XMAS: find shortest: problem generating CSV/TSV file

[Yokoyama@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
tsv or pb file not generated after "find shortest"
KeyError: None

File "C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\pandas\core\indexes\base.py", line 3819, in get_loc
raise KeyError(key) from err

See log for complete Python traceback.


Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/yokoyama.nanako/Documents/ChimeraX_structures/ZZH_structure_pred/MapXLonVatpase/6WM2.cif

6WM2.cif title:  
Human V-ATPase in state 1 with SidK and ADP [more info...]  
  
Chain information for 6WM2.cif #1  
---  
Chain | Description | UniProt  
0 | V-type proton ATPase 21 kDa proteolipid subunit | VATO_HUMAN 1-205  
1 2 3 4 5 6 7 8 9 | V-type proton ATPase 16 kDa proteolipid subunit | VATL_HUMAN 1-155  
A B C | V-type proton ATPase catalytic subunit A | VATA_HUMAN 1-617  
D E F | V-type proton ATPase subunit B, brain isoform | VATB2_HUMAN 1-511  
G | V-type proton ATPase subunit D | VATD_HUMAN 1-247  
H I J | V-type proton ATPase subunit E 1 | VATE1_HUMAN 1-226  
K L M | V-type proton ATPase subunit G 1 | VATG1_HUMAN 1-118  
N | V-type proton ATPase subunit F | VATF_HUMAN 1-119  
O | V-type proton ATPase subunit C 1 | VATC1_HUMAN 1-382  
P | V-type proton ATPase subunit H | VATH_HUMAN 1-483  
Q | V-type proton ATPase subunit d 1 | VA0D1_HUMAN 1-351  
R | V-type proton ATPase 116 kDa subunit a isoform 1 | VPP1_HUMAN 1-837  
S | V-type proton ATPase subunit e 1 | VA0E1_HUMAN 1-81  
T | Ribonuclease kappa | RNK_HUMAN 1-137  
U | V-type proton ATPase subunit S1 | VAS1_HUMAN 1-470  
V | Renin receptor | RENR_HUMAN 1-350  
X Y Z | SidK | A0A4T1L9X6_LEGPN 1-573  
  
Non-standard residues in 6WM2.cif #1  
---  
ADP — adenosine-5'-diphosphate  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CLR — cholesterol  
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)  
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
NGA — 2-acetamido-2-deoxy-beta-D-galactopyranose (N-acetyl-beta-D-
galactosamine; 2-acetamido-2-deoxy-beta-D-galactose; 2-acetamido-2-deoxy-D-
galactose; 2-acetamido-2-deoxy-galactose; N-ACETYL-D-GALACTOSAMINE)  
PSF — 1,2-dicaproyl-Sn-phosphatidyl-L-serine (phosphatidylserine)  
PTY — phosphatidylethanolamine  
SIA — N-acetyl-alpha-neuraminic acid (N-acetylneuraminic acid; sialic acid;
alpha-sialic acid; O-SIALIC ACID)  
WJP — methyl
(3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl
dihydrogen diphosphate (dolichol-pp)  
WJS — (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-
propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid  
WSS —
tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-
phosphoryl]oxyethyl]azanium  
  

> show cartoons

> hide atoms

> ui tool show XMAS

  
Peptide pair mapping of XlinkX evidence file:
C:/Users/yokoyama.nanako/Documents/ChimeraX_structures/ZZH_structure_pred/MapXLonVatpase/heklopit_pl3017_frd1ppi_sc151_fdr1rp_rcsb_pdb_sequence_clusters_20251128111153_v_atpase.csv.csv  
Unique peptide pairs: 156 out of 215  
Unique peptide pairs with pseudobonds: 101  
Pseudobonds are stored in
C:/Users/yokoyama.nanako/Documents/ChimeraX_structures/ZZH_structure_pred/MapXLonVatpase/heklopit_pl3017_frd1ppi_sc151_fdr1rp_rcsb_pdb_sequence_clusters_20251128111153_v_atpase.csv_1.pb  
Mapping information is stored in
C:/Users/yokoyama.nanako/Documents/ChimeraX_structures/ZZH_structure_pred/MapXLonVatpase/heklopit_pl3017_frd1ppi_sc151_fdr1rp_rcsb_pdb_sequence_clusters_20251128111153_v_atpase.csv_1.tsv  
Traceback (most recent call last):  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexes\base.py", line 3812, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "pandas/_libs/index.pyx", line 167, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index.pyx", line 175, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index_class_helper.pxi", line 70, in
pandas._libs.index.Int64Engine._check_type  
KeyError: None  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\frame.py", line 4573, in _set_value  
iindex = self.index.get_loc(index)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexes\base.py", line 3819, in get_loc  
raise KeyError(key) from err  
KeyError: None  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexes\base.py", line 3812, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "pandas/_libs/index.pyx", line 167, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index.pyx", line 175, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index_class_helper.pxi", line 19, in
pandas._libs.index.Float64Engine._check_type  
KeyError: None  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\XMAS\tool.py", line 1015, in <lambda>  
self.get_names(names_menu, pbs_dict, f))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\XMAS\tool.py", line 1246, in get_names  
function(pbs_dict, names)  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\XMAS\tool.py", line 1225, in update_distances  
file.df.at[index, "Distance (A)"] = distance  
~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexing.py", line 2603, in __setitem__  
return super().__setitem__(key, value)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexing.py", line 2543, in __setitem__  
self.obj._set_value(*key, value=value, takeable=self._takeable)  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\frame.py", line 4586, in _set_value  
self.loc[index, col] = value  
~~~~~~~~^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexing.py", line 912, in __setitem__  
iloc._setitem_with_indexer(indexer, value, self.name)  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexing.py", line 1923, in _setitem_with_indexer  
nindexer.append(labels.get_loc(key))  
^^^^^^^^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexes\base.py", line 3819, in get_loc  
raise KeyError(key) from err  
KeyError: None  
  
KeyError: None  
  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexes\base.py", line 3819, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexes\base.py", line 3812, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "pandas/_libs/index.pyx", line 167, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index.pyx", line 175, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index_class_helper.pxi", line 19, in
pandas._libs.index.Float64Engine._check_type  
KeyError: None  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\frame.py", line 4573, in _set_value  
iindex = self.index.get_loc(index)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexes\base.py", line 3819, in get_loc  
raise KeyError(key) from err  
KeyError: None  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexes\base.py", line 3812, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "pandas/_libs/index.pyx", line 167, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index.pyx", line 175, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index_class_helper.pxi", line 19, in
pandas._libs.index.Float64Engine._check_type  
KeyError: None  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\XMAS\tool.py", line 1015, in <lambda>  
self.get_names(names_menu, pbs_dict, f))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\XMAS\tool.py", line 1246, in get_names  
function(pbs_dict, names)  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\XMAS\tool.py", line 1225, in update_distances  
file.df.at[index, "Distance (A)"] = distance  
~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexing.py", line 2603, in __setitem__  
return super().__setitem__(key, value)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexing.py", line 2543, in __setitem__  
self.obj._set_value(*key, value=value, takeable=self._takeable)  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\frame.py", line 4586, in _set_value  
self.loc[index, col] = value  
~~~~~~~~^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexing.py", line 912, in __setitem__  
iloc._setitem_with_indexer(indexer, value, self.name)  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexing.py", line 1923, in _setitem_with_indexer  
nindexer.append(labels.get_loc(key))  
^^^^^^^^^^^^^^^^^^^  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexes\base.py", line 3819, in get_loc  
raise KeyError(key) from err  
KeyError: None  
  
KeyError: None  
  
File
"C:\Users\yokoyama.nanako\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\pandas\core\indexes\base.py", line 3819, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4502
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex SFF 7010
OS: Microsoft Windows 11 Pro (Build 26200)
Memory: 34,033,348,608
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i5-13500
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    autocommand: 2.2.2
    babel: 2.17.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
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    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
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    ChimeraX-Centroids: 1.4
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    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
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    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
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    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
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    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
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    ChimeraX-MapFit: 2.0
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    ChimeraX-WebServices: 1.1.5
    ChimeraX-XMAS: 1.1.3
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    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.10.0
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    cycler: 0.12.1
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    executing: 2.2.0
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    imagesize: 1.4.1
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    ndindex: 1.10.0
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    OpenMM-CUDA-12: 8.2.0
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    packaging: 24.2
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    platformdirs: 4.2.2
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