[chimerax-users] alpha-fold error

[Tom Goddard]

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> 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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