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Questions and answers => General discussions (Q&As) => Topic started by: gwon on March 01, 2013, 10:31:40 pm

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Title: I want to make the DNA figure How to make it?
Post by: gwon on March 01, 2013, 10:31:40 pm

I want to make the DNA figure^^

I refer the paper : 2003 paper 

"3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
Xiang-Jun Lu and Wilma K. Olson*"

and I want to a figure1, figure4

Figure 1. Pictorial de®nitions of rigid body parameters used to describe the geometry of complementary (or non-complementary) base pairs and sequential base pair steps

Figure 4. In ̄uence of non-zero Slide and Roll at sequential dimer steps on overall DNA helical conformation. Images generated with 3DNA building upon  the principles of Calladine and Drew (42).


But i didn't look the webpage description, so How to make this figure^^

Title: Re: I want to make the DNA figure How to make it?
Post by: xiangjun on March 02, 2013, 12:13:23 pm

Did you read the 3DNA NP08 paper (http://www.nature.com/nprot/journal/v3/n7/abs/nprot.2008.104.html)? Pay special attention to recipe #1, Figure 2: "Schematic diagrams of three representative rigid-body parameters"), and recipe #2, Figure 3: "3DNA-generated images of 22-bp DNA duplexes with the same overall 45° curvature per helical turn".

Also, in 3DNA distribution, did you notice the directory $X3DNA/examples/calladine_drew? It contains further details (see the README file) on how to produce such schematics.

HTH,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University