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Opened 9 hours ago
Closed 29 minutes ago
#19521 closed defect (duplicate)
alignment widget not properly destroying when tool closed
| Reported by: | 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-10-10.0.22000
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:/Users/Pina/Desktop/Work/predictions based off 1LIL model.cxs"
Log from Tue Oct 14 10:05:07 2025UCSF 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 5bv7 format mmcif fromDatabase pdb
5bv7 title:
Crystal structure of human LCAT (L4F, N5D) in complex with Fab of an agonistic
antibody [more info...]
Chain information for 5bv7 #1
---
Chain | Description | UniProt
A | Phosphatidylcholine-sterol acyltransferase | LCAT_HUMAN 1-416
B | Fab1 light chain |
C | Fab1 heavy chain |
H | 27C3 heavy chain |
L | 27C3 light chain |
Non-standard residues in 5bv7 #1
---
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)
5bv7 mmCIF Assemblies
---
1| author_defined_assembly
2| author_and_software_defined_assembly
> open "C:/Users/olgad/Desktop/gLC C214 two chains.fasta"
Summary of feedback from opening C:/Users/olgad/Desktop/gLC C214 two
chains.fasta
---
notes | Alignment identifier is gLC C214 two chains.fasta
Associated 5bv7 chain L to chainA with 3 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment gLC C214 two chains.fasta
Opened 2 sequences from gLC C214 two chains.fasta
> select clear
[Repeated 1 time(s)]
> open 1lil fromDatabase pdb format mmcif
Summary of feedback from opening 1lil fetched from pdb
---
note | Fetching compressed mmCIF 1lil from http://files.rcsb.org/download/1lil.cif
1lil title:
Bence jones protein cle, A λ III immunoglobulin light-chain dimer [more
info...]
Chain information for 1lil #2
---
Chain | Description | UniProt
A B | LAMBDA III BENCE JONES PROTEIN CLE | LAC_HUMAN 2-213
> hide #!1 models
> sequence associate /A chainA
Associated 1lil chain A to chainA with 36 mismatches and/or gaps
> sequence associate /B chainB
Associated 5bv7 chain B to chainB with 35 mismatches and/or gaps
Associated 1lil chain B to chainB with 36 mismatches and/or gaps
> modeller comparative #1/A,B chainA,chainB multichain true nmodels 1 key
> MODELIRANJE
Missing or invalid "targets" argument: No sequences match '#1/A,B'
> ui tool show "Modeller Comparative"
> modeller comparative #2/A,B chainA,chainB multichain true nmodels 1 key
> MODELIRANJE
Missing or invalid "targets" argument: No sequences match '#2/A,B'
> ui tool show "Modeller Comparative"
> modeller comparative "gLC C214 two chains.fasta:1" numModels 5 fast false
> multichain true hetPreserve true hydrogens true waterPreserve true
Cannot preserve water/het with more than one template per target; not
preserving
Webservices job id: KRLU4SM7RM2PSGQD
> ui tool show "Modeller Comparative"
> modeller comparative "gLC C214 two chains.fasta:2" numModels 5 fast false
> multichain true hetPreserve true hydrogens true waterPreserve true
Cannot preserve water/het with more than one template per target; not
preserving
Webservices job id: KIC81ET5ZM3BWTHZ
> hide #2 atoms
[Repeated 1 time(s)]
> show #2 atoms
> hide #2 atoms
Webservices job finished: KRLU4SM7RM2PSGQD
Modeller job (ID KRLU4SM7RM2PSGQD) finished
Parameters
---
Chain pairing | ss
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 1lil, chain A (#2) with chainA, chain A (#), sequence alignment
score = 874.7
Matchmaker 1lil, chain B (#2) with chainA, chain B (#), sequence alignment
score = 948.7
RMSD between 184 pruned atom pairs is 0.691 angstroms; (across all 424 pairs:
20.495)
Parameters
---
Chain pairing | ss
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 1lil, chain A (#2) with chainA, chain A (#), sequence alignment
score = 851.9
Matchmaker 1lil, chain B (#2) with chainA, chain B (#), sequence alignment
score = 927.1
RMSD between 185 pruned atom pairs is 0.696 angstroms; (across all 424 pairs:
20.353)
Parameters
---
Chain pairing | ss
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 1lil, chain A (#2) with chainA, chain A (#), sequence alignment
score = 841.7
Matchmaker 1lil, chain B (#2) with chainA, chain B (#), sequence alignment
score = 927.1
RMSD between 186 pruned atom pairs is 0.637 angstroms; (across all 424 pairs:
20.377)
Parameters
---
Chain pairing | ss
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 1lil, chain A (#2) with chainA, chain A (#), sequence alignment
score = 859.7
Matchmaker 1lil, chain B (#2) with chainA, chain B (#), sequence alignment
score = 930.7
RMSD between 183 pruned atom pairs is 0.688 angstroms; (across all 424 pairs:
20.436)
Parameters
---
Chain pairing | ss
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 1lil, chain A (#2) with chainA, chain A (#), sequence alignment
score = 842.9
Matchmaker 1lil, chain B (#2) with chainA, chain B (#), sequence alignment
score = 941.5
RMSD between 189 pruned atom pairs is 0.694 angstroms; (across all 424 pairs:
19.295)
Associated chainA chain A to chainA with 0 mismatches
Associated chainA chain B to chainA with 0 mismatches
Associated chainA chain A to chainA with 0 mismatches
Associated chainA chain B to chainA with 0 mismatches
Associated chainA chain A to chainA with 0 mismatches
Associated chainA chain B to chainA with 0 mismatches
Associated chainA chain A to chainA with 0 mismatches
Associated chainA chain B to chainA with 0 mismatches
Associated chainA chain A to chainA with 0 mismatches
Associated chainA chain B to chainA with 0 mismatches
Chain information for chainA
---
Chain | Description
3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.1/B 3.2/B 3.3/B 3.4/B 3.5/B | No description available
Webservices job finished: KIC81ET5ZM3BWTHZ
Modeller job (ID KIC81ET5ZM3BWTHZ) finished
Parameters
---
Chain pairing | ss
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 1lil, chain A (#2) with chainB, chain A (#), sequence alignment
score = 874.7
Matchmaker 1lil, chain B (#2) with chainB, chain B (#), sequence alignment
score = 948.7
RMSD between 184 pruned atom pairs is 0.691 angstroms; (across all 424 pairs:
20.495)
Parameters
---
Chain pairing | ss
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 1lil, chain A (#2) with chainB, chain A (#), sequence alignment
score = 851.9
Matchmaker 1lil, chain B (#2) with chainB, chain B (#), sequence alignment
score = 927.1
RMSD between 185 pruned atom pairs is 0.696 angstroms; (across all 424 pairs:
20.353)
Parameters
---
Chain pairing | ss
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 1lil, chain A (#2) with chainB, chain A (#), sequence alignment
score = 841.7
Matchmaker 1lil, chain B (#2) with chainB, chain B (#), sequence alignment
score = 927.1
RMSD between 186 pruned atom pairs is 0.637 angstroms; (across all 424 pairs:
20.377)
Parameters
---
Chain pairing | ss
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 1lil, chain A (#2) with chainB, chain A (#), sequence alignment
score = 859.7
Matchmaker 1lil, chain B (#2) with chainB, chain B (#), sequence alignment
score = 930.7
RMSD between 183 pruned atom pairs is 0.688 angstroms; (across all 424 pairs:
20.436)
Parameters
---
Chain pairing | ss
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 1lil, chain A (#2) with chainB, chain A (#), sequence alignment
score = 842.9
Matchmaker 1lil, chain B (#2) with chainB, chain B (#), sequence alignment
score = 941.5
RMSD between 189 pruned atom pairs is 0.694 angstroms; (across all 424 pairs:
19.295)
Associated chainB chain A to chainB with 0 mismatches
Associated chainB chain B to chainB with 0 mismatches
Associated chainB chain A to chainB with 0 mismatches
Associated chainB chain B to chainB with 0 mismatches
Associated chainB chain A to chainB with 0 mismatches
Associated chainB chain B to chainB with 0 mismatches
Associated chainB chain A to chainB with 0 mismatches
Associated chainB chain B to chainB with 0 mismatches
Associated chainB chain A to chainB with 0 mismatches
Associated chainB chain B to chainB with 0 mismatches
Chain information for chainB
---
Chain | Description
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.1/B 4.2/B 4.3/B 4.4/B 4.5/B | No description available
> hide #!3 models
> hide #!4 models
> hide #4.1 models
> hide #2 models
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #3.5 models
> show #3.5 models
> hide #4.2 models
> hide #4.3 models
> hide #4.4 models
> hide #4.5 models
> show #4.3 models
> hide #4.3 models
> hide #!4 models
> hide #3.5 models
> show #3.5 models
> show #2 models
> hide #2 models
> save "C:/Users/olgad/Desktop/predictions based off 1LIL model.cxs"
——— End of log from Tue Oct 14 10:05:07 2025 ———
> view name session-start
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
QFileSystemWatcher::addPaths: list is empty
> select #1/B:64 #1/L:64 #2/A:65 #2/B:65 #3.1/A:65 #3.1/B:280 #3.2/A:65
> #3.2/B:280 #3.3/A:65 #3.3/B:280 #3.4/A:65 #3.4/B:280 #3.5/A:65 #3.5/B:280
> #4.1/A:65 #4.1/B:280 #4.2/A:65 #4.2/B:280 #4.3/A:65 #4.3/B:280 #4.4/A:65
> #4.4/B:280 #4.5/A:65 #4.5/B:280
244 atoms, 220 bonds, 24 residues, 12 models selected
> select
> #1/B:2,4,7,9-10,13-14,18-19,23,25-26,28-33,37-38,42,45,49-52,59,65,71,75,77,79-80,88-90,94-96,105,134,190
> #2/B:2,4,7,9-11,14-15,19-20,24,26-27,29-34,38-39,43,46,50-53,60,66,72,76,78,80-81,89-91,94-96,105,133,190
> #4.1/A:3,5,8,10-11,14-15,19-20,24,26-27,29-34,38-39,43,46,50-53,60,66,72,76,78,80-81,89-91,95-98,107,136,192/B:218,220,223,225-226,229-230,234-235,239,241-242,244-249,253-254,258,261,265-268,275,281,287,291,293,295-296,304-306,310-313,322,351,407
> #4.2/A:3,5,8,10-11,14-15,19-20,24,26-27,29-34,38-39,43,46,50-53,60,66,72,76,78,80-81,89-91,95-98,107,136,192/B:218,220,223,225-226,229-230,234-235,239,241-242,244-249,253-254,258,261,265-268,275,281,287,291,293,295-296,304-306,310-313,322,351,407
> #4.3/A:3,5,8,10-11,14-15,19-20,24,26-27,29-34,38-39,43,46,50-53,60,66,72,76,78,80-81,89-91,95-98,107,136,192/B:218,220,223,225-226,229-230,234-235,239,241-242,244-249,253-254,258,261,265-268,275,281,287,291,293,295-296,304-306,310-313,322,351,407
> #4.4/A:3,5,8,10-11,14-15,19-20,24,26-27,29-34,38-39,43,46,50-53,60,66,72,76,78,80-81,89-91,95-98,107,136,192/B:218,220,223,225-226,229-230,234-235,239,241-242,244-249,253-254,258,261,265-268,275,281,287,291,293,295-296,304-306,310-313,322,351,407
> #4.5/A:3,5,8,10-11,14-15,19-20,24,26-27,29-34,38-39,43,46,50-53,60,66,72,76,78,80-81,89-91,95-98,107,136,192/B:218,220,223,225-226,229-230,234-235,239,241-242,244-249,253-254,258,261,265-268,275,281,287,291,293,295-296,304-306,310-313,322,351,407
6982 atoms, 6738 bonds, 515 residues, 7 models selected
> select
> #1/L:2,4,7,9-10,13-14,18,23,25-26,28-30,32-33,38,42,45,49-50,52,59,71,75,77,79-80,88-90,92-97,135
> #2/A:2,4,7,9-11,14-15,19,24,26-27,29-31,33-34,39,43,46,50-51,53,60,72,76,78,80-81,89-91,93-96,133
> #3.1/A:3,5,8,10-11,14-15,19,24,26-27,29-31,33-34,39,43,46,50-51,53,60,72,76,78,80-81,89-91,93-98,136/B:218,220,223,225-226,229-230,234,239,241-242,244-246,248-249,254,258,261,265-266,268,275,287,291,293,295-296,304-306,308-313,351
> #3.2/A:3,5,8,10-11,14-15,19,24,26-27,29-31,33-34,39,43,46,50-51,53,60,72,76,78,80-81,89-91,93-98,136/B:218,220,223,225-226,229-230,234,239,241-242,244-246,248-249,254,258,261,265-266,268,275,287,291,293,295-296,304-306,308-313,351
> #3.3/A:3,5,8,10-11,14-15,19,24,26-27,29-31,33-34,39,43,46,50-51,53,60,72,76,78,80-81,89-91,93-98,136/B:218,220,223,225-226,229-230,234,239,241-242,244-246,248-249,254,258,261,265-266,268,275,287,291,293,295-296,304-306,308-313,351
> #3.4/A:3,5,8,10-11,14-15,19,24,26-27,29-31,33-34,39,43,46,50-51,53,60,72,76,78,80-81,89-91,93-98,136/B:218,220,223,225-226,229-230,234,239,241-242,244-246,248-249,254,258,261,265-266,268,275,287,291,293,295-296,304-306,308-313,351
> #3.5/A:3,5,8,10-11,14-15,19,24,26-27,29-31,33-34,39,43,46,50-51,53,60,72,76,78,80-81,89-91,93-98,136/B:218,220,223,225-226,229-230,234,239,241-242,244-246,248-249,254,258,261,265-266,268,275,287,291,293,295-296,304-306,308-313,351
5846 atoms, 5597 bonds, 455 residues, 7 models selected
> select #1/B:134 #1/L:135 #2/A:133 #2/B:133 #3.1/A:136 #3.1/B:351 #3.2/A:136
> #3.2/B:351 #3.3/A:136 #3.3/B:351 #3.4/A:136 #3.4/B:351 #3.5/A:136 #3.5/B:351
> #4.1/A:136 #4.1/B:351 #4.2/A:136 #4.2/B:351 #4.3/A:136 #4.3/B:351 #4.4/A:136
> #4.4/B:351 #4.5/A:136 #4.5/B:351
168 atoms, 144 bonds, 24 residues, 12 models selected
> view #3.1/A:136
No displayed objects specified.
> save "C:/Users/Pina/Desktop/gLC C214S V136G model Chimera based on 1LIL and
> alpha fold.cxs"
> hide #!1 models
> hide #!3 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #!1 models
> show #2 models
> hide #2 models
> hide #!1 models
> close session
> open 1lIL fromDatabase pdb format mmcif
1lil title:
Bence jones protein cle, A λ III immunoglobulin light-chain dimer [more
info...]
Chain information for 1lil #1
---
Chain | Description | UniProt
A B | LAMBDA III BENCE JONES PROTEIN CLE | LAC_HUMAN 2-213
> open "C:/Users/Pina/Desktop/patient LC WT .fasta"
Summary of feedback from opening C:/Users/Pina/Desktop/patient LC WT .fasta
---
note | Alignment identifier is patient LC WT .fasta
Opened 1 sequence from patient LC WT .fasta
> ui tool show AlphaFold
> alphafold predict #1/A
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> ui tool show "Modeller Comparative"
> modeller comparative "patient LC WT .fasta:1" numModels 5 fast false
> multichain true hetPreserve false hydrogens false waterPreserve false
Alignment patient LC WT .fasta has no associated chains
> show target m
[Repeated 1 time(s)]
> view clip false
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> ui tool show "Modeller Comparative"
> modeller comparative 1:1 "patient LC WT .fasta:1" numModels 5 fast false
> multichain true hetPreserve false hydrogens false waterPreserve false
Alignment patient LC WT .fasta has no associated chains
> select clear
[Repeated 1 time(s)]
> open "C:/Users/Pina/Desktop/pLC homodimer .fasta"
Summary of feedback from opening C:/Users/Pina/Desktop/pLC homodimer .fasta
---
notes | Alignment identifier is pLC homodimer .fasta
Showing conservation header ("seq_conservation" residue attribute) for
alignment pLC homodimer .fasta
Opened 2 sequences from pLC homodimer .fasta
> modeller comparative "pLC homodimer .fasta:1" numModels 5 fast false
> multichain true hetPreserve false hydrogens false waterPreserve false
Alignment pLC homodimer .fasta has no associated chains
> ui tool show "Modeller Comparative"
[Repeated 1 time(s)]
> modeller comparative "pLC homodimer .fasta:2" numModels 5 fast false
> multichain true hetPreserve false hydrogens false waterPreserve false
Alignment pLC homodimer .fasta has no associated chains
> info #1
1 models
#1, 1lil, shown
3314 atoms, 3273 bonds, 548 residues, 2 chains (A,B)
> info #1
1 models
#1, 1lil, shown
3314 atoms, 3273 bonds, 548 residues, 2 chains (A,B)
> info #1
1 models
#1, 1lil, shown
3314 atoms, 3273 bonds, 548 residues, 2 chains (A,B)
> fromstructure #1 chains A,B
Unknown command: sequence fromstructure #1 chains A,B
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 2
> ui tool show "Modeller Comparative"
> ui dockable false "Modeller Comparative"
> ui favorite true "Modeller Comparative"
> ui autostart true "Modeller Comparative"
> help help:user/tools/modeller.html
> ui tool show "Show Sequence Viewer"
[Repeated 1 time(s)]
> sequence chain /B
Alignment identifier is 1/B
> open "C:/Users/Pina/Desktop/pLC homodimer .fasta"
Summary of feedback from opening C:/Users/Pina/Desktop/pLC homodimer .fasta
---
notes | Alignment identifier is pLC homodimer .fasta
Showing conservation header ("seq_conservation" residue attribute) for
alignment pLC homodimer .fasta
Opened 2 sequences from pLC homodimer .fasta
> select
3314 atoms, 3273 bonds, 548 residues, 1 model selected
> select clear
[Repeated 5 time(s)]
> select add #1
3314 atoms, 3273 bonds, 548 residues, 1 model selected
> view clip false
> show target m
[Repeated 1 time(s)]
> hide target m
> log metadata #1
Metadata for 1lil #1
---
Title | Bence jones protein cle, A λ III immunoglobulin light-chain dimer
Citations | Huang, D.B., Ainsworth, C., Solomon, A., Schiffer, M. (1996). Pitfalls of molecular replacement: the structure determination of an immunoglobulin light-chain dimer. Acta Crystallogr.,Sect.D, 52, 1058-1066. PMID: 15299564. DOI: 10.1107/S090744499600813X
Stevens, F.J., Westholm, F.A., Panagiotopoulos, N., Solomon, A., Schiffer, M.
(1981). Preliminary Crystallographic Data on the Human Lambda III Bence Jones
Protein Dimer Cle. J.Mol.Biol., 147, 179
Source (natural) | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.65Å
> log chains #1
Chain information for 1lil #1
---
Chain | Description | UniProt
A B | LAMBDA III BENCE JONES PROTEIN CLE | LAC_HUMAN 2-213
> view clip false
> show #1 models
> log metadata #1
Metadata for 1lil #1
---
Title | Bence jones protein cle, A λ III immunoglobulin light-chain dimer
Citations | Huang, D.B., Ainsworth, C., Solomon, A., Schiffer, M. (1996). Pitfalls of molecular replacement: the structure determination of an immunoglobulin light-chain dimer. Acta Crystallogr.,Sect.D, 52, 1058-1066. PMID: 15299564. DOI: 10.1107/S090744499600813X
Stevens, F.J., Westholm, F.A., Panagiotopoulos, N., Solomon, A., Schiffer, M.
(1981). Preliminary Crystallographic Data on the Human Lambda III Bence Jones
Protein Dimer Cle. J.Mol.Biol., 147, 179
Source (natural) | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.65Å
> log chains #1
Chain information for 1lil #1
---
Chain | Description | UniProt
A B | LAMBDA III BENCE JONES PROTEIN CLE | LAC_HUMAN 2-213
> log metadata #1
Metadata for 1lil #1
---
Title | Bence jones protein cle, A λ III immunoglobulin light-chain dimer
Citations | Huang, D.B., Ainsworth, C., Solomon, A., Schiffer, M. (1996). Pitfalls of molecular replacement: the structure determination of an immunoglobulin light-chain dimer. Acta Crystallogr.,Sect.D, 52, 1058-1066. PMID: 15299564. DOI: 10.1107/S090744499600813X
Stevens, F.J., Westholm, F.A., Panagiotopoulos, N., Solomon, A., Schiffer, M.
(1981). Preliminary Crystallographic Data on the Human Lambda III Bence Jones
Protein Dimer Cle. J.Mol.Biol., 147, 179
Source (natural) | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.65Å
> log chains #1
Chain information for 1lil #1
---
Chain | Description | UniProt
A B | LAMBDA III BENCE JONES PROTEIN CLE | LAC_HUMAN 2-213
> log metadata #1
Metadata for 1lil #1
---
Title | Bence jones protein cle, A λ III immunoglobulin light-chain dimer
Citations | Huang, D.B., Ainsworth, C., Solomon, A., Schiffer, M. (1996). Pitfalls of molecular replacement: the structure determination of an immunoglobulin light-chain dimer. Acta Crystallogr.,Sect.D, 52, 1058-1066. PMID: 15299564. DOI: 10.1107/S090744499600813X
Stevens, F.J., Westholm, F.A., Panagiotopoulos, N., Solomon, A., Schiffer, M.
(1981). Preliminary Crystallographic Data on the Human Lambda III Bence Jones
Protein Dimer Cle. J.Mol.Biol., 147, 179
Source (natural) | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.65Å
> log chains #1
Chain information for 1lil #1
---
Chain | Description | UniProt
A B | LAMBDA III BENCE JONES PROTEIN CLE | LAC_HUMAN 2-213
> ui tool show "Modeller Comparative"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 347, in _update_sequence_menus
row_info.fieldItem.widget().destroy()
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\seqalign\widgets.py", line 104, in destroy
self.alignment.remove_observer(self)
File "C:\Program Files\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 "C:\Program Files\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 "C:\Program Files\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 0x00000211BFC34550>
KeyError:
File "C:\Program Files\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.
OpenGL version: 3.3.0 NVIDIA 581.80
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1250
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Dell G15 5515
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 33,663,741,952
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics
OSLanguage: pl-PL
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 (2)
comment:1 by , 29 minutes ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → alignment widget not properly destroying when tool closed |
comment:2 by , 29 minutes ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate of #18702