Re: [modeller_usage] Modeling DNA

[Mensur Dlakic <mdlakic AT montana.edu>]

If you want to model DNA without worrying about restraints with protein or 
something else, Modeller is not the best tool to use. Take your pick from 
the links below:

http://rutchem.rutgers.edu/~xiangjun/3DNA/
http://www.t10.lanl.gov/namot/
http://www.scripps.edu/mb/case/casegr-sh-3.2.html
http://www.homepage.montana.edu/~mdlakic/software.html

If molecules built end up being slightly irregular, there is a script to 
fix that assuming one has CNS:

http://www.dl.ac.uk/list-archive-public/ccp4bb/2005-01/msg00420.html

Hope this helps,

Mensur


At 07:28 PM 6/22/2005, you wrote:
> Maybe Modeller won't even be necessary for this task,
> but, anyway, someone can point a simpler solution: how
> can I generate a PDB for a small DNA double helix
> (something like 10-15 base pairs)?
>
> Lucas

==========================================================================
| Mensur Dlakic, PhD                | Tel: (406) 994-6576                |
| Department of Microbiology        | Fax: (406) 994-4926                |
| Montana State University          |                                    |
| 109 Lewis Hall, P.O. Box 173520   | http://myprofile.cos.com/mensur    |
| Bozeman, MT 59717-3520            | E-mail: mdlakic AT montana.edu        |
==========================================================================