Opened 4 years ago

Closed 3 years ago

#6081 closed defect (fixed)

Symmetry handler using dead 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:        Linux-5.11.0-38-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/smith/Documents/Srp_structures/PTI-Chy-Try_PP/Refine_13/PTI-Chy-
> Try_PP_refine_13.pdb

Chain information for PTI-Chy-Try_PP_refine_13.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> addh hbond true

Summary of feedback from adding hydrogens to PTI-Chy-Try_PP_refine_13.pdb #1  
---  
warnings | Not adding hydrogens to /A LYS 36 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 79 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 145 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B ASN 97 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /C LYS 132 CB because it is missing heavy-atom bond
partners  
3 messages similar to the above omitted  
notes | No usable SEQRES records for PTI-Chy-Try_PP_refine_13.pdb (#1) chain
A; guessing termini instead  
No usable SEQRES records for PTI-Chy-Try_PP_refine_13.pdb (#1) chain B;
guessing termini instead  
No usable SEQRES records for PTI-Chy-Try_PP_refine_13.pdb (#1) chain C;
guessing termini instead  
Chain-initial residues that are actual N termini: /A CYS 1, /B ILE 1, /C PRO 7  
Chain-initial residues that are not actual N termini: /A ILE 16, /A THR 151,
/C GLN 77, /C PHE 162  
Chain-final residues that are actual C termini: /A ASN 245, /B ASN 223, /C GLN
193  
Chain-final residues that are not actual C termini: /A LEU 10, /A ARG 145, /C
SER 71, /C VAL 148  
682 hydrogen bonds  
Adding 'H' to /A ILE 16  
Adding 'H' to /A THR 151  
Adding 'H' to /C GLN 77  
Adding 'H' to /C PHE 162  
4722 hydrogens added  
  

> isolde start

> set selectionWidth 4

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 10.1 - if installed, please make sure this is
on your library path before starting ChimeraX.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 19 residues in model #1 to IUPAC-IUB
standards.  
Chain information for PTI-Chy-Try_PP_refine_13.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
  
Done loading forcefield  
Discarding unrecognised/unsupported data array /crystal/Original-experimental-
data-mapped-to-asu/HLA A  
Discarding unrecognised/unsupported data array /crystal/Original-experimental-
data-mapped-to-asu/HLB A  
Discarding unrecognised/unsupported data array /crystal/Original-experimental-
data-mapped-to-asu/HLC A  
Discarding unrecognised/unsupported data array /crystal/Original-experimental-
data-mapped-to-asu/HLD A  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,46,44, pixel
0.544,0.557,0.568, shown at level 0.338, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,46,44, pixel
0.544,0.557,0.568, shown at level -0.123,0.123, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_9 as #1.1.1.4, grid size 50,46,44, pixel
0.544,0.557,0.568, shown at level 0.307, step 1, values float32  
Opened (STATIC) (Model-structure-factors-(bulk-solvent-and-all-scales-
included)) F-model, PHIF-model as #1.1.1.5, grid size 50,46,44, pixel
0.544,0.557,0.568, shown at level -0.517,0.517, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT as #1.1.1.6,
grid size 50,46,44, pixel 0.544,0.557,0.568, shown at level 0.385, step 1,
values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill
as #1.1.1.7, grid size 50,46,44, pixel 0.544,0.557,0.568, shown at level
0.367, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT as #1.1.1.8, grid
size 50,46,44, pixel 0.544,0.557,0.568, shown at level -0.258,0.258, step 1,
values float32  
Opened (LIVE) MDFF potential as #1.1.1.9, grid size 50,46,44, pixel
0.544,0.557,0.568, shown at level 0.282, step 1, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 9217, resource id:
18005511, major code: 40 (TranslateCoords), minor code: 0  

> set bgColor white

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1.2/A  

> 123angle

123angle is provided by the uninstalled bundle SEQCROW versions 0.13 – 0.15  
ISOLDE: started sim  
ISOLDE: paused sim  

> close #1.2

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

> close #1.1

Deleting atomic symmetry model...  
Deleting Crystallographic maps (PTI-Chy-Try_PP_refine_13.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_9  
Deleting (LIVE) MDFF potential  

> open /home/smith/Documents/Srp_structures/PTI-Chy-Try_PP/Refine_13/PTI-Chy-
> Try_PP_refine_13.pdb

Chain information for PTI-Chy-Try_PP_refine_13.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Traceback (most recent call last):  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1306, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1332, in add_xtal_data  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 183, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> close #2.1

Deleting atomic symmetry model...  

> close #2

Deleting atomic symmetry model...  

> open /home/smith/Documents/Srp_structures/PTI-Chy-Try_PP/Refine_2/PTI-Chy-
> Try_PP_refine_2-modAS.pdb

Chain information for PTI-Chy-Try_PP_refine_2-modAS.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Traceback (most recent call last):  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1306, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1332, in add_xtal_data  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 183, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> close #2

Deleting atomic symmetry model...  

> close

Deleting atomic symmetry model...  

> open /home/smith/Documents/Srp_structures/PTI-Chy-Try_PP/Refine_2/PTI-Chy-
> Try_PP_refine_2.pdb

Chain information for PTI-Chy-Try_PP_refine_2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> color #1 #75507b transparency 0

> color #1 #5c3566 transparency 0

Traceback (most recent call last):  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1306, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1332, in add_xtal_data  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 183, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> close #1

> open /home/smith/Documents/Srp_structures/PTI-Chy-Try_PP/Refine_13/PTI-Chy-
> Try_PP_refine_13.pdb

Chain information for PTI-Chy-Try_PP_refine_13.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Traceback (most recent call last):  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1306, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 1332, in add_xtal_data  
map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 183, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/home/smith/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 21.0.3
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CML GT2)
OpenGL vendor: Intel
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B460MDS3HV2
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
Cache Size: 16384 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi       8.0Gi        11Gi       1.3Gi        12Gi        21Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:9bc5] (rev 05)	
	DeviceName: Onboard - Video	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:d000]
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    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: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Symmetry handler using dead structure

comment:2 by Tristan Croll, 4 years ago

Hmm... problem started when the user specifically closed model #1.2 (the actual atomic structure) rather than just closing #1 (Clipper's top-level SymmetryManager object). Never really designed things to support that eventuality... I guess I should add a callback to automatically close the top-level SymmetryManager object if the child structure is closed.

comment:3 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed
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