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#10122 closed defect (fixed)

CheckWaterViewer holding reference to dead Residue

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
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:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:\下载\5a07.pdb format pdb

5a07.pdb title:  
X-ray structure of the mannosyltransferase KTR4P from S. Cerevisiae In complex
with GDP [more info...]  
  
Chain information for 5a07.pdb #1  
---  
Chain | Description | UniProt  
A B | KTR4P | KTR4_YEAST 33-464  
  
Non-standard residues in 5a07.pdb #1  
---  
ACT — acetate ion  
GDP — guanosine-5&#x27;-diphosphate  
MN — manganese (II) ion  
  

> select /A:70-464

3307 atoms, 3408 bonds, 395 residues, 1 model selected  

> select /A:70-464

3307 atoms, 3408 bonds, 395 residues, 1 model selected  

> select /A:70-464

3307 atoms, 3408 bonds, 395 residues, 1 model selected  

> ui tool show "Check Waters"

> hbonds /A:2001-2300/B:2001-2278 interModel false reveal true restrict any
> name "water H-bonds"

742 hydrogen bonds found  

> select /A:2001-2300/B:2001-2278

578 atoms, 578 residues, 1 model selected  

> display /A:2001-2300/B:2001-2278 :<4

> view /A:2001-2300/B:2001-2278 @<4

> select /B:2205

1 atom, 1 residue, 1 model selected  

> display /B:2205 :<4

> view /B:2205 @<4

> select /A:2001-2300/B:2001-2278

578 atoms, 578 residues, 1 model selected  

> display /A:2001-2300/B:2001-2278 :<4

> view /A:2001-2300/B:2001-2278 @<4

> ~select

Nothing selected  

> select /A:70-464

3307 atoms, 3408 bonds, 395 residues, 1 model selected  

> select /A:70-464

3307 atoms, 3408 bonds, 395 residues, 1 model selected  

> select /A:70-464

3307 atoms, 3408 bonds, 395 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

Alignment identifier is 1/B  

> select /B:463

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:462-463

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B:320-321

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select /B:320-326

55 atoms, 57 bonds, 7 residues, 1 model selected  

> select
> /B:72-84,94-111,142-164,177-187,200-204,211-225,232-253,274-282,295-299,301-317,322-328,332-339,356-380,383-399,439-445,447-462

1844 atoms, 1878 bonds, 218 residues, 1 model selected  

> select /B:297

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /B:297-300

33 atoms, 32 bonds, 4 residues, 1 model selected  

> select add #1

3365 atoms, 3466 bonds, 6 pseudobonds, 400 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select :ACT

8 atoms, 6 bonds, 2 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select :GDP

56 atoms, 60 bonds, 2 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select :MN

2 atoms, 2 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save D:/下载/5a07.cxs

Traceback (most recent call last):  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 624, in take_snapshot  
data = {'structure': self.structure,  
File "atomic_cpp\cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__  
RuntimeError: Residue already deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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 0x0000019C9A282C40> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x0000019CB90AF7C0> ->
<chimerax.atomic.molobject.Residue object at 0x0000019CB8C35AC0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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
0x0000019C9A282C40> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x0000019CB90AF7C0> -> <chimerax.atomic.molobject.Residue object at
0x0000019CB8C35AC0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000019C9A282C40> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x0000019CB90AF7C0> ->
<chimerax.atomic.molobject.Residue object at 0x0000019CB8C35AC0>  
  
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->  
  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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 "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 624, in take_snapshot  
data = {'structure': self.structure,  
File "atomic_cpp\cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__  
RuntimeError: Residue already deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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 0x0000019C9A282C40> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x0000019CB90AF7C0> ->
<chimerax.atomic.molobject.Residue object at 0x0000019CB8C35AC0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\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 "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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
0x0000019C9A282C40> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x0000019CB90AF7C0> -> <chimerax.atomic.molobject.Residue object at
0x0000019CB8C35AC0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000019C9A282C40> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x0000019CB90AF7C0> ->
<chimerax.atomic.molobject.Residue object at 0x0000019CB8C35AC0>  
  
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->  
  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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 D:/下载/ddd.cxs

Traceback (most recent call last):  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 624, in take_snapshot  
data = {'structure': self.structure,  
File "atomic_cpp\cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__  
RuntimeError: Residue already deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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 0x0000019C9A282C40> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x0000019CB90AF7C0> ->
<chimerax.atomic.molobject.Residue object at 0x0000019CB8C35AC0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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
0x0000019C9A282C40> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x0000019CB90AF7C0> -> <chimerax.atomic.molobject.Residue object at
0x0000019CB8C35AC0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000019C9A282C40> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x0000019CB90AF7C0> ->
<chimerax.atomic.molobject.Residue object at 0x0000019CB8C35AC0>  
  
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->  
  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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 "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 624, in take_snapshot  
data = {'structure': self.structure,  
File "atomic_cpp\cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__  
RuntimeError: Residue already deleted  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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 0x0000019C9A282C40> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x0000019CB90AF7C0> ->
<chimerax.atomic.molobject.Residue object at 0x0000019CB8C35AC0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\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 "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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
0x0000019C9A282C40> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x0000019CB90AF7C0> -> <chimerax.atomic.molobject.Residue object at
0x0000019CB8C35AC0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x0000019C9A282C40> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x0000019CB90AF7C0> ->
<chimerax.atomic.molobject.Residue object at 0x0000019CB8C35AC0>  
  
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->  
  
File "D:\下载\wechat\WeChat
Files\wxid_gf8ayzt8g6pd21\FileStorage\File\2023-10\ChimeraX\ChimeraX\bin\lib\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 - Build 31.0.101.4502
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 83AL
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 16,891,371,520
MaxProcessMemory: 137,438,953,344
CPU: 16 13th Gen Intel(R) Core(TM) i5-13500H
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component:	Unassigned → Sessions
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → CheckWaterViewer holding reference to dead Residue

comment:2 by Eric Pettersen, 2 years ago

Resolution:	→ fixed
Status:	accepted → closed

Fixed in develop and release candidate

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