id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1429 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 (2018-11-08) Description I'm trying to load a pseudobond set of ditances, either on a custom PDB or on the 5xnl form the PDB database. However i see errors as the atom don't exist, for any atom. I tought it was a problem of the custom PDB (built in chimera as well) ... but is not. The same happens when i try just to se the distance (e.g.: distance #1/P:166@CA #1/P:170@CA radius 0.5 dashes 12 color gold) Log: UCSF ChimeraX version: 0.8 (2018-11-08) How to cite UCSF ChimeraX > 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 > set bgColor white > hide selAtoms > show selAtoms ribbons > open D:/UTRECHT_MS/Xlink_results/Pres_data/mAPPING/All_dsso_on5xnl.pb Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py"", line 542, 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 2581, 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 117, 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 583, in open session, filenames, format=format, name=name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py"", line 461, 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 416, 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 33, in read_pseudobond_file % (i, len(a), aspec)) File """", line None SyntaxError: Line 0, got 0 atoms for spec ""#1/P:166@CA"", require exactly 1 File """", line None SyntaxError: Line 0, got 0 atoms for spec ""#1/P:166@CA"", require exactly 1 File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\read_pbonds\readpbonds.py"", line 33, in read_pseudobond_file % (i, len(a), aspec)) See log for complete Python traceback. > sequence chain #1/P Chains must have same sequence Chains must have same sequence OpenGL version: 3.3.0 NVIDIA 388.75 OpenGL renderer: GeForce 940M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed critical 0.8 Command Line fixed chimera-staff all ChimeraX