Recent Posts

91

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!

92

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

93

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

94

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

95

w3DNA -- web interface to 3DNA / Analyze multiple models

« Last post by bbobay on April 14, 2023, 10:58:50 am »

Good morning -

I was trying to run an example using PDB code 1RGO and when analyzing one structure from the NMR ensemble it works fine but when clicking on the "Analyze multiple models" the resulting files are empty (with the download button) and the link results in "404 Page Not Found" errors.

How can I analyze multiple models from an NMR ensemble?

Best,

Ben

96

w3DNA -- web interface to 3DNA / Re: can't open the baselist file error for 2 PDB IDs

« Last post by xiangjun on December 25, 2022, 11:49:24 am »

The modified nucleotide J0C in 7E9E and 7E9I does not follow the naming convention of canonical bases. 3DNA can not handle it and thus the error message you reported.

DSSR can run successfully on these two PDB entries.

97

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on December 25, 2022, 11:37:20 am »

See the FAQ "How to make the best use of the Forum".

Your account has been granted download access.

98

w3DNA -- web interface to 3DNA / Re: Cannot understand what a base pair type means from web-3DNA output

« Last post by xiangjun on December 25, 2022, 11:33:44 am »

See the paper "DSSR: an integrated software tool for dissecting the spatial structure of RNA" (https://doi.org/10.1093/nar/gkv716).

Identification of nucleotides

        Note that pseudouridine (PSU) is shortened to ‘P’, due to its special C1′–C5 glycosidic link- age (Figure 2).

The M–N versus M+N relative base orientations

99

w3DNA -- web interface to 3DNA / Cannot understand what a base pair type means from web-3DNA output

« Last post by sowmya on November 16, 2022, 06:33:32 am »

Dear Dr. Xiang,

I was analyzing the base pair type distribution among a dataset of RNAs that I have collected for my study using the pair.csv file for those PDB IDs obtained using web-3DNA. When I compiled the list of unique base pair types I noticed certain base pairs with a P, which are: P+A, A-P, P-G, P+G, C-P and P-A.
I got information on the other base pair types from the x3DNA website: http://x3dna.org/highlights/named-base-pairs, but I'm unable to find information on the above mentioned base pairs. Can you share some resources to understand what these named base pairs mean and how they are identified (in terms of the structural orientation of the bases and other parameters)?

Thank you
- Sowmya

100

FAQs / Re: Where to download x3DNA

« Last post by sahithjayceion on November 09, 2022, 12:55:46 am »

I waited after registration but still cannot view the download section. It would be great if you could give me access! regards.

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