Recent Posts

31

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

« Last post by xiangjun 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

32

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

« Last post by luka86 on February 02, 2024, 09:20:33 am »

Thank you, I am sending the file in the attachment of the PDB file and also of the .out file that I got. But I am on mac, I am not sure if I have successfully uploaded the files.

33

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

« Last post by junkaiWang on February 02, 2024, 07:39:46 am »

Hi Xiangjun,

I apologize for not providing specific details when I asked my question. Below, I will present my process and concerns.

I obtained the RNA annotation dictionary 'annot' using x3dna-dssr --json -i=2tob.cif.

Then, I filtered(filter(lambda x: x['nt_type'] == 'RNA', annot['nts']) the 'annot' dictionary to retain only the RNA content nt_annot.

I can retrieve information about the target base by using nt_annot['nt_id'].
For example, on base with ID 2tob.A.10, the coordinates in nt_annot['2tob.A.10'] are as follows:
C5' atom coordinate       C5prime_xyz: [-1.405, 8.313, 1.694]
P atom coordinate          P_xyz: [1.204, 8.473, 2.116]

However, the atomic coordinates for this base in the PDB file are as follows. The same situation exists for other bases of this RNA.
ATOM    191  P     U A  10     -16.156  -3.688 -12.208  1.00  0.30           P 
ATOM    195  C5'  U A  10     -15.795  -3.890 -14.824  1.00  0.34           C 

Clearly, they are different. Therefore, I would like to know what processing has been done on them(from PDB_xyz to DSSR_xyz).
I hope I've stated my question clearly.

Best regards,
Junkai Wang

34

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

« Last post by xiangjun on February 01, 2024, 11:05:25 am »

Please attach the file: AATAAA_dna.pdb

35

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

« Last post by luka86 on February 01, 2024, 10:58:43 am »

I have run the find_pair program combined with analyze on a PDB file of the single stranded DNA of this sequence GCGCGAATAAACGCGC. The exact command that I run was this: find_pair AATAAA_dna.pdb | analyze and I got some output files from which I believe that AATAAA_dna.out is the main output with some base pair information. It contains a section like this that is somewhat similar to .ct file:

****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

            Strand I                    Strand II          Helix
   1   (0.022) ....>-:...1_:[.DG]G-----C[.DC]:..16_:-<.... (0.021)     |
   2   (0.024) ....>-:...2_:[.DC]C-----G[.DG]:..15_:-<.... (0.044)     |
   3   (0.042) ....>-:...3_:[.DG]G-----C[.DC]:..14_:-<.... (0.025)     |
   4   (0.025) ....>-:...4_:[.DC]C-----G[.DG]:..13_:-<.... (0.024)     |
   5   (0.024) ....>-:...5_:[.DG]G-----C[.DC]:..12_:-<.... (0.030)     |
   6   (0.029) ....>-:...8_:[.DT]T-**+-A[.DA]:..11_:-<.... (0.020)     |
   7   (0.030) ....>-:...7_:[.DA]A-*---A[.DA]:..10_:-<.... (0.023)     |

Note: This structure contains 2[1] non-Watson-Crick base-pairs.
****************************************************************************

I would like to get the output in the .ct format like this:
     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

or in dot-bracket format like this:

(((((......)))))

36

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

« Last post by xiangjun 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

37

RNA structures (DSSR) / 2D DNA structure

« Last post by luka86 on February 01, 2024, 09:57:09 am »

Dear Dr. Xiang-Jun,
I am working on single stranded DNA aptamers and would like to be able to retrieve the 2D DNA structure of single-stranded DNA based on the PDB file. I would like to obtain the output in .ct or dot-bracket format, the same format as it is created by Mfold from the sequence. Is this feature already included in some of the tools?
Thank you in advance,
Best regards, Luka

38

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

« Last post by xiangjun 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

39

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

« Last post by junkaiWang on February 01, 2024, 07:21:19 am »

Hi Xiangjun,

I encountered an issue while analyzing RNA structures using the 3dna-dssr program: I noticed that the XYZ coordinates of atoms such as base C5' in the output results are not consistent with those in the PDB file, indicating that some transformation has been applied. I found that there seems to be a relative coordinate system between base pairs in the output file, and I attempted to use it for conversion, but the results did not meet my expectations. Could you please clarify how the coordinates in the PDB file are transformed into the format used in the program's output?

40

FAQs / Re: Where to download x3DNA

« Last post by xiangjun 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