Hi Maik, The residue names come from the input, so chain B in your input file must have those single-letter codes. The PDB-standard DNA residue names are two letters starting with D, whereas RNA names are one letter, but your one-letter residues names clearly are not RNA since there is a ’T” in them. Anyway, whatever created the input file is the culprit here. For getting the sequences cleanly, I would use the Chain objects, which know both the residues and corresponding sequence. Assuming your selections on the chains are contiguous, this should work: selection = run(session, "select ...") for chain in selection.chains: indices = [i for i, r in enumerate(chain.residues) if r and r.atoms.selecteds.any()] print(chain, "".join(chain.characters[min(indices):max(indices)+1])) --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 6, 2024, at 2:02 PM, Engeholm, Maik via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi there,
I'm looking for a neat way to retrieve the sequence of an atom selection (in this case part of a double-stranded DNA molecule) from within a python script.
I've been playing around with:
selection = run (session, 'select #1/A:2-4|#1/B:6-9') for a in selection.atoms.unique_residues: print(a)
which gives me:
151 atoms, 169 bonds, 7 residues, 1 model selected /A DG 2 /A DG 3 /A DG 4 /B G 6 /B G 7 /B A 8 /B T 9
This is a good start, but ideally I'd like to get back a contiguous sequence string for each chain (like (('A', 'GGG'), ('B', GGAT'))). Also, I do not really understand, why residue names are reported as 'DG' for strand A, but 'G' for strand B, which makes extracting a sequence string from the above output quite difficult.
I've also tried:
selection = run (session, 'select #1/A:2-4|#1/B:6-9') for a in selection.atoms.by_chain: print(a[1]) print(a[2].unique_residues.unique_sequences[0][1])
which gives me:
151 atoms, 169 bonds, 7 residues, 1 model selected A AGGGAGTAATCCCCTTG B CAAGGGGATTACTCCCT
This is obviously also not what I want since it returns the entire sequence of each chain.
I guess I could take the residue numbers from the first command and use those to slice the strings returned by the second, but that feels a little awkward, and so I was wondering if there was a better, more direct way to achieve this seemingly simple task.
Your help would be much appreciated.
Cheers,
Maik
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