To add to what Cameron said:
* Cameron Mura <cm...@ucsd.edu> [2005-03-24 09:44] wrote:
> Hi Hyun-Chul,
>
> It's easy to use PyMOL to build protein fragments in standard geometries
> ("Build" menu in the Tcl/Tk GUI window), but I'm not sure about DNA.
> Three non-PyMOL methods that I'm aware of are:
>
> (1) The program "B" (aka "Biomer") from Dave Case's group at Scripps
> (http://www.scripps.edu/mb/case/Biomer/). It's a Java-based online
> biopolymer-building package, and is freely accessible.
>
> (2) The utility "nucgen" that comes with the Amber software package is
> useful for generating single- or double-stranded DNA and RNA structures
> in a variety of geometries (see pg. 236 of the Amber v8 manual --
> http://amber.scripps.edu/doc8/amber8.pdf). Unlike "B", this runs from a
> unix shell given plaintext input files, so would be more useful for
> scripting and things like that. However, Amber is not free.
>
> (3) There used to be a web-based server known as "RBSCM: Rapid Building
> of Standard 3D-Conformations of DNA/Protein" available at
> "http://www.bioinf.co.uk/bsps/bsps_N.html";, and I found it very useful
> for quickly building standard geometries. The www.bioinf.co.uk site
> doesn't seem to exist anymore (no redirects), but maybe you can track it
> down elsewhere...
>
> There are probably other ways to go about this too (e.g., InsightII
> biopolymer builder), but I think they're all
> proprietary/closed-source/not-free.
There is an easy to use open-source program called NAMOT
(http://namot.lanl.gov/) that allows one to type in a sequence and
create a DNA molecule with options for single- or double-stranded and
A, B or Z conformations.
Cheers,
Rob
--
Robert L. Campbell, Ph.D. <r...@post.queensu.ca>
Senior Research Associate phone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
