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Author Topic: How does 3dna-dssr convert the atomic coordinates from PDB files into its output  (Read 1091 times)

Offline junkaiWang

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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?

Offline xiangjun

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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

Offline junkaiWang

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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

Offline xiangjun

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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?
« Last Edit: February 02, 2024, 09:40:11 pm by xiangjun »

Offline junkaiWang

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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

Offline xiangjun

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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.

 

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.