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1

RNA structures (DSSR) / Re: overlapping area calculation - stacking interactions

« Last post by xiangjun on Today at 01:02:59 pm »

Hi Agnieszka,

The issue you reported should have been fixed by Shuxiang. Below is a part of the output from a user-uploaded PDB file on wDSSR.

Code: [Select]

****************************************************************************
Overlap area, in Angstrom^2, between polygons defined by atoms on successive
bases. Polygons projected in the mean plane of the associated base-pair step.

Values in parentheses measure the overlap of base ring atoms only. Those
outside parentheses include exocyclic atoms on the ring. Intra- and inter-
strand overlap is designated according to the following diagram:

                    i2  3'      5' j2
                       /|\      |
                        |       |
               Strand I |       | II
                        |       |
                        |       |
                        |      \|/
                    i1  5'      3' j1

     bp      i1-i2        i1-j2        j1-i2        j1-j2        sum
   1 G-C  6.90( 3.38)  0.00( 0.00)  0.00( 0.00)  0.96( 0.00)  7.86( 3.38)    # |1|A|G|3||||   |1|A|C|261|||| 19-XIX    cWW  cW-W  WC
   2 U-G  5.92( 2.45)  0.00( 0.00)  0.03( 0.00)  2.31( 1.07)  8.26( 3.52)    # |1|A|U|4||||   |1|A|G|107|||| 28-XXVIII cWW  cW-W  Wobble
   3 G-A  0.00( 0.00)  0.00( 0.00)  0.00( 0.00)  0.00( 0.00)  0.00( 0.00)    # |1|A|G|5||||   |1|A|A|260|||| --        cSW  cm-W  --
   4 U-A  0.00( 0.00)  0.39( 0.00)  0.00( 0.00)  1.27( 1.26)  1.66( 1.26)    # |1|A|U|24||||  |1|A|A|247|||| 20-XX     cWW  cW-W  WC
   5 C-G  0.15( 0.00)  0.00( 0.00)  0.00( 0.00)  3.26( 1.82)  3.41( 1.82)    # |1|A|C|23||||  |1|A|G|248|||| 19-XIX    cWW  cW-W  WC
   6 U-A  6.41( 3.40)  0.00( 0.00)  0.00( 0.00)  3.96( 2.40) 10.37( 5.80)    # |1|A|U|22||||  |1|A|A|249|||| 20-XX     cWW  cW-W  WC
......
Please let us know if you still see the problem, or any other issues related to DSSR or wDSSR.

Best regards,

Xiang-Jun

2

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by JiaolongBao on August 27, 2026, 02:19:14 am »

Hi Xiang-Jun,

Thanks for the update. It is indeed a good way to distinguish C2'-endo and C3'-endo both in L-sugars and D-sugar circumstance. I believe the sugar-class classification in dssr-torsion.txt for 1BNA_L.pdb is correct.

Best regards,

Jiaolong

3

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by xiangjun on August 25, 2026, 11:33:26 pm »

Hi Jiaolong,

As a follow-up to your July 06, 2026 post:

The sugar class classification for L-sugar is omitted due to some compatibility reason with D-sugar.

As of v2.9.3-2026aug26, DSSR employs ssZp to classify L-sugars and D-sugars into C2'-endo or C3'-endo conformations. Below are related excerpts from the dssr-torsions.txt output file:

  phase-angle: the phase angle of pseudorotation and puckering
  sugar-type: ~C2'-endo for C2'-endo like conformation (|ssZp| <= 2.5 A), or
               ~C3'-endo for C3'-endo like conformation (|ssZp| >= 3.3 A)
              Note the ONE column offset (for easy visual distinction)

ssZp: single-stranded Zp, defined as the z-coordinate of the 3' phosphorus atom
      (P) expressed in the standard reference frame of the 5' base; the value is
      POSITIVE when P lies on the +z-axis side (base in anti conformation);
      NEGATIVE if P is on the -z-axis side (base in syn conformation)
  Dp: perpendicular distance of the 3' P atom to the glycosidic bond
      [Ref: Chen et al. (2010): "MolProbity: all-atom structure
            validation for macromolecular crystallography."
            Acta Crystallogr D Biol Crystallogr, 66(1):12-21]

Attached is an example DSSR run on 1BNA_L.pdb (1BNA.pdb with negated x-coordinates: xL=-x) and the related dssr-torsions.txt file.

Best regards,

Xiang-Jun

4

RNA structures (DSSR) / Re: overlapping area calculation - stacking interactions

« Last post by shuxiang on August 25, 2026, 10:09:46 am »

Hi Agnieszka,

The wDSSR server has been updated with overlapping area calculations for the user-uploaded structures. Thanks.

Best,
Shuxiang

5

RNA structures (DSSR) / Re: overlapping area calculation - stacking interactions

« Last post by xiangjun on August 25, 2026, 09:51:06 am »

Hi Agnieszka,

Thanks for reporting this issue. I was able to reproduce it and can confirm that it happens on my end as well. The pre-processed PDB files have the option specified for overlapping area calculation, but the script processing user-uploaded files does not. I have notified Shuxiang (who recently joined our team) about this. It should be fixed soon, and we will let you know once it is resolved.

Best regards,

Xiang-Jun

6

RNA structures (DSSR) / Re: overlapping area calculation - stacking interactions

« Last post by Agnieszka on August 25, 2026, 07:02:21 am »

Dear Xiang-Jun,
Recently, we have noticed that when using the 3DNA server and uploading a PDB file directly from a computer, the output does not include the overlapping area calculation. However, when a PDB code is entered instead, the output does contain this calculation.

Could you please check this issue and, if possible, restore this functionality for uploaded files?

Thank you very much,
Agnieszka

7

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on August 16, 2026, 11:38:51 pm »

Hi,

The issue should be fixed now. It was due to my negligence.

Best regards.

Xiang-Jun

8

FAQs / Re: Where to download x3DNA

« Last post by deantuan on August 16, 2026, 07:50:12 pm »

Hello Dr. Lu,

My account has already been manually activated, and I can log in successfully. However, I still cannot see the “Download” link or the member-only “Downloads” section on the forum homepage.

I registered using my University of Washington email address and would like to download 3DNA for non-commercial academic research on DNA molecular dynamics trajectory analysis.

Could you please check whether my account still requires approval for download access?

Thank you very much for your help.

9

General discussions (Q&As) / Re: Could you tell me where l can download 3DNA?

« Last post by xiangjun on July 24, 2026, 09:16:16 am »

Hi Gai,

You should now be able to see the Download link in the top of the Forum.

Because you registered with a personal email address, it is difficult to verify your account and filter out spam. By default, new unverified accounts are assigned to a restricted category where the Download link is hidden and posts are moderated. This policy prevents spam and ensures the Forum remains clean and trustworthy.

Best regards,

Xiang-Jun

10

General discussions (Q&As) / Could you tell me where l can download 3DNA?

« Last post by gai on July 24, 2026, 07:51:15 am »

Dear Dr. xiangjun
I hope to download 3DNA v2.4 to carry out structural analysis of nucleic acids in my project. All usage will be limited to non-commercial academic research.

Thank you very much for your maintenance of this excellent software.

Best regards
Gai