id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2918 Blast Protein failure + Attempted instantiation of HeaderSequence during session save noemi.ruiz@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.92 (2020-03-03) Description (Describe the actions that caused this problem to occur here) Log: Unknown command: refresh > save session C:/Users/leole/Documents/SYT1SYT3.cxs Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 556, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 288, in process return copy_state(data, convert=convert) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 210, in copy_state return _copy(data) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 205, in _copy return data.__class__(items) TypeError: __init__() missing 1 required positional argument: 'refresh_callback' TypeError: __init__() missing 1 required positional argument: 'refresh_callback' File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 205, in _copy return data.__class__(items) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 929, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 647, in file_save_cb self.save_dialog.display(self, session) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\ui\save_dialog.py"", line 139, in display fmt.save(session, filename) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 1100, in save run(session, cmd) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2845, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 992, in save_session save(session, filename, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\save.py"", line 64, in save _handle_unexpected_keyword_error(e, 5) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 229, in export result = self.export_func(session, path, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 556, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\session.py"", line 288, in process return copy_state(data, convert=convert) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 210, in copy_state return _copy(data) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in _copy items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 204, in items = [_copy(o) for o in data] File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 205, in _copy return data.__class__(items) TypeError: __init__() missing 1 required positional argument: 'refresh_callback' TypeError: __init__() missing 1 required positional argument: 'refresh_callback' File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py"", line 205, in _copy return data.__class__(items) See log for complete Python traceback. > select #1:268 #2:230 16 atoms, 14 bonds, 2 models selected Seqview [ID: 1] region Consensus..201801_SYT3_1623pb_intensive.pdb, chain (blank) [1-555] RMSD: 3.412 > save ""C:/Users/leole/Documents/05 Univ Malaga_2016_2017/20 Manuscrito > SYT/Figuras Noemi/AlineamientoSYT1SYT3"" format aln alignment 1 > toolshed show ""Modeller Comparative"" No target sequence chosen for alignment 1 Seqview [ID: 1] region Consensus..201801_SYT3_1623pb_intensive.pdb, chain (blank) [1-555] RMSD: 3.412 Seqview [ID: 1] region Consensus..201801_SYT3_1623pb_intensive.pdb, chain (blank) [1-555] RMSD: 3.412 > save ""C:/Users/leole/Documents/05 Univ Malaga_2016_2017/20 Manuscrito > SYT/Figuras Noemi/AlineamientoSYT1SYT3"" format fasta alignment 1 > select #1 3819 atoms, 3915 bonds, 1 model selected > select #2 4367 atoms, 4470 bonds, 1 model selected > ~select #2 Nothing selected > blastprotein #1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name > bp3 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: appBlastProtein2Service15833203481191424442245 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15833203481191424442245 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 376.54 OpenGL renderer: GeForce 920M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Sequence duplicate Greg Couch all ChimeraX