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Opened 3 years ago
Closed 3 years ago
#7883 closed defect (nonchimerax)
Saving various files: No space left on device
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-52-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF 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 /home/dell/Desktop/Manuscripts/C5aR1-Go-
> Structure/C5apep-C5aR1-Go/C5apep-sharpened_map.ccp4
Opened C5apep-sharpened_map.ccp4 as #1, grid size 360,360,360, pixel 0.82,
shown at level 3.36, step 2, values float32
> set bgColor white
> open /home/dell/Desktop/Manuscripts/C5aR1-Go-
> Structure/C5apep-C5aR1-Go/C5a-pep-C5aR1-Go-model.pdb
Chain information for C5a-pep-C5aR1-Go-model.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
G | No description available
H | No description available
> show cartoons
> hide atoms
> volume #1 step 1
> volume #1 level 11.28
> surface dust #1 size 8.2
> volume #1 level 12.03
> lighting simple
> lighting flat
> open /home/dell/Desktop/Manuscripts/C5aR1-Go-
> Structure/C5apep-C5aR1-Go/C5apep-sharpened_map.ccp4
Opened C5apep-sharpened_map.ccp4 as #3, grid size 360,360,360, pixel 0.82,
shown at level 3.36, step 2, values float32
> hide #!1 models
> volume #3 level 5.792
> surface dust #3 size 8.2
> vop gaussian #3 sdev 2.46
Opened C5apep-sharpened_map.ccp4 gaussian as #4, grid size 360,360,360, pixel
0.82, shown at step 1, values float32
> volume #4 color #b2b2b280
> volume #4 color #ebdcdc
> volume #4 color #ebdcdc00
> volume #4 color #c9bbbb00
> volume #4 color #c9bbbb00
> volume #4 color #f7f1f100
> show #!1 models
> hide #!4 models
> color zone #1 near #2 distance 4.92
> hide #!2 models
> show #!4 models
> lighting soft
> volume #4 level 4.724
> volume #4 level 3.243
> ui tool show "Side View"
> volume #1 level 10.05
> volume #4 level 2.801
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/I1.png width 1281
> height 804 supersample 3 transparentBackground true
> graphics silhouettes false
> graphics silhouettes true
> volume #4 color #bf40401f
> volume #4 color #eee4e40c
> volume #4 color #f5efef27
> volume #4 color #f5efef22
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/I12.png width 1281
> height 804 supersample 3 transparentBackground true
> lighting full
> lighting shadows false
> show #!2 models
> hide #!2 models
> hide #!4 models
> lighting flat
> volume #1 level 9.304
> volume #1 level 10.05
> volume #1 level 9.675
> ui tool show "Map Eraser"
> volume erase #1 center 191.77,145.61,111.44 radius 18.21
Opened C5apep-sharpened_map.ccp4 copy as #6, grid size 360,360,360, pixel
0.82, shown at step 1, values float32
> volume #6 level 11.9
> volume #6 level 9.68
> surface dust #6 size 8.2
> volume erase #6 center 120,168.21,104.28 radius 18.155
> volume erase #6 center 116.8,128.28,112.47 radius 18.155
> volume erase #6 center 122.21,124.36,96.575 radius 18.155
> volume erase #6 center 168.62,142.99,147.22 radius 6.0516
> show #!2 models
> hide #!6 models
Drag select of 15 residues
> select up
713 atoms, 726 bonds, 94 residues, 1 model selected
> select up
2127 atoms, 2181 bonds, 270 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light slate gray
> select clear
Drag select of 9 residues
> select up
263 atoms, 268 bonds, 34 residues, 1 model selected
> select up
1654 atoms, 1681 bonds, 214 residues, 1 model selected
> color sel tomato
> select clear
Drag select of 11 residues
> select up
354 atoms, 358 bonds, 46 residues, 1 model selected
> select up
2538 atoms, 2585 bonds, 338 residues, 1 model selected
> color sel deep sky blue
> select clear
Drag select of 4 residues
> select up
116 atoms, 115 bonds, 17 residues, 1 model selected
> select up
403 atoms, 409 bonds, 56 residues, 1 model selected
> color sel yellow green
> select clear
Drag select of 10 residues
> select up
200 atoms, 204 bonds, 24 residues, 1 model selected
> select up
1743 atoms, 1789 bonds, 235 residues, 1 model selected
> color sel indigo
> color sel medium purple
> select clear
Drag select of 2 residues
> select up
74 atoms, 77 bonds, 7 residues, 1 model selected
> color sel gold
> show sel atoms
> select clear
> select /A:316@CD1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel light slate gray
> select clear
> show #!6 models
> color zone #6 near #2 distance 4.92
> hide cartoons
> lighting soft
> lighting flat
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 2.147
> volume #4 level 2.458
> lighting soft
> lighting flat
> lighting soft
> lighting flat
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-C5aR1-Go-
> Overall.png width 2000 height 1434 supersample 3 transparentBackground true
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5aR1-Go-F2.cxs
> includeMaps true
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-C5aR1-Go-
> Overall2.png width 2000 height 1434 supersample 3 transparentBackground true
> lighting flat
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5aR1-Go-F2.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save
fserialize(stream, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 130, in write
self._f.write(buf)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 695, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 880, in save
output.close("exceptional")
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 122, in close
self.__exit__(type(exception), exception, None)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 85, in __exit__
self._f.close()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
See log for complete Python traceback.
> graphics silhouettes width 5
> graphics silhouettes width 2
> graphics silhouettes width 1.5
> graphics silhouettes width 1
> graphics silhouettes width 1.2
> graphics silhouettes width 1.3
> graphics silhouettes width 1.5
> lighting soft
> lighting flat
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-C5aR1-Go-
> Overall3.png width 2000 height 1434 supersample 3 transparentBackground true
> graphics silhouettes width 2
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-C5aR1-Go-
> Overall4.png width 2000 height 1434 supersample 3 transparentBackground true
> lighting flat
> graphics silhouettes width 1
> hide #!4 models
> lighting soft
> lighting flat
> lighting soft
> hide #!2 models
> lighting flat
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-Side1.png
> width 2000 height 1434 supersample 3 transparentBackground true
> lighting flat
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-Side2.png
> width 2000 height 1434 supersample 3 transparentBackground true
> lighting flat
> volume #1 level 9.675
> volume #6 level 9.589
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-Side3.png
> width 2000 height 1434 supersample 3 transparentBackground true
> lighting flat
> show #!2 models
> hide #!6 models
> show cartoons
Drag select of 41 residues
> select up
756 atoms, 770 bonds, 102 residues, 1 model selected
> select up
1743 atoms, 1789 bonds, 235 residues, 1 model selected
> hide sel cartoons
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-
> Side2-ribbon.png width 2000 height 1434 supersample 3 transparentBackground
> true
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-
> Side3-ribbon.png width 2000 height 1434 supersample 3 transparentBackground
> true
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5aR1-Go-F2.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save
fserialize(stream, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 130, in write
self._f.write(buf)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 695, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 880, in save
output.close("exceptional")
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 122, in close
self.__exit__(type(exception), exception, None)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 85, in __exit__
self._f.close()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
See log for complete Python traceback.
> lighting flat
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> open /home/dell/Desktop/Manuscripts/C5aR1-Go-
> Structure/C5a-C5aR1-Go/C5a-C5aR1-sharpened_map.ccp4
Opened C5a-C5aR1-sharpened_map.ccp4 as #5, grid size 360,360,360, pixel 0.82,
shown at level 3.37, step 2, values float32
> volume #5 level 3.369
> volume #5 step 1
> volume #5 level 10.96
> hide #!2 models
> volume #5 level 10.17
> surface dust #5 size 8.2
> open /home/dell/Desktop/Manuscripts/C5aR1-Go-
> Structure/C5a-C5aR1-Go/C5a-C5ar1-refined.pdb
Chain information for C5a-C5ar1-refined.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
G | No description available
H | No description available
> show #!7 cartoons
> hide #!7 atoms
> select #5
3 models selected
> color sel light gray
> color sel light gray
> color sel dark gray
> color sel light gray
> select clear
> color zone #5 near #7 distance 4.92
> select clear
> hide #!7 models
> ui tool show "Map Eraser"
> volume erase #5 center 155.54,115.88,109.13 radius 7.6304
Opened C5a-C5aR1-sharpened_map.ccp4 copy as #9, grid size 360,360,360, pixel
0.82, shown at step 1, values float32
> show #!7 models
> color zone #9 near #7 distance 4.92
> hide #!7 models
> volume erase #9 center 168.18,121.51,108.6 radius 7.5276
> volume erase #9 center 154.88,121.42,113.28 radius 7.5276
> volume erase #9 center 157.16,121.26,113.49 radius 7.5276
> volume erase #9 center 152.16,116.15,103.3 radius 7.5276
> volume erase #9 center 141.66,121.38,105.73 radius 7.5276
> volume erase #9 center 133.67,126.64,102.33 radius 7.5276
> volume erase #9 center 136.44,123.13,98.4 radius 7.5276
> volume erase #9 center 129.95,132.07,96.645 radius 7.5276
> volume erase #9 center 132.09,131.54,89.584 radius 7.5276
> volume erase #9 center 128.53,142.66,94.375 radius 7.5276
> volume erase #9 center 129.59,138.74,86.018 radius 7.5276
> volume erase #9 center 132.49,148.99,89.336 radius 7.5276
> volume erase #9 center 135.87,155.81,94.872 radius 7.5276
> volume erase #9 center 140.64,156.39,90.084 radius 7.5276
> volume erase #9 center 147.21,160.93,87.766 radius 7.5276
> volume erase #9 center 155.95,164.41,89.28 radius 7.5276
> volume erase #9 center 164.38,164.18,92.857 radius 7.5276
> volume erase #9 center 171.53,159.71,99.741 radius 7.5276
> volume erase #9 center 169.44,161.15,96.494 radius 7.5276
> volume erase #9 center 177.92,151.3,98.808 radius 7.5276
> volume erase #9 center 179.5,141.19,102.25 radius 7.5276
> volume erase #9 center 175.58,133.51,107.23 radius 7.5276
> volume erase #9 center 171.99,126.31,104.97 radius 7.5276
> surface dust #9 size 8.2
> volume erase #9 center 169.8,120.63,102.73 radius 7.5276
> volume erase #9 center 179.78,145.66,98.612 radius 7.5276
> volume erase #9 center 139.5,179.27,126.25 radius 7.5276
> volume erase #9 center 143.73,175.68,121.6 radius 7.5276
> volume erase #9 center 123.13,159.21,123.53 radius 7.5276
> volume erase #9 center 164.04,166.41,131.78 radius 7.5276
> volume erase #9 center 164.84,122.88,139.02 radius 7.5276
> volume erase #9 center 169.09,131.33,140.79 radius 7.5276
> volume erase #9 center 158.82,134.36,136.06 radius 7.5276
> volume erase #9 center 145.74,132.82,134.32 radius 7.5276
> volume erase #9 center 131.98,131.68,132.86 radius 7.5276
> volume erase #9 center 123.01,140.54,128.63 radius 7.5276
> volume erase #9 center 141.65,187.7,174.66 radius 7.5276
> volume erase #9 center 147.43,181.76,173.14 radius 7.5276
> volume #9 level 10.17
> volume #9 level 8.095
> surface dust #9 size 8.2
> lighting soft
> lighting flat
> volume erase #9 center 165.85,132.67,131.85 radius 7.5276
> volume erase #9 center 126.64,168.86,121.92 radius 7.5276
> volume erase #9 center 163.82,163.14,122.27 radius 7.5276
> volume erase #9 center 180.83,132.93,97.552 radius 7.5276
> volume erase #9 center 135.16,150.81,82.899 radius 7.5276
> volume erase #9 center 134.85,131.6,90.138 radius 7.5276
> volume erase #9 center 164.65,160.09,93.412 radius 7.5276
> volume erase #9 center 174.39,156.82,88.236 radius 7.5276
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!9 models
Drag select of 16 residues
> select up
665 atoms, 677 bonds, 89 residues, 1 model selected
> select up
2126 atoms, 2179 bonds, 273 residues, 1 model selected
> color sel light slate gray
> color sel slate gray
> select clear
Drag select of 14 residues
> select up
399 atoms, 403 bonds, 52 residues, 1 model selected
> select up
1654 atoms, 1681 bonds, 214 residues, 1 model selected
> color sel tomato
> select clear
Drag select of 11 residues
> select up
240 atoms, 239 bonds, 34 residues, 1 model selected
> select up
2544 atoms, 2591 bonds, 338 residues, 1 model selected
> color sel deep sky blue
> color sel dodger blue
> select clear
Drag select of 2 residues
> select up
157 atoms, 156 bonds, 22 residues, 1 model selected
> select up
403 atoms, 409 bonds, 56 residues, 1 model selected
> color sel yellow green
> select clear
Drag select of 18 residues
> select up
282 atoms, 288 bonds, 35 residues, 1 model selected
> select up
1743 atoms, 1789 bonds, 235 residues, 1 model selected
> color sel gray
> color sel medium purple
> select clear
Drag select of 5 residues
> select up
191 atoms, 193 bonds, 26 residues, 1 model selected
> select up
561 atoms, 569 bonds, 75 residues, 1 model selected
> color sel cyan
> select clear
> show #!2 models
> hide #!7 models
Drag select of 21 residues
> select up
521 atoms, 528 bonds, 67 residues, 1 model selected
> select up
2538 atoms, 2585 bonds, 338 residues, 1 model selected
> color sel dodger blue
> select clear
> show #!7 models
> ui tool show "Show Sequence Viewer"
> ui tool show Matchmaker
> matchmaker #!7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker C5a-pep-C5aR1-Go-model.pdb, chain C (#2) with
C5a-C5ar1-refined.pdb, chain C (#7), sequence alignment score = 1579.9
RMSD between 337 pruned atom pairs is 0.680 angstroms; (across all 338 pairs:
0.689)
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> close #1
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!4 models
> hide #!4 models
> close #3
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!6 models
> hide #!2 models
> fitmap #7 inMap #9
Fit molecule C5a-C5ar1-refined.pdb (#7) to map C5a-C5aR1-sharpened_map.ccp4
copy (#9) using 9031 atoms
average map value = 10.53, steps = 148
shifted from previous position = 8.15
rotated from previous position = 14 degrees
atoms outside contour = 2981, contour level = 8.0952
Position of C5a-C5ar1-refined.pdb (#7) relative to
C5a-C5aR1-sharpened_map.ccp4 copy (#9) coordinates:
Matrix rotation and translation
0.99999999 0.00007967 0.00007308 -0.01903435
-0.00007965 0.99999998 -0.00020556 0.05220501
-0.00007309 0.00020555 0.99999998 -0.00901832
Axis 0.88505612 0.31468649 -0.34299866
Axis point 0.00000000 39.43856395 249.86571520
Rotation angle (degrees) 0.01330709
Shift along axis 0.00267502
> show #!4 models
> hide #!4 models
> show #!2 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> hide #!7 models
> fitmap #2 inMap #9
Fit molecule C5a-pep-C5aR1-Go-model.pdb (#2) to map
C5a-C5aR1-sharpened_map.ccp4 copy (#9) using 8465 atoms
average map value = 9.62, steps = 144
shifted from previous position = 7.96
rotated from previous position = 14.5 degrees
atoms outside contour = 3379, contour level = 8.0952
Position of C5a-pep-C5aR1-Go-model.pdb (#2) relative to
C5a-C5aR1-sharpened_map.ccp4 copy (#9) coordinates:
Matrix rotation and translation
0.98069124 0.18830446 0.05278370 -32.16413399
-0.17749979 0.97037155 -0.16392947 49.34289110
-0.08208845 0.15139510 0.98505889 -12.07825717
Axis 0.62884966 0.26897462 -0.72952091
Axis point 241.49435698 201.77331471 0.00000000
Rotation angle (degrees) 14.51984943
Shift along axis 1.85692170
> show #!7 models
> hide #!9 models
> show #!6 models
> select #6
3 models selected
> select clear
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> hide #!6 models
> show #!6 models
> hide #!7 models
> fitmap #2 inMap #6
Fit molecule C5a-pep-C5aR1-Go-model.pdb (#2) to map C5apep-sharpened_map.ccp4
copy (#6) using 8465 atoms
average map value = 12.15, steps = 172
shifted from previous position = 8.26
rotated from previous position = 14.5 degrees
atoms outside contour = 3138, contour level = 9.5886
Position of C5a-pep-C5aR1-Go-model.pdb (#2) relative to C5apep-
sharpened_map.ccp4 copy (#6) coordinates:
Matrix rotation and translation
0.99999538 0.00240287 0.00186296 -0.80895796
-0.00240804 0.99999325 0.00277629 0.02187508
-0.00185627 -0.00278076 0.99999441 1.05268449
Axis -0.67459422 0.45149328 -0.58401751
Axis point 0.00000000 366.16176533 -16.61455755
Rotation angle (degrees) 0.23599106
Shift along axis -0.05919135
> show #!9 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> fitmap #6 inMap #9
Fit map C5apep-sharpened_map.ccp4 copy in map C5a-C5aR1-sharpened_map.ccp4
copy using 92467 points
correlation = 0.9169, correlation about mean = 0.4603, overlap = 1.443e+07
steps = 168, shift = 8.45, angle = 14.5 degrees
Position of C5apep-sharpened_map.ccp4 copy (#6) relative to
C5a-C5aR1-sharpened_map.ccp4 copy (#9) coordinates:
Matrix rotation and translation
0.98149174 0.18553916 0.04742552 -30.87112884
-0.17535683 0.97026854 -0.16682010 49.47715653
-0.07696716 0.15541617 0.98484612 -13.81434709
Axis 0.64504603 0.24900674 -0.72243426
Axis point 245.00091734 199.12382666 0.00000000
Rotation angle (degrees) 14.46436005
Shift along axis 2.38680411
> fitmap #6 inMap #9
Fit map C5apep-sharpened_map.ccp4 copy in map C5a-C5aR1-sharpened_map.ccp4
copy using 92467 points
correlation = 0.9169, correlation about mean = 0.4604, overlap = 1.443e+07
steps = 44, shift = 0.0034, angle = 0.00139 degrees
Position of C5apep-sharpened_map.ccp4 copy (#6) relative to
C5a-C5aR1-sharpened_map.ccp4 copy (#9) coordinates:
Matrix rotation and translation
0.98149024 0.18554986 0.04741473 -30.86912231
-0.17537050 0.97026917 -0.16680204 49.47380241
-0.07695515 0.15539943 0.98484970 -13.81592877
Axis 0.64498994 0.24896634 -0.72249826
Axis point 244.96370109 199.10679102 0.00000000
Rotation angle (degrees) 14.46404888
Shift along axis 2.38902254
> hide #!9 models
> show #!2 models
> fitmap #2 inMap #6
Fit molecule C5a-pep-C5aR1-Go-model.pdb (#2) to map C5apep-sharpened_map.ccp4
copy (#6) using 8465 atoms
average map value = 12.15, steps = 136
shifted from previous position = 8.25
rotated from previous position = 14.5 degrees
atoms outside contour = 3144, contour level = 9.5886
Position of C5a-pep-C5aR1-Go-model.pdb (#2) relative to C5apep-
sharpened_map.ccp4 copy (#6) coordinates:
Matrix rotation and translation
0.99999573 0.00224584 0.00187205 -0.78410378
-0.00225118 0.99999340 0.00285340 -0.01029623
-0.00186563 -0.00285761 0.99999418 1.05190315
Axis -0.69870748 0.45728143 -0.55018320
Axis point 0.00000000 361.25705330 -1.25873839
Rotation angle (degrees) 0.23415926
Shift along axis -0.03558854
> volume #6 level 9.954
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!7 models
> fitmap #2 inMap #6
Fit molecule C5a-pep-C5aR1-Go-model.pdb (#2) to map C5apep-sharpened_map.ccp4
copy (#6) using 8465 atoms
average map value = 12.15, steps = 44
shifted from previous position = 0.00534
rotated from previous position = 0.00778 degrees
atoms outside contour = 3374, contour level = 9.9543
Position of C5a-pep-C5aR1-Go-model.pdb (#2) relative to C5apep-
sharpened_map.ccp4 copy (#6) coordinates:
Matrix rotation and translation
0.99999547 0.00234829 0.00188429 -0.80140680
-0.00235349 0.99999341 0.00276504 0.01320027
-0.00187778 -0.00276946 0.99999440 1.04102060
Axis -0.67669870 0.45998627 -0.57488390
Axis point 0.00000000 365.52173257 -12.23427415
Rotation angle (degrees) 0.23430223
Shift along axis -0.05008310
> show #!7 models
> hide #!2 models
> fitmap #7 inMap #6
Fit molecule C5a-C5ar1-refined.pdb (#7) to map C5apep-sharpened_map.ccp4 copy
(#6) using 9031 atoms
average map value = 10.17, steps = 60
shifted from previous position = 0.0265
rotated from previous position = 0.0638 degrees
atoms outside contour = 4703, contour level = 9.9543
Position of C5a-C5ar1-refined.pdb (#7) relative to C5apep-sharpened_map.ccp4
copy (#6) coordinates:
Matrix rotation and translation
0.98150339 -0.17556633 -0.07633852 37.83992044
0.18567548 0.97012586 0.15614237 -40.20096555
0.04664463 -0.16742845 0.98478017 23.53071552
Axis -0.64672971 -0.24580972 0.72202373
Axis point 245.27763285 198.52797511 0.00000000
Rotation angle (degrees) 14.48693512
Shift along axis 2.39932237
> fitmap #7 inMap #6
Fit molecule C5a-C5ar1-refined.pdb (#7) to map C5apep-sharpened_map.ccp4 copy
(#6) using 9031 atoms
average map value = 10.17, steps = 84
shifted from previous position = 0.0112
rotated from previous position = 0.0123 degrees
atoms outside contour = 4698, contour level = 9.9543
Position of C5a-C5ar1-refined.pdb (#7) relative to C5apep-sharpened_map.ccp4
copy (#6) coordinates:
Matrix rotation and translation
0.98148867 -0.17570915 -0.07619904 37.83791066
0.18578907 0.97011822 0.15605470 -40.19868747
0.04650184 -0.16732287 0.98480487 23.52445516
Axis -0.64635515 -0.24524998 0.72254928
Axis point 245.10168051 198.34898126 0.00000000
Rotation angle (degrees) 14.48666745
Shift along axis 2.39957717
> show #!9 models
> hide #!6 models
> color zone #9 near #7 distance 4.92
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!9 models
> show #!2 models
> color zone #6 near #2 distance 4.92
> hide #!2 models
> show #!2 models
> show #!9 models
> hide #!9 models
> hide #!2 models
> lighting soft
> show #!4 models
> hide #!4 models
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-C5aR1-Go-
> front.png width 2000 height 1439 supersample 3 transparentBackground true
> volume #4 level 2.507
> volume #6 level 9.68
> volume #6 level 9.68
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-C5aR1-Go-
> top.png width 2000 height 1439 supersample 3 transparentBackground true
> lighting flat
> show #!9 models
> hide #!6 models
> volume #9 level 9.985
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5a-C5aR1-Go-
> front.png width 2000 height 1439 supersample 3 transparentBackground true
> lighting flat
> volume #9 level 10.29
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5a-C5aR1-Go-
> top.png width 2000 height 1439 supersample 3 transparentBackground true
> lighting flat
> show #!5 models
> hide #!5 models
> show #!5 models
> close #5
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5aR1-Go-F2.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save
fserialize(stream, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 130, in write
self._f.write(buf)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 695, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 880, in save
output.close("exceptional")
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 122, in close
self.__exit__(type(exception), exception, None)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 85, in __exit__
self._f.close()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
See log for complete Python traceback.
> show #!7 models
> hide #!9 models
> lighting soft
Drag select of 29 residues
> select up
392 atoms, 402 bonds, 52 residues, 1 model selected
> select up
1743 atoms, 1789 bonds, 235 residues, 1 model selected
> hide sel cartoons
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5a-C5aR1-Go-
> ribbon.png width 2000 height 1439 supersample 3 transparentBackground true
> lighting flat
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-C5aR1-Go-
> ribbon.png width 200 height 144 supersample 3 transparentBackground true
> show #!7 models
> hide #!2 models
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5a-C5aR1-Go-
> ribbon.png width 2000 height 1439 supersample 3 transparentBackground true
> lighting flat
> show #!6 models
> hide #!7 models
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-C5aR1-Go-
> front.png width 2000 height 1439 supersample 3 transparentBackground true
> show #!2 models
> hide #!6 models
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5apep-C5aR1-Go-
> ribbon.png width 2000 height 1439 supersample 3 transparentBackground true
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F2/C5aR1-Go-F2.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save
fserialize(stream, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 130, in write
self._f.write(buf)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 695, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 880, in save
output.close("exceptional")
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 122, in close
self.__exit__(type(exception), exception, None)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 85, in __exit__
self._f.close()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
See log for complete Python traceback.
> lighting flat
> show #!6 models
> hide #!2 models
> select #6
3 models selected
> select clear
> select #6
3 models selected
> select clear
> select #6
3 models selected
> select #6
3 models selected
> select clear
> lighting soft
> lighting flat
> lighting soft
> lighting flat
> lighting soft
> select #6
3 models selected
> select clear
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5apep-G-prot-
> Map.png width 2000 height 1439 supersample 3 transparentBackground true
> lighting flat
> show #!9 models
> hide #!6 models
> volume #9 level 9.456
> volume #9 level 8.624
> lighting soft
> volume #9 level 9.229
> lighting flat
> volume #9 level 9.531
> lighting soft
> show #!6 models
> hide #!9 models
> show #!9 models
> hide #!6 models
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5a-G-prot-Map.png
> width 2000 height 1439 supersample 3 transparentBackground true
> lighting flat
> show #!2 models
> hide #!9 models
Drag select of 2 residues
> select up
252 atoms, 255 bonds, 33 residues, 1 model selected
> select up
2127 atoms, 2181 bonds, 270 residues, 1 model selected
> show sel surfaces
> color sel slate gray
> select clear
> color sel light gray
> select clear
> lighting soft
> lighting flat
> lighting soft
> lighting flat
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5apep-G-prot-
> Sur.png width 2000 height 1439 supersample 3 transparentBackground true
> show #!7 models
> lighting flat
> hide #!2 models
Drag select of 3 residues
> select up
242 atoms, 245 bonds, 32 residues, 1 model selected
> select up
2126 atoms, 2179 bonds, 273 residues, 1 model selected
> show sel surfaces
> color sel slate gray
> select clear
> color sel light gray
> select clear
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5a-G-prot-Sur.png
> width 2000 height 1439 supersample 3 transparentBackground true
> lighting flat
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5aR1-G-prot.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save
fserialize(stream, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 130, in write
self._f.write(buf)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 695, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 880, in save
output.close("exceptional")
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 122, in close
self.__exit__(type(exception), exception, None)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 85, in __exit__
self._f.close()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
See log for complete Python traceback.
> color sel dark gray
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> lighting soft
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5a-G-prot-Sur.png
> width 2000 height 1439 supersample 3 transparentBackground true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/ImageFile.py",
line 506, in _save
fh = fp.fileno()
AttributeError: '_idat' object has no attribute 'fileno'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/image_formats/__init__.py", line 45, in save
save_image(session, path, format_name, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/image_formats/save.py", line 123, in save_image
i.save(path, format_name, **metadata)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/Image.py", line
2158, in save
save_handler(self, fp, filename)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 1284, in _save
ImageFile._save(im, _idat(fp, chunk), [("zip", (0, 0) + im.size, 0, rawmode)])
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/ImageFile.py",
line 521, in _save
fp.write(d)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 989, in write
self.chunk(self.fp, b"IDAT", data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 976, in putchunk
fp.write(data)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 976, in putchunk
fp.write(data)
See log for complete Python traceback.
> show #!2 models
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> hide #!7 models
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> color sel dark gray
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5apep-G-prot-
> Sur.png width 2000 height 1439 supersample 3 transparentBackground true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/ImageFile.py",
line 506, in _save
fh = fp.fileno()
AttributeError: '_idat' object has no attribute 'fileno'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/image_formats/__init__.py", line 45, in save
save_image(session, path, format_name, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/image_formats/save.py", line 123, in save_image
i.save(path, format_name, **metadata)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/Image.py", line
2158, in save
save_handler(self, fp, filename)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 1284, in _save
ImageFile._save(im, _idat(fp, chunk), [("zip", (0, 0) + im.size, 0, rawmode)])
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/ImageFile.py",
line 521, in _save
fp.write(d)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 989, in write
self.chunk(self.fp, b"IDAT", data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 976, in putchunk
fp.write(data)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 976, in putchunk
fp.write(data)
See log for complete Python traceback.
> lighting flat
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5aR1-G-prot.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save
fserialize(stream, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 130, in write
self._f.write(buf)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 695, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 880, in save
output.close("exceptional")
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 122, in close
self.__exit__(type(exception), exception, None)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 85, in __exit__
self._f.close()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 548, in close
self._fp.close()
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 548, in close
self._fp.close()
See log for complete Python traceback.
> lighting soft
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5apep-G-prot-
> Sur.png width 2000 height 1439 supersample 3 transparentBackground true
> show #!7 models
> hide #!2 models
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5a-G-prot-Sur.png
> width 2000 height 1439 supersample 3 transparentBackground true
> lighting flat
> hide #!7 surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> show #!2 models
> hide surfaces
> hide #!7 models
> show #!7 models
> hide #!2 models
> select #7/A:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:71,237
19 atoms, 17 bonds, 2 residues, 1 model selected
> select #7/A:71,237-238
25 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 25 atom styles
> color sel byhetero
> hide #!7 models
> show #!2 models
> show #!7 models
> hide #!2 models
> select #7/A:71,146,237-238
34 atoms, 31 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 34 atom styles
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B #7/B
Alignment identifier is 1
> select #2/B:350 #7/B:350
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #2/B:350 #7/B:350
8 atoms, 6 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 2 chains [210] RMSD: 0.827
> select #2/B:350,354 #7/B:350,354
34 atoms, 32 bonds, 4 residues, 2 models selected
Seqview [ID: 1] region 2 chains [210] + 1 other block RMSD: 2.289
> select #2/B:317,350,354 #7/B:317,350,354
52 atoms, 48 bonds, 6 residues, 2 models selected
Seqview [ID: 1] region 2 chains [210] + 2 other blocks RMSD: 1.950
> select #2/B:315,317,350,354 #7/B:315,317,350,354
66 atoms, 62 bonds, 8 residues, 2 models selected
Seqview [ID: 1] region 2 chains [210] + 3 other blocks RMSD: 1.858
> select #2/B:315,317-318,350,354 #7/B:315,317-318,350,354
84 atoms, 80 bonds, 10 residues, 2 models selected
Seqview [ID: 1] region 2 chains [210] + 4 other blocks RMSD: 1.712
> select #2/B:194,315,317-318,350,354 #7/B:194,315,317-318,350,354
100 atoms, 94 bonds, 12 residues, 2 models selected
Seqview [ID: 1] region 2 chains [210] + 5 other blocks RMSD: 1.651
> show sel & #!7 atoms
> style sel & #!7 stick
Changed 50 atom styles
> show sel & #!7 atoms
> show sel & #!7 atoms
> show sel & #!7 atoms
> hide sel & #!7 cartoons
> show sel & #!7 cartoons
> color sel byhetero
> select clear
Drag select of 40 residues
> select up
586 atoms, 591 bonds, 80 residues, 1 model selected
> select up
2947 atoms, 3000 bonds, 394 residues, 1 model selected
> hide sel cartoons
> select #7/B:350
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> cartoon style width 0.8
> select #7/A:238
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #7/B:318
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #7/B:318@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
58 atoms, 58 bonds, 7 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #7/B:315
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> cartoon style width 1
> select clear
> lighting soft
> lighting flat
> select #7/B:317
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #7/B:318
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> select #7/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select add #7/B:354
13 atoms, 13 bonds, 1 residue, 1 model selected
> select add #7/B:351
19 atoms, 18 bonds, 2 residues, 1 model selected
> select subtract #7/B:351
13 atoms, 13 bonds, 1 residue, 1 model selected
> select up
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
17 atoms, 16 bonds, 2 residues, 1 model selected
> select add #7/A:71
25 atoms, 23 bonds, 3 residues, 1 model selected
> select add #7/A:146
34 atoms, 31 bonds, 4 residues, 2 models selected
> select add #7/B:194
42 atoms, 38 bonds, 5 residues, 2 models selected
> select add #7/B:317@CA
43 atoms, 38 bonds, 6 residues, 2 models selected
> select subtract #7/B:317@CA
42 atoms, 38 bonds, 5 residues, 2 models selected
> select up
44 atoms, 39 bonds, 6 residues, 2 models selected
> select up
51 atoms, 46 bonds, 6 residues, 2 models selected
> select up
53 atoms, 47 bonds, 7 residues, 2 models selected
> select up
58 atoms, 53 bonds, 7 residues, 2 models selected
> select add #7/A:237
69 atoms, 63 bonds, 8 residues, 2 models selected
> select add #7/A:238@CA
70 atoms, 63 bonds, 9 residues, 2 models selected
> select up
75 atoms, 69 bonds, 9 residues, 2 models selected
> select ~sel
17421 atoms, 17794 bonds, 10 pseudobonds, 2295 residues, 15 models selected
> transparency sel 60 target r
> transparency sel 70 target r
> select clear
Drag select of 2 residues
> select up
159 atoms, 158 bonds, 22 residues, 1 model selected
> select up
1654 atoms, 1681 bonds, 214 residues, 1 model selected
> select down
159 atoms, 158 bonds, 22 residues, 1 model selected
> select add #7/B:34
166 atoms, 164 bonds, 23 residues, 1 model selected
> select up
207 atoms, 205 bonds, 28 residues, 1 model selected
> select up
1654 atoms, 1681 bonds, 214 residues, 1 model selected
> select down
207 atoms, 205 bonds, 28 residues, 1 model selected
> select add #7/B:33
215 atoms, 212 bonds, 29 residues, 1 model selected
> select add #7/B:32
224 atoms, 220 bonds, 30 residues, 1 model selected
> select add #7/B:31
229 atoms, 224 bonds, 31 residues, 1 model selected
> select add #7/B:261
237 atoms, 231 bonds, 32 residues, 1 model selected
> select add #7/B:262
242 atoms, 235 bonds, 33 residues, 1 model selected
> select add #7/B:263
249 atoms, 241 bonds, 34 residues, 1 model selected
> select add #7/B:264
255 atoms, 246 bonds, 35 residues, 1 model selected
> select add #7/B:265
263 atoms, 253 bonds, 36 residues, 1 model selected
> select add #7/B:260
274 atoms, 264 bonds, 37 residues, 1 model selected
> select add #7/B:266
282 atoms, 271 bonds, 38 residues, 1 model selected
Drag select of 3 residues
> select add #7/B:220
313 atoms, 277 bonds, 42 residues, 1 model selected
> select add #7/B:221
318 atoms, 281 bonds, 43 residues, 1 model selected
> select subtract #7/B:221
313 atoms, 277 bonds, 42 residues, 1 model selected
> select add #7/B:222
321 atoms, 284 bonds, 43 residues, 1 model selected
> select add #7/B:221
326 atoms, 288 bonds, 44 residues, 1 model selected
> select add #7/B:216
337 atoms, 299 bonds, 45 residues, 1 model selected
> hide sel cartoons
> select add #7/B:259
348 atoms, 310 bonds, 46 residues, 1 model selected
> select add #7/B:256
356 atoms, 317 bonds, 47 residues, 1 model selected
> select add #7/B:255
362 atoms, 322 bonds, 48 residues, 1 model selected
> select add #7/B:267
370 atoms, 329 bonds, 49 residues, 1 model selected
> select add #7/B:223
378 atoms, 336 bonds, 50 residues, 1 model selected
> select add #7/B:215
384 atoms, 341 bonds, 51 residues, 1 model selected
> hide sel cartoons
> select clear
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5a-G-prot-
> interface-ribbon.png width 2000 height 1159 supersample 3
> transparentBackground true
> show #!2 models
> hide #!7 models
Drag select of 25 residues
> select up
557 atoms, 557 bonds, 77 residues, 1 model selected
> select up
2941 atoms, 2994 bonds, 394 residues, 1 model selected
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B #7/B
Alignment identifier is 2
> select #2/B:44 #7/B:44
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #2/B:44-46 #7/B:44-46
38 atoms, 36 bonds, 6 residues, 2 models selected
Seqview [ID: 2] region 2 chains [40-42] RMSD: 0.943
> select clear
> select #2/B:44-46,354 #7/B:44-46,354
64 atoms, 62 bonds, 8 residues, 2 models selected
Seqview [ID: 2] region 2 chains [40-42] + 1 other block RMSD: 1.765
> select #2/B:44-46,351,354 #7/B:44-46,351,354
76 atoms, 72 bonds, 10 residues, 2 models selected
Seqview [ID: 2] region 2 chains [40-42] + 2 other blocks RMSD: 1.691
> select #2/B:44-46,350-351,354 #7/B:44-46,350-351,354
84 atoms, 80 bonds, 12 residues, 2 models selected
Seqview [ID: 2] region 2 chains [40-42] + 3 other blocks RMSD: 1.580
> select #2/B:44-46,350-351,354 #7/B:44-46,350-351,354
84 atoms, 80 bonds, 12 residues, 2 models selected
Seqview [ID: 2] region 2 chains [40-42] + 4 other blocks RMSD: 1.400
> select clear
> select #2/B:354 #7/B:354
26 atoms, 26 bonds, 2 residues, 2 models selected
> select #2/B:354 #7/B:354
26 atoms, 26 bonds, 2 residues, 2 models selected
Seqview [ID: 2] region 2 chains [214] RMSD: 3.130
> select #2/B:351,354 #7/B:351,354
38 atoms, 36 bonds, 4 residues, 2 models selected
Seqview [ID: 2] region 2 chains [214] + 1 other block RMSD: 2.412
> select #2/B:350-351,354 #7/B:350-351,354
46 atoms, 44 bonds, 6 residues, 2 models selected
Seqview [ID: 2] region 2 chains [214] + 2 other blocks RMSD: 2.026
> select #2/B:350-351,353-354 #7/B:350-351,353-354
62 atoms, 60 bonds, 8 residues, 2 models selected
Seqview [ID: 2] region 2 chains [214] + 3 other blocks RMSD: 2.191
> select #2/B:341,350-351,353-354 #7/B:341,350-351,353-354
78 atoms, 74 bonds, 10 residues, 2 models selected
Seqview [ID: 2] region 2 chains [214] + 4 other blocks RMSD: 2.048
> select #2/B:337,341,350-351,353-354 #7/B:337,341,350-351,353-354
94 atoms, 88 bonds, 12 residues, 2 models selected
Seqview [ID: 2] region 2 chains [214] + 5 other blocks RMSD: 1.905
> select #2/B:315,337,341,350-351,353-354 #7/B:315,337,341,350-351,353-354
108 atoms, 102 bonds, 14 residues, 2 models selected
Seqview [ID: 2] region 2 chains [214] + 6 other blocks RMSD: 1.859
> select #2/B:315,317,337,341,350-351,353-354
> #7/B:315,317,337,341,350-351,353-354
126 atoms, 118 bonds, 16 residues, 2 models selected
Seqview [ID: 2] region 2 chains [214] + 7 other blocks RMSD: 1.772
> select #2/B:194,315,317,337,341,350-351,353-354
> #7/B:194,315,317,337,341,350-351,353-354
142 atoms, 132 bonds, 18 residues, 2 models selected
Seqview [ID: 2] region 2 chains [214] + 8 other blocks RMSD: 1.726
> show sel & #!2 atoms
> style sel & #!2 stick
Changed 71 atom styles
> select clear
> select #2/A:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:71,134
19 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/A:71,134,235
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #2/A:71,134,235,237-238
41 atoms, 37 bonds, 5 residues, 1 model selected
> select #2/A:71,134,235,237-238,241
48 atoms, 43 bonds, 6 residues, 1 model selected
> select #2/A:71,134,146,235,237-238,241
57 atoms, 51 bonds, 7 residues, 1 model selected
> select #2/A:71,134,146,233,235,237-238,241
68 atoms, 61 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 68 atom styles
> color sel byhetero
> select clear
> select #2/B:354
13 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select #2/B:353
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> color sel byhetero
> select clear
> select #2/B:351
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> color sel byhetero
> select clear
Drag select of 22 residues
> select up
181 atoms, 180 bonds, 25 residues, 1 model selected
Drag select of 3 residues
> select add #2/B:8
209 atoms, 188 bonds, 29 residues, 1 model selected
> hide sel cartoons
Drag select of 10 residues
> select up
138 atoms, 137 bonds, 17 residues, 1 model selected
> hide sel cartoons
Drag select of 3 residues
> select up
30 atoms, 29 bonds, 4 residues, 1 model selected
> select up
1654 atoms, 1681 bonds, 214 residues, 1 model selected
> select down
30 atoms, 29 bonds, 4 residues, 1 model selected
Drag select of 2 residues
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> hide sel cartoons
Drag select of 4 residues
> select up
1654 atoms, 1681 bonds, 214 residues, 1 model selected
> select down
30 atoms, 4 residues, 1 model selected
> hide sel cartoons
Drag select of 32 residues, 1 pseudobonds
> hide sel cartoons
> undo
> select clear
Drag select of 8 residues
> hide sel cartoons
> select #2/A:235
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #2/B:337
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> color sel byhetero
> select clear
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5aR1-G-prot.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save
fserialize(stream, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 130, in write
self._f.write(buf)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 695, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 880, in save
output.close("exceptional")
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 122, in close
self.__exit__(type(exception), exception, None)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/safesave.py", line 85, in __exit__
self._f.close()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/lz4/frame/__init__.py", line 543, in close
self._fp.write(self._compressor.flush())
See log for complete Python traceback.
> select #2/B:317
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select up
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select #2/B:341
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> color sel byhetero
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select #2/A:238
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
56 atoms, 55 bonds, 7 residues, 2 models selected
> select down
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
6 atoms, 5 bonds, 1 residue, 2 models selected
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select #2/B:354@CA
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
1 atom, 1 residue, 1 model selected
> hide sel cartoons
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
Drag select of 14 residues
> hide sel cartoons
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select up
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select #2/B:350
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> hide sel cartoons
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
Drag select of 27 atoms, 6 residues, 23 bonds
> hide sel atoms
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> show sel cartoons
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> lighting soft
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> lighting full
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> lighting flat
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> lighting flat
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> lighting full
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> lighting shadows false
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> lighting soft
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> lighting soft
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
> save /home/dell/Desktop/Manuscripts/C5aR1-Go-Structure/F3/C5apep-G-prot-
> interface-TMs.png width 2000 height 1205 supersample 3 transparentBackground
> true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 308, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 406, in add
self._history.enqueue((item, typed))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/json/__init__.py", line 180, in
dump
fp.write(chunk)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/ImageFile.py",
line 506, in _save
fh = fp.fileno()
AttributeError: '_idat' object has no attribute 'fileno'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/Image.py", line
2158, in save
save_handler(self, fp, filename)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 1284, in _save
ImageFile._save(im, _idat(fp, chunk), [("zip", (0, 0) + im.size, 0, rawmode)])
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/ImageFile.py",
line 521, in _save
fp.write(d)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 989, in write
self.chunk(self.fp, b"IDAT", data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/PIL/PngImagePlugin.py", line 976, in putchunk
fp.write(data)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/image_formats/__init__.py", line 45, in save
save_image(session, path, format_name, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/image_formats/save.py", line 123, in save_image
i.save(path, format_name, **metadata)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/Image.py", line
2162, in save
fp.close()
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/PIL/Image.py", line
2162, in save
fp.close()
See log for complete Python traceback.
OpenGL version: 4.3 (Core Profile) Mesa 21.2.6
OpenGL renderer: NV106
OpenGL vendor: nouveau
Manufacturer: Dell Inc.
Model: OptiPlex 5080
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i5-10500 CPU @ 3.10GHz
Cache Size: 12288 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 7.8Gi 1.1Gi 103Mi 6.4Gi 7.1Gi
Swap: 2.0Gi 2.0Mi 2.0Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK208B [GeForce GT 730] [10de:1287] (rev a1)
Subsystem: ZOTAC International (MCO) Ltd. GK208B [GeForce GT 730] [19da:730b]
Kernel driver in use: nouveau
Locale: ('en_IN', 'ISO8859-1')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
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-LinuxSupport: 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
distro: 1.5.0
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
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: 1.2.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Saving various files: No space left on device |
comment:2 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | accepted → closed |
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