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srnas / barnaba

Analyse Nucleic Acids Structure and Simulations with baRNAba
GNU General Public License v3.0
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Modified residues #42

Open ghost opened 4 years ago

ghost commented 4 years ago

Hello,

Does BARNABA have the ability to read modified residues. And can it calculate features of these residues like eRMSD, RMSD and gvectors? If yes, how?

Thank you,

Tia

valeriopiomponi commented 4 years ago

I had the same issue few weeks ago. I simply added my modified nucleotide (m6A) to the residue dictionary here https://github.com/srnas/barnaba/blob/master/barnaba/definitions.py I simply added 'm6A' : 'A' in the list on line 24. In this way, any time barnba see a residue named m6a, I will treat it as a simple adenine (that i think is good in terms of gvectors/ermds calculations)

sbottaro commented 4 years ago

Thanks @valeriopiomponi. You can add any modifications you need, as long as you make sure the name of atoms C2/C4/C6 are present in the modified base.