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Questions and answers > RNA structures (DSSR)
Creation of customized structures using DSSR
curiousphoton:
Hello,
I am a Computer Science Master's student working at the intersection between Computer Science and Computational Chemistry.
We have an RNA sequence, and the 9 torsional angles (calculated by 3DNA v2.4) for each residue. Would it be possible to reconstruct the full-atom 3D structure of the RNA using DSSR Pro's rebuild program from just these two pieces of information - the sequence and the 9 torsional angles?
I apologize if this question is irrelevant for the forum, I wanted to confirm if DSSR Pro could satisfy our requirements before buying the license since the Pro version of the manual is not available.
Thank you.
xiangjun:
Hi,
Thanks for your using 3DNA, and your inquiries about DSSR Pro.
--- Quote ---I apologize if this question is irrelevant for the forum, I wanted to confirm if DSSR Pro could satisfy our requirements before buying the license since the Pro version of the manual is not available.
--- End quote ---
It is directly relevant to the Forum. You are very welcome to post this question, and any more you may have.
--- Quote ---We have an RNA sequence, and the 9 torsional angles (calculated by 3DNA v2.4) for each residue. Would it be possible to reconstruct the full-atom 3D structure of the RNA using DSSR Pro's rebuild program from just these two pieces of information - the sequence and the 9 torsional angles?
--- End quote ---
No, at least for now, even though it is not clear to me what exactly are the 9 torsional angles you refer to. DSSR employs 6 rigid-body parameters to quantity the relative spatial geometry between two bases (or base pairs) and uses them to build 3D models with approximate backbones. I have long been interested in adding more modeling features to DSSR ...
Best regards,
Xiang-Jun
curiousphoton:
Hi,
By the 9 torsional angles, I meant the torsional and pseudotorsional angles - alpha, beta, gamma, delta, chi, epsilon, zeta, eta, theta - calculated by 3DNA's `analyze` program.
DSSR would indeed benefit from more modeling features! I'll be following the release notes to see if this particular modeling feature is ever introduced to DSSR.
Thank you for your work on this wonderful program!
xiangjun:
Thanks for your follow-up.
--- Quote ---By the 9 torsional angles, I meant the torsional and pseudotorsional angles - alpha, beta, gamma, delta, chi, epsilon, zeta, eta, theta - calculated by 3DNA's `analyze` program.
--- End quote ---
Among the 9 torsion angles, only the first 7 are independent. The last two, eta and theta, could in principle be deduced from (alpha, beta, gamma, delta, epsilon, zeta). I vaguely remember reading about software tools of building nucleic acid structures using backbone torsion angles, including only eta and theta. I just do not know how useable they are from a general user's perspective.
--- Quote ---DSSR would indeed benefit from more modeling features! I'll be following the release notes to see if this particular modeling feature is ever introduced to DSSR.
--- End quote ---
If you have info in modeling nucleic acids, please share them along this thread. I appreciate your kind words on DSSR.
Best regards,
Xiang-Jun
curiousphoton:
--- Quote ---I vaguely remember reading about software tools of building nucleic acid structures using backbone torsion angles, including only eta and theta. I just do not know how useable they are from a general user's perspective.
--- End quote ---
Oh wow! No issues with their usability, I will try to figure them out. Please let me know if you ever remember the names of these software tools.
And yes, I will share any comments or suggestions I have about modelling in this thread when I think of any.
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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.
