Opened 5 months ago

Last modified 5 months ago

#17650 assigned defect

XMAS: KeyError: 'PSMID'

Reported by: chimerax-bug-report@… Owned by: Richard Scheltema
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-15.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202503080840 (2025-03-08 08:40:29 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10.dev202503080840 (2025-03-08)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show XMAS

> open " 8JRI" fromDatabase pdb format mmcif

PDB identifiers are either 4 or 8 characters long, got " 8JRI"  

> open 8jri fromDatabase pdb format mmcif

Summary of feedback from opening 8jri fetched from pdb  
---  
notes | Fetching compressed mmCIF 8jri from http://files.rcsb.org/download/8jri.cif  
Fetching CCD ADP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif  
Fetching CCD ATP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
  
8jri title:  
Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) without
any bound substrate. [more info...]  
  
Chain information for 8jri #1  
---  
Chain | Description | UniProt  
A | 26S protease regulatory subunit 7 | PRS7_HUMAN 1-433  
B | 26S protease regulatory subunit 4 | PRS4_HUMAN 1-440  
C | 26S protease regulatory subunit 8 | PRS8_HUMAN 1-406  
D | 26S protease regulatory subunit 6B | PRS6B_HUMAN 1-418  
E | 26S protease regulatory subunit 10B | PRS10_HUMAN 1-389  
F | 26S protease regulatory subunit 6A | PRS6A_HUMAN 1-439  
G | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246  
H | Proteasome subunit alpha type-2 | PSA2_HUMAN 1-234  
I | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261  
J | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248  
K | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241  
L | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263  
M | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254  
U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN 1-953  
V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN 1-534  
W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN 1-456  
X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN 1-422  
Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN 1-389  
Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN 1-324  
a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN 1-376  
b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN 1-377  
c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN 1-310  
d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN -92-257  
e | 26S proteasome complex subunit DSS1 | DSS1_HUMAN 1-70  
f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN 1-908  
  
Non-standard residues in 8jri #1  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
  

> open 8jrt fromDatabase pdb format mmcif

Summary of feedback from opening 8jrt fetched from pdb  
---  
note | Fetching compressed mmCIF 8jrt from http://files.rcsb.org/download/8jrt.cif  
  
8jrt title:  
Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) bound to
K11/K48-branched ubiquitin (Ub) chain composed of three Ub. [more info...]  
  
Chain information for 8jrt #2  
---  
Chain | Description | UniProt  
A | 26S protease regulatory subunit 7 | PRS7_HUMAN 1-433  
B | 26S protease regulatory subunit 4 | PRS4_HUMAN 1-440  
C | 26S protease regulatory subunit 8 | PRS8_HUMAN 1-406  
D | 26S protease regulatory subunit 6B | PRS6B_HUMAN 1-418  
E | 26S protease regulatory subunit 10B | PRS10_HUMAN 1-389  
F | 26S protease regulatory subunit 6A | PRS6A_HUMAN 1-439  
G | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246  
H | Proteasome subunit alpha type-2 | PSA2_HUMAN 1-234  
I | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261  
J | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248  
K | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241  
L | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263  
M | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254  
U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN 1-953  
V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN 1-534  
W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN 1-456  
X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN 1-422  
Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN 1-389  
Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN 1-324  
a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN 1-376  
b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN 1-377  
c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN 1-310  
d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN -92-257  
e | 26S proteasome complex subunit DSS1 | DSS1_HUMAN 1-70  
f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN 1-908  
u v w | Polyubiquitin-B | UBB_HUMAN 1-76  
  
Non-standard residues in 8jrt #2  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
  

> open 8jti fromDatabase pdb format mmcif

Summary of feedback from opening 8jti fetched from pdb  
---  
note | Fetching compressed mmCIF 8jti from http://files.rcsb.org/download/8jti.cif  
  
8jti title:  
Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched
ubiquitin (Ub) chain composed of four Ub. [more info...]  
  
Chain information for 8jti #3  
---  
Chain | Description | UniProt  
A | 26S protease regulatory subunit 7 | PRS7_HUMAN 1-433  
B | 26S protease regulatory subunit 4 | PRS4_HUMAN 1-440  
C | 26S protease regulatory subunit 8 | PRS8_HUMAN 1-406  
D | 26S protease regulatory subunit 6B | PRS6B_HUMAN 1-418  
E | 26S protease regulatory subunit 10B | PRS10_HUMAN 1-389  
F | 26S protease regulatory subunit 6A | PRS6A_HUMAN 1-439  
G | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246  
H | Proteasome subunit alpha type-2 | PSA2_HUMAN 1-234  
I | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261  
J | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248  
K | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241  
L | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263  
M | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254  
U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN 1-953  
V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN 1-534  
W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN 1-456  
X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN 1-422  
Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN 1-389  
Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN 1-324  
a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN 1-376  
b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN 1-377  
c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN 1-310  
d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN -92-257  
e | 26S proteasome complex subunit DSS1 | DSS1_HUMAN 1-70  
f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN 1-908  
u v w x | Polyubiquitin-B | UBB_HUMAN 1-76  
  
Non-standard residues in 8jti #3  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
  

> open 8k0g fromDatabase pdb format mmcif

Summary of feedback from opening 8k0g fetched from pdb  
---  
note | Fetching compressed mmCIF 8k0g from http://files.rcsb.org/download/8k0g.cif  
  
8k0g title:  
Cryo-EM structure of human 26S RP (Ed state) bound to K11/K48-branched
ubiquitin (Ub) chain composed of four Ub. [more info...]  
  
Chain information for 8k0g #4  
---  
Chain | Description | UniProt  
A | 26S protease regulatory subunit 7 | PRS7_HUMAN 1-433  
B | 26S protease regulatory subunit 4 | PRS4_HUMAN 1-440  
C | 26S protease regulatory subunit 8 | PRS8_HUMAN 1-406  
D | 26S protease regulatory subunit 6B | PRS6B_HUMAN 1-418  
E | 26S protease regulatory subunit 10B | PRS10_HUMAN 1-389  
F | 26S protease regulatory subunit 6A | PRS6A_HUMAN 1-439  
G | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246  
H | Proteasome subunit alpha type-2 | PSA2_HUMAN 1-234  
I | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261  
J | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248  
K | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241  
L | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263  
M | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254  
U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN 1-953  
V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN 1-534  
W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN 1-456  
X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN 1-422  
Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN 1-389  
Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN 1-324  
a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN 1-376  
b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN 1-377  
c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN 1-310  
d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN -92-257  
e | 26S proteasome complex subunit DSS1 | DSS1_HUMAN 1-70  
f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN 1-908  
u v w x | Polyubiquitin-B | UBB_HUMAN 1-76  
y | Protein SIC1 | SIC1_YEAST -6-42  
  
Non-standard residues in 8k0g #4  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
  
Traceback (most recent call last):  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3805, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc  
File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'PSMID'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 105, in __init__  
self.engines[engine][1](df)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores  
function(peptide_pairs, df, xi_alternative)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 218, in parse_xi_pos_ids  
params[key] = df[col_name].tolist()  
~~^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/frame.py", line 4102, in __getitem__  
indexer = self.columns.get_loc(key)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
KeyError: 'PSMID'  
  
KeyError: 'PSMID'  
  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3805, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc  
File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'PSMID'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 105, in __init__  
self.engines[engine][1](df)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores  
function(peptide_pairs, df, xi_alternative)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 218, in parse_xi_pos_ids  
params[key] = df[col_name].tolist()  
~~^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/frame.py", line 4102, in __getitem__  
indexer = self.columns.get_loc(key)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
KeyError: 'PSMID'  
  
KeyError: 'PSMID'  
  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  
Please select pseudobonds  
Traceback (most recent call last):  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3805, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc  
File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'PSMID'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 105, in __init__  
self.engines[engine][1](df)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores  
function(peptide_pairs, df, xi_alternative)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 218, in parse_xi_pos_ids  
params[key] = df[col_name].tolist()  
~~^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/frame.py", line 4102, in __getitem__  
indexer = self.columns.get_loc(key)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
KeyError: 'PSMID'  
  
KeyError: 'PSMID'  
  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3805, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc  
File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'PSMID'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 105, in __init__  
self.engines[engine][1](df)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores  
function(peptide_pairs, df, xi_alternative)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 218, in parse_xi_pos_ids  
params[key] = df[col_name].tolist()  
~~^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/frame.py", line 4102, in __getitem__  
indexer = self.columns.get_loc(key)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
KeyError: 'PSMID'  
  
KeyError: 'PSMID'  
  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3805, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc  
File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'PSMID'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 105, in __init__  
self.engines[engine][1](df)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores  
function(peptide_pairs, df, xi_alternative)  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/XMAS/read_evidence.py", line 218, in parse_xi_pos_ids  
params[key] = df[col_name].tolist()  
~~^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/frame.py", line 4102, in __getitem__  
indexer = self.columns.get_loc(key)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
KeyError: 'PSMID'  
  
KeyError: 'PSMID'  
  
File "/Users/hsu/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/pandas/core/indexes/base.py", line 3812, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,8
      Model Number: MX2H3TA/A
      Chip: Apple M4 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 11881.41.5

Software:

    System Software Overview:

      System Version: macOS 15.1 (24B2083)
      Kernel Version: Darwin 24.1.0
      Time since boot: 12 days, 6 hours, 52 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL P2719H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    autocommand: 2.2.2
    babel: 2.17.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.2.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.19.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202503080840
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    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
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.7
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.0.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.44
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    coverage: 7.6.12
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    et_xmlfile: 2.0.0
    executing: 2.2.0
    filelock: 3.17.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    inflect: 7.3.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.collections: 5.1.0
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openpyxl: 3.1.5
    openvr: 1.26.701
    packaging: 24.2
    packaging: 24.2
    pandas: 2.2.3
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.1
    pyzmq: 26.2.1
    qtconsole: 5.5.2
    QtPy: 2.4.3
    QtRangeSlider: 0.1.5
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    seaborn: 0.13.2
    setuptools: 75.8.2
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.1.3
    sphinx-autodoc-typehints: 3.0.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2025.1
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel: 0.43.0
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (1)

comment:1 by pett, 5 months ago

Component: Unassigned → Third Party
Owner: set to Richard Scheltema
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → XMAS: KeyError: 'PSMID'
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