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.

Good luck,
Cam


=== pymol-users-request@lists.sourceforge.net wrote (on 03/23/2005 03:15 PM): ===

Subject:
[PyMOL] How to generate a DNA structure with given sequence?
From:
"HYUN-CHUL KIM" <sundol@saju.kaist.ac.kr>
Date:
Wed, 23 Mar 2005 19:40:56 +0900
To:
<pymol-users@lists.sourceforge.net>

I want to know how to generate a DNA structure with a given sequence.
I heard that Pymol can do that but I couldn't find such command.
Can you tell me how to do this?
 
Sincerely,
Hyun-Chul Kim