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Opened 4 weeks ago
Closed 4 weeks ago
#19122 closed defect (limitation)
MemoryError reading trajectory
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | MD/Ensemble Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:\project\MD\lacahulym\lig1_2_frame64538.pdb format pdb
Chain information for lig1_2_frame64538.pdb #1
---
Chain | Description
? | No description available
Computing secondary structure
> open "D:/project/SMILES/best pose 10-1/5hl1 (1).pdb"
5hl1 (1).pdb title:
Crystal structure of glutaminase C In complex with inhibitor CB-839 [more
info...]
Chain information for 5hl1 (1).pdb #2
---
Chain | Description | UniProt
A B C D | glutaminase kidney isoform, mitochondrial | GLSK_HUMAN 72-598
Non-standard residues in 5hl1 (1).pdb #2
---
63J —
2-(pyridin-2-yl)-N-(5-{4-[6-({[3-(trifluoromethoxy)phenyl]acetyl}amino)pyridazin-3-yl]butyl}-1,3,4-thiadiazol-2-yl)acetamide
> matchmaker #1 to #2
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5hl1 (1).pdb, chain B (#2) with lig1_2_frame64538.pdb, chain
(blank) (#1), sequence alignment score = 2066.6
RMSD between 324 pruned atom pairs is 0.763 angstroms; (across all 410 pairs:
2.036)
> select #1/?:1082
22 atoms, 21 bonds, 1 residue, 1 model selected
Drag select of 2 atoms, 2 bonds, 2 residues
> select add #2
13122 atoms, 12984 bonds, 3 pseudobonds, 2045 residues, 4 models selected
> select subtract #2
2 atoms, 2 bonds, 1 residue, 1 model selected
> select add #1
25632 atoms, 25928 bonds, 1642 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
13120 atoms, 12982 bonds, 3 pseudobonds, 2044 residues, 3 models selected
> select subtract #2
Nothing selected
> select protein
38126 atoms, 38692 bonds, 3 pseudobonds, 3260 residues, 3 models selected
> delete atoms (#1#!2 & sel)
> delete bonds (#1#!2 & sel)
> select clear
> open D:\project\MD\lacahulym\nowater20-41.nc structureModel #1
Specified structure has 124 atoms whereas the coordinates are for 25632 atoms
> select add #1
124 atoms, 132 bonds, 2 residues, 1 model selected
> close #2
> close
> open D:\project\MD\lacahulym\lig1_2_frame64538.pdb format pdb
Chain information for lig1_2_frame64538.pdb #1
---
Chain | Description
? | No description available
Computing secondary structure
> open "D:\project\SMILES\best pose 10-1\5hl1 (1).pdb" format pdb
5hl1 (1).pdb title:
Crystal structure of glutaminase C In complex with inhibitor CB-839 [more
info...]
Chain information for 5hl1 (1).pdb #2
---
Chain | Description | UniProt
A B C D | glutaminase kidney isoform, mitochondrial | GLSK_HUMAN 72-598
Non-standard residues in 5hl1 (1).pdb #2
---
63J —
2-(pyridin-2-yl)-N-(5-{4-[6-({[3-(trifluoromethoxy)phenyl]acetyl}amino)pyridazin-3-yl]butyl}-1,3,4-thiadiazol-2-yl)acetamide
> matchmaker #2 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker lig1_2_frame64538.pdb, chain (blank) (#1) with 5hl1 (1).pdb, chain
B (#2), sequence alignment score = 2066.6
RMSD between 324 pruned atom pairs is 0.763 angstroms; (across all 410 pairs:
2.036)
> open D:\project\MD\lacahulym\nowater20-41.nc structureModel #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\md_crds\\__init__.py", line 115, in open
num_coords = read_coords(session, data, structure_model, md_type,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 75, in read_coords
model.add_coordsets(coords, replace=replace)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1749, in add_coordsets
f(self._c_pointer, replace, pointer(xyzs), *xyzs.shape[:2])
MemoryError: not enough memory
MemoryError: not enough memory
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1749, in add_coordsets
f(self._c_pointer, replace, pointer(xyzs), *xyzs.shape[:2])
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 837, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 869, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 709, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 742, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1194, in first_intercept
b, f = _bond_intercept(bonds, mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2249, in _bond_intercept
cxyz1, cxyz2 = (a1.coords, a2.coords)
^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
ValueError: no active coordinate set
ValueError: no active coordinate set
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 208, in get_prop
cget(self._c_pointers, n, pointer(values))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 388.57
OpenGL renderer: GeForce 920M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1256
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: X555LJ
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 12,779,352,064
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-5005U CPU @ 2.00GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 4 weeks ago
| Component: | Unassigned → MD/Ensemble Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MemoryError reading trajectory |
comment:2 by , 4 weeks ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
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Hi Shahin,
--Eric