Input file for 3DNA

[donaldkellis]

I have just installed x3dna-dssr on my work computer.  All appears well, and I am able to import example PDB files and the software produces the output indicated in your tutorial.

I am curious to know how this file I found on the website was created, following is the link to the site:

http://www.fluortools.com/misc/scientific-illustration/w3dna

I have attached the txt document to this inquiry.

I am looking into creating an image for a journal publication using the methods shown in the link tutorial.

I am hopeful to begin using your software to model some of the structures I work with in my research lab.

Any assistance on this matter would be greatly appreciated

Ciao

Donald L Kellis

[xiangjun]

Thanks for using 3DNA!

The input file you attached can in principle be generated using any text editor (e.g., vi or emacs, if you are Unix orientated). However, it is more conveniently created by 3DNA itself after analyzing a structure. The point is best illustrated with an example. Download 1bna (the classic Dickerson B-DNA dodecamer) in PDB format (1bna.pdb), and do the followings:

Code: [Select]

find_pair 1bna.pdb 1bna.bps
analyze 1bna.bps
In addition to the main output file 1bna.out, you will also see a few other files including bp_step.par which is in the exact format as illustrated in your attachment.

An updated user manual for 3DNA v2.x is in progress. In the meantime, please try to reproduce all the recipes of the 2008 Nature Protocols paper to get a better understanding of what 3DNA has to offer. Remember any related questions are welcome on the Forum.

Best regards,

Xiang-Jun

[donaldkellis]

Xiangjun

Thank you so much for your quick response.  I will do as you suggested and go through the Nature article for practice.

I am hopeful this software package will solve a variety of problems our research group has been facing.

Ciao