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#17130 closed defect (duplicate)

MemoryError saving map in session

Reported by:	chimerax-bug-report@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open E:/LILab/20241112MtbRPo/cryosparc_P57_J282_003_volume_map.mrc

Opened cryosparc_P57_J282_003_volume_map.mrc as #1, grid size 640,640,640,
pixel 0.445, shown at level 0.0124, step 4, values float32  

> open E:/LILab/20241112MtbRPo/RealSpaceRefine_4/close_bubble_MtbRPo-
> coot-0_real_space_refined_real_space_refined.pdb

Chain information for close_bubble_MtbRPo-
coot-0_real_space_refined_real_space_refined.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  

> select add #2

26214 atoms, 26863 bonds, 3235 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> set bgColor white

> hide #!1 models

> select subtract #2

Nothing selected  

> volume #1 step 1

> windowsize 1000 1000

> volume all level 0.01

> show #!1 models

> hide #!1 models

> show #!1 models

> volume all level 0.012

> volume all level 0.01

> volume all level 0.02

> volume all level 0.015

> volume all level 0.012

> volume all level 0.01

> surface dust #1 size 4.45

> hide #!1 models

> lighting soft

> select #2/F:1-71

562 atoms, 573 bonds, 70 residues, 1 model selected  

> color sel comflower blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color sel cornflower blue

> dssp

> select #2/F:72-91

143 atoms, 147 bonds, 20 residues, 1 model selected  

> color sel blue

> select #2/F:92-158

498 atoms, 505 bonds, 67 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel #006bcbff

> select #2/F:159-312

281 atoms, 286 bonds, 40 residues, 1 model selected  

> color sel red

> select #2/A:1

1 atom, 1 residue, 1 model selected  

> size sel atomRadius 2

Changed 1 atom radii  

> select #2/A:1

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select #2/G,H,I

1875 atoms, 2099 bonds, 92 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> style sel stick

Changed 1875 atom styles  

> select #2/H:1

21 atoms, 22 bonds, 1 residue, 1 model selected  

> color sel #aaff7fff

> select #2:H:2-7

400 atoms, 428 bonds, 31 residues, 1 model selected  

> color sel #ffaaffff

> select #2/H:8-23

330 atoms, 368 bonds, 16 residues, 1 model selected  

> color sel #aaff7fff

> select #2/H:24-29

119 atoms, 131 bonds, 6 residues, 1 model selected  

> color sel #ffaaffff

> select #2/H:30-46

340 atoms, 380 bonds, 17 residues, 1 model selected  

> color sel #aaff7fff

> select #2/G:48

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select #2/G:42-47

124 atoms, 138 bonds, 6 residues, 1 model selected  

> color sel #ffaaffff

> select #2/G:26-41

326 atoms, 366 bonds, 16 residues, 1 model selected  

> color sel #aaff7fff

> select #2/G:24-25

41 atoms, 45 bonds, 2 residues, 1 model selected  

> color sel #ffaaffff

> select #2/G:12-23

245 atoms, 273 bonds, 12 residues, 1 model selected  

> color sel forest green

> select #2/G:3-11

186 atoms, 208 bonds, 9 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel #aaff7fff

> save E:/fig2d.cxs

> volume zone #1 nearAtoms #2/H:1 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #3, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/H:2-7 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #4, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> select add #3

186 atoms, 208 bonds, 9 residues, 3 models selected  

> select add #4

186 atoms, 208 bonds, 9 residues, 5 models selected  

> transparency (#2 & sel) 50

> select add #1

186 atoms, 208 bonds, 9 residues, 7 models selected  

> transparency (#2 & sel) 50

> select subtract #1

186 atoms, 208 bonds, 9 residues, 5 models selected  

> select add #2

26214 atoms, 26863 bonds, 3235 residues, 5 models selected  

> select subtract #3

26214 atoms, 26863 bonds, 3235 residues, 3 models selected  

> select subtract #2

2 models selected  

> select add #3

4 models selected  

> transparency #3.1#4.1 50

> volume zone #1 nearAtoms #2/H:8-23 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #5, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> select subtract #4

2 models selected  

> select subtract #3

Nothing selected  

> select add #5

2 models selected  

> transparency #5.1 50

> volume zone #1 nearAtoms #2/H:8-23 range 2 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #6, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> select subtract #5

Nothing selected  

> select add #6

2 models selected  

> transparency #6.1 50

> close #6

> volume zone #1 nearAtoms #2/H:8-23 range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #6, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> hide #!5 models

> show #!5 models

> hide #!6 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!5 models

> hide #!5 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!5 models

> select add #6

2 models selected  

> transparency #2-5 50

> show #!6 models

> hide #!5 models

> transparency #6.1 50

> show #!5 models

> close #6

> volume zone #1 nearAtoms #2/H:24-29 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #6, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/H:24-29 range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #7, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> hide #!6 models

> show #!6 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!6 models

> show #!7 models

> show #!6 models

> hide #!7 models

> hide #!6 models

> show #!6 models

> close #7

> volume zone #1 nearAtoms #2/H:30-46 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #7, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> select add #7

2 models selected  

> select add #6

4 models selected  

> transparency #6.1#7.1 50

> volume zone #1 nearAtoms #2/G:48 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #8, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/G:42-47 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #9, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/G:26-41 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #10, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/G:24-25 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #11, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/G:12-23 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #12, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/G:3-11 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #13, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> select add #8

6 models selected  

> select add #9

8 models selected  

> select add #10

10 models selected  

> select add #11

12 models selected  

> select add #12

14 models selected  

> select add #13

16 models selected  

> transparency #6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1 50

> ui tool show "Color Actions"

[Repeated 1 time(s)]

> color #3 #aaff7f

> color #5 #aaff7f

> hide #!5 models

> show #!5 models

> hide #!3 models

> show #!3 models

> hide #!7 models

> show #!7 models

> color #7 #aaff7f

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> color #8 #aaff7f

> hide #!8 models

> show #!8 models

> hide #!10 models

> show #!10 models

> color #10 #aaff7f

> hide #!10 models

> show #!10 models

> hide #!13 models

> show #!13 models

> color #13 #aaff7f

> hide #!13 models

> show #!13 models

> color #4 #ff55ff80 models

> color #4 #ffaaff80 models

> color #4 #ffaaff

> hide #!6 models

> show #!6 models

> color #6 #ffaaff

> hide #!6 models

> show #!6 models

> hide #!8 models

> show #!8 models

> hide #!9 models

> show #!9 models

> color #9 #ffaaff

> hide #!9 models

> show #!9 models

> hide #!11 models

> show #!11 models

> color #11 #ffaaff

> hide #!11 models

> show #!11 models

No visible atoms or bonds selected  

> color #12 #005500 models transparency 0

> color #12 #00aa00 models transparency 0

> transparency #6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1 50

> color #12 #00aa00

> select #2/A

1687 atoms, 1712 bonds, 222 residues, 1 model selected  

> color sel dark gray

> select #2/B

1800 atoms, 1827 bonds, 237 residues, 1 model selected  

> color sel dark gray

> select #2/C

8690 atoms, 8849 bonds, 1122 residues, 1 model selected  

> color sel dark gray

> select #2/D

10019 atoms, 10190 bonds, 1281 residues, 1 model selected  

> color sel light gray

> select #2/D

10019 atoms, 10190 bonds, 1281 residues, 1 model selected  

> color sel dark gray

> select #2/C

8690 atoms, 8849 bonds, 1122 residues, 1 model selected  

> color sel light gray

> select #2/E

659 atoms, 672 bonds, 84 residues, 1 model selected  

> color sel dark gray

> select clear

> volume zone #1 nearAtoms #2/F:1-71 range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #14, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> close #14

> save E:/fig2d.cxs

> volume zone #1 nearAtoms #2/F:1-71 range 2 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #14, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/F:1-71 range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #15, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> hide #!14 models

> show #!14 models

> hide #!14 models

> select add #15

2 models selected  

> show #!14 models

> select add #14

4 models selected  

> transparency #14.1#15.1 50

> hide #!15 models

> hide #!14 models

> select #2/F:1-71

562 atoms, 573 bonds, 70 residues, 1 model selected  

> color sel cornflower blue

> select clear

> show #!14 models

> hide #!14 models

> show #!15 models

> show #!14 models

> hide #!15 models

> surface dust #3 size 4.45

> surface dust #4 size 4.45

> surface dust #5 size 4.45

> surface dust #6 size 4.45

> surface dust #7 size 4.45

> surface dust #8 size 4.45

> surface dust #9 size 4.45

> surface dust #10 size 4.45

> surface dust #11 size 4.45

> surface dust #12 size 4.45

> surface dust #13 size 4.45

> surface dust #14 size 4.45

> hide #!14 models

> show #!15 models

> show #!14 models

> hide #!15 models

> hide #!14 models

> show #!15 models

> show #!14 models

> hide #!15 models

> hide #!14 models

> show #!15 models

> surface dust #3 size 4.45

> surface dust #4 size 4.45

> surface dust #5 size 4.45

> surface dust #6 size 4.45

> surface dust #7 size 4.45

> surface dust #8 size 4.45

> surface dust #9 size 4.45

> surface dust #10 size 4.45

> surface dust #11 size 4.45

> surface dust #12 size 4.45

> surface dust #13 size 4.45

> surface dust #15 size 4.45

> color #15 comflower blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> select add #15

2 models selected  

> select subtract #15

Nothing selected  

> hide #!15 models

> color #15 #55aaff80 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> color #15 #55aaff

> show #!15 models

> volume zone #1 nearAtoms #2/F:72-91 range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #16, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> select add #16

2 models selected  

> color #16.1 blue

> transparency #16.1 50

> transparency #16.1 70

> select add #15

4 models selected  

> transparency #15.1#16.1 70

> volume zone #1 nearAtoms #2/F:92-158 range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #17, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> color #17 #006bcb models transparency 0

> select add #17

6 models selected  

> transparency #15.1#16.1#17.1 70

> surface dust #15 size 4.45

> surface dust #16 size 4.45

> surface dust #17 size 4.45

> volume zone #1 nearAtoms #2/F:159-312 range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #18, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> color #18 red models transparency 0

> select add #18

8 models selected  

> transparency #15.1#16.1#17.1#18.1 70

> transparency #3-18 70 target s

> transparency #3-18 50 target s

> transparency #3-18 70 target s

> transparency #3-18 50 target s

> select clear

> volume zone #1 nearAtoms #2/A range 1 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #19, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> close #19

> volume zone #1 nearAtoms #2/A range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #19, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/B range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #20, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/C range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #21, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/D range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #22, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> volume zone #1 nearAtoms #2/E range 1.5 newMap true

Opened cryosparc_P57_J282_003_volume_map.mrc zone as #23, grid size
640,640,640, pixel 0.445, shown at step 1, values float32  

> color #19-23 darkred light

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #19-23 darkred light

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #19 darkred light

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #19-23 dark gray

> hide #!21 models

> show #!21 models

> color #21 light gray

> hide #!21 models

> show #!21 models

> hide #!20 models

> show #!20 models

> hide #!19 models

> show #!19 models

> transparency #19-23 70 target s

> save E:/fig2d.cxs

> hide #!23 models

> hide #!22 models

> show #!22 models

> show #!23 models

> voview name fig2d

Unknown command: voview name fig2d  

> view name fig2d

> turn y 180

> view name fig2d

> view fig2d

> turn y 180

> view name fig2d

> save Fig2d_1a.tiff width 2000 height 2000 transparentBackground true

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting flat

> lighting soft

> lighting flat

> graphics silhouettes false

> lighting flat

> lighting soft

> save Fig2d_1a.tiff width 2000 height 2000 transparentBackground true

> view fig2d

> surface dust #3 size 4.45

> surface dust #4 size 4.45

> surface dust #5 size 4.45

> surface dust #6 size 4.45

> surface dust #7 size 4.45

> surface dust #8 size 4.45

> surface dust #9 size 4.45

> surface dust #10 size 4.45

> surface dust #11 size 4.45

> surface dust #12 size 4.45

> surface dust #13 size 4.45

> surface dust #15 size 4.45

> surface dust #16 size 4.45

> surface dust #17 size 4.45

> surface dust #18 size 4.45

> surface dust #19 size 4.45

> surface dust #20 size 4.45

> surface dust #21 size 4.45

> surface dust #22 size 4.45

> surface dust #23 size 4.45

> save Fig2d_1a.tiff width 2000 height 2000 transparentBackground true

> turn y 180

> save Fig2d_2.tiff width 2000 height 2000 transparentBackground true

> save E:/fig2d.cxs

Traceback (most recent call last):  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 718, in write  
compressed = self._compressor.compress(data)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\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 "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 718, in write  
compressed = self._compressor.compress(data)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  

> save E:/fig2d.cxs

Traceback (most recent call last):  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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 "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\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 "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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 NVIDIA 556.39
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 34,206,019,584
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700F CPU @ 2.90GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 7 months ago

Cc:	Tom Goddard added
Component:	Unassigned → Sessions
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → MemoryError saving map in session

comment:2 by pett, 7 months ago

Resolution:	→ duplicate
Status:	assigned → closed

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