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
participants (3)
-
Antonio Díaz Quintana -
Elaine Meng -
Tom Goddard