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Opened 6 hours ago
#20552 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
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Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26200
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/mahamaya/OneDrive - Stanford/IVT_Structure/June
> 2026/cryosparc_P1_J258_002_volume_map.mrc"
Opened cryosparc_P1_J258_002_volume_map.mrc as #1, grid size 720,720,720,
pixel 0.92, shown at step 1, values float32
> volume #1 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #1 change image level -0.02563,0 level 0.1639,0.8 level 0.34,1
> volume #1 level 0.05866
> volume gaussian #31 sDev 2
> volume gaussian #1 sDev 2
Opened cryosparc_P1_J258_002_volume_map.mrc gaussian as #2, grid size
720,720,720, pixel 0.92, shown at step 1, values float32
> volume #2 level 0.04998
> vop flip #2
Opened cryosparc_P1_J258_002_volume_map.mrc gaussian z flip as #3, grid size
720,720,720, pixel 0.92, shown at step 1, values float32
> set bgColor white
> open
> "C:/Users/mahamaya/Downloads/Class1_J150_PostLocal_PostHomorefine_3.46Ang_flip_g2
> (1).mrc"
Opened Class1_J150_PostLocal_PostHomorefine_3.46Ang_flip_g2 (1).mrc as #4,
grid size 512,512,512, pixel 1.71, shown at level 0.105, step 2, values
float32
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #3
2 models selected
> ui mousemode right "move picked models"
> view matrix models #3,1,0,0,64.705,0,1,0,122.33,0,0,1,141.37
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.48518,0.82845,0.27976,-115.8,-0.77405,0.55575,-0.30331,612.84,-0.40675,-0.069391,0.9109,325.16
> select add #4
4 models selected
> select subtract #3
2 models selected
> transparency #4.1 80
> select subtract #4
Nothing selected
> select add #3
2 models selected
> view matrix models
> #3,0.14492,0.91611,0.37383,-62.583,-0.45242,0.39736,-0.79839,719.26,-0.87995,-0.053424,0.47205,618.96
> ui mousemode right "move picked models"
> view matrix models
> #3,0.14492,0.91611,0.37383,-196.96,-0.45242,0.39736,-0.79839,663.12,-0.87995,-0.053424,0.47205,411.48
> view matrix models
> #3,0.14492,0.91611,0.37383,-47.401,-0.45242,0.39736,-0.79839,732.04,-0.87995,-0.053424,0.47205,602.39
> view matrix models
> #3,0.14492,0.91611,0.37383,-49.181,-0.45242,0.39736,-0.79839,724.95,-0.87995,-0.053424,0.47205,607.31
> transparency #3.1 70
> select add #2
4 models selected
> view matrix models
> #3,0.14492,0.91611,0.37383,-44.999,-0.45242,0.39736,-0.79839,731.46,-0.87995,-0.053424,0.47205,601.04
> ui mousemode right "rotate selected models"
> select subtract #2
2 models selected
> view matrix models
> #3,0.59908,0.73584,0.31567,-118.5,-0.66049,0.67701,-0.32467,557.29,-0.45262,-0.013996,0.89159,311.39
> view matrix models
> #3,0.64753,0.70554,0.28795,-115.85,-0.65223,0.70854,-0.26937,526.66,-0.39408,-0.013388,0.91898,283.07
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> fitmap #3 inMap #4
Fit map cryosparc_P1_J258_002_volume_map.mrc gaussian z flip in map
Class1_J150_PostLocal_PostHomorefine_3.46Ang_flip_g2 (1).mrc using 8473772
points
correlation = 0.9411, correlation about mean = 0.7519, overlap = 2.622e+05
steps = 120, shift = 21.2, angle = 6.17 degrees
Position of cryosparc_P1_J258_002_volume_map.mrc gaussian z flip (#3) relative
to Class1_J150_PostLocal_PostHomorefine_3.46Ang_flip_g2 (1).mrc (#4)
coordinates:
Matrix rotation and translation
0.59159574 0.75439110 0.28444429 -104.87480763
-0.66323084 0.65596739 -0.36032159 558.08804133
-0.45840958 0.02451249 0.88840295 296.61745717
Axis 0.23378813 0.45128647 -0.86121056
Axis point 619.13688785 465.48923324 0.00000000
Rotation angle (degrees) 55.39030356
Shift along axis -28.11099133
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> save "C:/Users/mahamaya/OneDrive - Stanford/IVT_Structure/June
> 2026/J258_ALIGN_CLASS1_KRIOS_.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
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\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
> select add #4
4 models selected
> save "C:/Users/mahamaya/OneDrive - Stanford/IVT_Structure/June
> 2026/J258_ALIGN_CLASS1_KRIOS_.cxs" includeMaps true
Ran out of memory trying to save a session including 4 maps (4.7 Gbytes).
To save the session you will either have to save the maps to separate files
(then only the path to the file is included in the session) or close some of
the maps.
#1 "cryosparc_P1_J258_002_volume_map.mrc" (1423 MB)
#2 "cryosparc_P1_J258_002_volume_map.mrc gaussian" (1423 MB)
#3 "cryosparc_P1_J258_002_volume_map.mrc gaussian z flip" (1423 MB)
#4 "Class1_J150_PostLocal_PostHomorefine_3.46Ang_flip_g2 (1).mrc" (512 MB)
[Repeated 1 time(s)]
> save my_session.cxs includeMaps false
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
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\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
> close #1
> close #2
> save "C:/Users/mahamaya/OneDrive - Stanford/IVT_Structure/June
> 2026/J258_ALIGN_CLASS1_KRIOS_.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
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\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\bug_reporter\tool.py", line 249, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\webservices\post_form.py", line 45, in
post_multipart_formdata
return r.status, r.msg, r.getheaders(), r.read()
^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\http\client.py", line 482, in read
s = self._safe_read(self.length)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\http\client.py", line 633, in
_safe_read
raise IncompleteRead(data, amt-len(data))
http.client.IncompleteRead: IncompleteRead(666 bytes read, 6348 more expected)
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\bug_reporter\tool.py", line 249, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\webservices\post_form.py", line 45, in
post_multipart_formdata
return r.status, r.msg, r.getheaders(), r.read()
^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\http\client.py", line 482, in read
s = self._safe_read(self.length)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\http\client.py", line 633, in
_safe_read
raise IncompleteRead(data, amt-len(data))
http.client.IncompleteRead: IncompleteRead(666 bytes read, 6348 more expected)
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\bug_reporter\tool.py", line 249, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\webservices\post_form.py", line 45, in
post_multipart_formdata
return r.status, r.msg, r.getheaders(), r.read()
^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\http\client.py", line 482, in read
s = self._safe_read(self.length)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\http\client.py", line 633, in
_safe_read
raise IncompleteRead(data, amt-len(data))
http.client.IncompleteRead: IncompleteRead(666 bytes read, 6348 more expected)
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\bug_reporter\tool.py", line 249, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\webservices\post_form.py", line 45, in
post_multipart_formdata
return r.status, r.msg, r.getheaders(), r.read()
^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\http\client.py", line 482, in read
s = self._safe_read(self.length)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\http\client.py", line 633, in
_safe_read
raise IncompleteRead(data, amt-len(data))
http.client.IncompleteRead: IncompleteRead(666 bytes read, 6348 more expected)
> save "C:/Users/mahamaya/OneDrive - Stanford/IVT_Structure/June
> 2026/J258_ALIGN_CLASS1_Krios.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
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\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.4953
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex SFF Plus 7020
OS: Microsoft Windows 11 Education (Build 26200)
Memory: 16,851,456,000
MaxProcessMemory: 137,438,953,344
CPU: 28 Intel(R) Core(TM) i7-14700
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
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.24.0
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-ISOLDE: 1.9
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
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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
more-itertools: 10.3.0
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
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
zipp: 3.19.2
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