Rebuild B-DNA

[Xuan Liu]

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!