VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 16 2011 - 10:30:25 CDT

Hi,
  Do you get an error message from STRIDE when it tries to compute
the secondary structure? What is the location of the center of mass?
The STRIDE program communicates with VMD using the PDB file format,
which has a limited range of coordinate magnitudes, so this can
be a source of problems if you translate the center of mass far from
the origin. Since we didn't develop STRIDE, we are subject to its
limitations...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 16, 2011 at 01:45:21PM +0300, Ömer AN wrote:
> Hi,
>
> I have a homodimer model structure obtained from docking. When I
> move one of the molecules by its center of mass so that they orient at the
> xy plane, I lose the secondary structure of newly formed complex in New
> Cartoon representation. It shows only part of the helices and sheets,
> although they don't seem to overlap in 3-D. What may be the cause? How can
> I correct it? I want to keep all the secondary structure information in
> New Cartoon representation while still moving one of the chains.
>
> Thanks,
>
> O:mer AN 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078