Messages

1

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: June 02, 2025, 04:44:26 am »

Hi Xiang-Jun,

I've included my detailed procedure in this Evernote for your review: https://share.evernote.com/note/b6bd8283-bcad-58aa-0725-95dc61a9c6e0

I hope you can help explain why Y-shift is introduced when generating your B-DNA ring. Also, I think you would have a better idea than me of creating a Z-DNA ring with higher accuracy by taking into account the spatial relationship of the helical axis and the bp.

Thanks,

Di

2

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: June 01, 2025, 09:08:25 pm »

Hi Xiang-Jun,

I checked your model, and I can confirm that it is what I wanted.

I'm also attaching the model I've built. The screenshot is a comparison of yours (blue) and mine (pink). I think we were using the G84 ring I've created, so our models can be overlayed. An extra step required for your model is to link the dinucleotide steps.

By the way, I think I figured out why I didn't get the email notification. I indeed received a notification on April 30, but I thought (mistakenly, probably due to the early morning...) I had already viewed the reply because you posted a reply on April 29, which was assumed to be the same message, so I didn't open a link for your April 30 message. I saw in the email that "More replies may be posted, but you won't receive any more notifications until you read the topic." I believe this setting is the reason I didn't the email notification of your follow-up message on May 5.

Best,

Di

3

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: June 01, 2025, 08:39:40 pm »

Hi Xiang-Jun,

Thanks a lot for your following-up of my questions!

I'm sorry that I didn't look back into this question. And I don't know why I didn't receive an email notification about your reply. I remember that I always received an email notification whenever there was a reply to my message in the past...

I logged in today because I also have made progress to create the Z-DNA ring during the weekend, and wanted to let you know. Do you want me to post the details of my procedure?

Thanks again for your work, and I will check your model and let you know my opinion!

Best,

Di

4

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: April 25, 2025, 01:37:09 pm »

Hi Xiang-Jun, I used UCSF Chimera to manually align the dimer units onto G-C pair. It's very difficult to describe it in words and make it reproducible, and that's why I think it would be fantastic if you can help with it by slightly adjusting the codes you already have for generating atoms from helical parameters. 

5

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: April 25, 2025, 02:12:11 am »

Hi Xiang-Jun,

I manually aligned 5 dimer units onto the circle. As expected, it works. Only very minor adjustment of bond angles and lengths are required later. I'm attaching the screenshot and the pdb file.

Di

6

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: April 23, 2025, 06:49:40 pm »

I tried to make some progress on constructing a 168-bp circular Z-DNA structure. What I have achieved so far is determining the positions of the repeating units (each being a CG dimer) along the ring. Each position currently serves as a placeholder (a G:C pair; 84 in total), to be replaced by a Z-DNA dimer unit.

I'm attaching a screenshot of the current structure, as well as the corresponding PDB file. I think Xiang-Jun might be able to work his "tasks" magic to align and insert the Z-DNA dimer units into the specified positions.

If you think this direction makes sense, I’d be happy to post the detailed process of how I constructed this circle.

7

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

« on: April 22, 2025, 03:29:03 pm »

Hi Xiang-Jun,

Thank you for your detailed and insightful response. I'm truly impressed by your meticulous attention to details! It’s reassuring and strengthens my confidence in DSSR as a reliable tool!!! Also, thanks to your explanation and the referenced blog post, I now have a much clearer understanding of how the `--nt-mapping` option functions.​

I further tested `--nt-mapping`, and below is what I got:

Without `--nt-mapping`:

Code: [Select]

A.B8H7 has pseudo-uridine C1'...C5 glycosidic bond
B.B8H27 has pseudo-uridine C1'...C5 glycosidic bond
With `--nt-mapping='B8H:p'`, the result is the same as above, and the message reads:

Code: [Select]

uncommon base 'B8H' assigned to 'p' for A.B8H.7
uncommon base 'B8H' assigned to 'p' for B.B8H.27
A.B8H7 has pseudo-uridine C1'...C5 glycosidic bond
B.B8H27 has pseudo-uridine C1'...C5 glycosidic bond
With `--nt-mapping='B8H:u'`, I'm intentionally confusing the software to treat it as uridine, and I got the warning:

Code: [Select]

uncommon base 'B8H' assigned to 'u' for A.B8H.7
uncommon base 'B8H' assigned to 'u' for B.B8H.27
A.B8H7 has unusual GLYCOSIDIC bond!
B.B8H27 has unusual GLYCOSIDIC bond!
Best regards,

Di

8

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!

9

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!

10

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: April 21, 2025, 04:48:00 am »

Hi Xiang-Jun, following up on the Z-DNA rebuilding, is there a way to create a Z-DNA circle? I think the difficulty lies in how to rebuild to create a backbone of Z-DNA using the helical parameters. Thanks!

11

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

« on: October 25, 2024, 07:42:23 pm »

Thanks, Xiang-Jun!

Do you have any idea of how to easily find the axis of each 2-bp segment of a helix?

Also, I think an easier solution for A-form helix is to do a shift of the origin in the plane of the reference frame so that the shifted origin is where the axis passes through the plane.

Di

12

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

13

RNA structures (DSSR) / Re: running DSSR in windows

« on: December 12, 2017, 12:56:43 pm »

Hi Xiang-Jun,

Thanks a lot for the prompt response. You are very helpful! Now DSSR works well on my computer.

Best,

Di

14

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.