id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4455 BLAST failure kiernan1@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-19.6.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-05-03) Description I used the BLAST Protein function and got this error. Log: Startup Messages --- note | Updating list of available bundles failed: Internal Server Error libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile UCSF ChimeraX version: 0.9 (2019-05-03) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/Kaitlyn/Documents/Cryo-EM/Cas9 structures/Product-reb7-Cas9 only.pdb"" Summary of feedback from opening /Users/Kaitlyn/Documents/Cryo-EM/Cas9 structures/Product-reb7-Cas9 only.pdb --- warnings | Ignored bad PDB record found on line 20 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.008 0.065 11811 Ignored bad PDB record found on line 23 ANGLE : 0.786 9.688 16734 Ignored bad PDB record found on line 24 CHIRALITY : 0.049 0.296 2030 16 messages similar to the above omitted Chain information for Product-reb7-Cas9 only.pdb #1 --- Chain | Description A | No description available > style selAtoms sphere Changed 8100 atom styles > style selAtoms stick Changed 8100 atom styles > toolshed show ""Modeller Comparative"" > undo > toolshed show ""Blast Protein"" > blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 toolId 7 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: appBlastProtein2Service16175583085371107483065 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16175583085371107483065 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 320, in fetch_from_pdb f = urlopen(url) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 222, in urlopen return opener.open(url, data, timeout) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 531, in open response = meth(req, response) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 641, in http_response 'http', request, response, code, msg, hdrs) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 569, in error return self._call_chain(*args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 503, in _call_chain result = func(*args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 649, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 404: Not Found During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 544, in customEvent func(*args, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/job.py"", line 101, in on_finish self.tool.job_finished(self, p, self._params()) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py"", line 185, in job_finished self._show_results(job.atomspec, blast_results) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py"", line 218, in _show_results self._add_pdbinfo(pdb_chains) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py"", line 236, in _add_pdbinfo data = info.fetch_info(self.session, chain_ids) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 47, in fetch_info xml = fetch_from_pdb(session, 'describePDB', set(pdb_ids)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 323, in fetch_from_pdb except (URLError, HTTPError) as e: NameError: name 'HTTPError' is not defined NameError: name 'HTTPError' is not defined File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 323, in fetch_from_pdb except (URLError, HTTPError) as e: See log for complete Python traceback. > select #1.1 5 pseudobonds, 1 model selected > ~select #1.1 Nothing selected > select #1 8100 atoms, 8253 bonds, 5 pseudobonds, 1 model selected > blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 toolId 7 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: appBlastProtein2Service1617558365126895884501 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1617558365126895884501 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 320, in fetch_from_pdb f = urlopen(url) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 222, in urlopen return opener.open(url, data, timeout) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 531, in open response = meth(req, response) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 641, in http_response 'http', request, response, code, msg, hdrs) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 569, in error return self._call_chain(*args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 503, in _call_chain result = func(*args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 649, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 404: Not Found During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 544, in customEvent func(*args, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/job.py"", line 101, in on_finish self.tool.job_finished(self, p, self._params()) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py"", line 185, in job_finished self._show_results(job.atomspec, blast_results) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py"", line 218, in _show_results self._add_pdbinfo(pdb_chains) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py"", line 236, in _add_pdbinfo data = info.fetch_info(self.session, chain_ids) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 47, in fetch_info xml = fetch_from_pdb(session, 'describePDB', set(pdb_ids)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 323, in fetch_from_pdb except (URLError, HTTPError) as e: NameError: name 'HTTPError' is not defined NameError: name 'HTTPError' is not defined File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 323, in fetch_from_pdb except (URLError, HTTPError) as e: See log for complete Python traceback. > toolshed show ""Modeller Comparative"" > select /A 8100 atoms, 8253 bonds, 5 pseudobonds, 1 model selected > show #1 target m > select down 8100 atoms, 8253 bonds, 5 pseudobonds, 1 model selected > select sequence 1-1368 Nothing selected > select down Nothing selected > select up Nothing selected > select sequence 1-1366 Nothing selected > select sequence 1-1300 Nothing selected > select sequence 10-1366 Nothing selected > show #1 target m > show #1 target m > select sequence 10-1366 Nothing selected > select sequence 30-60 Nothing selected > select sequence 30-60 Nothing selected Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword Incomplete command: sequence > select 8100 atoms, 8253 bonds, 5 pseudobonds, 1 model selected > toolshed show ""Blast Protein"" > blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 toolId 9 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: appBlastProtein2Service1617558982109-55847901 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1617558982109-55847901 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 320, in fetch_from_pdb f = urlopen(url) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 222, in urlopen return opener.open(url, data, timeout) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 531, in open response = meth(req, response) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 641, in http_response 'http', request, response, code, msg, hdrs) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 569, in error return self._call_chain(*args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 503, in _call_chain result = func(*args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py"", line 649, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 404: Not Found During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 544, in customEvent func(*args, **kw) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/job.py"", line 101, in on_finish self.tool.job_finished(self, p, self._params()) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py"", line 185, in job_finished self._show_results(job.atomspec, blast_results) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py"", line 218, in _show_results self._add_pdbinfo(pdb_chains) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py"", line 236, in _add_pdbinfo data = info.fetch_info(self.session, chain_ids) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 47, in fetch_info xml = fetch_from_pdb(session, 'describePDB', set(pdb_ids)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 323, in fetch_from_pdb except (URLError, HTTPError) as e: NameError: name 'HTTPError' is not defined NameError: name 'HTTPError' is not defined File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py"", line 323, in fetch_from_pdb except (URLError, HTTPError) as e: See log for complete Python traceback. OpenGL version: 4.1 ATI-3.10.19 OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Sequence can't reproduce all ChimeraX