The following bug report has been submitted:
Platform: macOS-13.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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"procLaunch" : "2023-11-30 12:26:41.2318 -0500",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/lamiawahba/Downloads/AF-P90786-F1-model_v4.pdb format pdb
AF-P90786-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for piwi-like protein (P90786) [more
info...]
Chain information for AF-P90786-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | piwi-like protein | P90786_CAEEL 1-824
> style sphere
Changed 6589 atom styles
> show atoms
> hide atoms
> show atoms
> hide atoms
> label #1 text "{0.name} {0.number}{0.insertion_code}"
> ~label #1 residues
> select
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> help help:user/menu.html#selectzone
> style sel stick
Changed 6589 atom styles
> style sel stick
Changed 6589 atom styles
> style sel sphere
Changed 6589 atom styles
> select nucleic-acid
Nothing selected
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> volume style surface
No volumes specified
> volume step 1
No volumes specified
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right label
Alignment identifier is 1/A
> select
> /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817
2263 atoms, 2278 bonds, 277 residues, 1 model selected
> select /A:315
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:315-376
507 atoms, 515 bonds, 62 residues, 1 model selected
> select /A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:311-415
851 atoms, 868 bonds, 105 residues, 1 model selected
> select /A:215-216
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:215-217
27 atoms, 26 bonds, 3 residues, 1 model selected
> select /A:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:217-269
455 atoms, 463 bonds, 53 residues, 1 model selected
> select /A:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:217-354
1134 atoms, 1159 bonds, 138 residues, 1 model selected
> select /A:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:217-354
1134 atoms, 1159 bonds, 138 residues, 1 model selected
> select /A:217-354
1134 atoms, 1159 bonds, 138 residues, 1 model selected
> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762
1767 atoms, 1773 bonds, 213 residues, 1 model selected
> select /A:217-354
1134 atoms, 1159 bonds, 138 residues, 1 model selected
> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762
1767 atoms, 1773 bonds, 213 residues, 1 model selected
> select /A:217-354
1134 atoms, 1159 bonds, 138 residues, 1 model selected
> color sel red
> select /A:489
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:489
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762
1767 atoms, 1773 bonds, 213 residues, 1 model selected
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select
> /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817
2263 atoms, 2278 bonds, 277 residues, 1 model selected
> select /A:498
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:498-822
2560 atoms, 2610 bonds, 325 residues, 1 model selected
> color sel blue
> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762
1767 atoms, 1773 bonds, 213 residues, 1 model selected
> select
> /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817
2263 atoms, 2278 bonds, 277 residues, 1 model selected
> style sel sphere
Changed 2263 atom styles
> color sel bychain
> save /Users/lamiawahba/Desktop/prg-1.cxs
> color sel bychain
> style sel sphere
Changed 2263 atom styles
> hide target m
> show target m
> view clip false
> view orient
> view clip false
> show target m
> log metadata #1
Metadata for AF-P90786-F1-model_v4.pdb #1
---
Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786)
Source (natural) | Caenorhabditis elegans
> log chains #1
Chain information for AF-P90786-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | piwi-like protein | P90786_CAEEL 1-824
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762
1767 atoms, 1773 bonds, 213 residues, 1 model selected
> select /A:13
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:13-51
289 atoms, 292 bonds, 39 residues, 1 model selected
> select
> /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817
2263 atoms, 2278 bonds, 277 residues, 1 model selected
> select /A:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:220-228
83 atoms, 85 bonds, 9 residues, 1 model selected
> select /A:312-313
16 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:312-319
59 atoms, 61 bonds, 8 residues, 1 model selected
> select /A:367-403
296 atoms, 300 bonds, 37 residues, 1 model selected
> select /A:367-407
325 atoms, 329 bonds, 41 residues, 1 model selected
> select /A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:311-402
742 atoms, 756 bonds, 92 residues, 1 model selected
> color #1 #ebe0d1ff
> color #1 #ebe4d2ff
> ui tool show AlphaFold
> color sel byelement
> select /A:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:217-394
1458 atoms, 1487 bonds, 178 residues, 1 model selected
> select /A:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:217-360
1187 atoms, 1212 bonds, 144 residues, 1 model selected
> select /A:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:217-354
1134 atoms, 1159 bonds, 138 residues, 1 model selected
> color sel red
> select sequence EESMY
44 atoms, 44 bonds, 5 residues, 1 model selected
> select /A:498
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:498-821
2549 atoms, 2598 bonds, 324 residues, 1 model selected
> color sel medium blue
> save /Users/lamiawahba/Desktop/prg-1.cxs
> select ::name="LYS"
540 atoms, 482 bonds, 60 residues, 1 model selected
> color sel yellow
> color sel bychain
> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762
1767 atoms, 1773 bonds, 213 residues, 1 model selected
> select /A:498-821
2549 atoms, 2598 bonds, 324 residues, 1 model selected
> view clip false
> log metadata #1
Metadata for AF-P90786-F1-model_v4.pdb #1
---
Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786)
Source (natural) | Caenorhabditis elegans
> log chains #1
Chain information for AF-P90786-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | piwi-like protein | P90786_CAEEL 1-824
> view clip false
> select /A:636
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:636
9 atoms, 8 bonds, 1 residue, 1 model selected
> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762
1767 atoms, 1773 bonds, 213 residues, 1 model selected
> select /A:537-538
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:537-538
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:583-584
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:583-584
16 atoms, 15 bonds, 2 residues, 1 model selected
> style sel stick
Changed 16 atom styles
> style sel stick
Changed 16 atom styles
> style sel ball
Changed 16 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 16 atom styles
> rainbow sel
> style sel ball
Changed 16 atom styles
> style sel stick
Changed 16 atom styles
> style sel sphere
Changed 16 atom styles
> color sel bychain
> color sel byhetero
> color sel bypolymer
> rainbow sel
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel bynucleotide
> color sel byhetero
> color bfactor sel
16 atoms, 2 residues, 1 surfaces, atom bfactor range 89.8 to 94.4
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> style sel sphere
Changed 16 atom styles
> select /A:824
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> style sel sphere
Changed 6589 atom styles
> lighting full
> set bgColor black
> set bgColor white
> set bgColor black
> show sel surfaces
> show sel cartoons
> show sel atoms
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> show sel cartoons
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel atoms
> show sel surfaces
> hide sel surfaces
> save /Users/lamiawahba/Desktop/image1.png supersample 3
> ui tool show "Side View"
> view orient
> view
> view sel
> ui mousemode right "rotate selected models"
> ui mousemode right rotate
> save /Users/lamiawahba/Desktop/image2.png supersample 3
> save /Users/lamiawahba/Desktop/image3.png supersample 3
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel atoms
> style sel stick
Changed 6589 atom styles
> style sel ball
Changed 6589 atom styles
> show sel cartoons
> select /A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select /A:824
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:824
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:824
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:596-642
380 atoms, 389 bonds, 47 residues, 1 model selected
> select /A:596-643
389 atoms, 398 bonds, 48 residues, 1 model selected
> select /A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select /A:462
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:462-507
346 atoms, 350 bonds, 46 residues, 1 model selected
> select /A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select /A:641
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:641-642
16 atoms, 15 bonds, 2 residues, 1 model selected
> style sel stick
Changed 16 atom styles
> style sel ball
Changed 16 atom styles
> style sel ball
Changed 16 atom styles
> hide sel atoms
> show sel atoms
> show sel cartoons
> show sel surfaces
> style sel stick
Changed 16 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> select /A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> style sel ball
Changed 6589 atom styles
> style sel ball
Changed 6589 atom styles
> style sel sphere
Changed 6589 atom styles
> style sel sphere
Changed 6589 atom styles
> style sel stick
Changed 6589 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> hide sel atoms
> select /A:824
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:823-824
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /A:639
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:639-640
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select /A:643-644
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:642-644
24 atoms, 23 bonds, 3 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select /A:641
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:641
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel surfaces
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show sel surfaces
> hide sel surfaces
> select /A:561
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:561
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:824
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> show sel surfaces
> select /A:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:82
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:82-83
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /A:81-82
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /A:81-82
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /A:82-83
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /A:83
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:82
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:82
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel surfaces
> select /A:87
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:87
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:112
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:112
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:137-138
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:137-138
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:213
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:213
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:258
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:258
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:277
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:277
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:285
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:285
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:289
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:289
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:338
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:338
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:341
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:341
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:348
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:348
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:370
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:370
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:373
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:373
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:379
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:379
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:398
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:398
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:405
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:405
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:406
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:406
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:411
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:411
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:420
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:420
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:449
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:449
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:459
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:459
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:490-491
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:490-491
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:509
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:509
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:516
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:516-517
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:538
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:538-539
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /A:540
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:540
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:546
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:546
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:554
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:554
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:562
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:562
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select /A:569
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:569
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:575
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:575
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:591
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:591
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:593
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:593
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:632
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:632
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:665
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:665
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:670
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:670
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:682
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:682
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:689
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:689
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:695
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:695
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:703
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:703
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:711
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:711
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:770
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:770
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:777
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:777
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:800
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:800
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:820
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:820
9 atoms, 8 bonds, 1 residue, 1 model selected
> open "/Users/lamiawahba/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/753B9663-26C1-4821-942F-2BD094A26B5E/Undefined.pdb"
Chain information for Undefined.pdb #2
---
Chain | Description
? | No description available
> open "/Users/lamiawahba/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/753B9663-26C1-4821-942F-2BD094A26B5E/Undefined.pdb"
Chain information for Undefined.pdb #3
---
Chain | Description
? | No description available
> show #2 target m
> select add #2
6376 atoms, 6505 bonds, 793 residues, 3 models selected
> show #2 target m
> hide #!1 models
> show #!1 models
> hide #!1 models
> log metadata #2
The model has no metadata
> log chains #2
Chain information for Undefined.pdb #2
---
Chain | Description
? | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #2/? #3/?
Alignment identifier is 1
> select #2/*:84 #3/*:84
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/*:84-134 #3/*:84-134
866 atoms, 882 bonds, 102 residues, 2 models selected
1 [ID: 1] region 2 chains [52-102] RMSD: 0.000
> select #2/*:33 #3/*:33
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/*:33-37 #3/*:33-37
94 atoms, 94 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [1-5] RMSD: 0.000
> select add #1
6683 atoms, 6815 bonds, 834 residues, 3 models selected
> select add #3
13003 atoms, 13265 bonds, 1621 residues, 4 models selected
> close #3
> select add #2
12956 atoms, 13218 bonds, 1616 residues, 3 models selected
> show #!1 models
> hide #2 models
> select ::name="LYS"
1062 atoms, 948 bonds, 118 residues, 2 models selected
> select #1/A:779-824
376 atoms, 388 bonds, 46 residues, 1 model selected
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select #1/A:310
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:309-310
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309-310
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:310
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:309-310
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309-311
25 atoms, 25 bonds, 3 residues, 1 model selected
> coulombic sel
Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "AF-P90786-F1-model_v4.pdb_A SES surface": minimum
-29.33, mean -5.891, maximum 22.8
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "AF-P90786-F1-model_v4.pdb_A SES surface": minimum
-29.33, mean -5.891, maximum 22.8
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor sel
25 atoms, 3 residues, 1 surfaces, atom bfactor range 73.4 to 79.5
> rainbow sel
> color sel bypolymer
> rainbow sel
> color sel byhetero
> coulombic sel
Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36
To also show corresponding color key, enter the above coulombic command and
add key true
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> coulombic sel
Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel bychain
> select #1/A:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:217-337
992 atoms, 1014 bonds, 121 residues, 1 model selected
> select #1/A:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:217-354
1134 atoms, 1159 bonds, 138 residues, 1 model selected
> color (#!1 & sel) forest green
> select #1/A:498
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:498-808
2448 atoms, 2496 bonds, 311 residues, 1 model selected
> color (#!1 & sel) red
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #1/A:3-4
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/A:3-4
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309-311
25 atoms, 25 bonds, 3 residues, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:311-312
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select #1/A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:311
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309-311
25 atoms, 25 bonds, 3 residues, 1 model selected
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select #1/A:824
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:824
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select #1/A:823-824
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/A:823-824
20 atoms, 20 bonds, 2 residues, 1 model selected
> show target m
> log metadata #1
Metadata for AF-P90786-F1-model_v4.pdb #1
---
Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786)
Source (natural) | Caenorhabditis elegans
> log chains #1
Chain information for AF-P90786-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | piwi-like protein | P90786_CAEEL 1-824
> log metadata #2
The model has no metadata
> log chains #2
Chain information for Undefined.pdb #2
---
Chain | Description
? | No description available
> log metadata #1
Metadata for AF-P90786-F1-model_v4.pdb #1
---
Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786)
Source (natural) | Caenorhabditis elegans
> log chains #1
Chain information for AF-P90786-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | piwi-like protein | P90786_CAEEL 1-824
> log metadata #2
The model has no metadata
> log chains #2
Chain information for Undefined.pdb #2
---
Chain | Description
? | No description available
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> surface (#!1 & sel)
> surface hidePatches (#!1 & sel)
> hide #2 models
> select #1/A:97
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:97-98
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> select #1/A:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:48-49
16 atoms, 16 bonds, 2 residues, 1 model selected
> surface (#!1 & sel)
> select #1/A
6589 atoms, 6721 bonds, 824 residues, 1 model selected
> surface (#!1 & sel)
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16R0005YLL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 8419.60.44
OS Loader Version: 8419.60.44
Software:
System Software Overview:
System Version: macOS 13.1 (22C65)
Kernel Version: Darwin 22.2.0
Time since boot: 44 days, 7 hours, 34 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL SE2722HX:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Says faultingThread:30 with EXC_BREAKPOINT. The traceback for thread 30 was uninformative.