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Hi,
I am using DSSR v2.5.2 to build a DNA structure with the following command:
x3dna-dssr rebuild --backbone=B-DNA --par-file=dssr-dsStepPars.txt --o=new.pdb
The file dssr-dsStepPars.txt was generated using this command:
x3dna-dssr analyze --input=1hlo.pdb --rebuild-parameters
However, I noticed that in the rebuilt DNA structure (new.pdb), all thymine bases appear to be methylated—specifically, the C5M atom shows up in the output. There is no methylation in my initial input file(1hlo.pdb)
Snippets of the new.pdb file showing the issue have been attached to this message.
Could you please help me understand why the C5M atom appears in the rebuilt structure? Also, how can I generate the DNA structure without this methylation (without C5M)?
Thank you!
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Hi,
Thanks for using DSSR and for posting your question on the Forum. The two DSSR commands you used help illuminate the question well, and the snippets from your `new.pdb` file clearly show the issue.
However, I noticed that in the rebuilt DNA structure (new.pdb), all thymine bases appear to be methylated—specifically, the C5M atom shows up in the output. There is no methylation in my initial input file(1hlo.pdb)
The thymine base in DNA has a methyl group at the C5 position, which is named differently across various versions of the PDB
format. Historically, it was referred to as C5M, but in more recent versions (e.g., in `1hlo`), it is labeled as C7. For further
details, please refer to my blog post titled "Different names for the methyl group in DNA and RNA structures" at
https://x3dna.org/articles/different-names-for-the-methyl-group-in-dna-and-rna-structures
The presence of `C5M` in your `new.pdb` is because the building block in DSSR currently uses `C5M` to denote the methyl group on thymine instead of `C7`. Since you raised this point, I am considering updating DSSR to use `C7` for thymine in future versions. In the meantime, you can simply replace `C5M` with `C7` in your `new.pdb` file.
Best regads,
Xiang-Jun
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Thank you very much for your reply!
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University