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Opened 7 months ago
Closed 7 months ago
#17473 closed defect (can't reproduce)
Modeller update sequence menus: list.remove(x): x not in list
| 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-10-10.0.26100
ChimeraX Version: 1.9rc202411012347 (2024-11-01 23:47:45 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:/Users/yuuty/Desktop/HsHGPRT.cxs
Log from Tue Apr 22 13:47:40 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/yuuty/Downloads/1d6n.cif
Summary of feedback from opening C:/Users/yuuty/Downloads/1d6n.cif
---
notes | Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD PPO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/PPO/PPO.cif
Fetching CCD PRP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/PRP/PRP.cif
1d6n.cif title:
Ternary complex structure of human hgprtase, PRPP, MG2+, and the inhibitor HPP
reveals the involvement of the flexible loop In substrate binding [more
info...]
Chain information for 1d6n.cif #1
---
Chain | Description | UniProt
A B | PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE) | HPRT_HUMAN 4-217
Non-standard residues in 1d6n.cif #1
---
MG — magnesium ion
PPO — 3H-pyrazolo[4,3-D]pyrimidin-7-ol
PRP — 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose (ALPHA-
PHOSPHORIBOSYLPYROPHOSPHORIC ACID; 1-O-pyrophosphono-5-O-phosphono-alpha-D-
ribose; 1-O-pyrophosphono-5-O-phosphono-D-ribose;
1-O-pyrophosphono-5-O-phosphono-ribose)
1d6n.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> open C:/Users/yuuty/Downloads/1hmp.cif
Summary of feedback from opening C:/Users/yuuty/Downloads/1hmp.cif
---
note | Fetching CCD 5GP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/5GP/5GP.cif
1hmp.cif title:
The crystal structure of human hypoxanthine-guanine phosphoribosyltransferase
with bound GMP [more info...]
Chain information for 1hmp.cif #2
---
Chain | Description | UniProt
A B | HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE | HPRT_HUMAN 1-217
Non-standard residues in 1hmp.cif #2
---
5GP — guanosine-5'-monophosphate
1hmp.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open C:/Users/yuuty/Downloads/1z7g.cif
1z7g.cif title:
Free human HGPRT [more info...]
Chain information for 1z7g.cif #3
---
Chain | Description | UniProt
A B C D | Hypoxanthine-guanine phosphoribosyltransferase | HPRT_HUMAN 1-217
1z7g.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> open C:/Users/yuuty/Downloads/1bzy.cif
Summary of feedback from opening C:/Users/yuuty/Downloads/1bzy.cif
---
notes | Fetching CCD IMU from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/IMU/IMU.cif
Fetching CCD POP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/POP/POP.cif
1bzy.cif title:
Human hgprtase with transition state inhibitor [more info...]
Chain information for 1bzy.cif #4
---
Chain | Description | UniProt
A B C D | HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | HPRT_HUMAN 1-217
Non-standard residues in 1bzy.cif #4
---
IMU — phosphoric acid
mono-[5-(2-amino-4-oxo-4,5-dihydro-3H-pyrrolo[3,2-D]pyrimidin-7-yl)-3,4-dihydroxy-
pyrrolidin-2-ylmethyl] ester (modified quanosine-5-phosphate)
MG — magnesium ion
POP — pyrophosphate 2-
> ui tool show Matchmaker
> matchmaker #!2-4 to #1
Computing secondary structure
[Repeated 3 time(s)] 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 1d6n.cif, chain A (#1) with 1hmp.cif, chain B (#2), sequence
alignment score = 953
RMSD between 180 pruned atom pairs is 0.780 angstroms; (across all 209 pairs:
3.735)
Matchmaker 1d6n.cif, chain A (#1) with 1z7g.cif, chain B (#3), sequence
alignment score = 945.8
RMSD between 169 pruned atom pairs is 0.847 angstroms; (across all 199 pairs:
1.778)
Matchmaker 1d6n.cif, chain A (#1) with 1bzy.cif, chain B (#4), sequence
alignment score = 939.8
RMSD between 193 pruned atom pairs is 1.016 angstroms; (across all 214 pairs:
1.394)
> matchmaker #!2-4 to #1
Computing secondary structure
[Repeated 3 time(s)] 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 1d6n.cif, chain A (#1) with 1hmp.cif, chain B (#2), sequence
alignment score = 953
RMSD between 180 pruned atom pairs is 0.780 angstroms; (across all 209 pairs:
3.735)
Matchmaker 1d6n.cif, chain A (#1) with 1z7g.cif, chain B (#3), sequence
alignment score = 945.8
RMSD between 169 pruned atom pairs is 0.847 angstroms; (across all 199 pairs:
1.778)
Matchmaker 1d6n.cif, chain A (#1) with 1bzy.cif, chain B (#4), sequence
alignment score = 939.8
RMSD between 193 pruned atom pairs is 1.016 angstroms; (across all 214 pairs:
1.394)
> hide atoms
[Repeated 1 time(s)]
> show atoms
> hide atoms
> select #3/A:121
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:121
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
44 atoms, 43 bonds, 6 residues, 1 model selected
> select up
403 atoms, 404 bonds, 55 residues, 1 model selected
> select up
463 atoms, 464 bonds, 62 residues, 1 model selected
> select up
1558 atoms, 1587 bonds, 199 residues, 1 model selected
> select down
463 atoms, 464 bonds, 62 residues, 1 model selected
> select down
403 atoms, 404 bonds, 55 residues, 1 model selected
> select down
44 atoms, 43 bonds, 6 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/C:66
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
49 atoms, 48 bonds, 7 residues, 1 model selected
> select up
1695 atoms, 1728 bonds, 214 residues, 1 model selected
> select up
1801 atoms, 1762 bonds, 289 residues, 1 model selected
> select up
7216 atoms, 7048 bonds, 1168 residues, 1 model selected
> select down
1801 atoms, 1762 bonds, 289 residues, 1 model selected
> hide sel cartoons
> select #3/A:97
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
49 atoms, 49 bonds, 6 residues, 1 model selected
> select up
788 atoms, 805 bonds, 99 residues, 1 model selected
> select up
829 atoms, 845 bonds, 106 residues, 1 model selected
> select up
1191 atoms, 1209 bonds, 154 residues, 1 model selected
> select up
1227 atoms, 1246 bonds, 158 residues, 1 model selected
> select up
1558 atoms, 1587 bonds, 199 residues, 1 model selected
> select up
1663 atoms, 1587 bonds, 304 residues, 1 model selected
> select up
6777 atoms, 6392 bonds, 1308 residues, 1 model selected
> select down
1663 atoms, 1587 bonds, 304 residues, 1 model selected
> hide sel cartoons
> select #4/D:63
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
49 atoms, 48 bonds, 7 residues, 1 model selected
> select up
1695 atoms, 1728 bonds, 214 residues, 1 model selected
> select up
1796 atoms, 1762 bonds, 284 residues, 1 model selected
> select down
1695 atoms, 1728 bonds, 214 residues, 1 model selected
> select down
49 atoms, 48 bonds, 7 residues, 1 model selected
> select up
1695 atoms, 1728 bonds, 214 residues, 1 model selected
> hide sel cartoons
> select #4/A:147
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
109 atoms, 109 bonds, 13 residues, 1 model selected
> select up
1695 atoms, 1728 bonds, 214 residues, 1 model selected
> select down
109 atoms, 109 bonds, 13 residues, 1 model selected
> hide sel cartoons
> select clear
> select #2/A:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
102 atoms, 102 bonds, 15 residues, 1 model selected
> select up
1678 atoms, 1711 bonds, 214 residues, 1 model selected
> select down
102 atoms, 102 bonds, 15 residues, 1 model selected
> select up
1678 atoms, 1711 bonds, 214 residues, 1 model selected
> select down
102 atoms, 102 bonds, 15 residues, 1 model selected
> select up
1678 atoms, 1711 bonds, 214 residues, 1 model selected
> select down
102 atoms, 102 bonds, 15 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #4/A:115
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 4 residues, 1 model selected
> select up
1695 atoms, 1728 bonds, 214 residues, 1 model selected
> select down
28 atoms, 27 bonds, 4 residues, 1 model selected
> select up
1695 atoms, 1728 bonds, 214 residues, 1 model selected
> hide sel cartoons
> select #3/D:178
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
50 atoms, 51 bonds, 6 residues, 1 model selected
> select up
367 atoms, 378 bonds, 46 residues, 1 model selected
> select up
397 atoms, 408 bonds, 50 residues, 1 model selected
> select up
729 atoms, 742 bonds, 95 residues, 1 model selected
> select up
1694 atoms, 1594 bonds, 331 residues, 1 model selected
> select up
6777 atoms, 6392 bonds, 1308 residues, 1 model selected
> select down
1694 atoms, 1594 bonds, 331 residues, 1 model selected
> hide sel cartoons
> select #3/C:44
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
168 atoms, 169 bonds, 21 residues, 1 model selected
> select up
782 atoms, 799 bonds, 99 residues, 1 model selected
> select up
826 atoms, 842 bonds, 106 residues, 1 model selected
> select up
1590 atoms, 1621 bonds, 204 residues, 1 model selected
> hide sel cartoons
> select #1/B:47
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
168 atoms, 169 bonds, 21 residues, 1 model selected
> select up
1686 atoms, 1719 bonds, 214 residues, 1 model selected
> select up
1747 atoms, 1752 bonds, 245 residues, 1 model selected
> select up
3490 atoms, 3504 bonds, 486 residues, 1 model selected
> select down
1747 atoms, 1752 bonds, 245 residues, 1 model selected
> hide sel cartoons
> select #2/A:65
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
59 atoms, 59 bonds, 8 residues, 1 model selected
> select up
1678 atoms, 1711 bonds, 214 residues, 1 model selected
> select up
1749 atoms, 1737 bonds, 262 residues, 1 model selected
> select down
1678 atoms, 1711 bonds, 214 residues, 1 model selected
> select up
1749 atoms, 1737 bonds, 262 residues, 1 model selected
> select up
3430 atoms, 3412 bonds, 510 residues, 1 model selected
> select up
20913 atoms, 20356 bonds, 3472 residues, 4 models selected
> select down
3430 atoms, 3412 bonds, 510 residues, 1 model selected
> select down
1749 atoms, 1737 bonds, 262 residues, 1 model selected
> select down
1678 atoms, 1711 bonds, 214 residues, 1 model selected
> select up
1749 atoms, 1737 bonds, 262 residues, 1 model selected
> hide sel cartoons
> select ligand
244 atoms, 254 bonds, 14 residues, 3 models selected
> show sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 26 bonds, 1 residue, 1 model selected
> select up
1814 atoms, 1762 bonds, 302 residues, 1 model selected
> select up
7216 atoms, 7048 bonds, 1168 residues, 1 model selected
> select down
1814 atoms, 1762 bonds, 302 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 26 bonds, 1 residue, 1 model selected
> select up
1749 atoms, 1737 bonds, 262 residues, 1 model selected
> select up
3430 atoms, 3412 bonds, 510 residues, 1 model selected
> select down
1749 atoms, 1737 bonds, 262 residues, 1 model selected
> hide sel atoms
> select #1/B:301@N3
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 22 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 26 bonds, 1 residue, 1 model selected
> select up
1801 atoms, 1762 bonds, 289 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 26 bonds, 1 residue, 1 model selected
> select up
1796 atoms, 1762 bonds, 284 residues, 1 model selected
> hide sel atoms
> save C:/Users/yuuty/Desktop/faily.pdb
> save C:/Users/yuuty/Desktop/faily.cxs
——— End of log from Tue Apr 22 13:47:40 2025 ———
opened ChimeraX session
> show sel atoms
> hide sel atoms
> show sel cartoons
> select up
7216 atoms, 7048 bonds, 1168 residues, 1 model selected
> select down
1796 atoms, 1762 bonds, 284 residues, 1 model selected
> select down
1796 atoms, 1762 bonds, 284 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!1 cartoons
> select #1/B:123
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
52 atoms, 51 bonds, 7 residues, 1 model selected
> select up
1686 atoms, 1719 bonds, 214 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> hide #!1 models
> show #!2 cartoons
> select #2/A:150
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
97 atoms, 96 bonds, 12 residues, 1 model selected
> select up
1678 atoms, 1711 bonds, 214 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!3 models
> hide #!2 models
> show #!3 cartoons
> select #3/A:6
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
17 atoms, 17 bonds, 3 residues, 1 model selected
> select up
788 atoms, 805 bonds, 99 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
52 atoms, 52 bonds, 6 residues, 1 model selected
> select up
770 atoms, 782 bonds, 100 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/D:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
141 atoms, 144 bonds, 16 residues, 1 model selected
> select up
794 atoms, 811 bonds, 100 residues, 1 model selected
> select up
808 atoms, 824 bonds, 103 residues, 1 model selected
> select up
836 atoms, 852 bonds, 107 residues, 1 model selected
> select up
1694 atoms, 1594 bonds, 331 residues, 1 model selected
> select up
5219 atoms, 4805 bonds, 1109 residues, 1 model selected
> select down
1694 atoms, 1594 bonds, 331 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/C:34
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
54 atoms, 54 bonds, 6 residues, 1 model selected
> select up
782 atoms, 799 bonds, 99 residues, 1 model selected
> select up
826 atoms, 842 bonds, 106 residues, 1 model selected
> select up
1590 atoms, 1621 bonds, 204 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open C:/Users/yuuty/Downloads/OsHGPRT.fasta
Summary of feedback from opening C:/Users/yuuty/Downloads/OsHGPRT.fasta
---
note | Alignment identifier is OsHGPRT.fasta
Opened 1 sequence from OsHGPRT.fasta
> show #!1 models
> hide #!3 models
> sequence associate #1/A
Associated 1d6n.cif chain A to OsHGPRT (A0A0P0WIZ3) with 160 mismatches and/or
gaps
> undo
> redo
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
Drag select of 32 atoms, 214 residues, 33 bonds
> select clear
> sequence disassociate #1/A
Disassociated 1d6n.cif chain A from OsHGPRT (A0A0P0WIZ3)
> sequence associate #2/B
Associated 1hmp.cif chain B to OsHGPRT (A0A0P0WIZ3) with 161 mismatches and/or
gaps
> sequence associate #1/A
Associated 1d6n.cif chain A to OsHGPRT (A0A0P0WIZ3) with 160 mismatches and/or
gaps
> sequence disassociate #2/B
Disassociated 1hmp.cif chain B from OsHGPRT (A0A0P0WIZ3)
> ui tool show "Modeller Comparative"
> save C:/Users/yuuty/Desktop/HsHGPRT.cxs
> ui tool show "Modeller Comparative"
> sequence disassociate #1/A
Disassociated 1d6n.cif chain A from OsHGPRT (A0A0P0WIZ3)
> show #!2 models
> show #!3 models
> show #!4 models
Alignment identifier is 1/A
Alignment identifier is 1
> open C:/Users/yuuty/Downloads/OsHGPRT.fasta
Summary of feedback from opening C:/Users/yuuty/Downloads/OsHGPRT.fasta
---
note | Alignment identifier is OsHGPRT.fasta
Opened 1 sequence from OsHGPRT.fasta
> sequence associate #1/A OsHGPRT.fasta
Associated 1d6n.cif chain A to OsHGPRT (A0A0P0WIZ3) with 160 mismatches and/or
gaps
> ui tool show "Modeller Comparative"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 347, in _update_sequence_menus
row_info.fieldItem.widget().destroy()
File "C:\Program Files\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\seqalign\widgets.py", line 104, in destroy
self.alignment.remove_observer(self)
File "C:\Program Files\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 711, 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 1.9rc202411012347\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 711, in remove_observer
self.observers.remove(observer)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202411012347\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 0x0000028DB4CD3110>
KeyError:
File "C:\Program Files\ChimeraX 1.9rc202411012347\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 "C:\Program Files\ChimeraX 1.9rc202411012347\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 0x0000028D902AC890>
KeyError:
File "C:\Program Files\ChimeraX 1.9rc202411012347\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.
No alignments chosen for modeling
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9rc202411012347\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 0x0000028D902AC890>
KeyError:
File "C:\Program Files\ChimeraX 1.9rc202411012347\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 - Build 32.0.101.5763
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Python: 3.11.4
Locale: ja_JP.cp932
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: FUJITSU CLIENT COMPUTING LIMITED
Model: FMVUU7GUV1
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 8,209,092,608
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: ja-JP
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 2.4.1
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
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: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9rc202411012347
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.5
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.2
ChimeraX-Label: 1.1.11
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
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: 1.5.17
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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.1
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.2.4
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
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: 1.18.1
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
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: 1.41
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-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.7
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.54.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
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: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.1
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Modeller update sequence menus: list.remove(x): x not in list |
comment:2 by , 7 months ago
| Component: | Structure Prediction → Sequence |
|---|---|
| Resolution: | → can't reproduce |
| Status: | accepted → closed |
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It would seem like the only way for this to happen is if the sequence menu widget gets destroyed twice, but I can't reproduce it.