id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1060 Error assigning atom coordinate from a tuple Tom Goddard Eric Pettersen "IHM reader is broken by Cython changes because atom coordinate cannot be assigned from a tuple: ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 1809, in _add_spheres a.coord = xyz File ""cymol.pyx"", line 199, in core.atomic.cymol.CyAtom.coord.__set__ AttributeError: 'tuple' object has no attribute 'shape' Reproduce with open nup84.cif format ihm giving UCSF ChimeraX version: 0.5 (2018-03-15) OpenGL version: 4.1 NVIDIA-10.28.10 355.11.10.10.20.111 OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine OpenGL vendor: NVIDIA Corporation How to cite UCSF ChimeraX open /Users/goddard/ucsf/data/AllenInstitute/AICS-new/AICS-12_269.ome.tif Summary of feedback from opening /Users/goddard/ucsf/data/AllenInstitute/AICS-new/AICS-12_269.ome.tif notes image name 3500000523_100X_20170314_D04_P02.czi #1, dimension order XYCZT, grid spacing 0.1083, 0.1083, 0.29, grid size 924, 624, 47, times 1, channels 8, value type uint16 Opened multi-channel map AICS-12_269.ome.tif, 8 channels, grid size 924,624,47, pixel 0.108,0.108,0.29, shown at step 2, values uint16 close open /Users/goddard/ucsf/data/ihm-2016/examples/nup84/nup84.ihm Summary of feedback from opening /Users/goddard/ucsf/data/ihm-2016/examples/nup84/nup84.ihm notes Used PDBx fixed column width tables to speed up reading mmCIF file Used PDBx keywords to speed up reading mmCIF file Used PDBx fixed column width tables to speed up reading mmCIF file Used PDBx keywords to speed up reading mmCIF file Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ui/gui.py"", line 462, in customEvent func(*args, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ui/widgets/htmlview.py"", line 247, in defer help(session, topic) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/help_viewer/cmd.py"", line 40, in help ti.execute() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/cmd_line/tool.py"", line 205, in execute cmd.run(cmd_text) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py"", line 2569, in run result = ci.function(session, **kw_args) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 42, in open from_database=from_database, ignore_cache=ignore_cache, **kw)) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 112, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 63, in handle_unknown_kw return f(*args, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py"", line 461, in open session, filenames, format=format, name=name, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py"", line 444, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py"", line 404, in open_data models, status = open_func(*args, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/__init__.py"", line 24, in open_file return ihm.read_ihm(session, path, file_name, load_ensembles = ensembles) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 38, in read_ihm show_atom_crosslinks = show_atom_crosslinks) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 92, in __init__ smodels, emodels = self.make_sphere_models(mgroup, load_ensembles = load_ensembles) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 514, in make_sphere_models smodels = self.make_sphere_models_by_group(mspheres, mnames, model_group, group_coordsets) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 549, in make_sphere_models_by_group sm = SphereModel(self.session, mname, mid, slist, anames, adetail, asym_colors) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 1783, in __init__ self._add_spheres(sphere_list, entity_names, asym_detail_text) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py"", line 1809, in _add_spheres a.coord = xyz File ""cymol.pyx"", line 199, in core.atomic.cymol.CyAtom.coord.__set__ AttributeError: 'tuple' object has no attribute 'shape' AttributeError: 'tuple' object has no attribute 'shape' File ""cymol.pyx"", line 199, in core.atomic.cymol.CyAtom.coord.__set__ See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. " defect closed major 0.6 Core fixed all ChimeraX