Add Charges: Could not come up with unique atom name in mega-residue

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
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.  
How to cite UCSF ChimeraX  

> open "D:\Jessalyn's PhD\Cannulae A\CANA tube calcium labels.pdb" format pdb

No such file/path: D:\Jessalyn's PhD\Cannulae A\CANA tube calcium labels.pdb  

> open "C:\Users\roger\OneDrive - Emory University\Dissertation\All Minard lab
> work\Brick F\Brick F alpha2.pdb" format pdb

Chain information for Brick F alpha2.pdb #1  
---  
Chain | Description  
A B | No description available  
C E G | No description available  
  

> close

> open "D:\Jessalyn's PhD\Cannulae A\canA-017_BIOMT_expanded.pdb" format pdb

No such file/path: D:\Jessalyn's PhD\Cannulae A\canA-017_BIOMT_expanded.pdb  

> open "D:\Jessalyn's PhD\Hyper2\cryosparc_P128_J216_011_volume_map_sharp.mrc"
> format mrc

No such file/path: D:\Jessalyn's
PhD\Hyper2\cryosparc_P128_J216_011_volume_map_sharp.mrc  

> open "C:\Users\roger\OneDrive - Emory
> University\Dissertation\CanA\canA-017_BIOMT_expanded.pdb" format pdb

Summary of feedback from opening C:\Users\roger\OneDrive - Emory
University\Dissertation\CanA\canA-017_BIOMT_expanded.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
139387 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 125 125 ALAAA 67 LEUAA
70 1 4  
Start residue of secondary structure not found: HELIX 126 126 THRAA 126 TYRAA
128 1 3  
Start residue of secondary structure not found: SHEET 1 745 1 ALAAA 12 GLNAA
17 0  
Start residue of secondary structure not found: SHEET 2 746 1 ILEAA 23 HISAA
28 0  
Start residue of secondary structure not found: SHEET 3 747 1 GLYAA 30 THRAA
33 0  
9 messages similar to the above omitted  
  
Chain information for canA-017_BIOMT_expanded.pdb #1  
---  
Chain | Description  
0 1 2 3 4 5 6 7 8 9 A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AB AC AD AE AF AG AH AI AJ
AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ B BA BB C D E F G H I J K L M
N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z
| No description available  
A | No description available  
  

> hide /bb

> select /A:2-183

2808 atoms, 2870 bonds, 364 residues, 1 model selected  

> select add #1

140800 atoms, 143500 bonds, 18600 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 99, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 23, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,
query_user=query_user,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 198, in add_standard_charges  
fr = FakeRes(connected)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 775, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
ValueError: Could not come up with unique atom name in mega-residue  
  
ValueError: Could not come up with unique atom name in mega-residue  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 775, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
  
See log for complete Python traceback.  
  

> select /

Expected an objects specifier or a keyword  

> select /a

1408 atoms, 1435 bonds, 186 residues, 1 model selected  

> select /A

2812 atoms, 2870 bonds, 368 residues, 1 model selected  

> select ~sel

137988 atoms, 140630 bonds, 18232 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for canA-017_BIOMT_expanded.pdb_0 SES surface #1.1: minimum,
-23.28, mean -3.40, maximum 10.12  
Coulombic values for canA-017_BIOMT_expanded.pdb_1 SES surface #1.2: minimum,
-23.76, mean -3.43, maximum 10.11  
Coulombic values for canA-017_BIOMT_expanded.pdb_2 SES surface #1.3: minimum,
-23.59, mean -3.44, maximum 9.89  
Coulombic values for canA-017_BIOMT_expanded.pdb_3 SES surface #1.4: minimum,
-23.30, mean -3.42, maximum 9.90  
Coulombic values for canA-017_BIOMT_expanded.pdb_4 SES surface #1.5: minimum,
-24.18, mean -3.43, maximum 9.88  
Coulombic values for canA-017_BIOMT_expanded.pdb_5 SES surface #1.6: minimum,
-23.73, mean -3.44, maximum 9.91  
Coulombic values for canA-017_BIOMT_expanded.pdb_6 SES surface #1.7: minimum,
-23.37, mean -3.44, maximum 9.95  
Coulombic values for canA-017_BIOMT_expanded.pdb_7 SES surface #1.8: minimum,
-23.54, mean -3.41, maximum 9.89  
Coulombic values for canA-017_BIOMT_expanded.pdb_8 SES surface #1.9: minimum,
-23.64, mean -3.42, maximum 10.04  
Coulombic values for canA-017_BIOMT_expanded.pdb_9 SES surface #1.10: minimum,
-23.22, mean -3.44, maximum 9.80  
Coulombic values for canA-017_BIOMT_expanded.pdb_A0 SES surface #1.11:
minimum, -23.56, mean -3.42, maximum 9.94  
Coulombic values for canA-017_BIOMT_expanded.pdb_A1 SES surface #1.12:
minimum, -24.03, mean -3.41, maximum 9.97  
Coulombic values for canA-017_BIOMT_expanded.pdb_A2 SES surface #1.13:
minimum, -23.38, mean -3.42, maximum 9.96  
Coulombic values for canA-017_BIOMT_expanded.pdb_A3 SES surface #1.14:
minimum, -23.63, mean -3.44, maximum 9.86  
Coulombic values for canA-017_BIOMT_expanded.pdb_A4 SES surface #1.15:
minimum, -23.19, mean -3.42, maximum 9.90  
Coulombic values for canA-017_BIOMT_expanded.pdb_A5 SES surface #1.16:
minimum, -23.58, mean -3.44, maximum 9.96  
Coulombic values for canA-017_BIOMT_expanded.pdb_A6 SES surface #1.17:
minimum, -23.72, mean -3.45, maximum 10.11  
Coulombic values for canA-017_BIOMT_expanded.pdb_A7 SES surface #1.18:
minimum, -23.86, mean -3.45, maximum 10.13  
Coulombic values for canA-017_BIOMT_expanded.pdb_A8 SES surface #1.19:
minimum, -24.07, mean -3.43, maximum 9.92  
Coulombic values for canA-017_BIOMT_expanded.pdb_A9 SES surface #1.20:
minimum, -23.22, mean -3.46, maximum 10.06  
Coulombic values for canA-017_BIOMT_expanded.pdb_AB SES surface #1.21:
minimum, -23.48, mean -3.41, maximum 9.94  
Coulombic values for canA-017_BIOMT_expanded.pdb_AC SES surface #1.22:
minimum, -23.80, mean -3.43, maximum 9.90  
Coulombic values for canA-017_BIOMT_expanded.pdb_AD SES surface #1.23:
minimum, -23.62, mean -3.46, maximum 9.98  
Coulombic values for canA-017_BIOMT_expanded.pdb_AE SES surface #1.24:
minimum, -23.56, mean -3.43, maximum 9.91  
Coulombic values for canA-017_BIOMT_expanded.pdb_AF SES surface #1.25:
minimum, -23.71, mean -3.45, maximum 10.12  
Coulombic values for canA-017_BIOMT_expanded.pdb_AG SES surface #1.26:
minimum, -23.66, mean -3.45, maximum 10.18  
Coulombic values for canA-017_BIOMT_expanded.pdb_AH SES surface #1.27:
minimum, -23.67, mean -3.42, maximum 10.05  
Coulombic values for canA-017_BIOMT_expanded.pdb_AI SES surface #1.28:
minimum, -23.45, mean -3.42, maximum 9.97  
Coulombic values for canA-017_BIOMT_expanded.pdb_AJ SES surface #1.29:
minimum, -24.00, mean -3.44, maximum 10.08  
Coulombic values for canA-017_BIOMT_expanded.pdb_AK SES surface #1.30:
minimum, -23.79, mean -3.42, maximum 9.85  
Coulombic values for canA-017_BIOMT_expanded.pdb_AL SES surface #1.31:
minimum, -24.07, mean -3.44, maximum 10.02  
Coulombic values for canA-017_BIOMT_expanded.pdb_AM SES surface #1.32:
minimum, -23.57, mean -3.46, maximum 9.93  
Coulombic values for canA-017_BIOMT_expanded.pdb_AN SES surface #1.33:
minimum, -23.29, mean -3.44, maximum 9.81  
Coulombic values for canA-017_BIOMT_expanded.pdb_AO SES surface #1.34:
minimum, -23.61, mean -3.43, maximum 9.98  
Coulombic values for canA-017_BIOMT_expanded.pdb_AP SES surface #1.35:
minimum, -23.47, mean -3.44, maximum 9.87  
Coulombic values for canA-017_BIOMT_expanded.pdb_AQ SES surface #1.36:
minimum, -23.77, mean -3.44, maximum 9.80  
Coulombic values for canA-017_BIOMT_expanded.pdb_AR SES surface #1.37:
minimum, -24.12, mean -3.44, maximum 9.81  
Coulombic values for canA-017_BIOMT_expanded.pdb_AS SES surface #1.38:
minimum, -23.08, mean -3.47, maximum 9.93  
Coulombic values for canA-017_BIOMT_expanded.pdb_AT SES surface #1.39:
minimum, -23.72, mean -3.46, maximum 9.83  
Coulombic values for canA-017_BIOMT_expanded.pdb_AU SES surface #1.40:
minimum, -23.40, mean -3.41, maximum 9.87  
Coulombic values for canA-017_BIOMT_expanded.pdb_AV SES surface #1.41:
minimum, -24.19, mean -3.44, maximum 9.92  
Coulombic values for canA-017_BIOMT_expanded.pdb_AW SES surface #1.42:
minimum, -23.59, mean -3.44, maximum 10.10  
Coulombic values for canA-017_BIOMT_expanded.pdb_AX SES surface #1.43:
minimum, -24.22, mean -3.43, maximum 10.01  
Coulombic values for canA-017_BIOMT_expanded.pdb_AY SES surface #1.44:
minimum, -23.81, mean -3.44, maximum 9.85  
Coulombic values for canA-017_BIOMT_expanded.pdb_AZ SES surface #1.45:
minimum, -24.16, mean -3.43, maximum 9.88  
Coulombic values for canA-017_BIOMT_expanded.pdb_B SES surface #1.46: minimum,
-23.81, mean -3.44, maximum 9.94  
Coulombic values for canA-017_BIOMT_expanded.pdb_BA SES surface #1.47:
minimum, -25.26, mean -3.43, maximum 10.07  
Coulombic values for canA-017_BIOMT_expanded.pdb_BB SES surface #1.48:
minimum, -23.72, mean -3.40, maximum 9.98  
Coulombic values for canA-017_BIOMT_expanded.pdb_C SES surface #1.49: minimum,
-23.79, mean -3.43, maximum 9.96  
Coulombic values for canA-017_BIOMT_expanded.pdb_D SES surface #1.50: minimum,
-23.67, mean -3.43, maximum 9.88  
Coulombic values for canA-017_BIOMT_expanded.pdb_E SES surface #1.51: minimum,
-23.92, mean -3.44, maximum 10.01  
Coulombic values for canA-017_BIOMT_expanded.pdb_F SES surface #1.52: minimum,
-23.77, mean -3.45, maximum 10.07  
Coulombic values for canA-017_BIOMT_expanded.pdb_G SES surface #1.53: minimum,
-24.17, mean -3.43, maximum 10.01  
Coulombic values for canA-017_BIOMT_expanded.pdb_H SES surface #1.54: minimum,
-23.28, mean -3.45, maximum 9.84  
Coulombic values for canA-017_BIOMT_expanded.pdb_I SES surface #1.55: minimum,
-23.88, mean -3.45, maximum 10.07  
Coulombic values for canA-017_BIOMT_expanded.pdb_J SES surface #1.56: minimum,
-23.45, mean -3.42, maximum 9.89  
Coulombic values for canA-017_BIOMT_expanded.pdb_K SES surface #1.57: minimum,
-23.65, mean -3.45, maximum 9.88  
Coulombic values for canA-017_BIOMT_expanded.pdb_L SES surface #1.58: minimum,
-24.06, mean -3.42, maximum 9.93  
Coulombic values for canA-017_BIOMT_expanded.pdb_M SES surface #1.59: minimum,
-23.75, mean -3.45, maximum 10.09  
Coulombic values for canA-017_BIOMT_expanded.pdb_N SES surface #1.60: minimum,
-23.99, mean -3.44, maximum 9.92  
Coulombic values for canA-017_BIOMT_expanded.pdb_O SES surface #1.61: minimum,
-23.77, mean -3.43, maximum 9.84  
Coulombic values for canA-017_BIOMT_expanded.pdb_P SES surface #1.62: minimum,
-23.80, mean -3.42, maximum 10.13  
Coulombic values for canA-017_BIOMT_expanded.pdb_Q SES surface #1.63: minimum,
-23.18, mean -3.44, maximum 9.97  
Coulombic values for canA-017_BIOMT_expanded.pdb_R SES surface #1.64: minimum,
-23.86, mean -3.44, maximum 9.88  
Coulombic values for canA-017_BIOMT_expanded.pdb_S SES surface #1.65: minimum,
-23.39, mean -3.42, maximum 9.88  
Coulombic values for canA-017_BIOMT_expanded.pdb_T SES surface #1.66: minimum,
-23.63, mean -3.43, maximum 9.87  
Coulombic values for canA-017_BIOMT_expanded.pdb_U SES surface #1.67: minimum,
-23.66, mean -3.42, maximum 10.18  
Coulombic values for canA-017_BIOMT_expanded.pdb_V SES surface #1.68: minimum,
-24.10, mean -3.42, maximum 9.96  
Coulombic values for canA-017_BIOMT_expanded.pdb_W SES surface #1.69: minimum,
-23.81, mean -3.44, maximum 9.97  
Coulombic values for canA-017_BIOMT_expanded.pdb_X SES surface #1.70: minimum,
-23.91, mean -3.44, maximum 9.87  
Coulombic values for canA-017_BIOMT_expanded.pdb_Y SES surface #1.71: minimum,
-23.49, mean -3.41, maximum 9.86  
Coulombic values for canA-017_BIOMT_expanded.pdb_Z SES surface #1.72: minimum,
-23.30, mean -3.46, maximum 9.88  
Coulombic values for canA-017_BIOMT_expanded.pdb_a SES surface #1.73: minimum,
-23.85, mean -3.45, maximum 9.92  
Coulombic values for canA-017_BIOMT_expanded.pdb_b SES surface #1.74: minimum,
-23.71, mean -3.42, maximum 9.96  
Coulombic values for canA-017_BIOMT_expanded.pdb_c SES surface #1.75: minimum,
-23.60, mean -3.44, maximum 10.13  
Coulombic values for canA-017_BIOMT_expanded.pdb_d SES surface #1.76: minimum,
-23.12, mean -3.45, maximum 10.00  
Coulombic values for canA-017_BIOMT_expanded.pdb_e SES surface #1.77: minimum,
-23.26, mean -3.43, maximum 9.97  
Coulombic values for canA-017_BIOMT_expanded.pdb_f SES surface #1.78: minimum,
-23.71, mean -3.43, maximum 9.98  
Coulombic values for canA-017_BIOMT_expanded.pdb_g SES surface #1.79: minimum,
-23.98, mean -3.42, maximum 10.12  
Coulombic values for canA-017_BIOMT_expanded.pdb_h SES surface #1.80: minimum,
-23.36, mean -3.43, maximum 9.85  
Coulombic values for canA-017_BIOMT_expanded.pdb_i SES surface #1.81: minimum,
-23.88, mean -3.46, maximum 9.97  
Coulombic values for canA-017_BIOMT_expanded.pdb_j SES surface #1.82: minimum,
-23.75, mean -3.44, maximum 9.80  
Coulombic values for canA-017_BIOMT_expanded.pdb_k SES surface #1.83: minimum,
-23.77, mean -3.43, maximum 9.94  
Coulombic values for canA-017_BIOMT_expanded.pdb_l SES surface #1.84: minimum,
-24.15, mean -3.46, maximum 9.96  
Coulombic values for canA-017_BIOMT_expanded.pdb_m SES surface #1.85: minimum,
-23.69, mean -3.41, maximum 10.01  
Coulombic values for canA-017_BIOMT_expanded.pdb_n SES surface #1.86: minimum,
-24.00, mean -3.43, maximum 10.11  
Coulombic values for canA-017_BIOMT_expanded.pdb_o SES surface #1.87: minimum,
-23.44, mean -3.42, maximum 9.86  
Coulombic values for canA-017_BIOMT_expanded.pdb_p SES surface #1.88: minimum,
-23.62, mean -3.47, maximum 9.99  
Coulombic values for canA-017_BIOMT_expanded.pdb_q SES surface #1.89: minimum,
-23.88, mean -3.42, maximum 9.92  
Coulombic values for canA-017_BIOMT_expanded.pdb_r SES surface #1.90: minimum,
-23.88, mean -3.44, maximum 10.14  
Coulombic values for canA-017_BIOMT_expanded.pdb_s SES surface #1.91: minimum,
-23.45, mean -3.42, maximum 9.87  
Coulombic values for canA-017_BIOMT_expanded.pdb_t SES surface #1.92: minimum,
-23.71, mean -3.45, maximum 9.88  
Coulombic values for canA-017_BIOMT_expanded.pdb_u SES surface #1.93: minimum,
-24.06, mean -3.43, maximum 10.09  
Coulombic values for canA-017_BIOMT_expanded.pdb_v SES surface #1.94: minimum,
-24.03, mean -3.45, maximum 9.93  
Coulombic values for canA-017_BIOMT_expanded.pdb_w SES surface #1.95: minimum,
-24.02, mean -3.41, maximum 9.91  
Coulombic values for canA-017_BIOMT_expanded.pdb_x SES surface #1.96: minimum,
-23.80, mean -3.41, maximum 9.88  
Coulombic values for canA-017_BIOMT_expanded.pdb_y SES surface #1.97: minimum,
-23.84, mean -3.42, maximum 9.89  
Coulombic values for canA-017_BIOMT_expanded.pdb_z SES surface #1.98: minimum,
-23.94, mean -3.43, maximum 9.91  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select /A

2812 atoms, 2870 bonds, 368 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 99, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 23, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,
query_user=query_user,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 198, in add_standard_charges  
fr = FakeRes(connected)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 775, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
ValueError: Could not come up with unique atom name in mega-residue  
  
ValueError: Could not come up with unique atom name in mega-residue  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 775, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.14756 Core Profile Forward-Compatible Context 20.40.68.03 27.20.14068.3000
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Microsoft Corporation
Model: Surface Laptop 4
OS: Microsoft Windows 10 Home (Build 19044)
Memory: 8,002,080,768
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 Microsoft Surface (R) Edition
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    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: 1.18.3
    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
    comtypes: 1.1.10
    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
    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: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    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
    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
    pywin32: 303
    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
    WMI: 1.5.1