pseudobond manager group_map property error when resetting session

[p.albanese@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Cant open this session anymore (always been there in the same folder)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> C:/Users/pasca/Desktop/Current_projects/__PsbS/PsbS_FreeLHCII_docking/S_interface_internal.cxs

Log from Tue Jul 7 17:04:30 2020UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\Users\pasca\Desktop\Current_projects\\__PsbS\ConSurf_pocket\Strim_ConSurfl.pdb
> format pdb

Summary of feedback from opening
C:\Users\pasca\Desktop\Current_projects\\__PsbS\ConSurf_pocket\Strim_ConSurfl.pdb  
---  
warnings | Ignored bad PDB record found on line 511  
END  
  
Ignored bad PDB record found on line 514  
END  
  
Ignored bad PDB record found on line 517  
END  
  
Ignored bad PDB record found on line 2284  
END  
  
Ignored bad PDB record found on line 4051  
END  
  
1 messages similar to the above omitted  
  
Chain information for Strim_ConSurfl.pdb  
---  
Chain | Description  
1.1/O 1.2/O | No description available  
1.3/X | No description available  
  

> open
> C:\Users\pasca\Desktop\Current_projects\\__PsbS\ConSurf_pocket\Strim_5xnl.pdb
> format pdb

Summary of feedback from opening
C:\Users\pasca\Desktop\Current_projects\\__PsbS\ConSurf_pocket\Strim_5xnl.pdb  
---  
warnings | Ignored bad PDB record found on line 511  
END  
  
Ignored bad PDB record found on line 514  
END  
  
Ignored bad PDB record found on line 517  
END  
  
Ignored bad PDB record found on line 520  
END  
  
Ignored bad PDB record found on line 523  
END  
  
2 messages similar to the above omitted  
  
Chain information for Strim_5xnl.pdb #2  
---  
Chain | Description  
g n y | No description available  
  

> select #2:CHL,CLA,

Expected an objects specifier or a keyword  

> select #2:CHL,CLA

2502 atoms, 2670 bonds, 168 pseudobonds, 2 models selected  

> lighting soft

> graphics silhouettes true

> select #2:CHL,CLA,LUT,XAT,NEX,BCR

3018 atoms, 3207 bonds, 168 pseudobonds, 2 models selected  

> select ~sel

10511 atoms, 10749 bonds, 42 pseudobonds, 6 models selected  

> hide sel cartoons

> select clear

> select #2:CHL,CLA

2502 atoms, 2670 bonds, 168 pseudobonds, 2 models selected  

> color sel green

> select #2:LUT,XAT,NEX,BCR

516 atoms, 537 bonds, 1 model selected  

> color sel orange

> select clear

> select #2

8243 atoms, 8511 bonds, 210 pseudobonds, 2 models selected  

> hide sel atoms

> select #2:CHL,CLA,LUT,XAT,NEX,BCR

3018 atoms, 3207 bonds, 168 pseudobonds, 2 models selected  

> show sel atoms

> select clear

> save C:\Users\pasca\Desktop\image13.png supersample 3

> select #1

5286 atoms, 5445 bonds, 4 models selected  

> show sel cartoons

> ui mousemode right "rotate selected models"

> matchmaker #1.2 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Strim_5xnl.pdb, chain g (#2) with Strim_ConSurfl.pdb, chain O
(#1.2), sequence alignment score = 1115.6  
RMSD between 217 pruned atom pairs is 0.435 angstroms; (across all 219 pairs:
0.528)  
  

> matchmaker #1.1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Strim_5xnl.pdb, chain g (#2) with Strim_ConSurfl.pdb, chain O
(#1.1), sequence alignment score = 1115.6  
RMSD between 217 pruned atom pairs is 0.434 angstroms; (across all 219 pairs:
0.528)  
  

> matchmaker #1.1 to #2/n

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 Strim_5xnl.pdb, chain n (#2) with Strim_ConSurfl.pdb, chain O
(#1.1), sequence alignment score = 1112  
RMSD between 217 pruned atom pairs is 0.432 angstroms; (across all 219 pairs:
0.531)  
  

> matchmaker #1.3 to #2/y

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 Strim_5xnl.pdb, chain y (#2) with Strim_ConSurfl.pdb, chain X
(#1.3), sequence alignment score = 995.1  
RMSD between 217 pruned atom pairs is 0.495 angstroms; (across all 219 pairs:
0.615)  
  

> open C:/Users/pasca/Desktop/utils/Chimera_Scripts/script_ConSurf.py

executed script_ConSurf.py  

> show sel atoms

> style sel sphere

Changed 5286 atom styles  

> select clear

> show surfaces

> transparency #1 60

> transparency #1 90

> hide surfaces

> show surfaces

> hide atoms

> show atoms

> style sphere

Changed 13529 atom styles  

> select #1

5286 atoms, 5445 bonds, 4 models selected  

> hide sel atoms

> select clear

> select #2

8243 atoms, 8511 bonds, 210 pseudobonds, 2 models selected  

> hide sel surfaces

> select clear

> select #1

5286 atoms, 5445 bonds, 4 models selected  

> hide sel atoms

> hide sel atoms

> select clear

> select #2

8243 atoms, 8511 bonds, 210 pseudobonds, 2 models selected  

> hide sel atoms

> hide sel surfaces

> select #1

5286 atoms, 5445 bonds, 4 models selected  

> hide sel surfaces

> select clear

> undo

> undo

> undo

> show sel atoms

> select #2:CHL,CLA,LUT,XAT,NEX,BCR

3018 atoms, 3207 bonds, 168 pseudobonds, 2 models selected  

> show sel atoms

> select clear

Drag select of 295 atoms, 47 residues, 10 pseudobonds, 161 bonds  
Drag select of 4 atoms, 7 residues  

> select clear

> set bgColor white

> lighting soft

> graphics silhouettes false

> style ball

Changed 13529 atom styles  

> undo

> select #1

5286 atoms, 5445 bonds, 4 models selected  

> style sel ball

Changed 5286 atom styles  

> style sel sphere

Changed 5286 atom styles  

> select clear

Drag select of 1 residues  

> select #1.1

1764 atoms, 1816 bonds, 1 model selected  

> hide #!1.2 models

> hide #!1.3 models

Drag select of 661 atoms, 41 pseudobonds, 710 bonds  

> select up

2445 atoms, 2531 bonds, 41 pseudobonds, 4 models selected  

> select up

2748 atoms, 2860 bonds, 41 pseudobonds, 4 models selected  

> select up

7263 atoms, 7489 bonds, 41 pseudobonds, 4 models selected  

> select down

2748 atoms, 2860 bonds, 41 pseudobonds, 6 models selected  

> select clear

Drag select of 328 atoms, 19 pseudobonds, 350 bonds  

> select up

346 atoms, 353 bonds, 19 pseudobonds, 2 models selected  

> select up

613 atoms, 654 bonds, 19 pseudobonds, 2 models selected  

> select up

5499 atoms, 5673 bonds, 19 pseudobonds, 2 models selected  

> hide sel atoms

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> save C:\Users\pasca\Desktop\image14.png supersample 3

> show #!1.2 models

> show #!1.3 models

> interfaces sel & ~solvent

1 buried areas: y g 1832  

> undo

> undo

> select #1

5286 atoms, 5445 bonds, 4 models selected  

> interfaces sel & #!1.1 & ~solvent

0 buried areas:  

> select #2

8243 atoms, 8511 bonds, 210 pseudobonds, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #2:CHL,CLA,LUT,XAT,NEX,BCR

3018 atoms, 3207 bonds, 168 pseudobonds, 2 models selected  

> show sel atoms

> style sel stick

Changed 3018 atom styles  

> select #2:CHL,CLA,

Expected an objects specifier or a keyword  

> select #2:CHL,CLA

2502 atoms, 2670 bonds, 168 pseudobonds, 2 models selected  

> color sel green

> select #2:LUT,XAT,NEX,BCR

516 atoms, 537 bonds, 1 model selected  

> color sel orange

> select clear

> select #1

5286 atoms, 5445 bonds, 4 models selected  

> interfaces sel & #!1.1 & ~solvent

0 buried areas:  

> interfaces sel & #!1.1 & ~solvent

0 buried areas:  

> show #!1.2 models

> show #!1.3 models

> interfaces sel & ~solvent

3 buried areas: #1.1/O #1.3/X 923, #1.1/O #1.2/O 843, #1.2/O #1.3/X 834  

> hide sel atoms

> select #2

8243 atoms, 8511 bonds, 210 pseudobonds, 2 models selected  

> hide #!2 models

> select clear

> save C:\Users\pasca\Desktop\image15.png supersample 3

> save C:\Users\pasca\Desktop\image16.png supersample 3

> save
> C:\Users\pasca\Desktop\Current_projects\\__PsbS\ConSurf_pocket\Strim_2to1_interface.pdb
> selectedOnly true

> save
> C:\Users\pasca\Desktop\Current_projects\\__PsbS\ConSurf_pocket\Strim_2to1_interface.png

> select #1.1

1764 atoms, 1816 bonds, 1 model selected  

> show sel atoms

> hide sel atoms

> select clear

> select #1.2/O:87

11 atoms, 10 bonds, 1 model selected  

> select up

273 atoms, 279 bonds, 2 models selected  

> select up

1764 atoms, 1816 bonds, 2 models selected  

> show sel atoms

> show sel atoms

> style sel sphere

Changed 1764 atom styles  

> select clear

> save
> C:\Users\pasca\Desktop\Current_projects\\__PsbS\ConSurf_pocket\Strim_1to1&2_interface.png

> save
> C:\Users\pasca\Desktop\Current_projects\\__PsbS\ConSurf_pocket\Strim_1to1&2_interface2.png

> save
> C:\Users\pasca\Desktop\Current_projects\\__PsbS\ConSurf_pocket\Strim_1to1&2_interface.pdb
> selectedOnly true

> close #2

> select #1

5286 atoms, 5445 bonds, 4 models selected  

> show sel cartoons

> open
> C:/Users/pasca/Desktop/Current_projects/__PsbS/PDB/PsbS_Haddock_dimer.pdb

Summary of feedback from opening
C:/Users/pasca/Desktop/Current_projects/__PsbS/PDB/PsbS_Haddock_dimer.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_47w.pdb0"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_47.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
30 messages similar to the above omitted  
  
Chain information for PsbS_Haddock_dimer.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open
> C:/Users/pasca/Desktop/Current_projects/__PsbS/PsbS_FreeLHCII_docking/L_trim.pb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 382, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.0\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 1.0\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 52, in read_pseudobond_file  
% (i, len(a), aspec))  
File "<string>", line None  
SyntaxError: Line 0, got 0 atoms for spec "#1.2/s:22@CA", require exactly 1  
  
File "", line None  
SyntaxError: Line 0, got 0 atoms for spec "#1.2/s:22@CA", require exactly 1  
  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 52, in read_pseudobond_file  
% (i, len(a), aspec))  
  
See log for complete Python traceback.  
  

> open
> C:/Users/pasca/Desktop/Current_projects/__PsbS/ConSurf_pocket/Strim_ConSurfl.pdb

Summary of feedback from opening
C:/Users/pasca/Desktop/Current_projects/__PsbS/ConSurf_pocket/Strim_ConSurfl.pdb  
---  
warnings | Ignored bad PDB record found on line 511  
END  
  
Ignored bad PDB record found on line 514  
END  
  
Ignored bad PDB record found on line 517  
END  
  
Ignored bad PDB record found on line 2284  
END  
  
Ignored bad PDB record found on line 4051  
END  
  
1 messages similar to the above omitted  
  
Chain information for Strim_ConSurfl.pdb  
---  
Chain | Description  
3.1/O 3.2/O | No description available  
3.3/X | No description available  
  
Drag select of 111 residues  

> close #3

> close #2

> save
> C:/Users/pasca/Desktop/Current_projects/__PsbS/PsbS_FreeLHCII_docking/S_interface_internal.cxs

opened ChimeraX session  

> open
> C:/Users/pasca/Desktop/Current_projects/__PsbS/ConSurf_pocket/Consurf_pocket_M.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\session.py", line 656, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\session.py", line 495, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 599, in reset_state  
for pbg in list(self.group_map.values()):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 65, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 451.22
OpenGL renderer: Quadro T1000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 20QTCTO1WW
OS: Microsoft Windows 10 Home (Build 18363)
Memory: 34,081,447,936
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Eric Pettersen]

Hi Pascal,

Thanks for reporting this problem. Does the C:/Users/pasca/Desktop/Current_projects/__PsbS/ConSurf_pocket/Consurf_pocket_M.cxs session restore when you try in a newly started ChimeraX?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[p.albanese@…]

Hi Eric, 

Thanks for taking care of this. It actually happens when I open the session on a different PC, but I thought all the files should be embedded in the session file, or some of them (i.e. .pb files) are linked and should be moved along?

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Monday, July 20, 2020 6:06 PM
Cc: Albanese, P. (Pascal) <p.albanese@uu.nl>; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #3527: pseudobond manager group_map property error when resetting session

#3527: pseudobond manager group_map property error when resetting session
-----------------------------------+----------------------------
          Reporter:  p.albanese@…  |      Owner:  Eric Pettersen
              Type:  defect        |     Status:  feedback
          Priority:  normal        |  Milestone:
         Component:  Sessions      |    Version:
        Resolution:                |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback


Comment:

 Hi Pascal,
         Thanks for reporting this problem.  Does the  C:/Users/pasca/Desktop/Current_projects/__PsbS/ConSurf_pocket/Consurf_pocket_M.cxs
 session restore when you try in a newly started ChimeraX?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3527#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Hi Pascal,

This would be way easier for me to debug if I had the actual session file to work with. You could send it directly to me (pett@…) if you don't want to have it attached to this ticket.

--Eric