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Opened 3 years ago
Closed 3 years ago
#7809 closed defect (duplicate)
Basic Actions session save: 'QEventLoop' object has no attribute 'exec_'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.14.0-1052-oem-x86_64-with-glibc2.31
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3/5Z2Q_AD_clean.pdb
> /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3/3KYS_AB_clean.pdb
> /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3/6Y20_BD_clean.pdb
Summary of feedback from opening
/home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3/3KYS_AB_clean.pdb
---
warnings | Cannot find LINK/SSBOND residue MET (343 )
Cannot find LINK/SSBOND residue P1L (344 )
Summary of feedback from opening
/home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3/6Y20_BD_clean.pdb
---
warnings | Cannot find LINK/SSBOND residue GLU (349 )
Cannot find LINK/SSBOND residue MYK (350 )
Cannot find LINK/SSBOND residue ACE (297 )
Cannot find LINK/SSBOND residue ASN (337 )
Cannot find LINK/SSBOND residue ACE (297 )
1 messages similar to the above omitted
5Z2Q_AD_clean.pdb title:
VGLL1-TEAD4 core complex [more info...]
Chain information for 5Z2Q_AD_clean.pdb #1
---
Chain | Description | UniProt
A | transcriptional enhancer factor tef-3 | TEAD4_MOUSE
D | transcription cofactor vestigial-like protein 1 | VGLL1_MOUSE
3KYS_AB_clean.pdb title:
Crystal structure of human yap and tead complex [more info...]
Chain information for 3KYS_AB_clean.pdb #2
---
Chain | Description | UniProt
A | transcriptional enhancer factor tef-1 | TEAD1_HUMAN
B | 65 kda yes-associated protein | YAP1_HUMAN
6Y20_BD_clean.pdb title:
Crystal structure of protein scalloped (222-440) bound to protein vestigial
(298-337) [more info...]
Chain information for 6Y20_BD_clean.pdb #3
---
Chain | Description | UniProt
B | protein scalloped | SCAL_DROME
D | protein vestigial | VG_DROME
> ui tool show Matchmaker
> matchmaker #!2-3 to #1
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 5Z2Q_AD_clean.pdb, chain A (#1) with 3KYS_AB_clean.pdb, chain A
(#2), sequence alignment score = 923.9
RMSD between 184 pruned atom pairs is 0.676 angstroms; (across all 204 pairs:
2.260)
Matchmaker 5Z2Q_AD_clean.pdb, chain A (#1) with 6Y20_BD_clean.pdb, chain B
(#3), sequence alignment score = 844.4
RMSD between 185 pruned atom pairs is 0.610 angstroms; (across all 205 pairs:
2.049)
> set bgColor white
> color #1 #d3d7cf transparency 0
> color #2 #d3d7cf transparency 0
> color #3 #d3d7cf transparency 0
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> color #2 #babdb6 transparency 0
> color #2 #888a85 transparency 0
> color #2 #babdb6 transparency 0
[Repeated 1 time(s)]
> select #0:60-73.B
Expected an objects specifier or a keyword
> select: #0:60-73.B
Unknown command: select: #0:60-73.B
> select #0 /B :60-73
Nothing selected
> select #0 /B :60-73
Nothing selected
> select #2 /B :60-73
107 atoms, 107 bonds, 14 residues, 1 model selected
> name YAP1-3KYS sel #2 /B :60-73
"sel #2 /B :60-73": contains extra trailing text
> name YAP1-3KYS #2 /B :60-73
> ui tool show "Model Panel"
> ui tool show Toolbar
> name YAP1-3KYS sel
> ui tool show Toolbar
> ui tool show "Basic Actions"
> name YAP1-3KYS sel #2 /B :60-73
"sel #2 /B :60-73": contains extra trailing text
> name YAP1-3KYS #2 /B :60-73
> color YAP1-3KYS #e07676 target c
> color YAP1-3KYS #e47373 target c
> hide #1/A target c
[Repeated 5 time(s)]
> hide #2/A target c
[Repeated 5 time(s)]
> show #2/A target c
[Repeated 2 time(s)]
> color #2/B #3465a4 target c
[Repeated 2 time(s)]
> color YAP1-3KYS #e47373 target s
> hide YAP1-3KYS target c
> show YAP1-3KYS target c
> hide #2/B target c
[Repeated 5 time(s)]
> show #2/B target c
[Repeated 2 time(s)]
> color #2/A #729fcf target c
[Repeated 2 time(s)]
> hide YAP1-3KYS target c
> show YAP1-3KYS target c
> color YAP1-3KYS #d3d7cf target c
> color YAP1-3KYS #e47373 target c
> lighting soft
> graphics silhouettes true
> hide #2/B target c
[Repeated 5 time(s)]
> show #2/B target c
[Repeated 2 time(s)]
> hide #2/A target c
[Repeated 5 time(s)]
> show #2/A target c
[Repeated 2 time(s)]
> hide #2/B target c
[Repeated 5 time(s)]
> color #2/B #c4a000 target c
[Repeated 2 time(s)]
> show #2/B target c
[Repeated 2 time(s)]
> color #2/B #b3a846 target c
[Repeated 2 time(s)]
> color YAP1-3KYS #ffcf00 target c
> color YAP1-3KYS #e47373 target c
> select clear
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> save
> /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3refine.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f4ec2186d00> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7f4e3f9db100> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/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/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f4ec2186d00> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7f4e3f9db100> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/test.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f4ec2186d00> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7f4e3f9db100> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/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/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f4ec2186d00> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7f4e3f9db100> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/red-yellow-
> blue_cartoon_s.png width 1979 height 1095 supersample 4
> graphics silhouettes false
> graphics silhouettes true
> save /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/red-yellow-
> blue_cartoon_s.png width 1979 height 1095 supersample 4
> save /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/tew.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f4ec2186d00> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7f4e3f9db100> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/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/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f4ec2186d00> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7f4e3f9db100> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e3f9db100> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> select YAP1-3KYS
107 atoms, 107 bonds, 14 residues, 1 model selected
> delete YAP1-3KYS
> undo
Undo failed, probably because structures have been modified.
> close session
> open
> /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3/5Z2Q_AD_clean.pdb
> /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3/3KYS_AB_clean.pdb
> /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3/6Y20_BD_clean.pdb
Summary of feedback from opening
/home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3/3KYS_AB_clean.pdb
---
warnings | Cannot find LINK/SSBOND residue MET (343 )
Cannot find LINK/SSBOND residue P1L (344 )
Summary of feedback from opening
/home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/sele3/6Y20_BD_clean.pdb
---
warnings | Cannot find LINK/SSBOND residue GLU (349 )
Cannot find LINK/SSBOND residue MYK (350 )
Cannot find LINK/SSBOND residue ACE (297 )
Cannot find LINK/SSBOND residue ASN (337 )
Cannot find LINK/SSBOND residue ACE (297 )
1 messages similar to the above omitted
5Z2Q_AD_clean.pdb title:
VGLL1-TEAD4 core complex [more info...]
Chain information for 5Z2Q_AD_clean.pdb #1
---
Chain | Description | UniProt
A | transcriptional enhancer factor tef-3 | TEAD4_MOUSE
D | transcription cofactor vestigial-like protein 1 | VGLL1_MOUSE
3KYS_AB_clean.pdb title:
Crystal structure of human yap and tead complex [more info...]
Chain information for 3KYS_AB_clean.pdb #2
---
Chain | Description | UniProt
A | transcriptional enhancer factor tef-1 | TEAD1_HUMAN
B | 65 kda yes-associated protein | YAP1_HUMAN
6Y20_BD_clean.pdb title:
Crystal structure of protein scalloped (222-440) bound to protein vestigial
(298-337) [more info...]
Chain information for 6Y20_BD_clean.pdb #3
---
Chain | Description | UniProt
B | protein scalloped | SCAL_DROME
D | protein vestigial | VG_DROME
> ui tool show Matchmaker
> ui tool show "Basic Actions"
> matchmaker #!2-3 to #1
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 5Z2Q_AD_clean.pdb, chain A (#1) with 3KYS_AB_clean.pdb, chain A
(#2), sequence alignment score = 923.9
RMSD between 184 pruned atom pairs is 0.676 angstroms; (across all 204 pairs:
2.260)
Matchmaker 5Z2Q_AD_clean.pdb, chain A (#1) with 6Y20_BD_clean.pdb, chain B
(#3), sequence alignment score = 844.4
RMSD between 185 pruned atom pairs is 0.610 angstroms; (across all 205 pairs:
2.049)
> matchmaker #!2-3 to #1
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 5Z2Q_AD_clean.pdb, chain A (#1) with 3KYS_AB_clean.pdb, chain A
(#2), sequence alignment score = 923.9
RMSD between 184 pruned atom pairs is 0.676 angstroms; (across all 204 pairs:
2.260)
Matchmaker 5Z2Q_AD_clean.pdb, chain A (#1) with 6Y20_BD_clean.pdb, chain B
(#3), sequence alignment score = 844.4
RMSD between 185 pruned atom pairs is 0.610 angstroms; (across all 205 pairs:
2.049)
> save /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/project.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e37fb6fa0> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f4ec2186d00> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7f4e37fb6fa0> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e37fb6fa0> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e37fb6fa0> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/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/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f4ec2186d00> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7f4e37fb6fa0> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e37fb6fa0> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> remove YAP1-3KYS
Unknown command: remove YAP1-3KYS
> uname YAP1-3KYS
Unknown command: uname YAP1-3KYS
> name delete YAP1-3KYS
> save /home/dinler/Dropbox/Antunes_PI/Collaborators/Lizee/VGLL1/project.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e37fb6fa0> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f4ec2186d00> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7f4e37fb6fa0> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e37fb6fa0> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e37fb6fa0> 'Basic
Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/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/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f4ec2186d00> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7f4e37fb6fa0> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7f4ec2186d00> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7f4e37fb6fa0> 'Basic
Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 470.141.03
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3650 Tower
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 11th Gen Intel(R) Core(TM) i9-11900K @ 3.50GHz
Cache Size: 16384 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 5.5Gi 19Gi 207Mi 6.4Gi 24Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:4c8a] (rev 04)
DeviceName: OnBoard - Video
Subsystem: Dell Device [1028:0a58]
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
distro: 1.6.0
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Basic Actions session save: 'QEventLoop' object has no attribute 'exec_' |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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