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#5744 closed defect (duplicate)

Interfaces: 'ContactPlot' object has no attribute '_handler'

Reported by:	jonathan.sheehan@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Structure Analysis	Version:
Keywords:		Cc:	Eric Pettersen
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.21.3.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3rc202112040407 (2021-12-04 04:07:47 UTC)
Description
I finished the Quick Start tutorial, and selected File->Close Session.

I got the message: AttributeError: 'ContactPlot' object has no attribute '_handler'

I got it again when closing some of the tools.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3rc202112040407 (2021-12-04)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> open 2bbv

Summary of feedback from opening 2bbv fetched from pdb  
---  
notes | Fetching compressed mmCIF 2bbv from
http://files.rcsb.org/download/2bbv.cif  
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
  
2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv #1  
---  
Chain | Description | UniProt  
A B C | protein (black beetle virus capsid protein) | COAT_BBV  
D E F | protein (black beetle virus capsid protein) | COAT_BBV  
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3') |  
  
Non-standard residues in 2bbv #1  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> color bychain

> style /b stick

Changed 2382 atom styles  

> color /n teal

> hide /c

> ribbon /c

> select /B

2382 atoms, 2372 bonds, 2 pseudobonds, 379 residues, 2 models selected  

> color (#!1 & sel) byhetero

> select clear

> focus /c

Unknown command: focus /c  

> select /C

2473 atoms, 2469 bonds, 6 pseudobonds, 388 residues, 3 models selected  

> view sel

> view /c

> select clear

> select /N:4@C5'

1 atom, 1 residue, 1 model selected  

> select up

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

> color sel gold

> select clear

> surface #1

> color /n fromatoms

> style solvent sphere

Changed 208 atom styles  

> color solvent red

> ui tool show "Side View"

> sym #1

2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly| 60 copies of chains A-F,N  
2| icosahedral asymmetric unit| 1 copy of chains A-F,N  
3| icosahedral pentamer| 5 copies of chains A-F,N  
4| icosahedral 23 hexamer| 6 copies of chains A-F,N  
5| icosahedral asymmetric unit, std point frame| 1 copy of chains A-F,N  
6| crystal asymmetric unit, crystal frame| 5 copies of chains A-F,N  
  

> sym #1 assembly 3 newModel false copies false

> view

> set bgColor white

> set silhouettes true

> save /home/jonathan/Desktop/2bbv.png

> view

> movie record

> turn y 2 180

> wait 180

> movie encode /home/jonathan/Desktop/movie1.mp4

Movie saved to /home/jonathan/Desktop/movie1.mp4  
  

> measure buriedarea /a withAtoms2 /b

Buried area between /a and /b = 1900.4  
area /a = 15385, area /b = 14989, area both = 26573  

> measure sasa #1 & ~solvent

Solvent accessible area for #1 & ~solvent = 34093  

> interfaces #1 & protein

6 buried areas: C A 1675, C B 1671, A B 1663, C F 739, A D 714, B E 699  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 333, in interceptRequest  
self._callback(info)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 92, in _intercept  
return interceptor(request_info, *args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 319, in intercept  
chimerax_intercept(request_info, *args, session=self.session,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 468, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 382, in thread_safe  
func(*args, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 459, in defer  
cxcmd(session, topic)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 477, in cxcmd  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/interfaces/cmd.py", line 49, in interfaces  
tool.ContactPlot(session, sg, ba, interface_residue_area_cutoff)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 25, in __init__  
Graph.__init__(self, session, groups, contacts,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/interfaces/graph.py", line 139, in __init__  
self.graph = self._make_graph()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/interfaces/graph.py", line 160, in _make_graph  
import networkx as nx  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/networkx/__init__.py", line 57, in <module>  
from networkx import utils  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/networkx/utils/__init__.py", line 2, in <module>  
from networkx.utils.decorators import *  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/networkx/utils/decorators.py", line 12, in <module>  
import re, gzip, bz2  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/bz2.py", line 18, in <module>  
from _bz2 import BZ2Compressor, BZ2Decompressor  
ModuleNotFoundError: No module named '_bz2'  
  
ModuleNotFoundError: No module named '_bz2'  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/bz2.py", line 18, in  
from _bz2 import BZ2Compressor, BZ2Decompressor  
  
See log for complete Python traceback.  
  

> view

> close

> set bgColor black

> set silhouettes false

> open 1080 fromDatabase emdb

Summary of feedback from opening 1080 fetched from emdb  
---  
note | Fetching compressed map 1080 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1080/map/emd_1080.map.gz  
  
Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32  

> lighting full

> volume #1 level 0.9

> volume #1 level 1.1

> volume #1 level 1.3

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right "contour level"

> volume #1 level 1.685

> volume #1 level 1.771

> volume #1 level 1.508

> volume #1 level 1.3

> volume #1 level 0.6366

> volume #1 level -0.03423

> volume #1 level 0.06584

> volume #1 level 0.4661

> volume #1 level 0.06955

> volume #1 encloseVolume 1e6 step 1 color tan

> volume #1 level 0.8287

> volume #1 level 1.07

> set bgColor gray

> set silhouettes true

> volume #1 level 1.574

> volume #1 level 1.099

> ui mousemode right translate

> open 1grl

Summary of feedback from opening 1grl fetched from pdb  
---  
note | Fetching compressed mmCIF 1grl from
http://files.rcsb.org/download/1grl.cif  
  
1grl title:  
The crystal structure of the bacterial chaperonin groel At 2.8 angstroms [more
info...]  
  
Chain information for 1grl #2  
---  
Chain | Description | UniProt  
A B C D E F G | groel (HSP60 class) | CH60_ECOLI  
  
1grl mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  
  

> lighting default

> select /E:126@CG1

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

202 atoms, 202 bonds, 22 residues, 1 model selected  

> select up

4182 atoms, 4143 bonds, 518 residues, 1 model selected  

> select up

29274 atoms, 29001 bonds, 3626 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,47.122,0,1,0,16.128,0,0,1,62.879

> fitmap #2 inMap #1

Fit molecule 1grl (#2) to map emdb 1080 (#1) using 29274 atoms  
average map value = 1.044, steps = 104  
shifted from previous position = 17.5  
rotated from previous position = 24.9 degrees  
atoms outside contour = 13428, contour level = 1.0993  
  
Position of 1grl (#2) relative to emdb 1080 (#1) coordinates:  
Matrix rotation and translation  
0.90776524 0.41924712 0.01393269 39.70701138  
-0.41947454 0.90740126 0.02576956 -18.28427061  
-0.00183872 -0.02923712 0.99957081 64.93505013  
Axis -0.06543184 0.01876049 -0.99768067  
Axis point -20.96735494 -88.75319448 0.00000000  
Rotation angle (degrees) 24.85578529  
Shift along axis -67.72556908  
  

> volume #1 transparency 0.5

> molmap #2 10

Opened 1grl map 10 as #3, grid size 63,63,41, pixel 3.33, shown at level
0.0611, step 1, values float32  

> volume #3 style mesh

> volume subtract #1 #3 minRms true

Opened volume difference as #4, grid size 100,100,100, pixel 2.7, shown at
step 1, values float32  
Minimum RMS scale factor for "1grl map 10 #3" above level 0.061077 is 3.6985  
  

> volume #4 color pink transparency 0

> hide atoms

> show ribbons

> volume #4 level 0.6499

> close

> set bgColor black

> set silhouettes false

> open 1a0m fromDatabase eds

Summary of feedback from opening 1a0m fetched from eds  
---  
note | Fetching map 1a0m from
http://www.ebi.ac.uk/pdbe/coordinates/files/1a0m.ccp4  
  
Opened eds 1a0m as #1, grid size 97,101,88, pixel 0.37,0.37,0.367, shown at
level 2.28, step 1, values float32  

> open 1a0m

Summary of feedback from opening 1a0m fetched from pdb  
---  
note | Fetching compressed mmCIF 1a0m from
http://files.rcsb.org/download/1a0m.cif  
  
1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m #2  
---  
Chain | Description | UniProt  
A B | α-conotoxin [TYR15]-epi | CXA1_CONEP  
  
Non-standard residues in 1a0m #2  
---  
NH2 — amino group  
  

> hide ribbons

> show

> volume #1 level 1.0 style mesh

> volume zone #1 nearAtoms #2 range 2

> volume #1 level 0.5 transparency 0.6

> show cartoons

> hide cartoons

> close

> open 1273 fromDatabase emdb

Summary of feedback from opening 1273 fetched from emdb  
---  
note | Fetching compressed map 1273 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1273/map/emd_1273.map.gz  
  
Opened emdb 1273 as #1, grid size 2048,2048,76, pixel 22.5, shown at step 1,
values int8  

> volume #1 region all showOutlineBox true

> close session

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1032, in <lambda>  
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 680, in file_close_cb  
run(session, 'close session')  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/std_commands/close.py", line 60, in close_session  
session.reset()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 535, in reset  
sm.reset_state(container, self)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2251, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 654, in close_request  
tool_instance.delete()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.43
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: TYAN
Model: B7105F48TV8HR-2T-G
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 48 Intel(R) Xeon(R) Gold 5118 CPU @ 2.30GHz
Cache Size: 16896 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           187G        4.0G        158G        135M         24G        182G
	Swap:            9G          0B          9G

Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]	
	Kernel driver in use: ast
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-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: 1.3rc202112040407
    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-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 (2)

comment:1 by Eric Pettersen, 4 years ago

Cc:	Eric Pettersen added
Component:	Unassigned → Structure Analysis
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Interfaces: 'ContactPlot' object has no attribute '_handler'

comment:2 by Eric Pettersen, 4 years ago

Resolution:	→ duplicate
Status:	assigned → closed

Hi Jonathan,

The earlier error with the 'interfaces' command prevented the tool from fully initializing, which in turn produced the later errors. When we fix the first error, these later errors will also be eliminated.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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