Various memory errors

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
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:
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 "C:\\\Users\\\andre\\\Downloads\\\step7_2_production (5).pdb"

Summary of feedback from opening
C:\\\Users\\\andre\\\Downloads\\\step7_2_production (5).pdb  
---  
warning | Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
step7_2_production (5).pdb title:  
Martini system [more info...]  
  
Chain information for step7_2_production (5).pdb #1  
---  
Chain | Description  
A C D | No description available  
B | No description available  
E F G H | No description available  
  
Non-standard residues in step7_2_production (5).pdb #1  
---  
ION — (ION)  
MET — (MET)  
POPC — (popc)  
W — (W)  
  

> open "C:/Users/andre/Downloads/MD CNGC 4atcam}/step7_1_production.xtc"

Replaced existing frames of step7_2_production (5).pdb #1 with 501 new frames  

> lighting full

> open "C:/Users/andre/Downloads/MD CNGC 4atcam}/step7_2_production.xtc"

Replaced existing frames of step7_2_production (5).pdb #1 with 501 new frames  

> select main

3510 atoms, 49 bonds, 3450 pseudobonds, 3507 residues, 2 models selected  

> select ~sel & ##selected

149264 atoms, 87 bonds, 1 pseudobond, 120331 residues, 2 models selected  

> hide (#!1 & sel) target a

> surface (#!1 & sel)

> undo

> surface (#!1 & sel)

> style (#!1 & sel) ball

Changed 149264 atom styles  

> select add #1

152774 atoms, 136 bonds, 3451 pseudobonds, 120510 residues, 10 models selected  

> select subtract #1

8 models selected  

> lighting full

> set bgColor white

> style sphere

Changed 152774 atom styles  

> style stick

Changed 152774 atom styles  

> style sphere

Changed 152774 atom styles  

> style ball

Changed 152774 atom styles  

> style sphere

Changed 152774 atom styles  

> transparency 80

> undo

> select add #1

152774 atoms, 136 bonds, 3451 pseudobonds, 120510 residues, 2 models selected  

> style sel sphere

Changed 152774 atom styles  

> surface hidePatches (#!1 & sel)

> hide (#!1 & sel) target a

> surface (#!1 & sel)

> style sel ball

Changed 152774 atom styles  

> style sel sphere

Changed 152774 atom styles  

> style sel stick

Changed 152774 atom styles  

> show (#!1 & sel) target ab

> style sel ball

Changed 152774 atom styles  

> style sel sphere

Changed 152774 atom styles  

> hide sel cartoons

> show sel cartoons

> style (#!1 & sel) ball

Changed 152774 atom styles  

> surface hidePatches (#!1 & sel)

> show (#!1 & sel) target ab

> style (#!1 & sel) ringFill thick

Changed 120510 residue ring styles  

> hide (#!1 & sel-residues & (protein|nucleic)) target a

> cartoon hide (#!1 & sel-residues)

> show (#!1 & sel-residues & backbone) target ab

> cartoon (#!1 & sel)

> style sel ball

Changed 152774 atom styles  

> style sel sphere

Changed 152774 atom styles  

> show (#!1 & sel) target ab

> select nucleic-acid

Nothing selected  

> select main

3510 atoms, 49 bonds, 3450 pseudobonds, 3507 residues, 2 models selected  

> select :POPC

29856 atoms, 2488 residues, 1 model selected  

> transparency sel 100

> surface sel

> transparency (#!1 & sel) 70

> hide (#!1 & sel) target a

> select :ION

2624 atoms, 2624 residues, 1 model selected  

> select :MET

224 atoms, 4 pseudobonds, 112 residues, 2 models selected  

> select :ION

2624 atoms, 2624 residues, 1 model selected  

> select :W

111890 atoms, 111890 residues, 1 model selected  

> surface sel

> hide (#!1 & sel) target a

> transparency (#!1 & sel) 70

> select :W

111890 atoms, 111890 residues, 1 model selected  

> select :ION

2624 atoms, 2624 residues, 1 model selected  

> hide sel target a

> surface sel

> style sel ball

Changed 2624 atom styles  

> style sel sphere

Changed 2624 atom styles  

> style sel stick

Changed 2624 atom styles  

> hide sel atoms

> select add #1

152774 atoms, 136 bonds, 3451 pseudobonds, 120510 residues, 3 models selected  

> style sel ball

Changed 152774 atom styles  

> style sel sphere

Changed 152774 atom styles  

> hide sel cartoons

> hide sel atoms

> show sel atoms

> surface (#!1 & sel)

> transparency (#!1 & sel) 50

> hide sel atoms

> show sel atoms

> hide #* target a

> show (#!1 & sel) target ab

> select :POPC

29856 atoms, 2488 residues, 1 model selected  

> hide (#!1 & sel) target a

> select :W

111890 atoms, 111890 residues, 1 model selected  

> transparency (#!1 & sel) 90

> hide (#!1 & sel) target a

> select :ION

2624 atoms, 2624 residues, 1 model selected  

> hide (#!1 & sel) target a

> surface hidePatches (#!1 & sel)

> select main

3510 atoms, 49 bonds, 3450 pseudobonds, 3507 residues, 2 models selected  

> style sel sphere

Changed 3510 atom styles  

> style sel stick

Changed 3510 atom styles  

> style sel sphere

Changed 3510 atom styles  

> style sel ball

Changed 3510 atom styles  

> style sel sphere

Changed 3510 atom styles  

> surface hidePatches (#!1 & sel)

> style sel ball

Changed 3510 atom styles  

> style sel sphere

Changed 3510 atom styles  

> style sel stick

Changed 3510 atom styles  

> cartoon hide (#!1 & sel)

> surface hidePatches (#!1 & sel)

> hide (#!1 & sel) target a

> select main

3510 atoms, 49 bonds, 3450 pseudobonds, 3507 residues, 2 models selected  

> surface hidePatches (#!1 & sel)

> select add #1.10

33366 atoms, 49 bonds, 3450 pseudobonds, 5995 residues, 10 models selected  

> select subtract #1.10

3510 atoms, 49 bonds, 3450 pseudobonds, 3507 residues, 11 models selected  

> select add #1.11

115400 atoms, 49 bonds, 3450 pseudobonds, 115397 residues, 10 models selected  

> select add #1.11

115400 atoms, 49 bonds, 3450 pseudobonds, 115397 residues, 11 models selected  

> select add #1.12

118024 atoms, 49 bonds, 3450 pseudobonds, 118021 residues, 11 models selected  

> select add #1.10

147880 atoms, 49 bonds, 3450 pseudobonds, 120509 residues, 12 models selected  

> surface hidePatches (#!1 & sel)

> select subtract #1.8

147719 atoms, 48 bonds, 3291 pseudobonds, 120348 residues, 13 models selected  

> select add #1

152774 atoms, 136 bonds, 3451 pseudobonds, 120510 residues, 12 models selected  

> select subtract #1

11 models selected  

> select add #1.12

2624 atoms, 2624 residues, 1 model selected  

> select add #1.11

114514 atoms, 114514 residues, 2 models selected  

> select add #1.10

144370 atoms, 117002 residues, 3 models selected  

> surface (#!1 & sel)

> transparency (#!1 & sel) 70

> select :POPC

29856 atoms, 2488 residues, 1 model selected  

> color (#!1 & sel) lime

> select :W

111890 atoms, 111890 residues, 1 model selected  

> color (#!1 & sel) cyan

> surface hidePatches (#!1 & sel)

> select :ION

2624 atoms, 2624 residues, 1 model selected  

> surface hidePatches (#!1 & sel)

> select :POPC

29856 atoms, 2488 residues, 1 model selected  

> color (#!1 & sel) yellow

> open "C:/Users/andre/Downloads/MD CNGC 4atcam}/step7_1_production.xtc"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py",
line 731, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py",
line 2117, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
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 40, in read_coords  
coords = array(coords_list, dtype=float64)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 1.71 GiB for an
array with shape (501, 152774, 3) and data type float64  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 1.71 GiB for an
array with shape (501, 152774, 3) and data type float64  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 40, in read_coords  
coords = array(coords_list, dtype=float64)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open "C:/Users/andre/Downloads/MD CNGC 4atcam}/step7_1_production.xtc"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py",
line 731, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\gui.py",
line 2117, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
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 40, in read_coords  
coords = array(coords_list, dtype=float64)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 1.71 GiB for an
array with shape (501, 152774, 3) and data type float64  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 1.71 GiB for an
array with shape (501, 152774, 3) and data type float64  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 40, in read_coords  
coords = array(coords_list, dtype=float64)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> preset "overall look" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> set bgColor white

> select /A:1-716

1748 atoms, 29 bonds, 706 pseudobonds, 716 residues, 2 models selected  

> select /A:1-716

1748 atoms, 29 bonds, 706 pseudobonds, 716 residues, 2 models selected  

> color (#!1 & sel) blue

> color (#!1 & sel) cornflower blue

> select /C:1-716

1748 atoms, 35 bonds, 703 pseudobonds, 716 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select /C:1-716

1748 atoms, 35 bonds, 703 pseudobonds, 716 residues, 2 models selected  

> select /A:1-716

1748 atoms, 29 bonds, 706 pseudobonds, 716 residues, 2 models selected  

> select /C:1-716

1748 atoms, 35 bonds, 703 pseudobonds, 716 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select /C:1-716

1748 atoms, 35 bonds, 703 pseudobonds, 716 residues, 2 models selected  

> select /C:1-716

1748 atoms, 35 bonds, 703 pseudobonds, 716 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select /D:1-716

1748 atoms, 30 bonds, 707 pseudobonds, 716 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select /B:2-716

1746 atoms, 30 bonds, 706 pseudobonds, 715 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> ui windowfill toggle

[Repeated 1 time(s)]

> ui tool show "Model Panel"

> ui tool show Toolbar

> style sel ball

Changed 1746 atom styles  

> hide sel atoms

> surface hidePatches (#!1 & sel)

> show sel atoms

> style sel sphere

Changed 1746 atom styles  

> style sel ball

Changed 1746 atom styles  

> style sel sphere

Changed 1746 atom styles  

> select main

3510 atoms, 49 bonds, 3450 pseudobonds, 3507 residues, 2 models selected  

> surface hidePatches (#!1 & sel)

> hide sel atoms

> show sel atoms

> style sel sphere

Changed 3510 atom styles  

> style sel ball

Changed 3510 atom styles  

> style sel sphere

Changed 3510 atom styles  

> surface (#!1 & sel)

> surface hidePatches (#!1 & sel)

> select add #1

152774 atoms, 136 bonds, 3451 pseudobonds, 120510 residues, 10 models selected  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
GLError(  
err = 1285,  
description = b'Memoria insuficiente',  
baseOperation = glBufferSubData,  
pyArgs = (  
34963,  
0,  
265120188,  
array([[ 91879, 91880, 91882],  
[ 91878, 91882, 91880],  
[ 91881, 91882, 91878],  
...,  
),  
cArgs = (  
34963,  
0,  
265120188,  
array([[ 91879, 91880, 91882],  
[ 91878, 91882, 91880],  
[ 91881, 91882, 91878],  
...,  
),  
cArguments = (  
34963,  
0,  
265120188,  
array([[ 91879, 91880, 91882],  
[ 91878, 91882, 91880],  
[ 91881, 91882, 91878],  
...,  
)  
)  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 84, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\view.py", line 266, in _draw_scene  
draw_transparent(r, transparent_drawings)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1559, in draw_transparent  
r.draw_transparent(  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1307, in draw_transparent  
draw_depth()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1560, in <lambda>  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DEPTH_DRAW_PASS),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 780, in draw  
self.draw_self(renderer, draw_pass)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self  
self._draw_geometry(renderer, transparent_only = any_opaque)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 814, in _draw_geometry  
ds.activate_bindings(renderer)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1924, in activate_bindings  
self.update_buffers()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1912, in update_buffers  
b.update_buffer_data(data)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 2831, in update_buffer_data  
GL.glBufferSubData(btype, 0, size, d)  
File "src\\\latebind.pyx", line 51, in
OpenGL_accelerate.latebind.Curry.__call__  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\OpenGL\GL\VERSION\GL_1_5.py", line 125, in glBufferSubData  
return baseOperation( target, offset, size, data )  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'Memoria insuficiente',  
baseOperation = glBufferSubData,  
pyArgs = (  
34963,  
0,  
265120188,  
array([[ 91879, 91880, 91882],  
[ 91878, 91882, 91880],  
[ 91881, 91882, 91878],  
...,  
),  
cArgs = (  
34963,  
0,  
265120188,  
array([[ 91879, 91880, 91882],  
[ 91878, 91882, 91880],  
[ 91881, 91882, 91878],  
...,  
),  
cArguments = (  
34963,  
0,  
265120188,  
array([[ 91879, 91880, 91882],  
[ 91878, 91882, 91880],  
[ 91881, 91882, 91878],  
...,  
)  
)  
  

> select subtract #1

9 models selected  
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\molsurf.py", line 560, in first_intercept  
p = Drawing.first_intercept(self, mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1095, in
_first_intercept_excluding_children  
ta = self.masked_triangles  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
  
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\molsurf.py", line 560, in first_intercept  
p = Drawing.first_intercept(self, mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1095, in
_first_intercept_excluding_children  
ta = self.masked_triangles  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
  
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\molsurf.py", line 560, in first_intercept  
p = Drawing.first_intercept(self, mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1095, in
_first_intercept_excluding_children  
ta = self.masked_triangles  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
  
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\molsurf.py", line 560, in first_intercept  
p = Drawing.first_intercept(self, mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1095, in
_first_intercept_excluding_children  
ta = self.masked_triangles  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
  
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\molsurf.py", line 560, in first_intercept  
p = Drawing.first_intercept(self, mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1095, in
_first_intercept_excluding_children  
ta = self.masked_triangles  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
  
See log for complete Python traceback.  
  

> select add #1

152774 atoms, 136 bonds, 3451 pseudobonds, 120510 residues, 11 models selected  

> select subtract #1

9 models selected  

> ui mousemode right select

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 656, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 556, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 70, in mouse_up  
mouse_select(event, mode, self.session, self.view)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 209, in mouse_select  
pick = 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\molsurf.py", line 560, in first_intercept  
p = Drawing.first_intercept(self, mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1095, in
_first_intercept_excluding_children  
ta = self.masked_triangles  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 656, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 556, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 70, in mouse_up  
mouse_select(event, mode, self.session, self.view)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 209, in mouse_select  
pick = 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\molsurf.py", line 560, in first_intercept  
p = Drawing.first_intercept(self, mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1095, in
_first_intercept_excluding_children  
ta = self.masked_triangles  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 253. MiB for an
array with shape (22093349, 3) and data type int32  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1355, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 25.9.1.250822
OpenGL renderer: AMD Radeon RX 6600
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: es_CO.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Gigabyte Technology Co., Ltd.
Model: B450 AORUS PRO WIFI
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 17,096,515,584
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5700X 8-Core Processor             
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: 3.10.3
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    narwhals: 1.39.1
    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: 2.2.6
    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
    plotly: 6.0.1
    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
    pyKVFinder: 0.8.0
    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
    tomlkit: 0.13.2
    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

[pett]

The last error was from picking on a surface. Earlier ones included opening a trajectory.

[Tom Goddard]

The memory errors are almost always on Windows. This machine has 16 GB. It appears the had a water box of 120,000 waters. Hopefully they understood the many different error messages that all said out of memory.