Opened 4 years ago

Closed 4 years ago

#5007 closed defect (duplicate)

Pick surface(?): index is out of bounds for axis

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> fetch 2hyy

Unknown command: fetch 2hyy  

> open 2hyy

Summary of feedback from opening 2hyy fetched from pdb  
---  
notes | Fetching compressed mmCIF 2hyy from
http://files.rcsb.org/download/2hyy.cif  
Fetching CCD STI from http://ligand-expo.rcsb.org/reports/S/STI/STI.cif  
  
2hyy title:  
Human Abl kinase domain in complex with imatinib (STI571, Glivec) [more
info...]  
  
Chain information for 2hyy #1  
---  
Chain | Description  
A B C D | Proto-oncogene tyrosine-protein kinase ABL1  
  
Non-standard residues in 2hyy #1  
---  
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib)  
  
2hyy mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> set lighting default

Expected a keyword  

> lighting simple

> sym #1 assembly 1

> view

> sym #1 assembly 1

> view

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\log\tool.py", line 204, in link_intercept  
chimerax_intercept(request_info, *args, session=self.session, view=self, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\view.py", line 50, in view  
undo = UndoView("view", session, models)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\view.py", line 555, in __init__  
self._before = NamedView(v, v.center_of_rotation, models)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 664, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 691, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 759, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 768, in _front_center_point  
p = self.picked_object(0.5 * w, 0.5 * h, max_transparent_layers = 0,
exclude=View.unpickable)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 787, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 819, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1036, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1036, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\structure.py", line 593, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\structure.py", line 626, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\ribbon.py", line 686, in first_intercept  
r = self._residues[tranges[n-1][0]]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
IndexError: index 470 is out of bounds for axis 0 with size 263  
  
IndexError: index 470 is out of bounds for axis 0 with size 263  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
  
See log for complete Python traceback.  
  

> sym #1 assembly 2

> view

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\log\tool.py", line 204, in link_intercept  
chimerax_intercept(request_info, *args, session=self.session, view=self, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\view.py", line 50, in view  
undo = UndoView("view", session, models)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\view.py", line 555, in __init__  
self._before = NamedView(v, v.center_of_rotation, models)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 664, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 691, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 759, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 768, in _front_center_point  
p = self.picked_object(0.5 * w, 0.5 * h, max_transparent_layers = 0,
exclude=View.unpickable)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 787, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 819, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1036, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1036, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\structure.py", line 593, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\structure.py", line 626, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\ribbon.py", line 686, in first_intercept  
r = self._residues[tranges[n-1][0]]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
IndexError: index 470 is out of bounds for axis 0 with size 265  
  
IndexError: index 470 is out of bounds for axis 0 with size 265  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
  
See log for complete Python traceback.  
  

> sym #1 assembly 3

> view

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\log\tool.py", line 204, in link_intercept  
chimerax_intercept(request_info, *args, session=self.session, view=self, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\view.py", line 50, in view  
undo = UndoView("view", session, models)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\view.py", line 555, in __init__  
self._before = NamedView(v, v.center_of_rotation, models)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 664, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 691, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 759, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 768, in _front_center_point  
p = self.picked_object(0.5 * w, 0.5 * h, max_transparent_layers = 0,
exclude=View.unpickable)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 787, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\view.py", line 819, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1036, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1036, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\structure.py", line 593, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\structure.py", line 626, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\ribbon.py", line 686, in first_intercept  
r = self._residues[tranges[n-1][0]]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
IndexError: index 470 is out of bounds for axis 0 with size 262  
  
IndexError: index 470 is out of bounds for axis 0 with size 262  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 156, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8935
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Inspiron 3670
OS: Microsoft Windows 10 Pro (Build 19041)
Memory: 16,996,343,808
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Pick surface(?): index is out of bounds for axis

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed

Fixed a month ago. #4828

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