id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1922 Non-ASCII PDB file should not raise bug-reportable error chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.9 (2019-05-08) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.9 (2019-05-08) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:quickstart > open ""C:/Users/sflsl/Desktop/HPV-18 Arif/HPV-18-E1/hpv_19_e1.pdb"" Summary of feedback from opening C:/Users/sflsl/Desktop/HPV-18 Arif/HPV-18-E1/hpv_19_e1.pdb --- error | Non-ASCII character on line 2 of PDB file warning | Ignored bad PDB record found on line 1 /data/8a76afc0d4654c1ba66b925e3 Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 564, in _qt_safe run(session, ""open "" + quote_if_necessary(paths[0])) 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 2631, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 64, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 602, in open session, filenames, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 477, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 433, in open_data models, status = open_func(*args, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\pdb\\__init__.py"", line 42, in open_file combine_sym_atoms=combine_sym_atoms) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\pdb\pdb.py"", line 27, in open_pdb pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic) ValueError: PDB file contains non-ASCII character or control character ValueError: PDB file contains non-ASCII character or control character File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\pdb\pdb.py"", line 27, in open_pdb pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic) See log for complete Python traceback. > open ""C:/Users/sflsl/Desktop/HPV-18 Arif/HPV-18-E1/hpv_19_e1.pdb"" Summary of feedback from opening C:/Users/sflsl/Desktop/HPV-18 Arif/HPV-18-E1/hpv_19_e1.pdb --- error | Non-ASCII character on line 2 of PDB file warning | Ignored bad PDB record found on line 1 /data/8a76afc0d4654c1ba66b925e3 Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 141, in lambda e, what=what, self=self: self.handle_scheme(what), File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 96, in handle_scheme run(self.session, f'{value}') 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 2631, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 64, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 602, in open session, filenames, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 477, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 433, in open_data models, status = open_func(*args, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\pdb\\__init__.py"", line 42, in open_file combine_sym_atoms=combine_sym_atoms) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\pdb\pdb.py"", line 27, in open_pdb pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic) ValueError: PDB file contains non-ASCII character or control character ValueError: PDB file contains non-ASCII character or control character File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\pdb\pdb.py"", line 27, in open_pdb pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 425.31 OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Input/Output fixed all ChimeraX