id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2314 MOLEonline in ChimeraX eackad@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-55-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.91 (2019-07-02) Description I downloaded the results of moleOnline (in chimera format) and tried to open them using chimeraX Log: UCSF ChimeraX version: 0.91 (2019-07-02) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/eddie/chimeratest.cxs opened ChimeraX session > select /A Nothing selected > select /B Nothing selected > select /P 7814 atoms, 8008 bonds, 2 models selected > select /P:54-90 604 atoms, 624 bonds, 2 models selected > open /home/eddie/code/namd/output/p450/analysis_apo/trajs/nowatmem.pdb Chain information for nowatmem.pdb #3 --- Chain | Description P | No description available > hide #!2 models > close #3 > close #1 > close > open /home/eddie/code/namd/output/p450/analysis_apo/trajs/nowatmem.pdb Chain information for nowatmem.pdb #1 --- Chain | Description P | No description available > select /P:218-235 149 atoms, 155 bonds, 1 model selected > color /P:218-235 grey > color /P:242-258 > select /P:242-258 147 atoms, 148 bonds, 1 model selected > style selAtoms stick Changed 147 atom styles > style selAtoms stick Changed 147 atom styles > color /P:242-258 violet > hide selAtoms > save session /home/eddie/code/namd/output/p450/p450_Nussinov.cxs > open /home/eddie/Downloads/mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 582, in _qt_safe run(session, ""open "" + "" "".join([quote_if_necessary(p) for p in paths])) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2646, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py"", line 616, in open session, filenames, format=format, name=name, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/io.py"", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/io.py"", line 433, in open_data models, status = open_func(*args, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 84, in open_python_script _exec_python(session, code, argv) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/scripting.py"", line 59, in _exec_python exec(code, sandbox.__dict__) File ""mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py"", line 1, in ModuleNotFoundError: No module named 'chimera' ModuleNotFoundError: No module named 'chimera' File ""mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py"", line 1, in See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 430.34 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation File attachment: mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py }}} [attachment:""mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py""] " defect closed normal Third Party nonchimerax all ChimeraX