suffering this
issue? The file is at:

http://www.toracat.org/work/testCD.pdb

Thank you in advance.

Akemi 

-- 
=========================================
Akemi Matsuno-Yagi, Ph.D.
The Scripps Research Institute
Dept of Molecular & Experimental Medicine
10550 N. Torrey Pines Rd., MEM256
La Jolla, CA 92037
email: ayagi <at> scripps.edu
=========================================