Error assigning atom coordinate from a tuple

[Tom Goddard]

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@… 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.