Recent Posts

51

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

« Last post by curiousphoton 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.

52

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

« Last post by xiangjun on October 12, 2023, 08:50:01 am »

Thanks for your follow-up.

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.

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.

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.

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

53

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

« Last post by curiousphoton 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!

54

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

« Last post by xiangjun on October 12, 2023, 08:18:44 am »

Hi,

Thanks for your using 3DNA, and your inquiries about DSSR Pro.

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.

It is directly relevant to the Forum. You are very welcome to post this question, and any more you may have.

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?

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

55

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

« Last post by curiousphoton 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.

56

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on September 22, 2023, 11:53:22 am »

Done.

57

FAQs / Re: Where to download x3DNA

« Last post by shumilio on September 22, 2023, 09:31:02 am »

Hello Xiangjun,

I faced the same issue, could you please grant access for me?

Thanks in advance!

58

General discussions (Q&As) / mutate_bases error

« Last post by dnalectronics on July 12, 2023, 03:05:59 pm »

Hello Sir,

Thank you for such a beautiful forum. I want to use mutate_bases to mutate the cytosine base pair. However, it shows this error.

$ mutate_bases -s fiber_model.pdb -m 4 5CM output.pdb
'mutate_bases' is not recognized as an internal or external command,
operable program or batch file.

Please help in understanding why I am getting this error.

Thank you

59

RNA structures (DSSR) / Re: Classification of helix versus loops

« Last post by xiangjun on July 06, 2023, 08:20:52 pm »

Hi Julia,

Please read the 2015 NAR paper "DSSR, an integrated software tool for dissecting the spatial structure of RNA" and the thread "Reproducing results published in the DSSR-NAR paper".

When asking questions, please be specific so other can understand exactly what you mean. I am glad the know that DSSR is being used by undergraduate students. Your instructor may provide you better help on the topics.

Also read the thread "No more grant funding for 3DNA/DSSR".

Best regards,

Xiang-Jun

60

RNA structures (DSSR) / Classification of helix versus loops

« Last post by jmmmggg on July 06, 2023, 03:04:18 pm »

Hello,
I am an undergraduate student interested in studying tetraloops.
My partner created a file using DSSR containing all hairpin loops, and now we are trying to determine which loops qualify as tetraloops.
We have some 6-nucleotide hairpin loops where it appears as if the first and last nucleotides are interacting as if they were a tetraloop, but we could not tell for sure. Thus, we are wondering what DSSR constitutes as a base pair, as well as how it defines helices versus hairpin loops.

Thank you!
-Julia