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.edumailto: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.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-usershttps://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)
-
Moustafa, Ibrahim M. -
Tom Goddard