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Messages - xiangjun

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1
Dear 3DNA/DSSR users,

It gives me great pleasure to announce that the 3DNA/DSSR project is now funded by the NIH R24GM153869 grant, "X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids". I am deeply grateful for the opportunity to continue working on a project that has basically defined who I am. It was a tough time during the funding gap over the past few years. Nevertheless, I have experienced and learned a lot, and witnessed miracles enabled by enthusiastic users.

Since late 2020 when I lost my R01 grant, DSSR has been licensed by the Columbia Technology Ventures (CTV). I appreciate the numerous users (including big pharma) who purchased a DSSR Pro License or a DSSR Basic paid License. Thanks to the NIH R24GM153869 grant, we are pleased to provide DSSR Basic free of charge to the academic community. Academic Users may submit a license request for DSSR Basic or DSSR Pro by clicking "Express Licensing" on the CTV landing page. Commercial users may inquire about pricing and licensing terms by emailing techtransfer@columbia.edu, copying xiangjun@x3dna.org.

The current version of DSSR is v2.4.5-2024sep24 which contains miscellaneous bug fixes (e.g., chain id with > 4 chars) and minor improvements. This release synchronizes with the new R24 funding, which will bring the project to the next stage. All existing users are encouraged to upgrade their installation.

Lots of exciting things will happen for the project. The first important thing is to make DSSR freely accessible to the academic community. I'm now starting to monitor the Forum closely and answer users questions promptly.

I am committed to making DSSR a brand that stands for quality and value. By virtue of its unmatched functionality, usability, and support, DSSR saves users a substantial amount of time and effort when compared to other options. My track record throughout the years has unambiguously demonstrated my dedication to this solid software product.

Xiang-Jun


DSSR Basic contains all features described in the three DSSR-related papers, and include the originally separate SNAP program (still unpublished) for analyzing DNA/RNA-protein complexes. The Pro version integrates the classic 3DNA functionality, plus advanced modeling routines, with email/Zoom/phone support.

2
RNA structures (DSSR) / Re: A pair is absent in dot-bracket notation ?
« on: September 05, 2024, 11:10:22 pm »
Pay attention to the following section:

# x3dna-dssr -i=8SH5.pdb

  stem#3[#2, #3]* bps=2 parallel
      strand-1 5'-GG-3'
       bp-type    ||
      strand-2 5'-CC-3'
      helix-form  .
   1 R.G19          R.C49          G-C WC           19-XIX    cWW  cW-W
   2 R.G20          R.C50          G-C WC           19-XIX    cWW  cW-W


These two WC pairs form a parallel mini-duplex. Both pairs (not just G19-C49 but also G20-C50) are excluded from the DBN notation.

Best regards,

Xiang-Jun

3
Hi,

DSSR is based on 3D structures of DNA/RNA, deriving features of base-pairing and stacking interactions. It also takes abasic sites into consideration in later releases, requiring only P or at least 5 out of the 6 main-chain backbone atoms (P, O5', C5', C4', C3', and O3'). In PDB entry 4AL5, nucleotide C4 has only one backbone atom (O3'), and C21 has 4 backbone atoms (P, O1P, O2P, and O5') as shown below.
ATOM   2826 O "O3'"  . C   B 2 3   ? 14.682 -18.630 19.841  1.00 152.11 ? 4    C   B "O3'"  1
......
ATOM   3343 P P      . C   B 2 20  ? 2.515  -3.243  14.608  1.00 43.27  ? 21   C   B P      1
ATOM   3344 O OP1    . C   B 2 20  ? 1.257  -3.732  14.022  1.00 60.70  ? 21   C   B OP1    1
ATOM   3345 O OP2    . C   B 2 20  ? 2.599  -1.863  15.133  1.00 37.31  ? 21   C   B OP2    1
ATOM   3346 O "O5'"  . C   B 2 20  ? 2.975  -4.175  15.812  1.00 40.82  ? 21   C   B "O5'"  1

So in previous DSSR versions, both nucleotides are ignored.

Following your question, I've revised DSSR to v2.4.4-2024sep06 which can recognize these two nucleotides. See below:

# x3dna-dssr -i=4AL5.cif
Secondary structures in dot-bracket notation (dbn) as a whole and per chain
>4AL5 nts=18 [whole]
CACUGCCGUAUAGGCAGC
..(((((.....))))).
-.AAAA..A...AAAA--

****************************************************************************
Summary of structural features of 18 nucleotides
  Note: the first five columns are: (1) serial number, (2) one-letter
    shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base
    ring atoms fitted against those in a standard base reference
    frame. The sixth (last) column contains a comma-separated list of
    features whose meanings are mostly self-explanatory, except for:
      turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees
      break: no backbone linkage between O3'(i-1) and P(i)
   1  C . B.C4      ---    non-stack,ss-non-loop
   2  A . B.A5      0.013  anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart
   3  C ( B.C6      0.007  anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart
   4  U ( B.U7      0.009  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate
   5  G ( B.G8      0.015  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate
   6  C ( B.C9      0.011  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate
   7  C ( B.C10     0.011  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate
   8  G . B.G11     0.043  u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate
   9  U . B.U12     0.019  turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop
  10  A . B.A13     0.022  u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate
  11  U . B.U14     0.006  turn,u-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart
  12  A . B.A15     0.007  anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart
  13  G ) B.G16     0.017  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop
  14  G ) B.G17     0.011  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem
  15  C ) B.C18     0.011  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem
  16  A ) B.A19     0.014  anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem
  17  G ) B.G20     0.018  anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end
  18  C . B.C21     ---    non-stack,ss-non-loop,phosphate


Best regards,

Xiang-Jun

4
General discussions (Q&As) / Re: All Possible Base Pairs
« on: August 08, 2024, 07:33:33 pm »
Hi Parivash,

DSSR (http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/) can find all base pairs and tertiary stacking interactions, among numerous other features. Using your RNA.pdb as an example, run the following commands:

Code: [Select]
x3dna-dssr -i=RNA.pdb -o=RNA.out
x3dna-dssr -i=RNA.pdb --non-pair | grep 'stacking:' | grep -v connected > long-stacks.txt

The output files RNA.out and long-stacks.txt are attached for your reference. The RNA.out contains a port of stacking interactions as listed below:

Code: [Select]
****************************************************************************
List of 63 base stacks
  Note: a stack is an ordered list of nucleotides assembled together via
        base-stacking interactions, regardless of backbone connectivity.
        Stacking interactions within a stem are *not* included.
   1 nts=2 AG A.A563,A.G567
   2 nts=2 GA A.G570,A.A873
   3 nts=2 AA A.A573,A.A574
   4 nts=2 GG A.G587,A.G755
   5 nts=2 GU A.G597,A.U598
   6 nts=2 GC A.G617,A.C618
   7 nts=2 AG A.A632,A.G633
   8 nts=2 AC A.A642,A.C643
   9 nts=2 GC A.G644,A.C645
  10 nts=2 GG A.G657,A.G658
  11 nts=2 GG A.G688,A.G700
  12 nts=2 CG A.C701,A.G703
  13 nts=2 GG A.G727,A.G731
  14 nts=2 CC A.C747,A.C748
  15 nts=2 AG A.A777,A.G778
  16 nts=2 UC A.U804,A.C805
  17 nts=2 CA A.C817,A.A819
  18 nts=2 GU A.G818,A.U820
  19 nts=2 UU A.U827,A.U870
  20 nts=2 GC A.G838,A.C840
  21 nts=2 CU A.C862,A.U863
  22 nts=2 CG A.C866,A.G867
  23 nts=2 AG A.A872,A.G874
  24 nts=2 CC A.C879,A.C880
  25 nts=2 GG A.G898,A.G902
  26 nts=2 CA A.C912,A.A913
  27 nts=3 CUC A.C562,A.U884,A.C883
  28 nts=3 CUG A.C564,A.U565,A.G566
  29 nts=3 AAA A.A572,A.A864,A.A865
  30 nts=3 GAU A.G577,A.A816,A.U813
  31 nts=3 GAG A.G662,A.A663,A.G664
  32 nts=3 AAG A.A728,A.A729,A.G730
  33 nts=3 CAA A.C732,A.A665,A.A733
  34 nts=3 GGG A.G774,A.G775,A.G776
  35 nts=3 GGG A.G821,A.G575,A.G881
  36 nts=3 GGU A.G890,A.G906,A.U905
  37 nts=3 CAA A.C899,A.A900,A.A901
  38 nts=4 UGGU A.U580,A.G581,A.G758,A.U757
  39 nts=4 GAGA A.G588,A.A753,A.G654,A.A655
  40 nts=4 GGUA A.G594,A.G595,A.U641,A.A640
  41 nts=4 CAAC A.C620,A.A621,A.A622,A.C623
  42 nts=4 CUGU A.C651,A.U652,A.G752,A.U751
  43 nts=4 GGGU A.G666,A.G741,A.G742,A.U743
  44 nts=4 GAGU A.G683,A.A684,A.G685,A.U686
  45 nts=4 CGGU A.C689,A.G690,A.G691,A.U692
  46 nts=4 CAGG A.C779,A.A780,A.G800,A.G799
  47 nts=4 GAUU A.G786,A.A787,A.U788,A.U789
  48 nts=4 CGGC A.C857,A.G858,A.G869,A.C868
  49 nts=4 GGAU A.G887,A.G888,A.A889,A.U891
  50 nts=5 GAUGG A.G584,A.A583,A.U582,A.G760,A.G761
  51 nts=5 AAUAC A.A687,A.A704,A.U705,A.A706,A.C707
  52 nts=5 CGCCC A.C764,A.G765,A.C812,A.C811,A.C810
  53 nts=5 GAAAA A.G769,A.A768,A.A767,A.A766,A.A814
  54 nts=5 CAUAG A.C783,A.A782,A.U801,A.A802,A.G803
  55 nts=5 GAAAG A.G829,A.A828,A.A859,A.A860,A.G861
  56 nts=6 UGGGGG A.U605,A.G606,A.G631,A.G630,A.G629,A.G628
  57 nts=6 AAAGAC A.A607,A.A608,A.A609,A.G610,A.A611,A.C612
  58 nts=6 GAAAUG A.G693,A.A694,A.A695,A.A696,A.U697,A.G698
  59 nts=6 AGGAAC A.A712,A.G713,A.G714,A.A715,A.A716,A.C717
  60 nts=6 AGAACC A.A790,A.G791,A.A792,A.A794,A.C795,A.C796
  61 nts=7 UUAAGGG A.U678,A.U677,A.A676,A.A675,A.G674,A.G673,A.G734
  62 nts=7 GCCGAGG A.G718,A.C719,A.C720,A.G721,A.A722,A.G724,A.G725
  63 nts=7 GCAAAAC A.G894,A.C893,A.A892,A.A907,A.A908,A.A909,A.C910

Best regards,

Xiang-Jun


5
General discussions (Q&As) / Re: All Possible Base Pairs
« on: June 09, 2024, 10:34:29 pm »
Hi Parivash,

Thanks for your interest in using 3DNA. The find_pair -p command should give you a list of all pairs, canonical or not. Please provide a concrete example to illustrate what base pairs are missing.

As for the availability of x3dna-dssr, please see the post "No more grant funding for 3DNA/DSSR" (http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/). You could use http://skmatics.x3dna.org to analyze/visualize a structure using x3dna-dssr.

Hope this helps.

Xiang-Jun

6
MD simulations / Re: Gromacs missing ' P ' atom
« on: May 27, 2024, 06:41:08 pm »
No, it is for information only: i.e., the first nucleotide (DG1) does not have the phosphate group.

7
Hi Junkai,

Thanks for the update. Getting DSSR-Basic, Academic license has been very straightforward from past experiences. As I heard from the CTV, your application has triggered a review of the license policy, and thus the delay. I am not sure of the exact details, but being patient seems to the best thing that can be done.

Let's stop this thread and put future communications via email.

Best regards,

Xiang-Jun

8
Hi Junkai,

Thanks for your interest in purchasing a DSSR Basic Academic License. Sorry for the unexpected delay in response from the CTV. I've communicated with people in charge, and hopefully the issue will be resolved shortly.

Best regards,

Xiang-Jun

9
Code: [Select]
what are the criteria for selecting the origin and XYZ axis vectors for the coordinate system?

It helps that you reads 3DNA/DSSR-related publications, and report back what you find.

10
Hi Junkai,

Thanks for your follow-up. Now your question can be answered, using C5' atom as an example:

ATOM    195  C5'  U A  10     -15.795  -3.890 -14.824  1.00  0.34           C  
C5' atom coordinate       C5prime_xyz: [-1.405, 8.313, 1.694]

C5prime_xyz is the original C5' atomic coordinates [-15.795  -3.890 -14.824] expressed in the local base reference frame,

Code: [Select]
{"rmsd":0.013,"origin":[-7.546,-2.079,-13.202],
              "x_axis":[-0.071,0.233,0.970],
              "y_axis":[-0.997,0.020,-0.078],
              "z_axis":[-0.037,-0.972,0.231],
"quaternion":[0.543,0.412,-0.464,0.566]}


dd = [-15.795  -3.890 -14.824] - [-7.546,-2.079,-13.202] = [-8.249  -1.811  -1.622]

dd * [ -0.071  -0.997  -0.037
        0.233   0.020  -0.972
        0.970  -0.078   0.231 ] = [-1.4096   8.3145   1.6908]

The slight difference between [-1.4096   8.3145   1.6908] and [-1.405, 8.313, 1.694] is due to round off errors.

Hope this helps.

Xiang-Jun


PS. Which version of DSSR are you using?

11
Feature requests / MOVED: 2D DNA structure
« on: February 02, 2024, 12:14:28 pm »

12
RNA structures (DSSR) / Re: 2D DNA structure
« on: February 02, 2024, 12:13:19 pm »
Hi Luka,

Thanks for attaching file AATAAA_dna.pdb (no need to copy-and-paste the content). DSSR does what you want, as shown below:

Code: [Select]
x3dna-dssr -i=AATAAA_dna.pdb -o=AATAAA_dna.out

# dssr-2ndstrs.dbn
>AATAAA_dna nts=16 [AATAAA_dna] -- secondary structure derived by DSSR
GCGCGAATAAACGCGC
(((((......)))))

# dssr-2ndstrs.ct
   16 ENERGY = 0.0 [AATAAA_dna] -- secondary structure derived by DSSR
    1 G     0     2    16     1
    2 C     1     3    15     2
    3 G     2     4    14     3
    4 C     3     5    13     4
    5 G     4     6    12     5
    6 A     5     7     0     6
    7 A     6     8     0     7
    8 T     7     9     0     8
    9 A     8    10     0     9
   10 A     9    11     0    10
   11 A    10    12     0    11
   12 C    11    13     5    12
   13 G    12    14     4    13
   14 C    13    15     3    14
   15 G    14    16     2    15
   16 C    15     0     1    16

It generates output file AATAAA_dna.out, and a few auxiliary files including dssr-2ndstrs.ct and dssr-2ndstrs.dbn which are all attached.

See the post [No more grant funding for 3DNA/DSSR](http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/).

Xiang-Jun

13
RNA structures (DSSR) / Re: 2D DNA structure
« on: February 01, 2024, 11:05:25 am »
Please attach the file: AATAAA_dna.pdb

14
RNA structures (DSSR) / Re: 2D DNA structure
« on: February 01, 2024, 10:07:44 am »
Hi Luka,

Please use a specific to illustrate unambiguously what you want to achieve. What you have tried and the results you got.

Xiang-Jun

15
Hi,

Please be specific with your questions by providing a minimal, reproducible example. What commands did you use? What results did you get? What did you expect? ....

Best regards,

Xiang-Jun

16
FAQs / Re: Where to download x3DNA
« on: January 30, 2024, 05:57:38 pm »
Hi Petr,

Thanks for coming back! You should now be able to see the download page.

Best regards,

Xiang-Jun

17
RNA structures (DSSR) / Re: How to look for abasic site using DSSR
« on: November 27, 2023, 11:54:06 am »
For PDB entry: 1FZL


x3dna-dssr -v

Code: [Select]
******************************************************************
           DSSR: an Integrated Software Tool for
          Dissecting the Spatial Structure of RNA
           v2.4.2-2023may01 by xiangjun@x3dna.org
******************************************************************


x3dna-dssr -i=1FZL.pdb

Code: [Select]
   1  C ( A.DC1   0.012  anti,~C2'-endo,BI,non-stack,canonical,helix-end,stem-end,coaxial-stack
   2  A ( A.DA2   0.020  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
   3  C ( A.DC3   0.007  anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack
   4  A ( A.DA4   0.018  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
   5  A ( A.DA5   0.015  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
   6  A ( A.DA6   0.015  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
   7  C ( A.DC7   0.009  anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack
   8  A ( A.DA8   0.013  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop
   9  ? . A.PYP9  ---    modified,~C2'-endo,BI,non-stack,internal-loop
  10  G ( A.DG10  0.013  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop


more dssr-torsions.txt
Code: [Select]
          nt               alpha    beta   gamma   delta  epsilon   zeta     e-z        chi            phase-angle   sugar-type    ssZp     Dp    splay
 1     C A.DC1               ---     ---    59.6   143.0  -178.2   -98.9    -79(BI)   -112.1(anti)   162.0(C2'-endo) ~C2'-endo     1.99    2.26   16.42
 2     A A.DA2             -92.0  -166.3    54.8   121.4   179.5   -87.3    -93(BI)   -112.9(anti)   143.5(C1'-exo)  ~C2'-endo     1.97    2.07   18.44
 3     C A.DC3             -62.7   166.0    58.6   144.3  -166.0  -165.5     -1(--)    -85.4(anti)   156.7(C2'-endo) ~C2'-endo     2.70    2.79   25.63
 4     A A.DA4             -75.7  -177.0    60.4   153.3  -175.3   -78.8    -97(BI)   -110.7(anti)   185.3(C3'-exo)  ~C2'-endo     1.72    1.82   18.57
 5     A A.DA5             -80.9   172.3    59.3   107.1  -166.5   -94.1    -72(BI)   -126.1(anti)   120.9(C1'-exo)  ~C2'-endo     2.48    2.58   18.91
 6     A A.DA6             -74.4   171.8    59.7   120.9   179.8   -99.1    -81(BI)   -120.3(anti)   134.2(C1'-exo)  ~C2'-endo     2.37    2.43   16.58
 7     C A.DC7             -74.1  -176.0    59.0   149.2  -164.1  -146.5    -18(--)    -93.5(anti)   168.5(C2'-endo) ~C2'-endo     2.04    2.06   24.91
 8     A A.DA8             -74.9   176.5    57.1   147.6  -173.6  -100.2    -73(BI)   -120.0(anti)   175.2(C2'-endo) ~C2'-endo      ---     ---     ---
 9     ? A.PYP9            -63.0   175.7    62.6   135.3  -178.2   -77.7   -101(BI)      ---         151.8(C2'-endo) ~C2'-endo      ---     ---     ---
 10    G A.DG10            -84.6   171.5    59.9   122.1  -176.2  -130.1    -46(BI)   -112.0(anti)   133.5(C1'-exo)  ~C2'-endo     2.63    2.71   21.35

18
RNA structures (DSSR) / Re: How to look for abasic site using DSSR
« on: November 27, 2023, 10:14:42 am »
Quote
2.  Be specific with your questions; provide a minimal, reproducible
        example if possible; use attachments where appropriate.


19
RNA structures (DSSR) / Re: A pair is absent in dot-bracket notation ?
« on: November 25, 2023, 12:01:52 am »
Hi,

Thanks for using DSSR, and for asking questions with specifics and for your followup.

6 A.A7           A.U16          A-U --           --        cWW  cW-W

Base-pair #6 is Watson-Crick like, but not a WC A-U pair, due to unconventional H-bonding patterns, as detailed below:

       [-153.4(anti) ~C3'-endo lambda=53.9] [-160.2(anti) ~C3'-endo lambda=88.0]
       d(C1'-C1')=10.02 d(N1-N9)=9.09 d(C6-C8)=10.56 tor(C1'-N1-N9-C1')=-7.1
       H-bonds[1]: "N1*O2(carbonyl)[2.91]"
       interBase-angle=12  Simple-bpParams: Shear=-2.57 Stretch=1.35 Buckle=9.9 Propeller=-7.0
       bp-pars: [-2.83   0.63    0.93    11.39   -4.17   30.82]


The DBN notation is for classic 2nd stratucure with WC and G-U wobble pairs.

Best regards,

Xiang-Jun

20
RNA structures (DSSR) / Re: Creation of customized structures using DSSR
« on: October 12, 2023, 11:11:25 am »
Also "RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2317-9):

Quote
Here, we present RNAfitme, a versatile webserver tool for remodeling of nucleobase- and nucleoside residue conformations in the fixed-backbone RNA 3D structures. Our approach makes use of dedicated libraries that define RNA conformational space. They have been built upon torsional angle characteristics of PDB-deposited RNA structures. RNAfitme can be applied to reconstruct full-atom model of RNA from its backbone; remodel user-selected nucleobase/nucleoside residues in a given RNA structure; predict RNA 3D structure based on the sequence and the template of a homologous molecule of the same size; refine RNA 3D model by reducing steric clashes indicated during structure quality assessment. RNAfitme is a publicly available tool with an intuitive interface. It is freely accessible at http://rnafitme.cs.put.poznan.pl/

21
RNA structures (DSSR) / Re: Creation of customized structures using DSSR
« on: October 12, 2023, 11:06:59 am »
Have a look at "The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs" (https://academic.oup.com/nar/article/49/1/79/6029180):

Quote
"To aid the development of novel XNA polymers and the search for possible pre-RNA candidates, this article presents the proto-Nucleic Acid Builder (https://github.com/GT-NucleicAcids/pnab), an open-source program for modeling nucleic acid analogs with alternative backbones and nucleobases. The torsion-driven conformation search procedure implemented here predicts structures with good accuracy compared to experimental structures, and correctly demonstrates the correlation between the helical structure and the backbone conformation in DNA and RNA."

Please report back how it goes.

Best regards,

Xiang-Jun

22
RNA structures (DSSR) / Re: Creation of customized structures using DSSR
« on: October 12, 2023, 08:50:01 am »
Thanks for your follow-up.

Quote
By the 9 torsional angles, I meant the torsional and pseudotorsional angles - alpha, beta, gamma, delta, chi, epsilon, zeta, eta, theta - calculated by 3DNA's `analyze` program.

Among the 9 torsion angles, only the first 7 are independent. The last two, eta and theta, could in principle be deduced from (alpha, beta, gamma, delta, epsilon, zeta). I vaguely remember reading about software tools of building nucleic acid structures using backbone torsion angles, including only eta and theta. I just do not know how useable they are from a general user's perspective.

Quote
DSSR would indeed benefit from more modeling features! I'll be following the release notes to see if this particular modeling feature is ever introduced to DSSR.

If you have info in modeling nucleic acids, please share them along this thread. I appreciate your kind words on DSSR.

Best regards,

Xiang-Jun


23
RNA structures (DSSR) / Re: Creation of customized structures using DSSR
« on: October 12, 2023, 08:18:44 am »
Hi,

Thanks for your using 3DNA, and your inquiries about DSSR Pro.

Quote
I apologize if this question is irrelevant for the forum, I wanted to confirm if DSSR Pro could satisfy our requirements before buying the license since the Pro version of the manual is not available.

It is directly relevant to the Forum. You are very welcome to post this question, and any more you may have.


Quote
We have an RNA sequence, and the 9 torsional angles (calculated by 3DNA v2.4) for each residue. Would it be possible to reconstruct the full-atom 3D structure of the RNA using DSSR Pro's rebuild program from just these two pieces of information - the sequence and the 9 torsional angles?

No, at least for now, even though it is not clear to me what exactly are the 9 torsional angles you refer to. DSSR employs 6 rigid-body parameters to quantity the relative spatial geometry between two bases (or base pairs) and uses them to build 3D models with approximate backbones. I have long been interested in adding more modeling features to DSSR ...

Best regards,

Xiang-Jun


24
FAQs / Re: Where to download x3DNA
« on: September 22, 2023, 11:53:22 am »
Done.

25
RNA structures (DSSR) / Re: Classification of helix versus loops
« 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


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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.