[Chimera-users] Output chain sequences

[Elaine Meng]

Hi Joe,
I can’t advise on the python, but our system was down for several days recently.  It’s up now, and I just used the Align Chains service successfully.

Saving fasta for structure chains might be slightly easier in ChimeraX, although still one-by-one.  When you open a structure, there are links in the Log to show each chain sequence with a single click, and then you can save fasta using the context menu within each sequence window.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> 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)
> ```