Cannot save session: bytes object is too large

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Using very big files

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/dparrell/Desktop/Cimera_session/all_together.cxs

Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__actin_seg.hdf
as #1, grid size 2048,2880,800, pixel 9.21, shown at level 0.631, step 4,
values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__F_prot_seg.hdf
as #2, grid size 2048,2880,800, pixel 9.21, shown at level 0.0894, step 2,
values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__Membrane_seg.hdf
as #3, grid size 2048,2880,800, pixel 9.21, shown at level 0.061, step 4,
values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__mito_seg_2.hdf
as #4, grid size 2048,2880,800, pixel 9.21, shown at level 0.182, step 4,
values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__ribosomes_seg.hdf
as #5, grid size 2048,2880,800, pixel 9.21, shown at level 0.195, step 4,
values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RSV_seg_2.hdf
as #6, grid size 2048,2880,800, pixel 9.21, shown at level 0.101, step 2,
values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__vesicles_seg.hdf
as #7, grid size 2048,2880,800, pixel 9.21, shown at level 0.154, step 4,
values float32  
Opened W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2.mrc as #8, grid
size 2046,2880,800, pixel 9.21,9.21,9.21, shown at step 1, values int16  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RNP_seg.hdf
as #9, grid size 2048,2880,800, pixel 9.21, shown at level 0.185, step 1,
values float32  
Log from Thu Oct 28 15:52:36 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__actin_seg.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__F_prot_seg.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__Membrane_seg.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__mito_seg_2.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__ribosomes_seg.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RSV_seg_2.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__vesicles_seg.hdf
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2.mrc

Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__actin_seg.hdf
as #1, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__F_prot_seg.hdf
as #2, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__Membrane_seg.hdf
as #3, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__mito_seg_2.hdf
as #4, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__ribosomes_seg.hdf
as #5, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RSV_seg_2.hdf
as #6, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__vesicles_seg.hdf
as #7, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  
Opened W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2.mrc as #8, grid
size 2046,2880,800, pixel 9.21,9.21,9.21, shown at step 1, values int16  

> volume #1 color #ff3300 color white color white

> volume #2 color #990099 color white color white

> volume #3 color #0033cc color white color white

> volume #4 color cyan color white color white

> volume #5 color #ffff33 color white color white

> volume #6 color magenta color white color white

> volume #7 color #3399ff color white color white

> volume #8 level -8.998,0 level 25.99,0.8 level 100,1

> volume #8 level -149,0 level 25.99,0.8 level 100,1

> volume #8 level -149,0 level -26.02,1 level 100,1

> volume #8 level -149,0 level -26.02,1 level 28.2,1

> volume #8 level -149,0 level 23.64,1 level 28.2,1

> volume #8 level -149,0 level 23.64,1 level 114.6,0.9706

> volume #8 level -66.42,0.01471 level 23.64,1 level 114.6,0.9706

> volume #8 level -66.42,0.01471 level 6.905,1 level 114.6,0.9706

> volume #8 level -74.52,0 level 6.905,1 level 114.6,0.9706

> volume #7 color black color white color white

> volume #7 color white color white color white

> volume #8 level -100.4,0 level 6.905,1 level 114.6,0.9706

> volume #8 level -100.4,0 level 27.41,1 level 114.6,0.9706

> volume #8 level -100.4,0 level 27.41,1 level 80.55,1

> volume #8 level -53.47,0 level 27.41,1 level 80.55,1

> volume #8 level -53.47,0 level 18.24,1 level 80.55,1

> volume #8 level -53.47,0 level 18.24,1 level 77.32,1

> volume #7 region 0,0,0,2047,2879,799 step 8

> volume #7 region 0,0,0,2047,2879,799 step 8

> volume #6 region 0,0,0,2047,2879,799 step 8

> volume #6 region 0,0,0,2047,2879,799 step 8

> volume #5 region 0,0,0,2047,2879,799 step 8

> volume #5 region 0,0,0,2047,2879,799 step 8

> volume #4 region 0,0,0,2047,2879,799 step 8

> volume #4 region 0,0,0,2047,2879,799 step 8

> ui tool show "Hide Dust"

> volume #3 region 0,0,0,2047,2879,799 step 8

> volume #3 region 0,0,0,2047,2879,799 step 8

> volume #2 region 0,0,0,2047,2879,799 step 8

> volume #2 region 0,0,0,2047,2879,799 step 8

> volume #1 region 0,0,0,2047,2879,799 step 8

> volume #1 region 0,0,0,2047,2879,799 step 8

> volume #1 step 4

> volume #2 step 4

> volume #3 step 4

> volume #4 step 4

> volume #5 step 4

> volume #6 step 4

> volume #1 color #ff6600

> volume #2 color #990099

> volume #3 color #3366ff

> volume #4 color cyan

> volume #5 color #ffcc00

> volume #1 color #33cc33

> volume #1 color #99ff99

> volume #6 color #ff33ff

> volume #7 color #3366cc

> volume #7 color #6699ff

> volume #7 step 4

> surface dust #3 size 809.79

> surface dust #6 size 1001.1

> surface dust #2 size 573.29

> surface dust #1 size 445.22

> surface dust #4 size 558.05

> surface dust #5 size 211.58

> surface dust #7 size 757.83

> volume #6 color #ff66cc

> volume #2 color #660066

> surface dust #2 size 588.53

> surface dust #2 size 311.08

> surface undust #2

> surface dust #2 size 311.08

> surface undust #1

> surface dust #1 size 831.33

> surface undust #4

> surface dust #4 size 1395.6

> surface undust #4

> surface dust #4 size 1945.7

> volume #7 color #3399ff

> volume #7 color #6699cc

> volume #7 color #3399cc

> volume #7 color #33ffff

> volume #7 color #00ffcc

> volume #7 color #669999

> volume #5 color #cc9900

> volume #5 color #ffcc33

> volume #5 color #cc9900

> volume #5 color #cc9933

> volume #5 color #ff9933

> volume #5 color #cc9933

> volume #6 step 2

> volume #2 step 2

> volume #6 color #990099

> volume #2 color #ff66ff

> volume #2 color #ff33cc

> volume #2 color #ff66cc

> surface undust #1

> surface dust #1 size 1945.7

> surface undust #3

> surface dust #3 size 1306.1

> surface dust #3 size 1359.5

> surface dust #3 size 488.73

> surface dust #3 size 495.19

> surface dust #3 size 411.22

> save /Users/dparrell/Desktop/Cimera_session/all_together.cxs

> surface dust #3 size 416.65

> surface dust #3 size 279.69

> surface dust #3 size 279.69

> surface undust #3

> surface dust #3 size 654.59

> open
> /Users/dparrell/Desktop/Cimera_session/W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RNP_seg.hdf

Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RNP_seg.hdf
as #9, grid size 2048,2880,800, pixel 9.21, shown at step 1, values float32  

> volume #9 region 0,0,0,2047,2879,799 step 8

> volume #9 region 0,0,0,2047,2879,799 step 8

> surface dust #9 size 355.2

> volume #9 step 2

> surface undust #9

> surface dust #9 size 1306.1

> volume #9 step 1

> volume #2 color #ffff33

> volume #5 color #ffcc66

> volume #5 color #996600

> volume #5 color #663300

> volume #5 color #cc9933

> volume #5 color #663300

> volume #5 color #996600

> volume #5 color #993300

> volume #5 color #996633

> volume #5 color #cc9966

> volume #5 color #996633

> volume #7 color #339999

> volume #7 color #3366ff

> save /Users/dparrell/Desktop/Cimera_session/all_together.cxs

——— End of log from Thu Oct 28 15:52:36 2021 ———

opened ChimeraX session  

> ui tool show "Map Coordinates"

> save /Users/dparrell/Desktop/Cimera_session/all_together.cxs

> save /Users/dparrell/Desktop/Cimera_session/all_together_clean.cxs

> ui tool show "Command Line Interface"

> hide #!9 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!9 models

> select #8

2 models selected  

> hide #!8 models

> show #!8 models

> select #8

2 models selected  

> ~select #8

Nothing selected  

> select #8

2 models selected  

> select #8.1

1 model selected  

> ~select #8.1

Nothing selected  

> hide #8.1 models

> show #8.1 models

> ui mousemode right "map eraser"

> ui tool show "Hide Dust"

> surface dust #6 size 9.21

> surface dust #6 size 92.93

> surface undust #6

> surface dust #6 size 590.57

> surface undust #6

> surface dust #6 size 1510

> volume erase #6 center -11018,-888.09,-816.96 radius 9664.1

Opened
W1617_G1_L4_Tilt1_insideER2_constantinside_30b_i30_bin2_preproc__RSV_seg_2.hdf
copy as #11, grid size 2048,2880,800, pixel 9.21, shown at step 1, values
float32  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py:2746: RuntimeWarning: invalid value
encountered in log  
h.show_data(log(counts + 1))  

> surface dust #6 size 1620.2

> surface dust #6 size 1224

> surface dust #6 size 1276.7

> surface dust #6 size 1063.8

> surface dust #6 size 1079.4

> surface dust #6 size 771.03

> surface undust #6

> surface dust #11 size 544.34

> surface undust #11

> surface dust #11 size 1058

> volume erase #11 center -3056.1,17906,-1628.7 radius 9664.1

> volume #11 step 2

> surface dust #11 size 1114.2

> surface dust #11 size 279.88

> surface dust #11 size 283.58

> surface dust #11 size 1427.8

> surface dust #11 size 1427.8

> volume erase #11 center -4614.6,5179.5,281.66 radius 5925.7

> volume erase #11 center -2586.9,-8922.9,-3605.5 radius 5925.7

> save /Users/dparrell/Desktop/Cimera_session/all_together_clean.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> select #11.1

1 model selected  

> ~select #11.1

Nothing selected  

> volume erase #11 center 2385.4,-2415.5,966.28 radius 1206.4

> volume erase #11 center 2001.2,-3093.6,259.84 radius 1206.4

> volume erase #11 center 2171.9,-8896.4,543.98 radius 980.99

> volume erase #11 center 471.1,-9712.2,1499 radius 980.99

> volume erase #11 center 3597,-13151,2500.3 radius 980.99

> volume erase #11 center 1459.1,606.9,-629.85 radius 980.99

> volume erase #11 center 4270.6,8440.7,3475.4 radius 980.99

> volume erase #11 center 4352.5,-4395.8,-422.88 radius 980.99

> volume erase #11 center 3820.9,8817.3,-568.62 radius 980.99

> save /Users/dparrell/Desktop/Cimera_session/all_together_clean.cxs
> includeMaps true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> close #6

> lighting simple

> toolshed show

> save /Users/dparrell/Desktop/Cimera_session/all_together_clean2.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.26
OpenGL renderer: AMD Radeon Pro Vega 64X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac Pro
      Model Identifier: iMacPro1,1
      Processor Name: Intel Xeon W
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 18
      L2 Cache (per Core): 1 MB
      L3 Cache: 24.8 MB
      Hyper-Threading Technology: Enabled
      Memory: 256 GB
      Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G9323)
      Kernel Version: Darwin 18.7.0
      Time since boot: 16 days 12:13

Graphics/Displays:

    Radeon Pro Vega 64X:

      Chipset Model: Radeon Pro Vega 64X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 16 GB
      Vendor: AMD (0x1002)
      Device ID: 0x686b
      Revision ID: 0x0000
      ROM Revision: 113-D0500D-114
      VBIOS Version: 113-D05001A1XX-021
      Option ROM Version: 113-D05001A1XX-021
      EFI Driver Version: 01.01.114
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
        LED Cinema Display:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 2A11515U6JL 
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0