[Chimera-users] Output chain sequences

[Healey, Joe]

Hi Elaine,


That's strange in that case. I still receive this error (and I reinstalled the latest stable version of Chimera today too).


I'm familiar with this type of Python error, but not sure what it means in the context of not being able to communicate with the servers.


The error:

ValueError: Too make values to unpack


File "/Applications/Chimera.app/Contents/Resources/share/AlignChains/gui.py, line 109, in __init__

  serviceName, inOutFlags, serviceOptions = serviceinfo




Joe Healey


M.Sc. B.Sc. (Hons) MRSB
PhD Student
MOAC CDT, Senate House
University of Warwick
Coventry
CV47AL
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
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 10 July 2018 18:00:39
To: Healey, Joe
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Output chain sequences

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)
> ```

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