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Messages - tanoramb

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Related topics / 3DNA published in Nature Protocols 2008
« on: July 17, 2008, 05:05:15 pm »
Hello,

I found a 3DNA protocol was published in last number of Nature Protocols (Nature Protocols, 3(7):1213 - 1227). I found it very clear and useful.

Thanks for this paper.

Tomas

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Related topics / What other software is available?
« on: May 06, 2008, 06:01:41 pm »
Hello everyone. I would like to know what other software besides 3DNA you know is available so as to build models of 3D DNA from sequence. I have read many papers and almost all of them describe software before 3DNA. Model.it, for instance, is a software currently available on-line but is very simple compared to 3DNA.

Thank you in advance for your replies.

Regards

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General discussions (Q&As) / How does rebuild work?
« on: October 26, 2007, 12:04:29 pm »
Dear Xiang-Jun,

This is a terrific forum! Just one thing is not clear to me in your 3DNA manual, given the conformational parameters (slide, shift, rise, tilt, roll, and twist), did you use a standard base-pair(coordinates for all atoms for a base-pair are given in a standard reference) to build coordinates for a base-pair in an experimental reference?

I got what you said in your manual about building bases (calculating experimental origins and transformation matrices), but how to get pairs is not clear to me, would you please help me on it? Thanks in advance.

Best,
Baoqiang

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.