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Opened 4 years ago
Closed 4 years ago
#5584 closed defect (duplicate)
wrapped C/C++ object of type QScreen has been deleted
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
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.
> open "C:\Users\vcouroub\Dropbox (Scripps
> Research)\Collaborations\COVID-19\Eddy Arnold\Mpro Polyprotein
> Structure\Mpronsp710-Cryo_dockednsp711run3model5.cxs" format session
Log from Wed Nov 10 13:36:37 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro
> structures/Mpro_nsp7-10.pdb"
Chain information for Mpro_nsp7-10.pdb #1
---
Chain | Description
A B | No description available
C D | No description available
> select /A:79
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
52 atoms, 52 bonds, 7 residues, 1 model selected
> select up
2366 atoms, 2419 bonds, 306 residues, 1 model selected
> color sel orange
> select /B:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
41 atoms, 42 bonds, 4 residues, 1 model selected
> select up
2366 atoms, 2419 bonds, 306 residues, 1 model selected
> color sel orange red
> select clear
> select /C:2
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
69 atoms, 67 bonds, 10 residues, 1 model selected
> select up
4870 atoms, 4972 bonds, 632 residues, 1 model selected
> select clear
> select /C:2
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
69 atoms, 67 bonds, 10 residues, 1 model selected
> color sel cornflower blue
> select /D:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
69 atoms, 67 bonds, 10 residues, 1 model selected
> color sel light sea green
> select clear
> set bgColor white
> lighting soft
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> sequence chain /C
Alignment identifier is 1/C
> open "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy
> Arnold/Polyproteins/nsp7-11/Run3/model5_updatedSS.pdb"
Summary of feedback from opening C:/Users/vcouroub/Dropbox (Scripps
Research)/Collaborations/COVID-19/Eddy
Arnold/Polyproteins/nsp7-11/Run3/model5_updatedSS.pdb
---
warnings | Ignored bad PDB record found on line 44
METHOD
Ignored bad PDB record found on line 45
METHOD The models are generated by I-TASSER which combines the
Ignored bad PDB record found on line 46
METHOD methods of threading, ab initio modeling and structural
Ignored bad PDB record found on line 47
METHOD refinement. The procedure is fully automated.
Ignored bad PDB record found on line 48
METHOD
7 messages similar to the above omitted
Chain information for model5_updatedSS.pdb #2
---
Chain | Description
A | No description available
> undo
> undo
> select clear
> select #2/A:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
171 atoms, 171 bonds, 21 residues, 1 model selected
> select up
4166 atoms, 4233 bonds, 548 residues, 1 model selected
> color sel lime
> select clear
> select #2/A:129
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
171 atoms, 171 bonds, 21 residues, 1 model selected
> select up
4166 atoms, 4233 bonds, 548 residues, 1 model selected
> toolshed show
> select #2/A:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:151
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
77 atoms, 76 bonds, 10 residues, 1 model selected
> select up
4166 atoms, 4233 bonds, 548 residues, 1 model selected
> ui tool show "Modeller Comparative"
> ui tool show "Modeller Comparative"
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> ui tool show "Modeller Comparative"
> modeller comparative 2/A:1 1/C:1 multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> ui tool show "Modeller Comparative"
> modeller comparative 1/C:1 2/A:1 multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread
self.run(*args, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run
self.launch(*args, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch
self._suds = Client(self.service_url + "?wsdl")
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 115, in __init__
self.wsdl = reader.open(url)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\reader.py",
line 150, in open
d = self.fn(url, self.options)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\wsdl.py",
line 136, in __init__
d = reader.open(url)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\reader.py",
line 74, in open
d = self.download(url)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\reader.py",
line 92, in download
fp = self.options.transport.open(Request(url))
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\https.py", line 62, in open
return HttpTransport.open(self, request)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 67, in open
return self.u2open(u2request)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open
return url.open(u2request, timeout=tm)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 525, in
open
response = self._open(req, data)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 542, in
_open
result = self._call_chain(self.handle_open, protocol, protocol +
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 502, in
_call_chain
result = func(*args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 1383,
in http_open
return self.do_open(http.client.HTTPConnection, req)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 1358,
in do_open
r = h.getresponse()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\http\client.py", line 1347, in
getresponse
response.begin()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\http\client.py", line 307, in
begin
version, status, reason = self._read_status()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\http\client.py", line 268, in
_read_status
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\socket.py", line 669, in
readinto
return self._sock.recv_into(b)
socket.timeout: timed out
Exception in thread 1:
socket.timeout: timed out
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\socket.py", line 669, in
readinto
return self._sock.recv_into(b)
See log for complete Python traceback.
Modeller job ID None finished
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 648, in customEvent
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 444, in on_finish
err = self.get_file("stderr.txt")
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file
url = self._status_url + '/' + filename
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file
url = self._status_url + '/' + filename
See log for complete Python traceback.
> help help:user
> select #2/A:118
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:118
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
171 atoms, 171 bonds, 21 residues, 1 model selected
> select up
4166 atoms, 4233 bonds, 548 residues, 1 model selected
> ui tool show "Basic Actions"
> ui tool show "Model Panel"
> ui tool show "Molecular Dynamics Viewer"
Please register the custom scheme 'kmd' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.
> ui tool show "Build Structure"
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> toolshed show
> open 1gcn
Summary of feedback from opening 1gcn fetched from pdb
---
note | Fetching compressed mmCIF 1gcn from
http://files.rcsb.org/download/1gcn.cif
1gcn title:
X-ray analysis of glucagon and its relationship to receptor binding [more
info...]
Chain information for 1gcn #3
---
Chain | Description
A | glucagon
> undo
> hide #3 models
> align
Missing or invalid "atoms" argument: empty atom specifier
> align chains
Missing or invalid "atoms" argument: invalid atoms specifier
> align "chains"
Missing or invalid "atoms" argument: invalid atoms specifier
> show #2 target m
> show #2 target m
> split
Split Mpro_nsp7-10.pdb (#1) into 4 models
Did not split model5_updatedSS.pdb, has only one piece
Did not split 1gcn, has only one piece
Chain information for Mpro_nsp7-10.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for Mpro_nsp7-10.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for Mpro_nsp7-10.pdb C #1.3
---
Chain | Description
C | No description available
Chain information for Mpro_nsp7-10.pdb D #1.4
---
Chain | Description
D | No description available
> hide #1.4 models
> show #1.4 models
> hide #1.2 models
> hide #1.1 models
> ui tool show "Structure Modification"
> ui tool show Matchmaker
> ui tool show Matchmaker
> matchmaker #2 to #1.3 showAlignment true
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 Mpro_nsp7-10.pdb C, chain C (#1.3) with model5_updatedSS.pdb, chain
A (#2), sequence alignment score = 35.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Mpro_nsp7-10.pdb C #1.3/C,
model5_updatedSS.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 4 pruned atom pairs is 1.265 angstroms; (across all 10 pairs:
4.578)
> show #1.1 models
> show #1.2 models
> select #1.3/C:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:1-10
69 atoms, 67 bonds, 10 residues, 1 model selected
> select clear
> select #2/A:390
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:390-399
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel blue
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 5 atomic models, 0 maps.
> select clear
> select clear
> select #2/A:183-184
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:183-192
77 atoms, 76 bonds, 10 residues, 1 model selected
> select #2/A:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
171 atoms, 171 bonds, 21 residues, 1 model selected
> select up
4166 atoms, 4233 bonds, 548 residues, 1 model selected
> color sel dark gray
> select clear
> select #2/A:390
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:390-399
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel cyan
> color sel purple
> select clear
> select #2/A:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:182-189
62 atoms, 61 bonds, 8 residues, 1 model selected
> select #2/A:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:183-196
109 atoms, 108 bonds, 14 residues, 1 model selected
> select #2/A:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:183-213
229 atoms, 230 bonds, 31 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lime green
> color sel lawn green
> color sel chartreuse
> color sel lime
> color sel yellow green
> color sel pale green
> color sel light green
> color sel pale green
> color sel light green
> color sel light green
> color sel pale green
> select clear
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5.cxs"
> select #2/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
171 atoms, 171 bonds, 21 residues, 1 model selected
> select up
4166 atoms, 4233 bonds, 548 residues, 1 model selected
> color sel dark gray
> select clear
> select #2/A:390
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:390-399
69 atoms, 68 bonds, 10 residues, 1 model selected
> color sel medium blue
> select clear
> select clear
> select #1.1/A:19
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
44 atoms, 43 bonds, 6 residues, 1 model selected
> select up
2366 atoms, 2419 bonds, 306 residues, 1 model selected
> show sel surfaces
> select clear
> select #1.1/A:143@CA
1 atom, 1 residue, 1 model selected
> select #1.1/A:26@O
1 atom, 1 residue, 1 model selected
> select #2/A:402
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1.1/A:273@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
107 atoms, 106 bonds, 14 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> color (#!1.1 & sel) orange
> select clear
> select #2/A:534
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
139 atoms, 140 bonds, 18 residues, 1 model selected
> select up
4166 atoms, 4233 bonds, 548 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> style sel sphere
Changed 4166 atom styles
> color sel bychain
> undo
> show sel cartoons
> show sel atoms
> transparency (#!2 & sel) 50
> show sel surfaces
> hide sel atoms
> select #1.1/A:277@C
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
133 atoms, 133 bonds, 18 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> transparency (#!1.1 & sel) 50
> select clear
> hide #1.2-4#!2#!1.1 surfaces
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/MproC145A_nsp711-run3model5_dock.pdb" models #2#1.1-2
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5.cxs"
——— End of log from Wed Nov 10 13:36:37 2021 ———
opened ChimeraX session
> split
Did not split model5_updatedSS.pdb, has only one piece
Did not split 1gcn, has only one piece
Did not split Mpro_nsp7-10.pdb A, has only one piece
Did not split Mpro_nsp7-10.pdb B, has only one piece
Did not split Mpro_nsp7-10.pdb C, has only one piece
Did not split Mpro_nsp7-10.pdb D, has only one piece
> open "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/XL_Mpro_nsp711model5_inter.pb"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\graphics.py", line 51, in event
if self.handle_drag_and_drop(event):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\graphics.py", line 116, in handle_drag_and_drop
mw.dropEvent(event)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 552, in dropEvent
_open_dropped_file(self.session, p)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 1812, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 421, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\read_pbonds\\__init__.py", line 25, in open
return readpbonds.read_pseudobond_file(session, data, file_name)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 51, in read_pseudobond_file
raise SyntaxError('Line %d, got %d atoms for spec "%s", require exactly 1'
File "<string>", line None
SyntaxError: Line 0, got 0 atoms for spec "/C:164@CA", require exactly 1
File "", line None
SyntaxError: Line 0, got 0 atoms for spec "/C:164@CA", require exactly 1
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 51, in read_pseudobond_file
raise SyntaxError('Line %d, got %d atoms for spec "%s", require exactly 1'
See log for complete Python traceback.
> setattr /A c chain_id E
Assigning chain_id attribute to 3 items
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> setattr /A r chain_id E
Assigning chain_id attribute to 0 items
> ui tool show "Show Sequence Viewer"
> setattr #1/A c chain_id A
Assigning chain_id attribute to 0 items
> setattr #1/A r chain_id A
Assigning chain_id attribute to 0 items
> ui tool show "Show Sequence Viewer"
> setattr Mpro_nsp7-10.pdb/A r chain_id A
Expected a keyword
> select clear
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5.jpg" width 1290 height 802
> supersample 3
> select #1.1/E:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
92 atoms, 93 bonds, 11 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> show sel surfaces
> select clear
> select #1.2/B:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
41 atoms, 42 bonds, 4 residues, 1 model selected
> select up
2366 atoms, 2419 bonds, 306 residues, 1 model selected
> show sel surfaces
> transparency (#!1.2 & sel) 50
> select clear
> undo
> undo
> hide sel surfaces
> select clear
> select #2/E:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
93 atoms, 94 bonds, 12 residues, 2 models selected
> select up
4166 atoms, 4233 bonds, 548 residues, 2 models selected
> show sel surfaces
> color (#!2 & sel) dark gray
> surface style #2 mesh
> surface style #2 solid
> transparency (#!2 & sel) 50
> select clear
> select #2/E:390
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/E:390-399
69 atoms, 68 bonds, 10 residues, 1 model selected
> color (#!2 & sel) medium blue
> select clear
> select #1.2/B:157
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
93 atoms, 96 bonds, 11 residues, 1 model selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> show sel surfaces
> select clear
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_surface.jpg" width 1290
> height 802 supersample 3
> select #1.2/B:83@NE2
1 atom, 1 residue, 1 model selected
> select clear
> select #1.2/B:88@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
48 atoms, 47 bonds, 6 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> hide sel surfaces
> select clear
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_surface2.jpg" width 1290
> height 802 supersample 3
> turn y
> turn y
> turn y
> turn y
> turn y
> turn y
> turn y
> turn y
> turn x
> turn x
> turn x
> turn x
> turn y 45
> select #1.2/B:19
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
44 atoms, 43 bonds, 6 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> hide #!1.2 models
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> show #!1.2 models
> hide #!1.2 models
> turn y 45
> turn y 45
> turn y 45
> show #!1.2 models
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> select clear
> select #1.2/B:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
41 atoms, 42 bonds, 4 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> show sel surfaces
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> undo
> undo
> turn y 45
> select clear
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> hide #1.3-4#!2#!1.1-2 surfaces
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> show #1.3-4#!2#!1.1-2 surfaces
> select #1.4/D:1@N
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
69 atoms, 67 bonds, 10 residues, 2 models selected
> hide sel surfaces
> select #2/E:196@NH1
1 atom, 1 residue, 1 model selected
> select clear
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #1.3/C:3@N
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
69 atoms, 67 bonds, 10 residues, 2 models selected
> hide sel surfaces
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> select clear
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_surface.jpg" width 1292
> height 744 supersample 3
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 45
> turn y 90
> turn y 90
> turn y 90
> turn y 90
> turn y 90
> turn y 90
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_surface180.jpg" width 1292
> height 744 supersample 3
> turn y 90
> turn y 90
> undo
> undo
> turn y 90
> turn y 90
> hide #!1.2 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.4 models
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_surface2.jpg" width 1292
> height 744 supersample 3
> turn y 180
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_surface2-180.jpg" width
> 1292 height 744 supersample 3
> turn y 180
> hide #!2#!1.1,3 surfaces
> turn y 180
> turn y 180
> show #!1.2 models
> turn y 180
> turn y 180
> hide #!2#!1.1-3 surfaces
> show #!1.4 models
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5.jpg" width 1292 height 744
> supersample 3
> turn y 180
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5-180y.jpg" width 1292 height
> 744 supersample 3
> turn y 180
> ui tool show "Show Sequence Viewer"
> setattr /E c chain_id A
Assigning chain_id attribute to 3 items
> setattr /E r chain_id A
Assigning chain_id attribute to 0 items
> setattr /#1A c chain_id E
Expected a keyword
> setattr /#1A c chain_id "E"
Expected a keyword
> setattr #1/A c chain_id E
Assigning chain_id attribute to 1 item
> setattr #1/A r chain_id E
Assigning chain_id attribute to 0 items
> ui tool show "Show Sequence Viewer"
> setattr #1/E c chain_id A
Assigning chain_id attribute to 1 item
> setattr #2/A c chain_id E
Assigning chain_id attribute to 1 item
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2149, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 626, in close_request
tool_instance.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 512, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 725, in remove_tool
tw._destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2189, in destroy
sbar.destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 51, in destroy
v.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 438, in delete
self.make_current()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 99, in make_current
qc = self._initialize_context()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2149, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 626, in close_request
tool_instance.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 512, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 725, in remove_tool
tw._destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2189, in destroy
sbar.destroy()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 51, in destroy
v.delete()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 438, in delete
self.make_current()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 99, in make_current
qc = self._initialize_context()
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
> ui tool show "Show Sequence Viewer"
> open "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/XL_Mpro_nsp711model5_interXL_test.pb"
Opened Pseudobonds XL_Mpro_nsp711model5_interXL_test.pb, 9 bonds
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #!1.1 models
> show #!1.1 models
> open "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/XL_Mpro_nsp711model5_interXLtoA.pb"
Opened Pseudobonds XL_Mpro_nsp711model5_interXLtoA.pb, 9 bonds
> turn y 180
> turn y 180
No model chosen to save relative to
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/MproC145A_nsp711-run3model5_dock_test2.pdb" models #2#1.1-2
> select #2/E:118
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
171 atoms, 171 bonds, 21 residues, 2 models selected
> select up
4166 atoms, 4233 bonds, 548 residues, 2 models selected
> select #1.1/A:19
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #5 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1 models
> show #!1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
No model chosen to save relative to
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/MproC145A_nsp711-run3model5_dock_test3.pdb" models #2#1.1-2
> displayedOnly true serialNumbering amber
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/MproC145A_nsp711-run3model5_dock_test4.pdb" models #2#1.1-2
> serialNumbering amber
> select clear
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/MproC145A_nsp711-run3model5_dock_Aandnsp711.pdb" models #2#1.1
> open "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/XL_Mpro_nsp711model5_interXLtoA_colorDistance.pb"
Opened Pseudobonds XL_Mpro_nsp711model5_interXLtoA_colorDistance.pb, 9 bonds
> turn y 180
> turn y 180
No model chosen to save relative to
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/MproC145A_nsp711-run3model5_dock_Bandnsp711.pdb" models #2#1.2
> open "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/XL_Mpro_nsp711model5_interXLtoB_colorDistance.pb"
Opened Pseudobonds XL_Mpro_nsp711model5_interXLtoB_colorDistance.pb, 9 bonds
> select #1.1/A:233
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
92 atoms, 93 bonds, 11 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light green
> color sel dark sea green
> select #1.2/B:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
48 atoms, 47 bonds, 6 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> color sel pale green
> color sel light green
> color sel moccasin
> color sel navajo white
> color sel peach puff
> color sel pink
> select #1.1/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
92 atoms, 93 bonds, 11 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> color sel lavender blush
> color sel lavender
> color sel plum
> select clear
> hide #6 models
> hide #7 models
> show #!1.3 models
> show #!1.4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/E
Alignment identifier is 2/E
> select #2/E:390-391
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #2/E:390-399
69 atoms, 68 bonds, 10 residues, 1 model selected
> color (#!2 & sel) lime
> color (#!2 & sel) forest green
> select clear
> show #6 models
> hide #6 models
> show #6 models
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_interXLtoA.jpg" width 1292
> height 744 supersample 3
> hide #6 models
> show #7 models
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_interXLtoB.jpg" width 1292
> height 744 supersample 3
> hide #7 models
> select #2/E:129
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/E:123
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
171 atoms, 171 bonds, 21 residues, 2 models selected
> select up
4166 atoms, 4233 bonds, 548 residues, 2 models selected
> show sel surfaces
> select #1.1/A:237
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
92 atoms, 93 bonds, 11 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> show sel surfaces
> transparency (#!1.1 & sel) 50
> select #1.2/B:157
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.2/B:158
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
93 atoms, 96 bonds, 11 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> show sel surfaces
> transparency (#!1.2 & sel) 20
> transparency (#!1.2 & sel) 50
> select clear
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5-colorscheme2.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 1983, in shown
return self.__toolkit.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002029CE753A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000202B76E7CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 1983, in shown
return self.__toolkit.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002029CE753A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000202B76E7CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> turn y 180
> turn y 180
> hide #!2#!1.1-4 surfaces
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> undo
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select clear
> graphics silhouettes false
> select #2/E:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
171 atoms, 171 bonds, 21 residues, 2 models selected
> select up
4166 atoms, 4233 bonds, 548 residues, 2 models selected
> graphics silhouettes true
> select clear
> graphics silhouettes false
> hide #!1 models
> graphics silhouettes true
> show #!1 models
> hide #!1 models
> show #!1 models
> graphics silhouettes false
> select #1.2/B:158
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
93 atoms, 96 bonds, 11 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> ui tool show "Color Actions"
> color sel thistle
> select clear
> select #1.2/B:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
41 atoms, 42 bonds, 4 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> color sel light steel blue
> select clear
> select #2/E:534
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
139 atoms, 140 bonds, 18 residues, 2 models selected
> select up
4166 atoms, 4233 bonds, 548 residues, 2 models selected
> select clear
> select clear
> turn y 180
> turn y 180
> turn y 90
> turn y 90
> turn y 90
> turn y 90
> turn y 90
> turn y 90
> view orient
> turn y 90
> turn y 90
> turn y 90
> turn y 90
> turn y 90
> turn y 90
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5.jpg" width 1294 height 918
> supersample 3
> select #1.1/A:68
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel surfaces
> show sel surfaces
> select clear
> show #!2#!1.1-4 surfaces
> select #1.2/B:242@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
51 atoms, 52 bonds, 6 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> transparency (#!1.2 & sel) 50
> select clear
> hide #!1.2 models
> hide #!1.1 models
> select #1.4/D:4@CG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> show #!1.2 models
> show #!1.1 models
> select clear
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_surface.jpg" width 1294
> height 918 supersample 3
> turn y 90
> turn y 90
> undo
> turn y 90
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_surface180y.jpg" width 1294
> height 918 supersample 3
> turn y 90
> turn y 90
Drag select of model5_updatedSS.pdb_A SES surface, 1106 of 589742 triangles,
Mpro_nsp7-10.pdb A_A SES surface, 619 of 262024 triangles, Mpro_nsp7-10.pdb
C_C SES surface, 230 of 16636 triangles, 22 residues
> select clear
> select #1.2/B:33@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
16 atoms, 15 bonds, 2 residues, 2 models selected
> hide #!1.2 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.4 models
> turn y 90
> turn y 90
Drag select of model5_updatedSS.pdb_A SES surface, 2900 of 589742 triangles,
Mpro_nsp7-10.pdb A_A SES surface, 276 of 262024 triangles, Mpro_nsp7-10.pdb
C_C SES surface, 154 of 16636 triangles, 26 residues
> select clear
> hide #!2#!1.1,3 surfaces
> show #!2#!1.1,3 surfaces
> ui tool show Clashes
Illegal clashes 'color' attribute value (Color([0.6666667, 0.0, 0.0, 1.0])),
leaving attribute unchanged
Illegal clashes 'color' attribute value (Color([0.6666667, 0.0, 0.0, 1.0])),
leaving attribute unchanged
Illegal clashes 'color' attribute value (Color([1.0, 0.33333334, 1.0, 1.0])),
leaving attribute unchanged
Illegal clashes 'color' attribute value (Color([1.0, 0.33333334, 1.0, 1.0])),
leaving attribute unchanged
> hide #!2#!1.1,3 surfaces
> select #2/E:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
129 atoms, 129 bonds, 17 residues, 2 models selected
> select up
4166 atoms, 4233 bonds, 548 residues, 2 models selected
> show sel atoms
> select #1.1/A:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
48 atoms, 47 bonds, 6 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> show sel atoms
> select clear
> turn y 90
> turn y 90
> show #!1.2 models
> hide #!1.2 models
> style #!2#!1.1,3 stick
Changed 6601 atom styles
> style #!2#!1.1,3 sphere
Changed 6601 atom styles
> style #!2#!1.1,3 ball
Changed 6601 atom styles
> turn y 90
> turn y 90
> style #!2#!1.1,3 sphere
Changed 6601 atom styles
> select #1.1/A:292@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
133 atoms, 133 bonds, 18 residues, 2 models selected
> select up
2366 atoms, 2419 bonds, 306 residues, 2 models selected
> hide sel atoms
> select clear
> turn y 90
> turn y 90
> hide #!2#!1.1,3 atoms
> show #!1.2 models
> hide #!2#!1.1-3 surfaces
> show #!1.4 models
> hide #!2#!1.1-4 surfaces
> turn y 180
> select clear
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_180y.jpg" width 1294 height
> 918 supersample 3
> show #6 models
> hide #6 models
> turn y 180
> show #6 models
> turn y 180
> turn y 180
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_interXLtoA.jpg" width 1294
> height 918 supersample 3
> hide #6 models
> show #7 models
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5_interXLtoB.jpg" width 1294
> height 918 supersample 3
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 1983, in shown
return self.__toolkit.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002029CE753A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000202B76E7CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 1983, in shown
return self.__toolkit.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002029CE753A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000202B76E7CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 1983, in shown
return self.__toolkit.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002029CE753A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000202B76E7CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 1983, in shown
return self.__toolkit.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002029CE753A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000202B76E7CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/MproC145A_nsp711-run3model5_dock.pdb" models #1-2
No map chosen to save
> save "C:/Users/vcouroub/Dropbox (Scripps
> Research)/Collaborations/COVID-19/Eddy Arnold/Mpro Polyprotein
> Structure/Mpronsp710-Cryo_dockednsp711run3model5.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 1983, in shown
return self.__toolkit.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002029CE753A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000202B76E7CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 1983, in shown
return self.__toolkit.shown
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002029CE753A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x00000202B76E7CD0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002029CE753A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x00000202B76E7CD0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.13507 Core Profile Forward-Compatible Context 23.20.15032.11
OpenGL renderer: AMD Radeon RX 550
OpenGL vendor: ATI Technologies Inc.
Manufacturer: Dell Inc.
Model: OptiPlex 3050
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 34,237,292,544
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
MolecularDynamicsViewer: 1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
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
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
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
Send2Trash: 1.7.1
SEQCROW: 1.1
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → wrapped C/C++ object of type QScreen has been deleted |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Fixed several months ago, soon after 1.2.5 release.