Topics

1

RNA structures (DSSR) / Can x3dna-dssr correctly handle N1-methyl-pseudouridine?

« on: April 22, 2025, 12:48:13 am »

Hi Xiang-Jun,

I understand that x3dna-dssr can handle pseudouridine (PDB Chem ID: PSU) correctly. I'm inquiring about its support for N1-methyl-pseudouridine (PDB Chem ID: B8H). Specifically,​ does x3dna-dssr recognize B8H based on its PDB chemical ID, or does it rely on atomic connectivity?

FYI, I've tested x3dna-dssr with PDB entries 8PFK and 8PFQ, both containing B8H, and the analysis proceeded without errors, with the results looking reasonable. However, given the unique C5-C1′ glycosidic bond for B8H, I want to confirm that x3dna-dssr interprets this modification accurately.

Further, is there a comprehensive list of modified nucleotides currently supported by x3dna-dssr?​ I came across these two pages (https://x3dna.org/highlights/automatic-identification-of-nucleotides ; https://x3dna.org/highlights/modified-nucleotides-in-the-pdb ), but could not find the exact answer.

Thank you for your assistance!

2

RNA structures (DSSR) / Rebuilding circular Z-DNA

« on: April 21, 2025, 08:10:12 pm »

Hi Xiang-Jun, I think three steps are needed for creating such a Z-DNA ring or more generally, any Z-form helical structures:

(1) Obtaining a helical parameter file in a similar way as the A- or B-form helices;
(2) Creating the atoms of the bases based on the helical parameter file;
(3) Putting the other atoms of the sugar and phosphate groups based on the position of the bases' atoms (there are only two conformations corresponding to the pyrimidines and purines, respectively).

Do you prefer that I start a new thread on this topic?

Thanks!

3

RNA structures (DSSR) / plotting the helical axis along curved helices

« on: October 24, 2024, 07:45:43 pm »

Hi Xiang-Jun,

I tried to extract the coordinates of the origin points of the base-pair reference frame from the json file. It appears working for DNA structures; but for RNA, the points form a spiral around the helical axis (see attached image), as we would expect due to the differences of how the axis passes through the base-pairs in B- and A-form helices.

Thanks,

Di

4

RNA structures (DSSR) / running DSSR in windows

« on: December 11, 2017, 09:31:44 pm »

When I'm trying to run DSSR in windows 7, an error message popped out saying "The program can't start because msys-2.0.dll is missing from your computer. Try reinstalling the program to fix this problem."
How can I deal with it?
Thanks in advance.