Hi Eric,
thanks a lot for your help. That is exactly what I wanted!
By the way, the example DNA file I created in ChimeraX using build start nucleic type DNA form B. And, yes, it has these different residue names for the two strands in the pdb file.
SEQRES 1 A 17 DA DG DG DG DA DG DT DA DA DT DC DC DC
SEQRES 2 A 17 DC DT DT DG
SEQRES 1 B 17 C A A G G G G A T T A C T
SEQRES 2 B 17 C C C T
ATOM 1 C4' DA A 1 212.165 192.028 187.380 1.00 0.00 C
ATOM 2 O5' DA A 1 214.218 191.381 188.348 1.00 0.00 O
ATOM 3 O3' DA A 1 210.239 190.586 187.380 1.00 0.00 O
...
Can you reproduce this?
Regards,
Maik
________________________________
From: Eric Pettersen
Sent: Monday, January 8, 2024 9:10:05 PM
To: Engeholm, Maik
Cc: chimerax-users@cgl.ucsf.edu
Subject: Re: [chimerax-users] retrieve the sequence of an atom selection
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 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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