The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\Users\BD2020212\Downloads\6yyt.pdb format pdb
6yyt.pdb title:
Structure of replicating sars-cov-2 polymerase [more info...]
Chain information for 6yyt.pdb #1
---
Chain | Description
A | NSP12
B D | NSP8
C | NSP7
P Q T U | RNA product
Non-standard residues in 6yyt.pdb #1
---
ZN — zinc ion
> show atoms
> show cartoons
> hide atoms
> show surfaces
> show cartoons
> show atoms
QFileSystemWatcher::removePaths: list is empty
> save C:/work/design/pdb/proteintest/test.obj
> hide atoms
> hide cartoons
> hide surfaces
> show surfaces
> show cartoons
> show surfaces
> interfaces ~solvent
8 buried areas: A B 2523, D C 1366, A T 1092, A C 796, A D 789, A P 625, P T
526, Q U 523
> select /C:1-73
559 atoms, 562 bonds, 73 residues, 1 model selected
> transparency (#!1 & sel) 50
> select clear
> close session
> open 2mr
'2mr' has no suffix
> open 2mfr
Summary of feedback from opening 2mfr fetched from pdb
---
note | Fetching compressed mmCIF 2mfr from
http://files.rcsb.org/download/2mfr.cif
2mfr title:
Solution structure of the transmembrane domain of the insulin receptor in
micelles [more info...]
Chain information for 2mfr
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | Insulin receptor
> select #1.1/A
958 atoms, 976 bonds, 57 residues, 1 model selected
> select ~sel
18202 atoms, 18544 bonds, 1083 residues, 20 models selected
> delete atoms sel
> delete bonds sel
> open 1irk
Summary of feedback from opening 1irk fetched from pdb
---
notes | Fetching compressed mmCIF 1irk from
http://files.rcsb.org/download/1irk.cif
Fetching CCD EMC from http://ligand-expo.rcsb.org/reports/E/EMC/EMC.cif
1irk title:
Crystal structure of the tyrosine kinase domain of the human insulin receptor
[more info...]
Chain information for 1irk #2
---
Chain | Description
A | insulin receptor tyrosine kinase domain
Non-standard residues in 1irk #2
---
EMC — ethyl mercury ion
> select #1.1/A
958 atoms, 976 bonds, 57 residues, 1 model selected
> select #2/A
2574 atoms, 2427 bonds, 2 pseudobonds, 504 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> hide #!2 models
> show #!2 models
> hide #!1 models
> sequence chain #2/A
Alignment identifier is 2/A
> show #!1 models
> select protein
3327 atoms, 3399 bonds, 360 residues, 2 models selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> select #2/A:981
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #2/A:983
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:981
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #1.1/A:57
18 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.1/A:57
18 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select #1.1/A:57
18 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select #2/A:981
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Build Structure"
> select #2/A:983
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:984
5 atoms, 4 bonds, 1 residue, 1 model selected
Drag select of 360 residues, 25 atoms, 2 pseudobonds, 20 bonds
> combin
Unknown command: combin
> combine
Unknown command: combine
> select clear
> combine
Unknown command: combine
> combine
Unknown command: combine
> combine
Unknown command: combine
> combine
Unknown command: combine
> combine
Unknown command: combine
> select #2/A:1220
9 atoms, 8 bonds, 1 residue, 1 model selected
> build start atom "custom built"
> build start atom "custom built"
> build start atom "custom built"
> delete atoms sel
> delete bonds sel
> delete atoms
> delete bonds
> undo
Undo failed, probably because structures have been modified.
> close session
> open 2mfr format mmcif fromDatabase pdb
2mfr title:
Solution structure of the transmembrane domain of the insulin receptor in
micelles [more info...]
Chain information for 2mfr
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | Insulin receptor
> delete atoms
> delete bonds
> close session
> open 2mfr format mmcif fromDatabase pdb
2mfr title:
Solution structure of the transmembrane domain of the insulin receptor in
micelles [more info...]
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 629, in customEvent
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 440, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 456, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 188, in provider_open
session.models.add(opened_models)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 670, in add
m.added_to_session(session)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1152, in added_to_session
super().added_to_session(session)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 124, in added_to_session
self.apply_auto_styling(set_lighting = self._is_only_model())
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1210, in apply_auto_styling
ions = atoms.filter(atoms.structure_categories == "ions")
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 238, in filter
return self._objects_class(self._pointers[mask_or_indices])
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 730, in __init__
Collection.__init__(self, atom_pointers, molobject.Atom, Atoms)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 122, in __init__
set_cvec_pointer(self, pointers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molc.py", line 238, in set_cvec_pointer
self._c_pointers = pointer(pointers)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molc.py", line 322, in pointer
p = a.ctypes.data_as(ctypes.POINTER(cty))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\numpy\core\\_internal.py", line 283, in data_as
ptr = self._ctypes.cast(self._data, obj)
File "C:\Program Files\ChimeraX 1.1\bin\lib\ctypes\\__init__.py", line 498, in
cast
return _cast(obj, obj, typ)
OSError: exception: access violation writing 0x000001DE8BCBD480
OSError: exception: access violation writing 0x000001DE8BCBD480
File "C:\Program Files\ChimeraX 1.1\bin\lib\ctypes\\__init__.py", line 498, in
cast
return _cast(obj, obj, typ)
See log for complete Python traceback.
> open 2mfr format mmcif fromDatabase pdb
2mfr title:
Solution structure of the transmembrane domain of the insulin receptor in
micelles [more info...]
Chain information for 2mfr
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A
2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A | Insulin receptor
> hide atoms
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1.1/A
958 atoms, 976 bonds, 57 residues, 1 model selected
> select ~sel
37362 atoms, 38064 bonds, 2223 residues, 41 models selected
> delete atoms (#1.2-20 & sel)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1144, in <lambda>
run(ses, cmd % (sel_or_all(ses, ['atoms', 'bonds']), sel_or_all(ses, ['atoms',
'bonds']))))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\std_commands\delete.py", line 41, in delete_atoms
session.models.close([s for s in session.models
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 886, in close
self.remove(mopen)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\models.py", line 856, in remove
m.removed_from_session(session)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 132, in removed_from_session
self._graphics_updater.remove_structure(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1554, in remove_structure
self._structures.remove(s)
KeyError: <chimerax.atomic.structure.AtomicStructure object at
0x000001DE8C8608C8>
KeyError:
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1554, in remove_structure
self._structures.remove(s)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1562, in
_update_graphics_if_needed
s = self._array()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1607, in _array
self._structures_array = sa =
StructureDatas(object_pointers(self._structures))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 1423, in object_pointers
pointers = array(tuple(o._c_pointer.value for o in objects), dtype = cptr,)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 1423, in <genexpr>
pointers = array(tuple(o._c_pointer.value for o in objects), dtype = cptr,)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute '_c_pointer'
Error processing trigger "graphics update":
AttributeError: 'Structure' object has no attribute '_c_pointer'
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 637, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 59, in mouse_up
mouse_select(event, mode, self.session, self.view)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 184, in mouse_select
select_pick(session, pick, mode)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 196, in select_pick
sel.undo_add_selected(undo_state, False)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 71, in undo_add_selected
items = self.items(oname)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 34, in items
for m in self.models():
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 30, in models
return [m for m in self._all_models if m.get_selected(include_children=True)]
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 30, in <listcomp>
return [m for m in self._all_models if m.get_selected(include_children=True)]
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 674, in get_selected
if self.atoms.num_selected > 0 or self.bonds.num_selected > 0:
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 529, in
_dispatch_mouse_event
lm.mouse_up(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 196, in select_pick
sel.undo_add_selected(undo_state, False)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 71, in undo_add_selected
items = self.items(oname)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 34, in items
for m in self.models():
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 30, in models
return [m for m in self._all_models if m.get_selected(include_children=True)]
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 30, in <listcomp>
return [m for m in self._all_models if m.get_selected(include_children=True)]
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 674, in get_selected
if self.atoms.num_selected > 0 or self.bonds.num_selected > 0:
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 637, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 56, in mouse_up
mouse_drag_select(self.mouse_down_position, event, mode, self.session,
self.view)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 190, in mouse_drag_select
select_pick(session, pick, mode)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 196, in select_pick
sel.undo_add_selected(undo_state, False)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 71, in undo_add_selected
items = self.items(oname)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 34, in items
for m in self.models():
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 30, in models
return [m for m in self._all_models if m.get_selected(include_children=True)]
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\selection.py", line 30, in <listcomp>
return [m for m in self._all_models if m.get_selected(include_children=True)]
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\structure.py", line 674, in get_selected
if self.atoms.num_selected > 0 or self.bonds.num_selected > 0:
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 442.70
OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 15 9560
OS: Microsoft Windows 10 家庭中文版 (Build 19042)
Memory: 34,204,643,328
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
MolecularDynamicsViewer: 1.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
Send2Trash: 1.5.0
SEQCROW: 0.25.2
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
I am baffled. The crash is during "open 2mfr", autostyling is making an Atoms object for ions by filtering all atoms. There are no ions. I the final step of making this empty Atoms Collection it is taking the numpy array of pointers (length 0, numpy type uintp) and creating a ctypes pointer value to the data and it gets a seg fault. This should merely be creating a ctypes pointer instance and filling in the 64-bit pointer value. I guess somehow the ctypes pointer instance is outside allocated memory. Not sure how Python works, maybe it is doing its own memory allocation and has corrupted state in its memory allocator.
The user successfully open 2mfr earlier in the session. I successfully open it on Windows in ChimeraX 1.1. I'd put my money on a memory corruption problem caused by the multiple commands deleting atoms and bonds tht preceded this error.