Session save: No bundle information for chimerax.atomic.molobject.PseudobondManager

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.9 (2019-02-08)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-02-08)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\Andrew\\\Desktop\\\4ybb (1).cif"

4ybb (1).cif title:  
High-resolution structure of the Escherichia coli ribosome [more info...]  
  
Chain information for 4ybb (1).cif #1  
---  
Chain | Description  
AA BA | 16S rRNA  
AB BB | 30S ribosomal protein S2  
AC BC | 30S ribosomal protein S3  
AD BD | 30S ribosomal protein S4  
AE BE | 30S ribosomal protein S5  
AF BF | 30S ribosomal protein S6  
AG BG | 30S ribosomal protein S7  
AH BH | 30S ribosomal protein S8  
AI BI | 30S ribosomal protein S9  
AJ BJ | 30S ribosomal protein S10  
AK BK | 30S ribosomal protein S11  
AL BL | 30S ribosomal protein S12  
AM BM | 30S ribosomal protein S13  
AN BN | 30S ribosomal protein S14  
AO BO | 30S ribosomal protein S15  
AP BP | 30S ribosomal protein S16  
AQ BQ | 30S ribosomal protein S17  
AR BR | 30S ribosomal protein S18  
AS BS | 30S ribosomal protein S19  
AT BT | 30S ribosomal protein S20  
AU BU | 30S ribosomal protein S21  
C0 D0 | 50S ribosomal protein L30  
C1 D1 | 50S ribosomal protein L32  
C2 D2 | 50S ribosomal protein L33  
C3 D3 | 50S ribosomal protein L34  
C4 D4 | 50S ribosomal protein L35  
C5 D5 | 50S ribosomal protein L36  
CA | 23S rRNA  
CB DB | 5S rRNA  
CC DC | 50S ribosomal protein L2  
CD DD | 50S ribosomal protein L3  
CE DE | 50S ribosomal protein L4  
CF DF | 50S ribosomal protein L5  
CG DG | 50S ribosomal protein L6  
CH DH | 50S ribosomal protein L9  
CJ DJ | 50S ribosomal protein L11  
CK DK | 50S ribosomal protein L13  
CL DL | 50S ribosomal protein L14  
CM DM | 50S ribosomal protein L15  
CN DN | 50S ribosomal protein L16  
CO DO | 50S ribosomal protein L17  
CP DP | 50S ribosomal protein L18  
CQ DQ | 50S ribosomal protein L19  
CR DR | 50S ribosomal protein L20  
CS DS | 50S ribosomal protein L21  
CT DT | 50S ribosomal protein L22  
CU DU | 50S ribosomal protein L23  
CV DV | 50S ribosomal protein L24  
CW DW | 50S ribosomal protein L25  
CX DX | 50S ribosomal protein L27  
CY DY | 50S ribosomal protein L28  
CZ DZ | 50S ribosomal protein L29  
DA | 23S rRNA  
DI | 50S ribosomal protein L10  
  
Non-standard residues in 4ybb (1).cif #1  
---  
1PE — pentaethylene glycol (PEG400)  
3TD —
(1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-
D-ribitol  
4D4 — (2S,3R)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid  
ACY — acetic acid  
D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid  
EDO — 1,2-ethanediol (ethylene glycol)  
GUN — guanine  
MG — magnesium ion  
MPD — (4S)-2-methyl-2,4-pentanediol  
PEG — di(hydroxyethyl)ether  
PG4 — tetraethylene glycol  
PGE — triethylene glycol  
PUT — 1,4-diaminobutane (putrescine)  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)  
ZN — zinc ion  
  
4ybb (1).cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> show selAtoms ribbons

> hide selAtoms surfaces

> hide selAtoms surfaces

> hide selAtoms ribbons

> style selAtoms ball

Changed 294856 atom styles  

> hide selAtoms surfaces

> show selAtoms ribbons

> hide #!1.3 models

> show #!1.2 models

> hide #!1.2 models

> hide #!1.1 models

> ~select #1.2

294856 atoms, 539 bonds, 8767 pseudobonds, 2 models selected  

> ~select #1.1

294856 atoms, 539 bonds, 2 pseudobonds, 1 model selected  

> ~select #1.3

294856 atoms, 539 bonds selected  

> ui mousemode rightMode select

> show selAtoms

> show #1 target m

> view #1 clip false

> ui mousemode rightMode clip

> ui mousemode rightMode clip

> ui mousemode rightMode clip

> ui mousemode rightMode clip

> ui mousemode rightMode clip

> ui mousemode rightMode clip

> ui mousemode rightMode clip

> show selAtoms surfaces

> set bgColor white

> set bgColor gray

> set bgColor black

> lighting simple

> lighting shadows true

> lighting soft

> toolshed show '"Side View"'

> save "C:\\\Users\\\Andrew\\\Desktop\\\image1.png" supersample 3

> save session "C:/Users/Andrew/vestibule trial.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 810, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 573, in file_save_cb  
self.save_dialog.display(self, session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 141, in display  
fmt.save(session, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 40, in save  
return self._save(session, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 93, in _session_save  
run(session, "save session %s" % quote_if_necessary(filename))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2615, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 916, in save_session  
save(session, filename, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 203, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 730, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 497, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 224, in discovery  
uid = _UniqueName.from_obj(self.session, value)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 128, in from_obj  
obj_cls.__module__, obj_cls.__name__))  
RuntimeError: No bundle information for
chimerax.atomic.molobject.PseudobondManager  
  
RuntimeError: No bundle information for
chimerax.atomic.molobject.PseudobondManager  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 128, in from_obj  
obj_cls.__module__, obj_cls.__name__))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 417.71
OpenGL renderer: GeForce GTX 970M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

duplicate of #1698