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Questions and answers => General discussions (Q&As) => Topic started by: nicalleb on July 13, 2020, 02:23:34 pm

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Title: Local base step parameters
Post by: nicalleb on July 13, 2020, 02:23:34 pm
Hello everyone,

I study the ionization of small complexes composed of several stacked DNA bases. The values of ionization potentials seem to be very dependent of the conformational parameters. I use web-X3DNA to determine the local base step parameters (shift, slide, rise, tilt, roll and twist) of my complexes. I would understand how these parameters are determined by the software (because My results are very variable).

In that purpose, I looked for information in the tutorial and in some articles related to the program but it doesn't really help me. I've namely found that X3DNA adopts the standard reference frame for the parameters but again, it doesn't help me much. Do you have detailed information about the determination of the parameters by X3DNA or can you indicate me where I can found more precise information ?

Thank you in advance,

Nicolas (PhD student at ULB, Belgium)
Title: Re: Local base step parameters
Post by: xiangjun on July 13, 2020, 02:58:12 pm
Hi Nicolas,

Thanks for your interest in using 3DNA and for posting on the Forum.

Since 3DNA v2.4 is open source, the best way to dig into the details you are interested is to read the code. The definition of base-pair step parameters is based on SCHNAaP (http://10.1006/jmbi.1997.1346)/SCHNArP (http://10.1006/jmbi.1997.1345) (), for which the source code is also available.

Depending on the 3DNA version you downloaded, you may find a PDF tech-details.pdf (attached) that provided step-by-step details on how 3DNA base-pair parameters are calculated.



Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.