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
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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Thank you Tom, I am trying it right now and it seems working! Ibrahim ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Thursday, November 4, 2021 6:14 PM To: Moustafa, Ibrahim M. <ria2@psu.edu> Cc: ChimeraX Users Help <chimerax-users@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@cgl.ucsf.edu<mailto: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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimerax-users&data=04%7C01%7Cria2%40psu.edu%7C8ad3ddc3fdcb4a48554808d99fe0860c%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637716608933340505%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=lmqvS7KdgghCJ7mKIh5x9EYDy6j3%2BGuWvBhU7GBFgks%3D&reserved=0>
participants (2)
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Moustafa, Ibrahim M. -
Tom Goddard