[chimerax-users] alpha-fold error

[Moustafa, Ibrahim M.]

Thank you Tom, I am trying it right now and it seems working!

  Ibrahim
________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Thursday, November 4, 2021 6:14 PM
To: Moustafa, Ibrahim M. <ria2 at psu.edu>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] alpha-fold error

Hi Ibrahim,

  ChimeraX AlphaFold prediction should be back to working now.  Thanks for reporting the problem.

  The DeepMind developers released a new AlphaFold version 2.1.0 at GitHub on November 2 which broke the ChimeraX capability to predict AlphaFold structures.  ChimeraX was using the most recent AlphaFold code but I have changed it now to use the specific AlphaFold version 2.0.1 which is the previous working version. You do not need a new ChimeraX  (this configuration change was to the ChimeraX AlphaFold Python code which is loaded from the web each time it is run).

Tom


On Nov 4, 2021, at 1:07 PM, Moustafa, Ibrahim M. via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Dear all,

  I am trying to use alpha fold in ChimeraX but I get the following error during computing multiple sequence alignmenet step:

--------------------------------------------------------
 TypeError
________________________________
2 frames
________________________________

<ipython-input-1-a242dc837c9a><https://localhost:8080/#> in multiple_seq_align(dbs)
    247       for i, result in enumerate(db_results):
    248         from alphafold.data import parsers
--> 249         msa, deletion_matrix, target_names = parsers.parse_stockholm(result['sto'])
    250         e_values_dict = parsers.parse_e_values_from_tblout(result['tbl'])
    251         e_values = [e_values_dict[t.split('/')[0]] for t in target_names]



TypeError: cannot unpack non-iterable Msa object


---------------------------------------------------------

  I followed the instructions of ChimeraX tutorial. I was able to use it successfully before, but not sure why I keep getting this error.

  Any idea what could be wrong?

I use ChimeraX version 1.3 (09-08-2021)

  Thanks for help
   Ibrahim

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