id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2917 BlaST web service: No alias or index file found for protein database petevseev@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.92 (2020-03-03) Description Blastprotein does not work :( blastprotein 1 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 id: appBlastProtein2Service15833070227471984832818 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15833070227471984832818 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 606, in customEvent func(*args, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\blastprotein\job.py"", line 96, in on_finish p = Parser(""query"", self.seq, results) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\blastprotein\blastp_parser.py"", line 47, in __init__ tree = ET.fromstring(output) File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() See log for complete Python traceback. Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.92 (2020-03-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/Peter/Downloads/05-modeller/05-modeller/076-tail sheath > protein.fasta"" Summary of feedback from opening C:/Users/Peter/Downloads/05-modeller/05-modeller/076-tail sheath protein.fasta --- note | Alignment identifier is 076-tail sheath protein.fasta Opened 1 sequences from 076-tail sheath protein.fasta > blastprotein 1 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 id: appBlastProtein2Service15833067449811830343188 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15833067449811830343188 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 606, in customEvent func(*args, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\job.py"", line 96, in on_finish p = Parser(""query"", self.seq, results) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\blastp_parser.py"", line 47, in __init__ tree = ET.fromstring(output) File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() See log for complete Python traceback. > blastprotein 1 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 id: appBlastProtein2Service1583306829274-1619047780 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1583306829274-1619047780 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 606, in customEvent func(*args, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\job.py"", line 96, in on_finish p = Parser(""query"", self.seq, results) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\blastp_parser.py"", line 47, in __init__ tree = ET.fromstring(output) File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() See log for complete Python traceback. > blastprotein 1 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 id: appBlastProtein2Service15833068734461897175413 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15833068734461897175413 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 606, in customEvent func(*args, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\job.py"", line 96, in on_finish p = Parser(""query"", self.seq, results) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\blastp_parser.py"", line 47, in __init__ tree = ET.fromstring(output) File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() See log for complete Python traceback. > toolshed show ""Blast Protein"" > blastprotein 1 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 id: appBlastProtein2Service1583307009054-562103175 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1583307009054-562103175 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 606, in customEvent func(*args, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\job.py"", line 96, in on_finish p = Parser(""query"", self.seq, results) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\blastp_parser.py"", line 47, in __init__ tree = ET.fromstring(output) File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() See log for complete Python traceback. > blastprotein 1 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 id: appBlastProtein2Service15833070227471984832818 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15833070227471984832818 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 606, in customEvent func(*args, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\job.py"", line 96, in on_finish p = Parser(""query"", self.seq, results) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\blastprotein\blastp_parser.py"", line 47, in __init__ tree = ET.fromstring(output) File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File """", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File ""C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py"", line 1316, in XML return parser.close() See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 441.41 OpenGL renderer: GeForce GTX 1060 with Max-Q Design/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Sequence fixed noemi.ruiz@… all ChimeraX