Opened 2 years ago

Closed 2 years ago

#10113 closed defect (duplicate)

ISOLDE holding ref to deleted structure

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:        Windows-10-10.0.22621
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/yuan/Desktop/cyclic_peptide/postprocess_masked_84.mrc

Opened postprocess_masked_84.mrc as #1, grid size 256,256,256, pixel 0.83,
shown at level 0.0133, step 1, values float32  

> open C:/Users/yuan/Desktop/cyclic_peptide/NEW_c6.pdb

Chain information for NEW_c6.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 123 residues in model #2 to IUPAC-IUB
standards.  
Chain information for NEW_c6.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
2.2/E | No description available  
2.2/F | No description available  
  

> clipper associate #1 toModel #2

Opened postprocess_masked_84.mrc as #2.1.1.1, grid size 256,256,256, pixel
0.83, shown at step 1, values float32  

> select /F

252 atoms, 257 bonds, 14 residues, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  

> volume #2.1.1.1 level 0.01702

> volume #2.1.1.1 style surface

> transparency 50

> set bgColor white

> volume #2.1.1.1 level 0.01325

> volume #2.1.1.1 level 0.0181

> volume #2.1.1.1 level 0.01325

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 8 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> open C:/Users/yuan/Desktop/cyclic_peptide/postprocess_masked_84.mrc

Opened postprocess_masked_84.mrc as #1, grid size 256,256,256, pixel 0.83,
shown at level 0.0133, step 1, values float32  

> volume zone #1 nearAtoms sel range 3 newMap true

Opened postprocess_masked_84.mrc zone as #3, grid size 256,256,256, pixel
0.83, shown at step 1, values float32  

> hide #!2 models

> show #!2 models

> select add #2.2

23283 atoms, 23544 bonds, 2 pseudobonds, 1512 residues, 12 models selected  

> save C:/Users/yuan/Desktop/cyclic_peptide/NEW_c6_isolde.pdb selectedOnly
> true relModel #2

> hide #!2.2 models

> open C:/Users/yuan/Desktop/cyclic_peptide/NEW_c6_isolde.pdb

Chain information for NEW_c6_isolde.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> select add #4

46566 atoms, 47088 bonds, 4 pseudobonds, 3024 residues, 14 models selected  

> hide sel & #!4 atoms

> show sel & #!4 cartoons

> select #4/F

252 atoms, 257 bonds, 14 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 252 atom styles  

> transparency #3.1 50

> surface dust #3 size 5

> volume #3 level 0.01074

> select clear

> hide #!4 cartoons

> show #!2.2 models

> hide #!4 models

> select #2.2/F#4/F

504 atoms, 514 bonds, 28 residues, 2 models selected  

> color (#!2.2 & sel) orange

> select clear

> select #2.2/F:1

21 atoms, 21 bonds, 1 residue, 1 model selected  

> delete atoms (#!2.2 & sel)

> delete bonds (#!2.2 & sel)

> isolde add aa Tyr #2.2/F:1

Please select a single residue!  

> isolde add aa Tyr #2.2/F:1

Please select a single residue!  

> isolde add aa Tyr #2.2/F:1

Please select a single residue!  

> isolde add aa Tyr #2.2/F:2

> 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 #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> delete atoms (#!2.2 & sel)

> delete bonds (#!2.2 & sel)

> 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 3 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select add #2.2

23277 atoms, 23539 bonds, 2 pseudobonds, 1511 residues, 12 models selected  

> hide #!2.2 models

> show #!2.2 models

> select add #2.2

23277 atoms, 23539 bonds, 2 pseudobonds, 1511 residues, 12 models selected  

> select add #2.2

23277 atoms, 23539 bonds, 2 pseudobonds, 1511 residues, 12 models selected  

> close #2.2

Deleting atomic symmetry model...  
Deleting atomic symmetry model...  

> show #!4 models

> hide #!4 models

> select add #2

6 models selected  

> show #!1 models

> hide #!1 models

Deleting atomic symmetry model...  

> close #1

Deleting atomic symmetry model...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #4 to IUPAC-IUB
standards.  
Chain information for NEW_c6_isolde.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  
Deleting atomic symmetry model...  

> show #!1.2 models

> select clear

> select #1/F:1

21 atoms, 21 bonds, 1 residue, 1 model selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> isolde add aa Tyr #1/F:2

> clipper associate #3 toModel #1

Deleting atomic symmetry model...  
Opened postprocess_masked_84.mrc zone as #1.1.1.1, grid size 256,256,256,
pixel 0.83, shown at step 1, values float32  
C:\Users\yuan\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py:2028: RuntimeWarning: divide by zero
encountered in double_scalars  
self.global_k = scaling_constant/ref_g  
Deleting atomic symmetry model...  

> volume #1.1.1.1 level 0.003428

> volume #1.1.1.1 style surface

> volume #1.1.1.1 style mesh

> isolde sim start sel

ISOLDE: started sim  

> volume #1.1.1.1 level 0.01215

> volume #2.1.1.1 level 0.01684

> volume #2.1.1.1 level 0.01325

> isolde sim stop

> isolde sim stop discardTo start

> close #1

Deleting atomic symmetry model...  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\yuan\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\position.py", line 118, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "C:\Users\yuan\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\yuan\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\distance.py", line 150, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "C:\Users\yuan\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\yuan\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\secondary_structure.py", line 79,
in _selection_changed_cb  
sel = self.isolde.selected_atoms.unique_residues  
File "C:\Users\yuan\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\yuan\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\register_shift.py", line 105, in
_selection_changed_cb  
sel = self.isolde.selected_atoms  
File "C:\Users\yuan\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\isolde.py", line 445, in selected_atoms  
return m.atoms[m.atoms.selecteds]  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 163, in get_prop  
vcount = getattr(self, value_count)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "selection changed":  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 512.15
OpenGL renderer: NVIDIA TITAN RTX/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_DE.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: TAROX
Model: Midrange Workstation
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 136,963,719,168
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Xeon(R) W-2245 CPU @ 3.90GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
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    ChimeraX-PDBLibrary: 1.0.2
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    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
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    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: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
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    imagecodecs: 2021.11.20
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    pyparsing: 3.0.9
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    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 2 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE holding ref to deleted structure

comment:2 by pett, 2 years ago

Resolution: → duplicate
Status: assigned → closed
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