id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2333 UTF-16 file p.albanese@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.9 (2019-06-06) Description I'm trying to map crosslinks in form of .pb files (i was already doing this with previous versions, daily releases actually) but now with this release i got this message: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte File ""C:\Program Files\ChimeraX\bin\lib\codecs.py"", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) See log for complete Python traceback. ___ is that somthing related to the PDB or the .pb file attached? Log: UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:\\\Users\\\Alban001\\\Downloads\\\4wjg.pdb"" 4wjg.pdb title: Structure of T. Brucei haptoglobin-hemoglobin receptor binding to human haptoglobin-hemoglobin [more info...] Chain information for 4wjg.pdb #1 --- Chain | Description 1 B G L Q V | hemoglobin subunit β 2 C H M R W | zonulin 3 D I N S X | iron-regulated surface determinant protein H 4 E J O T Y | haptoglobin-hemoglobin receptor A F K P U Z | hemoglobin subunit α Non-standard residues in 4wjg.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) NAG — N-acetyl-D-glucosamine OXY — oxygen molecule > select /4:36-296 1963 atoms, 1982 bonds selected > select /E:36-296 1963 atoms, 1982 bonds selected > select /1:1-146 1123 atoms, 1153 bonds selected > select /B:1-146 1123 atoms, 1153 bonds selected > select /B:1-146 1123 atoms, 1153 bonds selected > select /A:44@O 1 atom selected > select /1:1-146 1123 atoms, 1153 bonds selected > show selAtoms ribbons > hide selAtoms > select up 40807 atoms, 41616 bonds, 64 pseudobonds, 1 model selected > select up 41424 atoms, 42331 bonds, 64 pseudobonds, 1 model selected > select up 44086 atoms, 45092 bonds, 64 pseudobonds, 1 model selected > select up 46624 atoms, 47688 bonds, 64 pseudobonds, 1 model selected > select up 47792 atoms, 48888 bonds, 77 pseudobonds, 1 model selected > hide selAtoms > show selAtoms ribbons > select clear > select /B:9 6 atoms, 5 bonds selected > select up 1530 atoms, 1560 bonds selected > select up 9578 atoms, 9843 bonds selected > select ~sel 38214 atoms, 39045 bonds, 51 pseudobonds, 1 model selected > delete sel > save ""K:\\\HbHp_TP\\\PDB\\\HpHb_human.pdb"" > select clear > close #1 > open K:/HbHp_TP/PDB/HpHb_human.pdb Summary of feedback from opening K:/HbHp_TP/PDB/HpHb_human.pdb --- warning | Ignored bad PDB record found on line 21459 END HpHb_human.pdb title: Structure of T. Brucei haptoglobin-hemoglobin receptor binding to human haptoglobin-hemoglobin [more info...] Chain information for HpHb_human.pdb #1 --- Chain | Description A F | hemoglobin subunit α B G | hemoglobin subunit β C H | zonulin Non-standard residues in HpHb_human.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) NAG — N-acetyl-D-glucosamine OXY — oxygen molecule > open ""K:/HbHp_TP/PD results (tera2)/0_mapped.pb"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 572, 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 2632, 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 601, 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\read_pbonds\\__init__.py"", line 23, in open_file return readpbonds.read_pseudobond_file(session, stream, file_name) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\read_pbonds\readpbonds.py"", line 16, in read_pseudobond_file lines = stream.readlines() File ""C:\Program Files\ChimeraX\bin\lib\codecs.py"", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte File ""C:\Program Files\ChimeraX\bin\lib\codecs.py"", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) See log for complete Python traceback. > sequence chain #1/C#1/H Alignment identifier is 1 > select clear > open ""K:/HbHp_TP/PD results (tera2)/HbHp_75.pb"" Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 572, 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 2632, 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 601, 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\read_pbonds\\__init__.py"", line 23, in open_file return readpbonds.read_pseudobond_file(session, stream, file_name) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\read_pbonds\readpbonds.py"", line 16, in read_pseudobond_file lines = stream.readlines() File ""C:\Program Files\ChimeraX\bin\lib\codecs.py"", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte File ""C:\Program Files\ChimeraX\bin\lib\codecs.py"", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) See log for complete Python traceback. OpenGL version: 3.3.0 OpenGL renderer: Quadro FX 380/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation File attachment: 0_mapped.pb }}} [attachment:""0_mapped.pb""] " defect closed normal Input/Output not a bug Greg Couch Tom Goddard all ChimeraX