Opened 3 years ago

Last modified 3 years ago

#8544 assigned defect

ISOLDE: after session restore 'mgr' is None

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs

Opened P21_J80_009_volume_map_deepEMhanced-highRes.mrc as #1.1.1.1, grid size
384,384,384, pixel 0.835, shown at level 0.0292, step 1, values float32  
Opened P21_J80_009_volume_map_deepEMhanced.mrc as #3, grid size 384,384,384,
pixel 0.835, shown at level 0.0514, step 1, values float32  
Restoring stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb  
Log from Tue Feb 21 19:02:33 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/ts387/Documents/Work/Modelling/LTAg_ADP-CGfork/LTAg_ADP-
> CGfork_ISOLDE-3.cxs

Opened P21_J80_009_volume_map_deepEMhanced-highRes.mrc as #1.1.1.1, grid size
384,384,384, pixel 0.835, shown at level 0.0128, step 1, values float32  
Opened P21_J80_009_volume_map_deepEMhanced.mrc as #3, grid size 384,384,384,
pixel 0.835, shown at level 0.0674, step 1, values float32  
Restoring stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb  
Log from Mon Feb 20 20:35:10 2023

> ui tool show "Hide Dust"

UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde start

> set selectionWidth 4

Populating font family aliases took 329 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

> open /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/ISOLDE-2_Rsr/LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb format pdb

Chain information for LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb #1  
---  
Chain | Description  
A D | No description available  
B C E F | No description available  
M | No description available  
  

> style stick

Changed 36010 atom styles  

> color bychain

> color byhetero

> hide atoms

> show cartoons

> select ::name="ADP"

234 atoms, 246 bonds, 6 residues, 1 model selected  

> show sel target ab

> open /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/P21_J80_009_volume_map_deepEMhanced-highRes.mrc format mrc

Opened P21_J80_009_volume_map_deepEMhanced-highRes.mrc as #2, grid size
384,384,384, pixel 0.835, shown at level 0.00113, step 2, values float32  

> surface dust #2 size 10.02

> color #2 #b2b2b23d models

> color #2 #b2b2b240 models

> volume #2 level 0.03954

> volume #2 level 0.05235

> volume #2 step 1

> volume #2 level 0.06303

> volume #2 style mesh

> volume #2 color #b2b2b2

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb  
---  
Chain | Description  
1.2/A 1.2/D | No description available  
1.2/B 1.2/C 1.2/E 1.2/F | No description available  
1.2/M | No description available  
  

> clipper associate #2 toModel #1

Opened P21_J80_009_volume_map_deepEMhanced-highRes.mrc as #1.1.1.1, grid size
384,384,384, pixel 0.835, shown at step 1, values float32  
Loading residue template for ADP from internal database  

> save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true

> ui tool show "Ramachandran Plot"

> isolde restrain ligands #1

> save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true

> view #1.2/B:431

> volume #1.1.1.1 level 0.05647

> volume #1.1.1.1 level 0.0151

> view #1.2/A:431

> view #1.2/F:431

> save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true

> select #1

36010 atoms, 36389 bonds, 2187 residues, 15 models selected  

> open /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/ModelAngelo/deepEMhanced-highRes/model.cif

Summary of feedback from opening
/Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
CGfork/ModelAngelo/deepEMhanced-highRes/model.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model.cif #2  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
  

> select add #1

36010 atoms, 36389 bonds, 2187 residues, 15 models selected  

> select add #1

36010 atoms, 36389 bonds, 2187 residues, 15 models selected  

> select clear

> select add #2

14777 atoms, 15066 bonds, 14 pseudobonds, 1820 residues, 2 models selected  

> style sel stick

Changed 14777 atom styles  

> color sel bychain

> color sel byhetero

> select subtract #2

Nothing selected  

> open /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/P21_J80_009_volume_map_deepEMhanced.mrc

Opened P21_J80_009_volume_map_deepEMhanced.mrc as #3, grid size 384,384,384,
pixel 0.835, shown at level 9.44e-05, step 2, values float32  

> surface dust #3 size 5.01

> volume #3 level 0.03222

> hide #!2 models

> show #!3 models

> volume #3 level 0.03936

> volume #3 step 1

> volume #3 color #ffffb245

> volume #3 color #ffffb240

> volume #3 level 0.07938

> volume #3 level 0.04736

> volume #3 style mesh

> volume #3 color #ffffb2

> hide #!3 models

> save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true

> select #1

36010 atoms, 36389 bonds, 2187 residues, 15 models selected  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim pause

> isolde sim resume

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> isolde sim pause

> isolde sim resume

> select clear

[Repeated 1 time(s)]

> isolde sim pause

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 11 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> hide #!2 models

> save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true

Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb  

> show #!2 models

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> hide #!2 models

> show #!2 models

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #1.1.1.1 level 0.02228

> volume #3 level 0.02735

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #3 level 0.03535

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> volume #3 level 0.03936

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true

Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #1.1.1.1 level 0.002486

> hide #!2 models

> volume #3 level 0.02735

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #3 level 0.007337

> volume #1.1.1.1 level 0.009084

> select clear

> isolde sim start sel

ISOLDE: started sim  

> show #!2 models

> volume #1.1.1.1 level 0.009084

> hide #!2 models

> volume #1.1.1.1 level 0.05527

> volume #3 level 0.06737

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level -0.0008131

> volume #1.1.1.1 level 0.04208

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.01285

> hide #!2 models

> isolde sim start sel

ISOLDE: started sim  

> show #!2 models

> hide #!2 models

> show #!2 models

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true

Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb  

> save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP-
> CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true

Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb  

——— End of log from Mon Feb 20 20:35:10 2023 ———

opened ChimeraX session  

> isolde start

> set selectionWidth 4

Populating font family aliases took 273 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

> ui tool show "Ramachandran Plot"

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

Loading residue template for ADP from internal database  
ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.06233

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> hide #!2 models

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.02274

> volume #1.1.1.1 level 0.1052

> select clear

[Repeated 3 time(s)]

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/ts387/Documents/Work/Modelling/LTAg_ADP-CGfork/LTAg_ADP-
> CGfork_ISOLDE-3.cxs includeMaps true

Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb  

> open /Users/ts387/Documents/Work/Modelling/LTAg_ADP-
> CGfork/ModelAngelo/deepEMhanced/model.cif

Summary of feedback from opening
/Users/ts387/Documents/Work/Modelling/LTAg_ADP-
CGfork/ModelAngelo/deepEMhanced/model.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for model.cif #4  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
  

> select clear

> select add #4

14434 atoms, 14710 bonds, 18 pseudobonds, 1779 residues, 2 models selected  

> style sel stick

Changed 14434 atom styles  

> color sel bychain

> color sel byhetero

> select subtract #4

Nothing selected  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> show #!2 models

> show #!4 models

> hide #!4 models

> hide #!2 models

> select clear

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.06563

> select clear

> volume #1.1.1.1 level 0.02274

> volume #1.1.1.1 level 0.02604

> volume #1.1.1.1 level 0.04584

> isolde sim pause

> isolde sim resume

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!4 models

> select clear

> hide #!4 models

> volume #1.1.1.1 level 0.01944

> volume #3 level 0.03535

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> show #!2 models

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> show #!4 models

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 2 time(s)]

> hide #!4 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> volume #1.1.1.1 level 0.09937

> volume #1.1.1.1 level 0.05633

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> show #!2 models

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> hide #!2 models

> show #!4 models

> hide #!4 models

> isolde sim start sel

ISOLDE: started sim  

> select clear

> volume #1.1.1.1 level 0.02252

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> show #!2 models

> select clear

> isolde sim pause

> isolde sim resume

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> show #!4 models

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> hide #!4 models

> hide #!2 models

> isolde sim start sel

ISOLDE: started sim  

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!4 models

> hide #!4 models

> hide #!2 models

> show #!2 models

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> hide #!2 models

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> show #!2 models

> isolde sim start sel

ISOLDE: started sim  

> show #!4 models

> hide #!4 models

> hide #!2 models

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #1.1.1.1 level 0.07785

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> show #!2 models

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.01022

> volume #3 level 0.1154

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> volume #3 level 0.05136

> volume #1.1.1.1 level 0.05941

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.02924

> isolde sim start sel

ISOLDE: started sim  

> hide #!2 models

> show #!2 models

> show #!4 models

> hide #!4 models

> hide #!2 models

> show #!2 models

> show #!4 models

> hide #!4 models

> hide #!2 models

> show #!2 models

> show #!4 models

> hide #!4 models

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/ts387/Documents/Work/Modelling/LTAg_ADP-CGfork/LTAg_ADP-
> CGfork_ISOLDE-3.cxs includeMaps true

Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> hide #!2 models

> isolde sim start sel

ISOLDE: started sim  

> select clear

> show #!2 models

> show #!4 models

> hide #!4 models

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save /Users/ts387/Documents/Work/Modelling/LTAg_ADP-CGfork/LTAg_ADP-
> CGfork_ISOLDE-3.cxs includeMaps true

Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb  

——— End of log from Tue Feb 21 19:02:33 2023 ———

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1790, in _get_and_process_changes  
return self._process_changes(changes)  
File "/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1778, in _process_changes  
mgr.triggers.activate_trigger('changes', (mgr, processed_changeds))  
AttributeError: 'NoneType' object has no attribute 'triggers'  
  
Error processing trigger "new frame":  
AttributeError: 'NoneType' object has no attribute 'triggers'  
  
File "/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 1778, in _process_changes  
mgr.triggers.activate_trigger('changes', (mgr, processed_changeds))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/clipper/symmetry.py", line 1252, in _set_default_cartoon_cb  
set_to_default_cartoon(self.session, model = self.structure)  
File "/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/clipper/util.py", line 80, in set_to_default_cartoon  
cartoon.cartoon(session, atoms = atoms, suppress_backbone_display=False)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/cartoon.py", line 70, in cartoon  
residues = all_residues(session)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2389, in all_residues  
structures = all_structures(session, atomic_only=atomic_only)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2365, in all_structures  
return Structures([m for m in session.models.list() if
isinstance(m,class_obj)])  
AttributeError: 'NoneType' object has no attribute 'models'  
  
Error processing trigger "frame drawn":  
AttributeError: 'NoneType' object has no attribute 'models'  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2365, in all_structures  
return Structures([m for m in session.models.list() if
isinstance(m,class_obj)])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/clipper/symmetry.py", line 1905, in rebuild  
_copy_ribbon_drawing(self.master_ribbon, self, self.dim_factor)  
File "/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/clipper/symmetry.py", line 1883, in master_ribbon  
return self.structure._ribbons_drawing  
AttributeError: 'NoneType' object has no attribute '_ribbons_drawing'  
  
Error processing trigger "frame drawn":  
AttributeError: 'NoneType' object has no attribute '_ribbons_drawing'  
  
File "/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/clipper/symmetry.py", line 1883, in master_ribbon  
return self.structure._ribbons_drawing  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 555 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 499.40.2.0.0
      OS Loader Version: 564.40.4~66
      SMC Version (system): 2.45f5

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 4 days, 18 hours, 2 minutes

Graphics/Displays:

    Intel HD Graphics 630:

      Chipset Model: Intel HD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591b
      Revision ID: 0x0004
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Support: Metal 3

    Radeon Pro 555:

      Chipset Model: Radeon Pro 555
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c7
      ROM Revision: 113-C980AJ-927
      VBIOS Version: 113-C9801AP-A02
      EFI Driver Version: 01.A0.927
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-ISOLDE: 1.5
    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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
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    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
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    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
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    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
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    cxservices: 1.2
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    Cython: 0.29.32
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    executing: 1.2.0
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    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
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    PyQt6-sip: 13.4.0
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    RandomWords: 0.4.0
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Change History (3)

comment:1 by pett, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: after session restore 'mgr' is None

comment:2 by Tristan Croll, 3 years ago

Now that's an interesting one I've never seen before. Can't reproduce it so far, and I'm struggling to explain how it could come about. The objects managed here (ISOLDE's restraints and their visualisations) are modelled heavily on the ChimeraX molobject/molarray framework. The change tracker creates a nested {class name: {pointer:changes} }, and the _process_changes method uses c_ptr_to_existing_py_inst to find the matching Python objects. So the only ways I can see that mgr could be None is (a) if the pointer is zero (impossible, as far as I can tell), (b) the C++ code is registering changes before the Python object has been instantiated, or (c) the C++ object is somehow hanging around (and registering changes) after the Python object has been deleted, or (d) changes have been made *and* the Python object deleted in the same GUI update. The band-aid approach would be to just add:

if mgr is None:
    continue

... but I feel like I'm missing something deeper here.

comment:3 by pett, 3 years ago

You may have to wait until someone provides a relevant session in order to track this down.

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