Messages

1

RNA structures (DSSR) / Re: Creation of customized structures using DSSR

« on: October 12, 2023, 10:00:12 am »

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.

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.

2

RNA structures (DSSR) / Re: Creation of customized structures using DSSR

« on: October 12, 2023, 08:28:21 am »

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!

3

RNA structures (DSSR) / Creation of customized structures using DSSR

« on: October 12, 2023, 08:06:13 am »

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.