Messages

26

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

27

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.

28

RNA structures (DSSR) / Re: DSSR Basic Licence Application: Seeking Status Update and Assistance

« on: February 20, 2024, 06:02:31 pm »

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

29

RNA structures (DSSR) / Re: DSSR Basic Licence Application: Seeking Status Update and Assistance

« on: February 16, 2024, 09:05:42 am »

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

30

RNA structures (DSSR) / Re: How does 3dna-dssr convert the atomic coordinates from PDB files into its output

« on: February 04, 2024, 11:19:43 am »

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.

31

RNA structures (DSSR) / Re: How does 3dna-dssr convert the atomic coordinates from PDB files into its output

« on: February 02, 2024, 09:35:33 pm »

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?

32

Feature requests / MOVED: 2D DNA structure

« on: February 02, 2024, 12:14:28 pm »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=1020.0

33

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

34

RNA structures (DSSR) / Re: 2D DNA structure

« on: February 01, 2024, 11:05:25 am »

Please attach the file: AATAAA_dna.pdb

35

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

36

RNA structures (DSSR) / Re: How does 3dna-dssr convert the atomic coordinates from PDB files into its output

« on: February 01, 2024, 08:57:36 am »

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

37

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

38

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


39

RNA structures (DSSR) / Re: How to look for abasic site using DSSR

« on: November 27, 2023, 10:14:42 am »

2.  Be specific with your questions; provide a minimal, reproducible
        example if possible; use attachments where appropriate.

40

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

41

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):

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/

42

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):

"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

43

RNA structures (DSSR) / Re: Creation of customized structures using DSSR

« on: October 12, 2023, 08:50:01 am »

Thanks for your follow-up.

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.

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

44

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.

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.

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

45

FAQs / Re: Where to download x3DNA

« on: September 22, 2023, 11:53:22 am »

Done.

46

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

47

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

« 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.

48

FAQs / Re: Where to download x3DNA

« 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.

49

w3DNA -- web interface to 3DNA / Re: Cannot understand what a base pair type means from web-3DNA output

« 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

50

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

« 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