id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1322 Read pbonds: 'str' object has no attribute 'decode' pascal.albanese@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.8 (2018-09-07) Description (Describe the actions that caused this problem to occur here) Hi, sorry for bothering you but i hv some issues while trying to load .pb files, maybe i'm doing something wrong. the input is the following (a plain text file with "".pb"" in the name) #1.1/R:28@CA #1.2/R:170@CA #1.1/R:200@CA #1.2/R:28@CA #1.1/R:200@CA #1.2/G:38@CA #1.1/R:200@CA #1.2/V:38@CA #1.1/R:200@CA #1.2/U:38@CA #1.1/R:190@CA #1.2/R:28@CA #1.1/R:190@CA #1.2/G:38@CA #1.1/R:190@CA #1.2/V:38@CA #1.1/R:190@CA #1.2/U:38@CA #1.1/R:190@CA #1.2/R:32@CA i tried different combinations but i'm not able to generate Sets of pseudobonds (as i expect it will happen by loading different files... or not?) Thanks for your help, Pascal Log: UCSF ChimeraX version: 0.8 (2018-09-07) How to cite UCSF ChimeraX open D:/UTRECHT_MS/xls/Lhcb4_MDFF/DSSO_CL_Lhcb4_interP.pb ↵ Traceback (most recent call last):   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 517, 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 2561, in run     result = ci.function(session, **kw_args)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 41, in open     from_database=from_database, ignore_cache=ignore_cache, **kw))   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 110, in open     models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 62, in handle_unknown_kw     return f(*args, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 559, in open     session, filenames, format=format, name=name, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 444, 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 404, 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 27, in read_pseudobond_file     aspec1, aspec2 = line.decode('utf-8').split()[:2] AttributeError: 'str' object has no attribute 'decode' AttributeError: 'str' object has no attribute 'decode' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\read_pbonds\readpbonds.py"", line 27, in read_pseudobond_file aspec1, aspec2 = line.decode('utf-8').split()[:2] See log for complete Python traceback. open D:/UTRECHT_MS/xls/Lhcb4_MDFF/LHCB4.cxs ↵ opened ChimeraX session show selAtoms ribbons ↵ hide selAtoms ↵ show #!1.1 models ↵ hide #!1.1 models ↵ hide #!2 models ↵ show #!2 models ↵ show selAtoms ↵ hide selAtoms surfaces ↵ hide selAtoms ↵ select #2 ↵ 44 pseudobonds, 2 models selected ~select #2 ↵ select subtract #2 ↵ Nothing selected show selAtoms ↵ Traceback (most recent call last):   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\ui\mousemodes.py"", line 387, in     gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_up"")   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\ui\mousemodes.py"", line 326, in _dispatch_mouse_event     f(MouseEvent(event))   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\ui\mousemodes.py"", line 460, in mouse_up     mouse_drag_select(self.mouse_down_position, event, self.mode, self.session, self.view)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\ui\mousemodes.py"", line 603, in mouse_drag_select     select_pick(session, pick, mode)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\ui\mousemodes.py"", line 620, in select_pick     p.select(mode) AttributeError: 'PickedInstance' object has no attribute 'select' AttributeError: 'PickedInstance' object has no attribute 'select' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\ui\mousemodes.py"", line 620, in select_pick p.select(mode) See log for complete Python traceback. hide selAtoms ↵ select up ↵ 433 atoms, 436 bonds selected select up ↵ 3593 atoms, 3640 bonds selected show selAtoms surfaces ↵ open D:/UTRECHT_MS/xls/Lhcb4_MDFF/DSSO_CL_Lhcb4_interP.pb ↵ Traceback (most recent call last):   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 517, 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 2561, in run     result = ci.function(session, **kw_args)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 41, in open     from_database=from_database, ignore_cache=ignore_cache, **kw))   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 110, in open     models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py"", line 62, in handle_unknown_kw     return f(*args, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 559, in open     session, filenames, format=format, name=name, **kw)   File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 444, 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 404, 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 27, in read_pseudobond_file     aspec1, aspec2 = line.decode('utf-8').split()[:2] AttributeError: 'str' object has no attribute 'decode' AttributeError: 'str' object has no attribute 'decode' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\read_pbonds\readpbonds.py"", line 27, in read_pseudobond_file aspec1, aspec2 = line.decode('utf-8').split()[:2] See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 388.75 OpenGL renderer: GeForce 940M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal 1.0 Input/Output fixed all ChimeraX