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Opened 4 years ago
Closed 4 years ago
#5638 closed defect (duplicate)
Blast results problem: 'NoneType' object has no attribute 'split'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19043
ChimeraX Version: 1.3rc202111110135 (2021-11-11 01:35:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3rc202111110135 (2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\sheny\\\Desktop\\\Chimera_X_\\\zy3-100.cxs
Log from Fri Nov 19 11:15:07 2021UCSF ChimeraX version: 1.3rc202111110135
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\sheny\\\Desktop\\\Chimera_X_\\\zy3-100.cxs
Log from Thu Nov 18 21:34:11 2021UCSF ChimeraX version: 1.3rc202111110135
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\Users\sheny\Desktop\ZY3-100.pdb format pdb
ZY3-100.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) H120 [more info...]
Chain information for ZY3-100.pdb #1
---
Chain | Description
A B C | No description available
Non-standard residues in ZY3-100.pdb #1
---
NAG — (NAG)
> preset "molecular surfaces" "chain id coloring (opaque)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> lighting simple
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting soft
> cd C:/Users/sheny/Desktop/Chimera_X_
Current working directory is: C:\Users\sheny\Desktop\Chimera_X_
> save C:/Users/sheny/Desktop/Chimera_X_/zy3-100.cxs
——— End of log from Thu Nov 18 21:34:11 2021 ———
opened ChimeraX session
> open "C:/Users/sheny/Desktop/discovery studio/结果/ZY3-100Verify.dsv"
Unrecognized file suffix '.dsv'
Alignment identifier is 1
> select /A-C:247
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:247
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:264
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:264
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:271
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:271
24 atoms, 21 bonds, 3 residues, 1 model selected
> color (#!1 & sel) yellow
> ui tool show "Color Actions"
> select /A-C:276
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:276
24 atoms, 21 bonds, 3 residues, 1 model selected
> color (#!1 & sel) yellow
> select /A-C:281
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:281
24 atoms, 21 bonds, 3 residues, 1 model selected
> color (#!1 & sel) yellow
> select /A-C:283
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:283
24 atoms, 21 bonds, 3 residues, 1 model selected
> color (#!1 & sel) yellow
> select /A-C:289
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:289
24 atoms, 21 bonds, 3 residues, 1 model selected
> color (#!1 & sel) yellow
> select /A-C:305-306
57 atoms, 57 bonds, 6 residues, 1 model selected
> select /A-C:305-306
57 atoms, 57 bonds, 6 residues, 1 model selected
> select /A-C:305-306
57 atoms, 57 bonds, 6 residues, 1 model selected
> select /A-C:305-306
57 atoms, 57 bonds, 6 residues, 1 model selected
> select /A-C:306
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:306
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:337
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:337
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:338
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:338
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:343
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:343
24 atoms, 21 bonds, 3 residues, 1 model selected
> undo
[Repeated 9 time(s)]
> select /A-C:246-247
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:246-247
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:247
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:247
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:264
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:264
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:261
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:261
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:264
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:264
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:271
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:271
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:103
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:103
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:138
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:138
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:144
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:144
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:161-162
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:161-162
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:163
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:163
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:178
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:178
24 atoms, 21 bonds, 3 residues, 1 model selected
> color (#!1 & sel) cyan
> select /A-C:237
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:237
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:247
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:247
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:261
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:261
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:264-265
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:264
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:270-271
54 atoms, 54 bonds, 6 residues, 1 model selected
> select /A-C:270-271
54 atoms, 54 bonds, 6 residues, 1 model selected
> select /A-C:276
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:276
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:212
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:212
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:144
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:144
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:146
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /A-C:146
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /A-C:148
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:148
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:156-157
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:156-157
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:156-157
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:156-157
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:177
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:177
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:170
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:170
24 atoms, 21 bonds, 3 residues, 1 model selected
> hide sel surfaces
> help help:user/preferences.html#startup
> surface hidePatches (#!1 & sel)
> transparency (#!1 & sel) 40
> select /A-C:289
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:289
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:247
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:247
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:261
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:261
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:264
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:264
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:276
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:276
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:283
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:283
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:289
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:289
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:304
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:304
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:306
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:306
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:319
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:319
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:21-22
60 atoms, 60 bonds, 6 residues, 1 model selected
> select /A-C:21-1022
23187 atoms, 23685 bonds, 3006 residues, 1 model selected
> transparency (#!1 & sel) 60
> transparency (#!1 & sel) 40
> transparency (#!1 & sel) 30
> lighting soft
> lighting full
> lighting simple
> select /A-C:102
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:102-103
42 atoms, 39 bonds, 6 residues, 1 model selected
> select /A-C:138
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:138
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:143
36 atoms, 36 bonds, 3 residues, 1 model selected
> select /A-C:143-144
60 atoms, 60 bonds, 6 residues, 1 model selected
> select /A-C:144
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:144
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:147-148
39 atoms, 36 bonds, 6 residues, 1 model selected
> select /A-C:147-148
39 atoms, 36 bonds, 6 residues, 1 model selected
> select /A-C:148
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:148
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:494-495
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:494-495
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:495
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:495
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:456
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:456
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:454
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:454
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:451
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:451
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:449-450
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:449-450
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:447
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:447
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:21
36 atoms, 36 bonds, 3 residues, 1 model selected
> select /A-C:21-1022
23187 atoms, 23685 bonds, 3006 residues, 1 model selected
> transparency (#!1 & sel) 0
> lighting soft
> select /A-C:733
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:733
24 atoms, 21 bonds, 3 residues, 1 model selected
> save C:/Users/sheny/Desktop/Chimera_X_/zy3-100.cxs
——— End of log from Fri Nov 19 11:15:07 2021 ———
opened ChimeraX session
> open G:/黄勇老师课题组/多表位疫苗/序列/S蛋白/IBVsczy3100-S.fa
Summary of feedback from opening G:/黄勇老师课题组/多表位疫苗/序列/S蛋白/IBVsczy3100-S.fa
---
note | Alignment identifier is IBVsczy3100-S.fa
Opened 1 sequences from IBVsczy3100-S.fa
> blastprotein IBVsczy3100-S.fa:1
ChimeraX REST job id: job_uvw9btwm
BlastProtein finished.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\ui\gui.py", line 676, in customEvent
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 72, in on_finish
BlastProteinResults.from_job(
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 83, in from_job
return cls(
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 79, in __init__
self._build_ui()
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 197, in _build_ui
param_str = self._format_param_str()
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 174, in _format_param_str
model_no = int(float(values[0].split('/')[0][1:]))
AttributeError: 'NoneType' object has no attribute 'split'
AttributeError: 'NoneType' object has no attribute 'split'
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 174, in _format_param_str
model_no = int(float(values[0].split('/')[0][1:]))
See log for complete Python traceback.
> sequence associate /A IBVsczy3100-S.fa:1
Associated ZY3-100.pdb chain A to IBVsczy3-S.prot (1165 aa) Accession:
ADD62481.2 with 175 mismatches and/or gaps
> sequence associate /B IBVsczy3100-S.fa:1
Associated ZY3-100.pdb chain B to IBVsczy3-S.prot (1165 aa) Accession:
ADD62481.2 with 175 mismatches and/or gaps
> sequence associate /C IBVsczy3100-S.fa:1
Associated ZY3-100.pdb chain C to IBVsczy3-S.prot (1165 aa) Accession:
ADD62481.2 with 175 mismatches and/or gaps
> save G:/黄勇老师课题组/多表位疫苗/序列/S蛋白/N-Gly-zy3-100-S.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 142, in take_snapshot
, 'table_session': self.table.session_info()
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001A1965DD730> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001A1B3492190>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001A1965DD730> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x000001A1B3492190>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001A1965DD730> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001A1B3492190>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 142, in take_snapshot
, 'table_session': self.table.session_info()
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001A1965DD730> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001A1B3492190>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1284, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001A1965DD730> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x000001A1B3492190>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001A1965DD730> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001A1B3492190>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save G:/黄勇老师课题组/多表位疫苗/序列/S蛋白/N-zy3100.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 142, in take_snapshot
, 'table_session': self.table.session_info()
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001A1965DD730> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001A1B3492190>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001A1965DD730> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x000001A1B3492190>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001A1965DD730> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001A1B3492190>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 142, in take_snapshot
, 'table_session': self.table.session_info()
AttributeError: 'BlastProteinResults' object has no attribute 'table'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001A1965DD730> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001A1B3492190>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1284, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001A1965DD730> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x000001A1B3492190>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000001A1965DD730> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001A1B3492190>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\ui\gui.py", line 2251, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\ui\gui.py", line 648, in close_request
all_windows = self.tool_instance_to_windows[tool_instance]
KeyError: <chimerax.bug_reporter.bug_reporter_gui.BugReporter object at
0x000001A1B108D880>
KeyError:
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\ui\gui.py", line 648, in close_request
all_windows = self.tool_instance_to_windows[tool_instance]
See log for complete Python traceback.
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
[Repeated 1 time(s)]Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\ui\gui.py", line 2251, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\ui\gui.py", line 648, in close_request
all_windows = self.tool_instance_to_windows[tool_instance]
KeyError: <chimerax.bug_reporter.bug_reporter_gui.BugReporter object at
0x000001A1B108D880>
KeyError:
File "C:\Program Files\ChimeraX 1.3rc202111110135\bin\lib\site-
packages\chimerax\ui\gui.py", line 648, in close_request
all_windows = self.tool_instance_to_windows[tool_instance]
See log for complete Python traceback.
OpenGL version: 3.3.13596 Core Profile Forward-Compatible Context 20.10.35.02 27.20.1034.6
OpenGL renderer: AMD Radeon (TM) R7 M360
OpenGL vendor: ATI Technologies Inc.
Manufacturer: LENOVO
Model: 80NT
OS: Microsoft Windows 10 家庭版 (Build 19043)
Memory: 17,031,766,016
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
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: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.7
ChimeraX-AddCharge: 1.1.5
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.30.2
ChimeraX-AtomicLibrary: 4.1.5
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3rc202111110135
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
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: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
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: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
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: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.5.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.2
ParmEd: 3.2.0
parso: 0.8.2
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.22
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
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: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.2
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
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: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Blast results problem: 'NoneType' object has no attribute 'split' |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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