From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 03 2010 - 12:02:47 CST

Hi,
  VMD itself doesn't do any automated structure building. You could
use it in concert with scripting and/or with other tools, but it doesn't
provide any homology modeling functionality itself.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 30, 2010 at 01:43:11PM +1000, Seweryn Bialasiewicz wrote:
> Dear VMD users,
>
>
>
> I am hoping someone can help me out with a modelling quandary I am having
> (please forgive my ignorance of the issue, as I have just started using 3D
> protein modelling programs).
>
>
>
> I would like to generate a 3D model of a viral capsid (WUV) which has not
> had any of it's structures determined by x-ray crystallography; however,
> but a closely related virus (SV40) has. My question is; can I use VMD to
> build a predicted WUV capsid based off of it's capsid AA sequence, with
> the SV40 capsid .pdb file acting as a homology guide?
>
>
>
> So far, I have used I-TASSER to generate several .pdb candidate
> predictions of the WUV major capsid protein, but I am unsure of how to
> proceed in mapping it onto that of the SV40 capsid .pdb file (1SVA). Oh,
> and the capsid formation is fairly simple; the monomers form pentamers, of
> which 72 join together to form the capsid.
>
>
>
> Any help would be greatly appreciated!
>
>
>
> Cheers,
>
> -Seweryn
>
>
>
>
>
> Seweryn Bialasiewicz, PhD
>
> Queensland Paediatric Infectious Diseases Laboratory,
>
> Sir Albert Sakzewski Virus Research Centre
>
> Building C28, Back Rd.
>
> Herston, QLD 4029
>
> Australia
>
> t: +61.7.3636.8719
>
> f: +61.7.3636.1401
>
> e: seweryn_at_uq.edu.au
>
>

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