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#8061 closed defect (not a bug)

MD viewer: No self.atomLocations

Reported by:	chimerax-bug-report@…	Owned by:	pett
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: 1.4 (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.  

> open /Users/feng/Pictures/PhotosystemI/core.cxs format session

Log from Sun Nov 20 12:48:09 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/feng/Pictures/PhotosystemI/5oy0.pdb format pdb

5oy0.pdb title:  
Structure of synechocystis photosystem I trimer At 2.5A resolution [more
info...]  
  
Chain information for 5oy0.pdb #1  
---  
Chain | Description | UniProt  
0 | photosystem I reaction center subunit XI | PSAL_SYNY3  
1 | PSAA | PSAA_SYNY3  
2 B | PSAB | PSAB_SYNY3  
3 C | photosystem I iron-sulfur center | PSAC_SYNY3  
4 | photosystem I reaction center subunit II | PSAD_SYNY3  
5 E | photosystem I reaction center subunit IV | PSAE_SYNY3  
6 F f | PSI-F | PSAF_SYNY3  
7 J j | photosystem I reaction center subunit IX | PSAJ_SYNY3  
8 | photosystem I subunit X 2 | PSAK2_SYNY3  
9 M m | PSI-M | PSAM_SYNY3  
A a | PSAA | PSAA_SYNY3  
D d | photosystem I reaction center subunit II | PSAD_SYNY3  
I i | photosystem I reaction center subunit VIII | PSAI_SYNY3  
K | photosystem I subunit X 2 | PSAK2_SYNY3  
L l | photosystem I reaction center subunit XI | PSAL_SYNY3  
b | PSAB | PSAB_SYNY3  
c | photosystem I iron-sulfur center | PSAC_SYNY3  
e | photosystem I reaction center subunit IV | PSAE_SYNY3  
h | photosystem I reaction center subunit VIII | PSAI_SYNY3  
k | photosystem I subunit X 2 | PSAK2_SYNY3  
  
Non-standard residues in 5oy0.pdb #1  
---  
45D — β,β-carotene-4,4'-dione (isomer of canthaxanthin)  
ACT — acetate ion  
BCR — β-carotene  
CA — calcium ion  
CL — chloride ion  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
ECH — β,β-caroten-4-one (echinenone)  
EQ3 — (3'R)-3'-hydroxy-β,β-caroten-4-one (3'-hydroxyechinenone, 3'-oh-
echinenone)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
LMT — dodecyl-β-D-maltoside  
MG — magnesium ion  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
ZEX —
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol  
  

> cd /Users/feng/Pictures/PhotosystemI

Current working directory is: /Users/feng/Pictures/PhotosystemI  

> ui tool show "Basic Actions"

> hide /0 target c

[Repeated 1 time(s)]

> hide /1 target c

[Repeated 1 time(s)]

> hide /2 target c

[Repeated 1 time(s)]

> select

77111 atoms, 79086 bonds, 1250 pseudobonds, 8103 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> show /B target c

[Repeated 13 time(s)]

> show /A target c

[Repeated 6 time(s)]

> select ::name="CLA"

17482 atoms, 18620 bonds, 1141 pseudobonds, 285 residues, 2 models selected  

> show sel atoms

> select clear

> select ::name="PQN"

198 atoms, 204 bonds, 6 residues, 1 model selected  

> show sel atoms

> hide /A target c

[Repeated 6 time(s)]

> hide /B target c

[Repeated 6 time(s)]

> select up

4 atoms, 2 bonds, 2 residues, 1 model selected  

> select up

130 atoms, 138 bonds, 2 residues, 1 model selected  

> select add /A:1012@C1C

131 atoms, 140 bonds, 3 residues, 1 model selected  
Drag select of 4 atoms, 2 bonds  

> select up

139 atoms, 141 bonds, 7 residues, 1 model selected  

> select up

455 atoms, 483 bonds, 7 residues, 1 model selected  

> select /A:1140@C2B

1 atom, 1 residue, 1 model selected  

> select add /B:1023@C1C

1 atom, 3 bonds, 1 residue, 1 model selected  

> select up

13 atoms, 6 bonds, 6 residues, 1 model selected  

> select up

390 atoms, 414 bonds, 6 residues, 1 model selected  

> name frozen Chla sel

> select ::name="CLA"

17482 atoms, 18620 bonds, 1141 pseudobonds, 285 residues, 2 models selected  

> hide sel atoms

Drag select of 66 atoms, 68 bonds  

> name frozen PQ sel

> select Chla

390 atoms, 414 bonds, 24 pseudobonds, 6 residues, 2 models selected  

> show sel atoms

> hide /A target c

[Repeated 8 time(s)]

> show /A target c

[Repeated 8 time(s)]

> show /B target c

[Repeated 8 time(s)]

> hide /A target c

[Repeated 8 time(s)]

> hide /B target c

[Repeated 8 time(s)]

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

4 atoms, 2 bonds, 2 residues, 1 model selected  

> select up

130 atoms, 138 bonds, 2 residues, 1 model selected  

> color sel medium blue

> select Chla

390 atoms, 414 bonds, 24 pseudobonds, 6 residues, 2 models selected  

> color (#!1 & sel) forest green

> select add /A:1011@CMC

1 atom, 1 bond, 1 residue, 1 model selected  

> select up

3 atoms, 1 bond, 2 residues, 1 model selected  

> select up

130 atoms, 138 bonds, 2 residues, 1 model selected  

> name frozen P700 sel

> color sel blue

> select ::name="PQN"

198 atoms, 204 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select PQ

66 atoms, 68 bonds, 2 residues, 1 model selected  

> show sel atoms

> color sel hot pink

> select ::name="SF4"

72 atoms, 108 bonds, 9 residues, 1 model selected  

> show sel atoms

Drag select of 24 atoms, 36 bonds  

> select clear

Drag select of 23 atoms, 36 bonds  

> select clear

Drag select of 24 atoms, 36 bonds  

> name frozen SF sel

> select ::name="SF4"

72 atoms, 108 bonds, 9 residues, 1 model selected  

> hide sel atoms

> select SF

24 atoms, 36 bonds, 3 residues, 1 model selected  

> show sel atoms

> save "/Users/feng/Pictures/PhotosystemI/reaction core.cxs" includeMaps true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbd18384f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fbca8039910> 'Basic
Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbd18384f10> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7fbca8039910> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7fbd18384f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fbca8039910> 'Basic
Actions'  
  

Populating font family aliases took 374 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 225, in take_snapshot  
self.add_webview_state(data)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/basic_actions/tool.py", line 260, in add_webview_state  
event_loop.exec_()  
AttributeError: 'QEventLoop' object has no attribute 'exec_'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbd18384f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fbca8039910> 'Basic
Actions'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbd18384f10> -> <chimerax.basic_actions.tool.BasicActionsTool object at
0x7fbca8039910> 'Basic Actions': Error while saving session data for 'tools'
-> <chimerax.core.tools.Tools object at 0x7fbd18384f10> ->
<chimerax.basic_actions.tool.BasicActionsTool object at 0x7fbca8039910> 'Basic
Actions'  
  
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /Users/feng/Pictures/PhotosystemI/core.cxs

——— End of log from Sun Nov 20 12:48:09 2022 ———

opened ChimeraX session  

> ui tool show "Basic Actions"

> show /A target c

[Repeated 1 time(s)]

> show /B target c

[Repeated 1 time(s)]

> show /C target c

[Repeated 1 time(s)]

> show /D target c

[Repeated 1 time(s)]

> show /E target c

[Repeated 1 time(s)]

> show /F target c

[Repeated 1 time(s)]

> show /I target c

[Repeated 1 time(s)]

> show /J target c

[Repeated 1 time(s)]

> show /K target c

[Repeated 1 time(s)]

> show /L target c

[Repeated 1 time(s)]

> show /M target c

[Repeated 1 time(s)]

> select clear

> save /Users/feng/Desktop/PSI+core.png width 759 height 668 supersample 3
> transparentBackground true

> save "/Users/feng/Desktop/PSI Monomer + core.png" width 759 height 668
> supersample 3 transparentBackground true

> hide /D target c

[Repeated 1 time(s)]

> hide /E target c

[Repeated 1 time(s)]

> hide /F target c

[Repeated 1 time(s)]

> hide /I target c

[Repeated 1 time(s)]

> hide /J target c

[Repeated 1 time(s)]

> hide /K target c

[Repeated 1 time(s)]

> hide /L target c

[Repeated 1 time(s)]

> hide /M target c

[Repeated 1 time(s)]

> save /Users/feng/Desktop/3sub+core.png width 759 height 668 supersample 3
> transparentBackground true

> hide /A target c

[Repeated 1 time(s)]

> hide /B target c

[Repeated 1 time(s)]

> hide /C target c

[Repeated 1 time(s)]

> save /Users/feng/Desktop/core.png width 759 height 668 supersample 3
> transparentBackground true

> select PQ

66 atoms, 68 bonds, 2 residues, 1 model selected  

> hide sel atoms

> save "/Users/feng/Desktop/core no PQ.png" width 759 height 668 supersample 3
> transparentBackground true

> show /A target c

[Repeated 6 time(s)]

> show /B target c

[Repeated 6 time(s)]

> show /C target c

[Repeated 6 time(s)]

> save "/Users/feng/Desktop/3sub+core no PQ.png" width 759 height 668
> supersample 3 transparentBackground true

> ui tool show "Molecular Dynamics Viewer"

Please register the custom scheme 'kmd' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 335, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 399, in thread_safe  
func(*args, **kw)  
File "/Users/feng/Library/Application Support/ChimeraX/1.4/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme  
self.openFile()  
File "/Users/feng/Library/Application Support/ChimeraX/1.4/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 234, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
IndexError: list index out of range  
  

Populating font family aliases took 359 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

IndexError: list index out of range  
  
File "/Users/feng/Library/Application Support/ChimeraX/1.4/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 234, in openFile  
self.atomStruct.atoms.coords = self.atomLocation[0]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3D/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 5 days, 3 hours, 30 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          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
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.3
    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-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-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
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    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
    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: 2.6
    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: 1.2.1
    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
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 3 years ago

Component:	Unassigned → Third Party
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → MD viewer: No self.atomLocations

comment:2 by pett, 3 years ago

Resolution:	→ not a bug
Status:	accepted → closed

Not a trajectory (self.atomLocations only set on ENDMDL record).

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