How do I get Modeller structure if there was a connection timeout error on ChimeraX?
Dear ChimeraX, I used “Model Loops” on a large protein and even though ChimeraX indicated “Modeller Webservice: 1 of 1 models generated”, it also gave the following error message: modeller refine<help:user/commands/modeller.html#refine> 1:1:all-missing 1/A:1:all-missing numModels 1 fast false adjacentFlexible 1 protocol standard Webservices job id: RO5U9U0YU7YY6TM5 2025-05-23 15:51:56,220 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x32f0aa350>, 'Connection to webservices.rbvi.ucsf.edu timed out. (connect timeout=None)')': /cxservices/api/v1/chimerax/jobs/RO5U9U0YU7YY6TM5/files Am I able to retrieve the model from webservices.rbvi.ucsf.edu<http://webservices.rbvi.ucsf.edu/>? Sincerely yours, Andy LiWang Professor of Chemistry & Biochemistry University of California Merced, CA 95343
Hi Andy, Users can't login to webservices.rbvi.ucsf.edu <http://webservices.rbvi.ucsf.edu/>. I have located the generated model for your job and emailed it to you directly. --Eric Eric Pettersen UCSF Computer Graphics Lab
On May 23, 2025, at 4:01 PM, Andy Liwang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX,
I used “Model Loops” on a large protein and even though ChimeraX indicated “Modeller Webservice: 1 of 1 models generated”, it also gave the following error message: modeller refine <help:user/commands/modeller.html#refine> 1:1:all-missing 1/A:1:all-missing numModels 1 fast false adjacentFlexible 1 protocol standard Webservices job id: RO5U9U0YU7YY6TM5 2025-05-23 15:51:56,220 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x32f0aa350>, 'Connection to webservices.rbvi.ucsf.edu timed out. (connect timeout=None)')': /cxservices/api/v1/chimerax/jobs/RO5U9U0YU7YY6TM5/files
Am I able to retrieve the model from webservices.rbvi.ucsf.edu <http://webservices.rbvi.ucsf.edu/>?
Sincerely yours, Andy LiWang Professor of Chemistry & Biochemistry University of California Merced, CA 95343 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you very much, Eric!! By the way, after I had given up hope, a few hours after the job was finished the Modeller structure popped onto my ChimeraX screen, even with the timeout error. Go figure! Thanks again and have a great weekend! Andy LiWang Professor of Chemistry & Biochemistry University of California Merced, CA 95343 - - - On May 23, 2025, at 4:20 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Andy, Users can't login to webservices.rbvi.ucsf.edu<http://webservices.rbvi.ucsf.edu/>. I have located the generated model for your job and emailed it to you directly. --Eric Eric Pettersen UCSF Computer Graphics Lab On May 23, 2025, at 4:01 PM, Andy Liwang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear ChimeraX, I used “Model Loops” on a large protein and even though ChimeraX indicated “Modeller Webservice: 1 of 1 models generated”, it also gave the following error message: modeller refine<help:user/commands/modeller.html#refine> 1:1:all-missing 1/A:1:all-missing numModels 1 fast false adjacentFlexible 1 protocol standard Webservices job id: RO5U9U0YU7YY6TM5 2025-05-23 15:51:56,220 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x32f0aa350>, 'Connection to webservices.rbvi.ucsf.edu timed out. (connect timeout=None)')': /cxservices/api/v1/chimerax/jobs/RO5U9U0YU7YY6TM5/files Am I able to retrieve the model from webservices.rbvi.ucsf.edu<http://webservices.rbvi.ucsf.edu/>? Sincerely yours, Andy LiWang Professor of Chemistry & Biochemistry University of California Merced, CA 95343 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Pretty miraculous. :-) --Eric
On May 23, 2025, at 4:23 PM, Andy Liwang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you very much, Eric!!
By the way, after I had given up hope, a few hours after the job was finished the Modeller structure popped onto my ChimeraX screen, even with the timeout error. Go figure!
Thanks again and have a great weekend! Andy LiWang Professor of Chemistry & Biochemistry University of California Merced, CA 95343 - - -
On May 23, 2025, at 4:20 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Andy, Users can't login to webservices.rbvi.ucsf.edu <http://webservices.rbvi.ucsf.edu/>. I have located the generated model for your job and emailed it to you directly.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On May 23, 2025, at 4:01 PM, Andy Liwang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX,
I used “Model Loops” on a large protein and even though ChimeraX indicated “Modeller Webservice: 1 of 1 models generated”, it also gave the following error message: modeller refine <help:user/commands/modeller.html#refine> 1:1:all-missing 1/A:1:all-missing numModels 1 fast false adjacentFlexible 1 protocol standard Webservices job id: RO5U9U0YU7YY6TM5 2025-05-23 15:51:56,220 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x32f0aa350>, 'Connection to webservices.rbvi.ucsf.edu timed out. (connect timeout=None)')': /cxservices/api/v1/chimerax/jobs/RO5U9U0YU7YY6TM5/files
Am I able to retrieve the model from webservices.rbvi.ucsf.edu <http://webservices.rbvi.ucsf.edu/>?
Sincerely yours, Andy LiWang Professor of Chemistry & Biochemistry University of California Merced, CA 95343 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
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Andy Liwang -
Eric Pettersen