[Chimera-users] Output chain sequences

[Eric Pettersen]

Just to follow up on the Python question here, a model can have multiple sequences (one per chain), so your code should be:

from chimera import openModels
all_mods = chimera.openModels.list(modelTypes=[chimera.Molecule])
with open('output.fasta', 'w') as ofh:
     for mod in all_mods:
         for seq in mod.sequences():
             ofh.write('>%s.%s\n%s' % (mod.name, seq.chainID, seq)


What you were trying to use, mod.sequence, is a method that takes a chain ID as an argument and returns the Sequence object corresponding to that chain ID (e.g. mod.sequence(‘A’) returns the Sequence for chain A).

—Eric

> On Jul 10, 2018, at 4:48 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk> wrote:
> 
> Hi Chimera Team,
> 
> I've been experiencing issues with the "Align Chains" tools that connect to Clustal and Muscle - I think ostensibly this might be because the servers are no longer available or something.
> 
> I'm happy to make the alignments myself, but to do this I'd like to try and simply export the sequences of all open models to a fasta file or similar. I know this can be done manually sequence-by-sequence thtrough the GUI.
> 
> Could you tell me what the python (or chimera syntax) would be to do this if it's possible?
> 
> I'm envisaging something to the effect of this, but I can't quite get what I need back in terms of the sequence (it returns a `bound object'?):
> 
> ```
> from chimera import openModels
> all_mods = chimera.openModels.list(modelTypes=[chimera.Molecule])
> with open('output.fasta', 'w') as ofh:
>      for mod in all_mods:
>          ofh.write('>%s\n%s' % (mod.name, mod.sequence)
> ```
> 
> Thanks,
> 
> Joe Healey
> 
>                                        
> M.Sc. B.Sc. (Hons) MRSB
> PhD Student
> MOAC CDT, Senate House
> University of Warwick
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> 
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> 
> Twitter: @JRJHealey <https://twitter.com/JRJHealey>  |  Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738 <http://orcid.org/0000-0002-9569-6738>_______________________________________________
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