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Opened 3 years ago
Last modified 3 years ago
#8544 assigned defect
ISOLDE: after session restore 'mgr' is None
| Reported by: | 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:
alabaster: 0.7.12
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
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
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
ChimeraX-ToolshedUtils: 1.2.1
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
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.3.1
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (3)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE: after session restore 'mgr' is None |
comment:2 by , 3 years ago
comment:3 by , 3 years ago
You may have to wait until someone provides a relevant session in order to track this down.
Note:
See TracTickets
for help on using tickets.
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/molarrayframework. The change tracker creates a nested {class name: {pointer:changes} }, and the_process_changesmethod usesc_ptr_to_existing_py_instto find the matching Python objects. So the only ways I can see thatmgrcould beNoneis (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.