[Chimera-users] Output chain sequences

Healey, Joe J.R.J.Healey at warwick.ac.uk
Tue Jul 10 04:48:40 PDT 2018

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)



Joe Healey

M.Sc. B.Sc. (Hons) MRSB
PhD Student
MOAC CDT, Senate House
University of Warwick
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

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
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