HBonds: acc_phi_psi() takes 8 positional arguments but 9 were given

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2 (2021-04-27 05:33:30 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2 (2021-04-27)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/nantczak/Documents/ETH Work/Glycosylase Project/6m0w hogg1.cxs"
> format session

Log from Tue May 4 16:54:15 2021UCSF ChimeraX version: 1.2 (2021-04-27)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6W0M format mmcif fromDatabase pdb

6w0m title:  
Human 8-oxoguanine glycosylase crosslinked with oxoG lesion containing DNA
[more info...]  
  
Chain information for 6w0m #1  
---  
Chain | Description  
A | N-glycosylase/DNA lyase  
B | DNA (5'-D(P*CP*GP*TP*CP*CP*ap*(8OG)P*GP*TP*CP*TP*ap*C)-3')  
C | DNA (5'-D(P*GP*GP*TP*ap*GP*ap*CP*CP*TP*GP*GP*ap*CP*GP*C)-3')  
  
Non-standard residues in 6w0m #1  
---  
MG — magnesium ion  
S5Y — 2-(2-ethoxyethoxy)ethanethiol  
  

> set bgColor white

> color :.B :.C grey

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color :.B :.C gray

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color B C grey

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color B,C

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color B,C grey

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color grey bonds, cartoons

> color grey :.B, :.C

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> show #1.2 target m

> hide #1.2 target m

> show #1.1 target m

> show #1.3 target m

> nucleotides atoms

> style nucleic stick

Changed 575 atom styles  

> help color

> color /B /C grey

> color cyan /A

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color /A cyan

> color blue :288,322,231,232,280

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color :288,322,231,232,280 blue

> show :288,322,231,232,280 /B/C

> color :8og forest green

> color :8og dark green

> save /Users/nantczak/Desktop/image1.png supersample 3

> color :8og magenta

> color :8og purple

> help color

> color :8og hot pink

> color :8og deep pink

> save /Users/nantczak/Desktop/image2.png supersample 3

> save /Users/nantczak/Desktop/image3.png supersample 3

> help label

> label :D322

> label :322

> save "/Users/nantczak/Documents/ETH Work/Glycosylase Project/6m0w hogg1.cxs"

——— End of log from Tue May 4 16:54:15 2021 ———

opened ChimeraX session  

> show :45,147,319,144,152,155

> color :45,147,319,144,152,155 blue

> open "/Volumes/TOSHIBA EXT/ETH backup
> 28June2020/Documents/hogg1withfapyg1.pdb"

Summary of feedback from opening /Volumes/TOSHIBA EXT/ETH backup
28June2020/Documents/hogg1withfapyg1.pdb  
---  
warnings | Ignored bad PDB record found on line 6371  
END  
  
Cannot find LINK/SSBOND residue DA (22 )  
Cannot find LINK/SSBOND residue 8OG (23 )  
Cannot find LINK/SSBOND residue CA (302 )  
Cannot find LINK/SSBOND residue CA (302 )  
Cannot find LINK/SSBOND residue CA (302 )  
3 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 1 1 PRO A 20 LEU A 22 1
3  
Start residue of secondary structure not found: HELIX 2 2 LEU A 35 VAL A 38 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 90 PHE A 100 1
11  
Start residue of secondary structure not found: HELIX 4 4 LEU A 106 VAL A 116
1 11  
Start residue of secondary structure not found: HELIX 5 5 SER A 118 LYS A 126
1 9  
17 messages similar to the above omitted  
  
hogg1withfapyg1.pdb title:  
Structure of Q315F human 8-oxoguanine glycosylase distal crosslink to
8-oxoguanine DNA [more info...]  
  
Chain information for hogg1withfapyg1.pdb  
---  
Chain | Description  
2.1/A | AP lyase  
2.2/B | 5'-D(*GP*G*TP*ap*GP*ap*CP*CP*TP*GP*GP*ap*CP*GP*C)-3'  
2.2/C | 5'-D(*G*CP*GP*TP*CP*CP*ap*(G42)P*GP*TP*CP*TP*ap*CP*C)-3'  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  
Alignment identifier is 1/C  
Alignment identifier is 2.1/A  
Alignment identifier is 2.2/B  
Alignment identifier is 2.2/C  

> ui tool show Matchmaker

> matchmaker #!2.1 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6w0m, chain A (#1) with hogg1withfapyg1.pdb, chain A (#2.1),
sequence alignment score = 1609.5  
RMSD between 306 pruned atom pairs is 0.316 angstroms; (across all 309 pairs:
0.496)  
  

> undo

> ui tool show Matchmaker

> matchmaker #2.2#!2.1 to #1

No chains in match structure hogg1withfapyg1.pdb #2.2 compatible with
BLOSUM-62 similarity matrix  

> ui tool show Matchmaker

> matchmaker #2.2#!2.1 to #1/A pairing bs

No chains in match structure hogg1withfapyg1.pdb #2.2 compatible with
BLOSUM-62 similarity matrix  

> color :45,147,319,144,152,155 blue

> show :45,147,319,144,152,155 blue

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #1:45,147,319,144,152,155 blue

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #1:45,147,319,144,152,155

> show #2:45,147,319,144,152,155

> color #2:45,147,319,144,152,155 green

> ui tool show Matchmaker

> matchmaker #2.2 to #1/B pairing bs

Reference chain (6w0m (#1) chain B) not compatible with BLOSUM-62 similarity
matrix  

> select #1

3169 atoms, 3203 bonds, 38 pseudobonds, 443 residues, 5 models selected  

> ~select #1

Nothing selected  

> select :8OG

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

donor: 6w0m #1/A ARG 30 NH1 acceptor: hogg1withfapyg1.pdb #2.1/A ASP 36 OD1  
Traceback (most recent call last):  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1333, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in try_shortcut  
self.run_shortcut(keys)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 407, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 326, in run  
f(s)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 568, in run_expanded_command  
run(session, cmd)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 511, in run  
run_command(session, command, **kw)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/cmd.py", line 83, in cmd_hbonds  
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> mlp sel

mlp: no amino acids specified  

> hbonds sel reveal true

donor: 6w0m #1/A ARG 30 NH1 acceptor: hogg1withfapyg1.pdb #2.1/A ASP 36 OD1  
Traceback (most recent call last):  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1333, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in try_shortcut  
self.run_shortcut(keys)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 407, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 326, in run  
f(s)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 568, in run_expanded_command  
run(session, cmd)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 511, in run  
run_command(session, command, **kw)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/cmd.py", line 83, in cmd_hbonds  
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File
"/private/var/folders/lt/_2j4nd4d06vc1w5zylytk770g98_4k/T/AppTranslocation/AB93754D-FC8B-4DB9-B2B2-6AF8F68D3CB9/d/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.30
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir7,2
      Processor Name: Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 427.0.0.0.0
      SMC Version (system): 2.27f2

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G9216)
      Kernel Version: Darwin 18.7.0
      Time since boot: 2:45

Graphics/Displays:

    Intel HD Graphics 6000:

      Chipset Model: Intel HD Graphics 6000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1626
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
          UI Looks like: 1440 x 900
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    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: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.2
    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: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2
    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: 1.1.1
    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
    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
    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: 1.7.3
    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: 5.0.7
    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: 1.1.1
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    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

[Eric Pettersen]

Something wonky about user's custom PDB file; probably bad CONECT records