Hi Antonio, The error "ImportError: No module named replyobj" means Chimera cannot find its message logging module called "replyobj". That suggests that your Chimera installation is broken, and does not appear to be a problem specifically with BLAST. I would suggest installing the current Chimera version 1.16. If that does not fix it, use the Report a Bug... button that should appear when this error message is shown. Or if that button does not appear use Chimera menu entry Help / Report a Bug.... Tom
On May 31, 2022, at 8:05 AM, Antonio Díaz Quintana via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all,
Recently, I stopped being able to perform a BLAST search from the SEQUENCE tool in UCSF Chimera. Is there anything I could do to fix this?
Log message follows:
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr or pdb for sequences similar to the given protein sequence Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service <http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service> Opal job URL: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16540092552761301435... <http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16540092552761301435050> Traceback (most recent call last): File "C:\Program Files\Chimera 1.15rc\share\chimera\tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "C:\Program Files\Chimera 1.15rc\share\blastpdb\ParserBlastP.py", line 434, in _statusCB self.finishCB(self.params, output) File "C:\Program Files\Chimera 1.15rc\share\blastpdb\gui.py", line 424, in _finish self.fetchColumnValues() File "C:\Program Files\Chimera 1.15rc\share\blastpdb\gui.py", line 449, in fetchColumnValues info = fetch_pdb_info(pdb_ids) File "C:\Program Files\Chimera 1.15rc\share\blastpdb\pdbinfo.py", line 151, in fetch_pdb_info import replyobj ImportError: No module named replyobj
Best,
Antonio
-- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain
Phone: +34 954 48 9631 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
At least in my own test case just now, I can confirm that running Blast from the Sequence tool works in both the 1.16 release and today's 1.17 daily build. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 31, 2022, at 10:07 PM, Tom Goddard via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Antonio,
The error "ImportError: No module named replyobj" means Chimera cannot find its message logging module called "replyobj". That suggests that your Chimera installation is broken, and does not appear to be a problem specifically with BLAST. I would suggest installing the current Chimera version 1.16.
If that does not fix it, use the Report a Bug... button that should appear when this error message is shown. Or if that button does not appear use Chimera menu entry Help / Report a Bug....
Tom
On May 31, 2022, at 8:05 AM, Antonio Díaz Quintana via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all,
Recently, I stopped being able to perform a BLAST search from the SEQUENCE tool in UCSF Chimera. Is there anything I could do to fix this?
Log message follows:
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr or pdb for sequences similar to the given protein sequence Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service Opal job URL: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16540092552761301435... Traceback (most recent call last): File "C:\Program Files\Chimera 1.15rc\share\chimera\tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "C:\Program Files\Chimera 1.15rc\share\blastpdb\ParserBlastP.py", line 434, in _statusCB self.finishCB(self.params, output) File "C:\Program Files\Chimera 1.15rc\share\blastpdb\gui.py", line 424, in _finish self.fetchColumnValues() File "C:\Program Files\Chimera 1.15rc\share\blastpdb\gui.py", line 449, in fetchColumnValues info = fetch_pdb_info(pdb_ids) File "C:\Program Files\Chimera 1.15rc\share\blastpdb\pdbinfo.py", line 151, in fetch_pdb_info import replyobj ImportError: No module named replyobj
Best,
Antonio
-- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain
Phone: +34 954 48 9631
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Thank you, Elaine. I fixed it already by using the 1.16 version instead of 1.15rc, upon advice from other colleagues. Best, Antonio El 01/06/2022 a las 17:52, Elaine Meng escribió:
At least in my own test case just now, I can confirm that running Blast from the Sequence tool works in both the 1.16 release and today's 1.17 daily build. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 31, 2022, at 10:07 PM, Tom Goddard via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Antonio,
The error "ImportError: No module named replyobj" means Chimera cannot find its message logging module called "replyobj". That suggests that your Chimera installation is broken, and does not appear to be a problem specifically with BLAST. I would suggest installing the current Chimera version 1.16.
If that does not fix it, use the Report a Bug... button that should appear when this error message is shown. Or if that button does not appear use Chimera menu entry Help / Report a Bug....
Tom
On May 31, 2022, at 8:05 AM, Antonio Díaz Quintana via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all,
Recently, I stopped being able to perform a BLAST search from the SEQUENCE tool in UCSF Chimera. Is there anything I could do to fix this?
Log message follows:
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr or pdb for sequences similar to the given protein sequence Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service Opal job URL: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16540092552761301435... Traceback (most recent call last): File "C:\Program Files\Chimera 1.15rc\share\chimera\tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "C:\Program Files\Chimera 1.15rc\share\blastpdb\ParserBlastP.py", line 434, in _statusCB self.finishCB(self.params, output) File "C:\Program Files\Chimera 1.15rc\share\blastpdb\gui.py", line 424, in _finish self.fetchColumnValues() File "C:\Program Files\Chimera 1.15rc\share\blastpdb\gui.py", line 449, in fetchColumnValues info = fetch_pdb_info(pdb_ids) File "C:\Program Files\Chimera 1.15rc\share\blastpdb\pdbinfo.py", line 151, in fetch_pdb_info import replyobj ImportError: No module named replyobj
Best,
Antonio
-- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain
Phone: +34 954 48 9631
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
-- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain Phone: +34 954 48 9631
participants (3)
-
Antonio Díaz Quintana -
Elaine Meng -
Tom Goddard