id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1431 Atom specifiers not handling chain case correctly pascal.albanese@… Conrad Huang "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17134 ChimeraX Version: 0.8 (2018-11-03) Description Hello there, again i have the same bug opening with older daily builds, that used to works before ... i have no clue anymore So for instance the atoms : #1/o:15@ca #1/o:49@ca both exists, there are 2 chains, how is possible that the software see 4 atoms specified?? Expected two atoms to be specified (4 specified) Log: UCSF ChimeraX version: 0.8 (2018-11-03) How to cite UCSF ChimeraX open D:\Chimera_PSIIsc\PSII06\5xnl.pdb open D:\Chimera_PSIIsc\PSII06\5xnl.pdb 5xnl.pdb title: Structure of stacked C2S2M2-type psii-lhcii supercomplex from pisum sativum [more info...] Chain information for 5xnl.pdb #1 --- Chain | Description 1 2 5 6 G N Y g n y | lhcii TYPE I CAB-8 3 7 | chlorophyll A-B binding protein, chloroplastic 4 8 | light harvesting chlorophyll A/B-binding protein LHCB6, CP24 A a | photosystem II protein D1 B b | photosystem II CP47 reaction center protein C c | photosystem II CP43 reaction center protein D d | photosystem II D2 protein E e | PSII reaction center subunit V F f | cytochrome B559 subunit β, PSBF H h | photosystem II reaction center protein H I i | photosystem II reaction center protein I, PSBI J j | PSII-J K k | PSII-K L l | PSII-L M m | PSII-M O o | oxygen-evolving enhancer protein 1, chloroplastic P p | oxygen-evolving enhancer protein 2, chloroplastic Q q | oxygen-evolving enhancer protein 3 R r | light harvesting chlorophyll A/B-binding protein LHCB4, CP29 S s | light harvesting chlorophyll A/B-binding protein LHCB5, CP26 T t | PSII-T W w | photosystem II reaction center protein W X x | photosystem II reaction center protein X Z z | PSII-Z distance #1/o:77@ca #1/o:160@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (4 specified) distance #1/P:11@ca #1/P:166@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (0 specified) distance #1/O:50@ca #1/C:382@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (0 specified) distance #1/R:190@ca #1/R:170@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (0 specified) distance #1/P:33@ca #1/p:166@ca radius 0.5 dashes 12 color gold distance #1/P:33@ca #1/p:166@ca radius 0.5 dashes 12 color gold Distance between /P LYS 166 CA and /p LYS 166 CA: 99.969Å distance #1/c:382@ca #1/o:49@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (4 specified) distance #1/o:15@ca #1/o:5@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (4 specified) distance #1/5:91@ca #1/O:5@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (1 specified) distance #1/o:187@ca #1/B:419@ca radius 0.5 dashes 12 color gold distance #1/o:187@ca #1/B:419@ca radius 0.5 dashes 12 color gold Distance between /O LYS 187 CA and /o LYS 187 CA: 32.478Å distance #1/P:143@ca #1/P:38@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (0 specified) distance #1/P:11@ca #1/p:166@ca radius 0.5 dashes 12 color gold distance #1/P:11@ca #1/p:166@ca radius 0.5 dashes 12 color gold Distance already exists; modify distance properties with 'distance style' distance #1/r:190@ca #1/R:200@ca radius 0.5 dashes 12 color gold distance #1/r:190@ca #1/R:200@ca radius 0.5 dashes 12 color gold Distance between /R LYS 190 CA and /r LYS 190 CA: 161.685Å distance #1/B:438@ca #1/o:160@ca radius 0.5 dashes 12 color gold distance #1/B:438@ca #1/o:160@ca radius 0.5 dashes 12 color gold Distance between /O LYS 160 CA and /o LYS 160 CA: 47.854Å distance #1/o:15@ca #1/o:49@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (4 specified) close #1.2 close #1.2 Traceback (most recent call last):   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 126, in invoke     return self._func(self._name, data)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label3d.py"", line 334, in _structure_changed     self.delete_labels([l.object for l in self._labels if l.object_deleted])   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label3d.py"", line 334, in     self.delete_labels([l.object for l in self._labels if l.object_deleted])   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label3d.py"", line 581, in object_deleted     return self.location() is None   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label3d.py"", line 681, in location     xyz = scene_position.inverse() * sxyz AttributeError: 'NoneType' object has no attribute 'inverse' Error processing trigger ""changes"": 'NoneType' object has no attribute 'inverse': AttributeError: 'NoneType' object has no attribute 'inverse' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label3d.py"", line 681, in location xyz = scene_position.inverse() * sxyz See log for complete Python traceback. close #1.1 close #1.1 Traceback (most recent call last):   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 126, in invoke     return self._func(self._name, data)   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label3d.py"", line 334, in _structure_changed     self.delete_labels([l.object for l in self._labels if l.object_deleted])   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label3d.py"", line 334, in     self.delete_labels([l.object for l in self._labels if l.object_deleted])   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label3d.py"", line 581, in object_deleted     return self.location() is None   File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label3d.py"", line 681, in location     xyz = scene_position.inverse() * sxyz AttributeError: 'NoneType' object has no attribute 'inverse' Error processing trigger ""changes"": 'NoneType' object has no attribute 'inverse': AttributeError: 'NoneType' object has no attribute 'inverse' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\label\label3d.py"", line 681, in location xyz = scene_position.inverse() * sxyz See log for complete Python traceback. distance #1/o:77@ca #1/o:160@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (4 specified) distance #1/P:11@ca #1/P:166@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (0 specified) distance #1/O:50@ca #1/C:382@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (0 specified) distance #1/R:190@ca #1/R:170@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (0 specified) distance #1/P:33@ca #1/p:166@ca radius 0.5 dashes 12 color gold distance #1/P:33@ca #1/p:166@ca radius 0.5 dashes 12 color gold Distance already exists; modify distance properties with 'distance style' distance #1/c:382@ca #1/o:49@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (4 specified) distance #1/o:15@ca #1/o:5@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (4 specified) distance #1/5:91@ca #1/O:5@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (1 specified) distance #1/o:187@ca #1/B:419@ca radius 0.5 dashes 12 color gold distance #1/o:187@ca #1/B:419@ca radius 0.5 dashes 12 color gold Distance already exists; modify distance properties with 'distance style' distance #1/P:143@ca #1/P:38@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (0 specified) distance #1/P:11@ca #1/p:166@ca radius 0.5 dashes 12 color gold distance #1/P:11@ca #1/p:166@ca radius 0.5 dashes 12 color gold Distance already exists; modify distance properties with 'distance style' distance #1/r:190@ca #1/R:200@ca radius 0.5 dashes 12 color gold distance #1/r:190@ca #1/R:200@ca radius 0.5 dashes 12 color gold Distance already exists; modify distance properties with 'distance style' distance #1/B:438@ca #1/o:160@ca radius 0.5 dashes 12 color gold distance #1/B:438@ca #1/o:160@ca radius 0.5 dashes 12 color gold Distance already exists; modify distance properties with 'distance style' distance #1/o:15@ca #1/o:49@ca radius 0.5 dashes 12 color gold Missing or invalid ""atoms"" argument: Expected two atoms to be specified (4 specified) sequence chain #1/o sequence chain #1/o Alignment identifier is 1 sequence chain #1/O sequence chain #1/O Chains must have same sequence Chains must have same sequence QLineEdit::setSelection: Invalid start position (-1) OpenGL version: 3.3.0 NVIDIA 388.75 OpenGL renderer: GeForce 940M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed critical Command Line duplicate all ChimeraX