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General discussions (Q&As) / Re: Rebuild B-DNA
« on: July 06, 2025, 10:41:34 am »
Thanks for your feedback.
I've revised DSSR to replace C5M with C7 for thymine in A- and B-DNA. See the attached `new2.pdb` file.
As a side note, you could use the following command with the DSSR version you currently have installed:
Basically, it mutats T to T using the `mutate` subcommand. The net effect is C5M being replaced with C7 (see attached).
Best regards,
Xiang-Jun
I've revised DSSR to replace C5M with C7 for thymine in A- and B-DNA. See the attached `new2.pdb` file.
As a side note, you could use the following command with the DSSR version you currently have installed:
Code: [Select]
x3dna-dssr mutate -i=new.pdb --entry='name=T to=T' -o=newx.pdb
Basically, it mutats T to T using the `mutate` subcommand. The net effect is C5M being replaced with C7 (see attached).
Best regards,
Xiang-Jun