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#18702 accepted defect

alignment widget not properly destroying when tool closed

Reported by:	2231014@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
KeyError: 

File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\modeller\tool.py", line 264, in launch_modeller
seq_menu = self.seq_menu[aln]
~~~~~~~~~~~~~^^^^^

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 D:\Desktop\突变测序\M483.pdb format pdb

M483.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for M483.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in M483.pdb #1  
---  
CU — (CU)  
O — (O)  
  
Computing secondary structure  

> select :CU

4 atoms, 4 residues, 1 model selected  

> select :O

1 atom, 1 residue, 1 model selected  

> select :O

1 atom, 1 residue, 1 model selected  

> select :CU

4 atoms, 4 residues, 1 model selected  

> select :O

1 atom, 1 residue, 1 model selected  

> select :O

1 atom, 1 residue, 1 model selected  

> select :CU

4 atoms, 4 residues, 1 model selected  

> select :CU

4 atoms, 4 residues, 1 model selected  

> select :O

1 atom, 1 residue, 1 model selected  

> select :CU

4 atoms, 4 residues, 1 model selected  

> select :CU

4 atoms, 4 residues, 1 model selected  

> select :CU

4 atoms, 4 residues, 1 model selected  

> select :CU

4 atoms, 4 residues, 1 model selected  

> select :CU

4 atoms, 4 residues, 1 model selected  

> select :O

1 atom, 1 residue, 1 model selected  

> select /A:63-490

3367 atoms, 3451 bonds, 428 residues, 1 model selected  

> select /A:63-490

3367 atoms, 3451 bonds, 428 residues, 1 model selected  

> select add #1

3372 atoms, 3451 bonds, 433 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

3372 atoms, 3451 bonds, 433 residues, 1 model selected  

> select subtract #1

Nothing selected  

> mlp

Map values for surface "M483.pdb_A SES surface": minimum -28.45, mean -5.085,
maximum 25.95  

> set bgColor white

Fetching url
https://www.colourlovers.com/api/palettes?keywords=Giant%20Goldfish&format=json&numResults=100
failed:  
HTTP Error 403: Forbidden  

> mlp method type5 palette

Missing "palette" keyword's argument  

> mlp method type5

Map values for surface "M483.pdb_A SES surface": minimum -95.36, mean -19.5,
maximum 99.07  

> mlp method type5

Map values for surface "M483.pdb_A SES surface": minimum -95.36, mean -19.5,
maximum 99.07  

> mlp method type5 palette piyg

Map values for surface "M483.pdb_A SES surface": minimum -95.36, mean -19.5,
maximum 99.07  
Fetching url
https://www.colourlovers.com/api/palettes?keywords=Giant%20Goldfish&format=json&numResults=100
failed:  
HTTP Error 403: Forbidden  

> mlp method type5 palette piyg

Map values for surface "M483.pdb_A SES surface": minimum -95.36, mean -19.5,
maximum 99.07  

> select add #1

3372 atoms, 3451 bonds, 433 residues, 2 models selected  

> select subtract #1

1 model selected  

> hide #!1 target m

[Repeated 1 time(s)]

> close #1

> open D:\Desktop\突变测序\M483.pdb format pdb

M483.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for M483.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in M483.pdb #1  
---  
CU — (CU)  
O — (O)  
  
Computing secondary structure  

> open D:/Desktop/脚本.cxc

> setattr :asp res kdh -3.5 create true

Assigning kdh attribute to 38 items  

> setattr :glu res kdh -3.5 create true

Assigning kdh attribute to 27 items  

> setattr :asn res kdh -3.5 create true

Assigning kdh attribute to 26 items  

> setattr :gln res kdh -3.5 create true

Assigning kdh attribute to 15 items  

> setattr :lys res kdh -3.9 create true

Assigning kdh attribute to 30 items  

> setattr :arg res kdh -4.5 create true

Assigning kdh attribute to 8 items  

> setattr :his res kdh -3.2 create true

Assigning kdh attribute to 19 items  

> setattr :gly res kdh -0.4 create true

Assigning kdh attribute to 33 items  

> setattr :pro res kdh -1.6 create true

Assigning kdh attribute to 23 items  

> setattr :ser res kdh -0.8 create true

Assigning kdh attribute to 22 items  

> setattr :thr res kdh -0.7 create true

Assigning kdh attribute to 30 items  

> setattr :cys res kdh 2.5 create true

Assigning kdh attribute to 1 item  

> setattr :met res kdh 1.9 create true

Assigning kdh attribute to 21 items  

> setattr :mse res kdh 1.9 create true

Assigning kdh attribute to 0 items  

> setattr :ala res kdh 1.8 create true

Assigning kdh attribute to 23 items  

> setattr :val res kdh 4.2 create true

Assigning kdh attribute to 36 items  

> setattr :ile res kdh 4.5 create true

Assigning kdh attribute to 17 items  

> setattr :leu res kdh 3.8 create true

Assigning kdh attribute to 22 items  

> setattr :phe res kdh 2.8 create true

Assigning kdh attribute to 16 items  

> setattr :trp res kdh -0.9 create true

Assigning kdh attribute to 6 items  

> setattr :tyr res kdh -1.3 create true

Assigning kdh attribute to 15 items  

> surface protein

> hide protein atoms

> color byattribute kdh protein target rs palette dodgerblue:white:orangered
> noValueColor gray

428 residues, 1 surfaces, atom kdh range -4.5 to 4.5  
executed 脚本.cxc  

> undo

[Repeated 2 time(s)]

> close

> open D:\Desktop\突变测序\M483.pdb format pdb

M483.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for M483.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in M483.pdb #1  
---  
CU — (CU)  
O — (O)  
  
Computing secondary structure  

> open D:/Desktop/脚本.cxc

> setattr :asp res kdh -3.5 create true

Assigning kdh attribute to 38 items  

> setattr :glu res kdh -3.5 create true

Assigning kdh attribute to 27 items  

> setattr :asn res kdh -3.5 create true

Assigning kdh attribute to 26 items  

> setattr :gln res kdh -3.5 create true

Assigning kdh attribute to 15 items  

> setattr :lys res kdh -3.9 create true

Assigning kdh attribute to 30 items  

> setattr :arg res kdh -4.5 create true

Assigning kdh attribute to 8 items  

> setattr :his res kdh -3.2 create true

Assigning kdh attribute to 19 items  

> setattr :gly res kdh -0.4 create true

Assigning kdh attribute to 33 items  

> setattr :pro res kdh -1.6 create true

Assigning kdh attribute to 23 items  

> setattr :ser res kdh -0.8 create true

Assigning kdh attribute to 22 items  

> setattr :thr res kdh -0.7 create true

Assigning kdh attribute to 30 items  

> setattr :cys res kdh 2.5 create true

Assigning kdh attribute to 1 item  

> setattr :met res kdh 1.9 create true

Assigning kdh attribute to 21 items  

> setattr :mse res kdh 1.9 create true

Assigning kdh attribute to 0 items  

> setattr :ala res kdh 1.8 create true

Assigning kdh attribute to 23 items  

> setattr :val res kdh 4.2 create true

Assigning kdh attribute to 36 items  

> setattr :ile res kdh 4.5 create true

Assigning kdh attribute to 17 items  

> setattr :leu res kdh 3.8 create true

Assigning kdh attribute to 22 items  

> setattr :phe res kdh 2.8 create true

Assigning kdh attribute to 16 items  

> setattr :trp res kdh -0.9 create true

Assigning kdh attribute to 6 items  

> setattr :tyr res kdh -1.3 create true

Assigning kdh attribute to 15 items  

> surface protein

> hide protein atoms

> color byattribute kdh protein target rs palette dodgerblue:white:orangered
> noValueColor gray

428 residues, 1 surfaces, atom kdh range -4.5 to 4.5  
executed 脚本.cxc  

> select :CU

4 atoms, 4 residues, 1 model selected  

> undo

[Repeated 2 time(s)]

> close

> open D:\Desktop\突变测序\M483.pdb format pdb

M483.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for M483.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in M483.pdb #1  
---  
CU — (CU)  
O — (O)  
  
Computing secondary structure  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> ui mousemode right "link markers"

> ui mousemode right "mark surface"

> ui mousemode right distance

> select //chain_id='_':1@CU

Nothing selected  

> select /A:478@ND1

1 atom, 1 residue, 1 model selected  

> select //chain_id='_':1@CU

Nothing selected  

> ui mousemode right distance

> select //chain_id='_':1@CU

Nothing selected  

> ui mousemode right distance

> close

> ui tool show "Blast Protein"

> open D:/Desktop/突变测序/新建文本文档.fasta

Summary of feedback from opening D:/Desktop/突变测序/新建文本文档.fasta  
---  
note | Alignment identifier is 新建文本文档.fasta  
  
Opened 1 sequence from 新建文本文档.fasta  

> open D:\Desktop\突变测序\新建文本文档.fasta format fasta

Summary of feedback from opening D:\Desktop\突变测序\新建文本文档.fasta  
---  
notes | Destroying pre-existing alignment with identifier 新建文本文档.fasta  
Alignment identifier is 新建文本文档.fasta  
  
Opened 1 sequence from 新建文本文档.fasta  

> ui tool show "Blast Protein"

> open D:/Desktop/突变测序/McoF.fasta

Summary of feedback from opening D:/Desktop/突变测序/McoF.fasta  
---  
note | Alignment identifier is McoF.fasta  
  
Opened 1 sequence from McoF.fasta  

> open D:\Desktop\突变测序\McoF.fasta format fasta

Summary of feedback from opening D:\Desktop\突变测序\McoF.fasta  
---  
notes | Destroying pre-existing alignment with identifier McoF.fasta  
Alignment identifier is McoF.fasta  
  
Opened 1 sequence from McoF.fasta  

> ui tool show "Blast Protein"

> ui tool show "Modeller Comparative"

> open D:\Desktop\突变测序\McoF.fasta format fasta

Summary of feedback from opening D:\Desktop\突变测序\McoF.fasta  
---  
note | Alignment identifier is McoF.fasta  
  
Opened 1 sequence from McoF.fasta  

> open D:\Desktop\突变测序\McoF.fasta format fasta

Summary of feedback from opening D:\Desktop\突变测序\McoF.fasta  
---  
notes | Destroying pre-existing alignment with identifier McoF.fasta  
Alignment identifier is McoF.fasta  
  
Opened 1 sequence from McoF.fasta  

> open D:\Desktop\突变测序\McoF.fasta format fasta

Summary of feedback from opening D:\Desktop\突变测序\McoF.fasta  
---  
note | Alignment identifier is McoF.fasta  
  
Opened 1 sequence from McoF.fasta  

> ui tool show "Blast Protein"

Cannot run BLAST without some kind of sequence. Please open a model and select
a chain, or input sequences or a UniProt ID.  

> open D:\Desktop\突变测序\McoF.fasta format fasta

Summary of feedback from opening D:\Desktop\突变测序\McoF.fasta  
---  
notes | Destroying pre-existing alignment with identifier McoF.fasta  
Alignment identifier is McoF.fasta  
  
Opened 1 sequence from McoF.fasta  
Cannot run BLAST without some kind of sequence. Please open a model and select
a chain, or input sequences or a UniProt ID.  

> blastprotein
> MKAAILRTIILASSVAVFAAGCSKVSNMNGMDHSKMSMGSNPTSNSSESATSAKLTTATPVVDGKEFTITAQESNLEVEKGKTIPVWTFNNSVPGPQIRVKVGDTVKVNLKNQLKQPVSIHWHGYPVPNNMDGIPGVTQDAVEPGKTFTYEFKATVPGTYWYHSHQDSVNQVDKGLYGSLVVEDPQDTADRDYTLVLDEWMSSGDMDMDNDGMNMSGHDMSMYDLYTINGKTGDAIDKLTVKEGEKVKLRLINAGYITHRMHLHGHSFKVVASDGQPVNDPAVIKDQFVSIAPGERYDIEFTADYPGNWLLEEHAKDNRAQNMRAVIQYEGSNAKPDPSDAFEELPDFDLEKYGTMSASAFSLDQSFDEDVTMNLNTEMRNGDMVYTINGKVFPDTDTIKVKKGDKVKVTFVNQSRMDDHPMHLHGHFFQVLSKNGKPVQGSPIMKDTLNVKPGETYEVAFEADNPGEWMFHCHDLHHASAGMVTDVMYDDYQNNYTPDPNVNNVPE
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 600 version None name bp1

Webservices job id: YGXN8ZKRZH2MCGM2  
Webservices job finished: YGXN8ZKRZH2MCGM2  
Alignment identifier is bp1 [1]  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]  

> ui tool show "Modeller Comparative"

Traceback (most recent call last):  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\modeller\tool.py",
line 347, in _update_sequence_menus  
row_info.fieldItem.widget().destroy()  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\seqalign\widgets.py",
line 104, in destroy  
self.alignment.remove_observer(self)  
File "D:\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 780, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "D:\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 780, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  
Alignment identifier is bp1 [2]  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [2]  
Alignment identifier is bp1 [3]  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [3]  

> ui tool show "Modeller Comparative"

> modeller comparative "bp1 [2]:2" numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Alignment bp1 [2] has no associated chains  

> modeller comparative "bp1 [2]:2" numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Alignment bp1 [2] has no associated chains  

> open D:\Desktop\突变测序\McoF.fasta format fasta

Summary of feedback from opening D:\Desktop\突变测序\McoF.fasta  
---  
note | Alignment identifier is McoF.fasta  
  
Opened 1 sequence from McoF.fasta  

> ui tool show "Blast Protein"

> select clear

[Repeated 1 time(s)]

> blastprotein
> MKAAILRTIILASSVAVFAAGCSKVSNMNGMDHSKMSMGSNPTSNSSESATSAKLTTATPVVDGKEFTITAQESNLEVEKGKTIPVWTFNNSVPGPQIRVKVGDTVKVNLKNQLKQPVSIHWHGYPVPNNMDGIPGVTQDAVEPGKTFTYEFKATVPGTYWYHSHQDSVNQVDKGLYGSLVVEDPQDTADRDYTLVLDEWMSSGDMDMDNDGMNMSGHDMSMYDLYTINGKTGDAIDKLTVKEGEKVKLRLINAGYITHRMHLHGHSFKVVASDGQPVNDPAVIKDQFVSIAPGERYDIEFTADYPGNWLLEEHAKDNRAQNMRAVIQYEGSNAKPDPSDAFEELPDFDLEKYGTMSASAFSLDQSFDEDVTMNLNTEMRNGDMVYTINGKVFPDTDTIKVKKGDKVKVTFVNQSRMDDHPMHLHGHFFQVLSKNGKPVQGSPIMKDTLNVKPGETYEVAFEADNPGEWMFHCHDLHHASAGMVTDVMYDDYQNNYTPDPNVNNVPE
> database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 600 version 1 name bp2

Webservices job id: OAGR7M51IM7PT4V0  

> blastprotein
> MKAAILRTIILASSVAVFAAGCSKVSNMNGMDHSKMSMGSNPTSNSSESATSAKLTTATPVVDGKEFTITAQESNLEVEKGKTIPVWTFNNSVPGPQIRVKVGDTVKVNLKNQLKQPVSIHWHGYPVPNNMDGIPGVTQDAVEPGKTFTYEFKATVPGTYWYHSHQDSVNQVDKGLYGSLVVEDPQDTADRDYTLVLDEWMSSGDMDMDNDGMNMSGHDMSMYDLYTINGKTGDAIDKLTVKEGEKVKLRLINAGYITHRMHLHGHSFKVVASDGQPVNDPAVIKDQFVSIAPGERYDIEFTADYPGNWLLEEHAKDNRAQNMRAVIQYEGSNAKPDPSDAFEELPDFDLEKYGTMSASAFSLDQSFDEDVTMNLNTEMRNGDMVYTINGKVFPDTDTIKVKKGDKVKVTFVNQSRMDDHPMHLHGHFFQVLSKNGKPVQGSPIMKDTLNVKPGETYEVAFEADNPGEWMFHCHDLHHASAGMVTDVMYDDYQNNYTPDPNVNNVPE
> database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 600 version 1 name bp3

Webservices job id: THJAE5KRGE365TJT  

> blastprotein
> MKAAILRTIILASSVAVFAAGCSKVSNMNGMDHSKMSMGSNPTSNSSESATSAKLTTATPVVDGKEFTITAQESNLEVEKGKTIPVWTFNNSVPGPQIRVKVGDTVKVNLKNQLKQPVSIHWHGYPVPNNMDGIPGVTQDAVEPGKTFTYEFKATVPGTYWYHSHQDSVNQVDKGLYGSLVVEDPQDTADRDYTLVLDEWMSSGDMDMDNDGMNMSGHDMSMYDLYTINGKTGDAIDKLTVKEGEKVKLRLINAGYITHRMHLHGHSFKVVASDGQPVNDPAVIKDQFVSIAPGERYDIEFTADYPGNWLLEEHAKDNRAQNMRAVIQYEGSNAKPDPSDAFEELPDFDLEKYGTMSASAFSLDQSFDEDVTMNLNTEMRNGDMVYTINGKVFPDTDTIKVKKGDKVKVTFVNQSRMDDHPMHLHGHFFQVLSKNGKPVQGSPIMKDTLNVKPGETYEVAFEADNPGEWMFHCHDLHHASAGMVTDVMYDDYQNNYTPDPNVNNVPE
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 600 version 1 name bp4

Webservices job id: SF79N1CA897G6H3K  
Webservices job finished: SF79N1CA897G6H3K  
Alignment identifier is bp4 [1]  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp4 [1]  

> open pdb:6VOX

Summary of feedback from opening 6VOX fetched from pdb  
---  
notes | Fetching compressed mmCIF 6vox from http://files.rcsb.org/download/6vox.cif  
Fetching CCD C2O from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/C2O/C2O.cif  
Fetching CCD CU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/CU/CU.cif  
  
6vox title:  
Crystal structure of multi-copper oxidase from Pseudomonas Parafulva [more
info...]  
  
Chain information for 6vox #1  
---  
Chain | Description | UniProt  
A | Copper oxidase | A0A0A7JLK4_9PSED 40-459  
  
Non-standard residues in 6vox #1  
---  
C2O — Cu-O-Cu linkage  
CU — copper (II) ion  
  

> open pdb:9CPM

Summary of feedback from opening 9CPM fetched from pdb  
---  
notes | Fetching compressed mmCIF 9cpm from http://files.rcsb.org/download/9cpm.cif  
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif  
  
9cpm title:  
Thermus thermophilus HB27 laccase (Tth-Lac) mutant with partial deletion of
beta-hairpin sequence [more info...]  
  
Chain information for 9cpm #2  
---  
Chain | Description | UniProt  
A | Laccase | Q72HW2_THET2 23-462  
  
Non-standard residues in 9cpm #2  
---  
CU — copper (II) ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
9 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> matchmaker #2/A to #1/A

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 6VOX_A, chain A (#1) with 9CPM_A, chain A (#2), sequence alignment
score = 467  
RMSD between 208 pruned atom pairs is 1.090 angstroms; (across all 362 pairs:
5.762)  
  

> ui tool show "Modeller Comparative"

Traceback (most recent call last):  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\modeller\tool.py",
line 347, in _update_sequence_menus  
row_info.fieldItem.widget().destroy()  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\seqalign\widgets.py",
line 104, in destroy  
self.alignment.remove_observer(self)  
File "D:\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 780, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "D:\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 780, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\modeller\tool.py",
line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x000001EA0F5AA210>  
  
KeyError:  
  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\modeller\tool.py",
line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\modeller\tool.py",
line 264, in launch_modeller  
seq_menu = self.seq_menu[aln]  
~~~~~~~~~~~~~^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x000001EA0F5AA210>  
  
KeyError:  
  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\modeller\tool.py",
line 264, in launch_modeller  
seq_menu = self.seq_menu[aln]  
~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 24.7.1.240711
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: LENOVO
Model: 21D0
OS: Microsoft Windows 10 家庭中文版 (Build 19045)
Memory: 14,702,026,752
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 6800H with Radeon Graphics         
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    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
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    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
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    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: 2.5.1
    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: 1.6.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    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: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    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: 3.2.3
    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: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

Change History (4)

comment:1 by Eric Pettersen, 2 months ago

Platform:	→ all
Project:	→ ChimeraX

Hi Huang,

Thanks for reporting this problem. It took me awhile to work out the steps to reproduce it, but I have figured them out now. The steps are:

open an alignment
open Modeller Comparative
close the alignment
open Modeller Comparative

I'll look into fixing this in the next few days.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:2 by Eric Pettersen, 2 months ago

Component:	Unassigned → Sequence
Owner:	set to Eric Pettersen
Status:	new → accepted
Summary:	ChimeraX bug report submission → alignment widget not properly destroying when tool closed

comment:3 by Eric Pettersen, 2 months ago

Message that was rejected by email-to-Trac:

Thank you very much for your reply. The bug has been resolved somehome . Additionally, the note pointed to the line of code with "launch modeller" (I should have included the text when submitting the bug report, as there were two differents segments before and after click). Buy I Did select "web service" at that time, I urgently installed Modeller as a supplementary measure, followed online guidance to configure it, and then restarted ChimeraX to successfully complete the homology modeling（without closing any widgets）. I am still unsure whether not having Modeller installed initially had any impact.
Huang

comment:4 by Eric Pettersen, 2 months ago

The bug isn't really related to having Modeller installed. I'm glad you got things to work.

--Eric

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