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@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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