id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1533 ChimeraX bug report submission Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-12-13) Description open attached bild file (works fine in 0.7) Log: UCSF ChimeraX version: 0.8 (2018-12-13) How to cite UCSF ChimeraX > open /Users/meng/Desktop/simple.bild Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/gui.py"", line 529, in customEvent func(*args, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/widgets/htmlview.py"", line 302, in defer cxcmd(session, topic) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/widgets/htmlview.py"", line 394, in cxcmd run(session, cmd) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2582, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/open.py"", line 41, in open from_database=from_database, ignore_cache=ignore_cache, **kw)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/open.py"", line 117, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/open.py"", line 62, in handle_unknown_kw return f(*args, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/models.py"", line 587, in open session, filenames, format=format, name=name, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/io.py"", line 461, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/io.py"", line 416, in open_data models, status = open_func(*args, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/bild/__init__.py"", line 32, in open_file return bild.read_bild(session, stream, file_name) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/bild/bild.py"", line 561, in read_bild return b.parse_stream(stream) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/bild/bild.py"", line 112, in parse_stream func(self, tokens) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/bild/bild.py"", line 251, in cylinder_command radius, p0, p1, closed=closed, xform=self.transforms[-1], pure=self.pure[-1]) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/bild/bild.py"", line 589, in get_cylinder xform.tranform_normals(normals, in_place=True, is_rotation=pure) AttributeError: 'Place' object has no attribute 'tranform_normals' AttributeError: 'Place' object has no attribute 'tranform_normals' File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/bild/bild.py"", line 589, in get_cylinder xform.tranform_normals(normals, in_place=True, is_rotation=pure) See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation File attachment: simple.bild }}} [attachment:""simple.bild""] " defect closed normal Depiction fixed all ChimeraX