Recent Posts

61

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

62

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.

63

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.

64

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

65

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

66

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.

An Error Has Occurred!
The topic or board you are looking for appears to be either missing or off limits to you.

67

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

« Last post by sowmya on October 19, 2022, 07:54:02 am »

Dear Dr. Xiang,

I was trying to calculate the base pair and base step parameters for PDB IDs - 7E9E and 7E9I by uploading the PDB files to the web interface of 3DNA. I am getting a "can't open the baselist file error" for these 2 IDs. I am yet to come across this error for other PDB IDs - I have calculated for around 20 other PDB IDs (deposited after 2019) in the web interface and they were parsed fine. Requesting your suggestions to resolve this error in the web interface.

With regards,
Sowmya

68

General discussions (Q&As) / Re: Calculate torsion angles of the DNA, without taking into account the bases

« Last post by xiangjun on September 10, 2022, 09:38:10 pm »

Hi Andrea,

DSSR Pro can do what you want very easily, especially in combination with the --json option. See No more grant funding for 3DNA/DSSR.

Base atoms have always been necessary for the identification of nucleotides in order to calculate base-pair and backbone parameters in 3DNA v2.x, including the command you mentioned: analyze -t=torsions.out. However, since 3DNA v2.x is open source for academic uses, you can modify it to meet your needs.

Best regards,

Xiang-Jun

69

General discussions (Q&As) / Calculate torsion angles of the DNA, without taking into account the bases

« Last post by Andrea R on September 10, 2022, 06:48:52 pm »

Dear Dr. Xiang-Jun Lu,

I used versions of 3DNA earlier than the 2018 versions some time ago, in those versions it was possible to calculate the torsion angles of the sugar-phosphate backbone of DNA, without taking into account the bases, with the following command:

analyze -t = name.tor name.pdb

However in the new versions, this task is not possible anymore, it is necessary to have the nitrogenous bases or at least   N1, C2 or N9, C4 atoms. 

I was wondering if there is a new instruction or way to do that, because it would shorten my work route considerably. One of my study purposes is the optimized fragments of the Sugar-Phosphate Backbone, in these fragments the nitrogenous bases of the DNA are eliminated and replaced by a hydrogen (position N1 or N9) as shown in file attached .

Thank you very much,

Andrea R.

70

Site announcements / Re: Clarification on DSSR licensing

« Last post by xiangjun on August 11, 2022, 09:24:51 am »

Hi Dr. Baulin,

is it safe to freely use the old DSSR version for academic use according to the old license?

Yes. Keep in mind that such outdated versions are no longer supported or maintained.

Best regards,

Xiang-Jun