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51

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

« Last post by xiangjun 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.

52

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

« Last post by junkaiWang on February 04, 2024, 02:28:43 am »

Hi Xiangjun,

Thank you for your patient reply. I now understand the issue.
I have one final question:
what are the criteria for selecting the origin and XYZ axis vectors for the coordinate system?

Best regards,
Junkai Wang

53

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

« Last post by xiangjun 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,

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{"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?

54

Feature requests / MOVED: 2D DNA structure

« Last post by xiangjun 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

55

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

56

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.

57

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

58

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

59

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:

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

60

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