id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16608	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.1.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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    ""base"" : 140703361540096,
    ""CFBundleShortVersionString"" : ""2.1.1"",
    ""CFBundleIdentifier"" : ""com.apple.HIToolbox"",
    ""size"" : 3002356,
    ""uuid"" : ""f01dcd65-0a63-39f5-b7a1-f4c790a6ce5c"",
    ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"",
    ""name"" : ""HIToolbox""
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  {
    ""size"" : 0,
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    ""size"" : 245760,
    ""uuid"" : ""1b806694-216b-3869-9a82-0094a1ad6ba0"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"",
    ""name"" : ""libsystem_kernel.dylib""
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  {
    ""source"" : ""P"",
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    ""base"" : 140703165419520,
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    ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"",
    ""name"" : ""libsystem_pthread.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703164563456,
    ""size"" : 511996,
    ""uuid"" : ""d09eb0d4-5624-30a0-9b5a-745d78ce3591"",
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],
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},
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  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
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},
  ""logWritingSignature"" : ""66193842042a1230cecee9471ff0aac45453f0c4"",
  ""trialInfo"" : {
  ""rollouts"" : [
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  ""PC register does not match crashing frame (0x0 vs 0x144724944)""
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-62.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-62.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 193 193 PRO I 1336 ALA I 1343 1 8  
Start residue of secondary structure not found: HELIX 194 194 ASP I 1344 ALA I
1346 1 3  
Start residue of secondary structure not found: HELIX 195 195 MET I 1354 LEU I
1363 1 10  
Start residue of secondary structure not found: HELIX 196 196 LEU I 1366 ALA I
1371 1 6  
Start residue of secondary structure not found: HELIX 197 197 GLU I 1376 LYS I
1385 1 10  
17 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-62.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide atoms

> show cartoons

> dssp

> open
> /Users/farnung/Downloads/fold_2024_05_09_01_21(2)/fold_2024_05_09_01_21_model_0.cif

Chain information for fold_2024_05_09_01_21_model_0.cif #2  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
  

> mmaker #2/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker JF1086_model2-coot-62.pdb, chain A (#1) with
fold_2024_05_09_01_21_model_0.cif, chain A (#2), sequence alignment score =
4069.2  
RMSD between 304 pruned atom pairs is 1.153 angstroms; (across all 1016 pairs:
9.324)  
  

> hide atoms

> show cartoons

> hide #2 models

> open /Users/farnung/Desktop/JF1086/Krios/Refined_fromJ92/composite_map.ccp4

Opened composite_map.ccp4 as #3, grid size 616,616,616, pixel 0.851, shown at
level -0.0032, step 4, values float32  

> volume #3 step 1

> volume #3 level -0.003198

> volume #3 level 3.856

> combine #2

> hide #4 models

> delete #4/B-X

> delete #4/A:1-1200

> mmaker #4/A:1200-1900 #1/A:1200-1900

> matchmaker #4/A:1200-1900 #1/A:1200-1900

Missing required ""to"" argument  

> mmaker #4/A:1200-1900 to #1/A:1200-1900

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 JF1086_model2-coot-62.pdb, chain A (#1) with copy of
fold_2024_05_09_01_21_model_0.cif, chain A (#4), sequence alignment score =
1293.6  
RMSD between 156 pruned atom pairs is 1.102 angstroms; (across all 331 pairs:
4.593)  
  

> show #4 models

> hide #!3 models

> hide #!1 models

> delete #4/A:1430-1657

> show #!1 models

> delete #4/A:100-1300

> combine #4

> mmaker #5/A to #5/H:1300-1900

No 'to' model specified  

> mmaker #5/A to #1/H:1300-1900

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 JF1086_model2-coot-62.pdb, chain H (#1) with copy of copy of
fold_2024_05_09_01_21_model_0.cif, chain A (#5), sequence alignment score =
1097.9  
RMSD between 116 pruned atom pairs is 0.802 angstroms; (across all 285 pairs:
5.216)  
  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> delete #5/A:1000-1480

> mmaker #5/A:1655-1900 to #1/H:1655-1900

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 JF1086_model2-coot-62.pdb, chain H (#1) with copy of copy of
fold_2024_05_09_01_21_model_0.cif, chain A (#5), sequence alignment score =
771.2  
RMSD between 80 pruned atom pairs is 0.687 angstroms; (across all 159 pairs:
3.797)  
  

> undo

> hide #!5 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!4 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> delete #4/A:1-1408, 1450-1900

> show #!5 models

> hide #!5 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> combine #2

> hide #6 models

> delete #6/B-X

> delete #6/A:1-1200, 1430-1660

> show #!6 models

> mmaker #6/A:1200-1900 to #1/A:1200-1900

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 JF1086_model2-coot-62.pdb, chain A (#1) with copy of
fold_2024_05_09_01_21_model_0.cif, chain A (#6), sequence alignment score =
1285.2  
RMSD between 156 pruned atom pairs is 1.102 angstroms; (across all 326 pairs:
4.573)  
  

> combine #6

> hide #!7 models

> delete #6/A:1-1387,1430-1900

> delete #1/A:1388-1429

> show #!5 models

> hide #!5 models

> combine #1,6

Remapping chain ID 'A' in copy of fold_2024_05_09_01_21_model_0.cif #6 to 'I'  

> hide #!1 models

> hide #!6 models

> save /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-62_newC-term.pdb
> models #8

> show #!3 models

> ui tool show ""Fit in Map""

> hide #!3 models

> show #!3 models

> hide #!8 models

> hide #!3 models

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> show #!8 models

> show #!3 models

> fitmap #6 inMap #3

Fit molecule copy of fold_2024_05_09_01_21_model_0.cif (#6) to map
composite_map.ccp4 (#3) using 332 atoms  
average map value = 8.215, steps = 104  
shifted from previous position = 0.988  
rotated from previous position = 3.16 degrees  
atoms outside contour = 145, contour level = 3.8563  
  
Position of copy of fold_2024_05_09_01_21_model_0.cif (#6) relative to
composite_map.ccp4 (#3) coordinates:  
Matrix rotation and translation  
-0.12613499 0.15760077 -0.97941409 255.44967363  
0.90779391 0.41643741 -0.04990098 209.06491895  
0.40000024 -0.89540040 -0.19559634 227.14447058  
Axis -0.47409952 -0.77348328 0.42065813  
Axis point -57.73663339 0.00000000 236.55561528  
Rotation angle (degrees) 116.91363758  
Shift along axis -187.26661865  
  

> hide #!3 models

> show #!3 models

> hide #!3 models

> open
> /Users/farnung/Downloads/fold_armc5_cul3_dimer/fold_armc5_cul3_dimer_model_0.cif

Chain information for fold_armc5_cul3_dimer_model_0.cif #9  
---  
Chain | Description  
A B | .  
C D | .  
  

> hide #!8 models

> color #9 bychain

> delete #9/A-C

> show #!8 models

> mmaker #9/D:1-189 to #8/F:1-189

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 combination, chain F (#8) with fold_armc5_cul3_dimer_model_0.cif,
chain D (#9), sequence alignment score = 758.2  
RMSD between 121 pruned atom pairs is 1.135 angstroms; (across all 174 pairs:
3.884)  
  

> show #!3 models

> hide #!3 models

> combine #9

> hide #10 models

> delete #9/1-26,190-1000

> delete #9/D:1-26,190-1000

> combine #9

> mmaker #9/D to #8/G:26-189

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 combination, chain G (#8) with fold_armc5_cul3_dimer_model_0.cif,
chain D (#9), sequence alignment score = 668.5  
RMSD between 114 pruned atom pairs is 1.169 angstroms; (across all 163 pairs:
2.813)  
  

> hide #9 models

> hide #11 models

> delete #8/F,G:27-500

> show #9 models

> show #11 models

> combine #8,9,11

Remapping chain ID 'D' in fold_armc5_cul3_dimer_model_0.cif #9 to 'M'  
Remapping chain ID 'D' in copy of fold_armc5_cul3_dimer_model_0.cif #11 to 'N'  

> hide #!8 models

> hide #9 models

> hide #11 models

> dssp

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-64.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-64.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 211 211 ASN I 1389 GLU I 1401 1 13  
Start residue of secondary structure not found: HELIX 212 212 ALA I 1402 GLY I
1405 1 4  
Start residue of secondary structure not found: HELIX 213 213 PRO I 1410 ALA I
1428 1 19  
  
Chain information for JF1086_model2-coot-64.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!12 models

> show #9 models

> show #!12 models

> hide #9#!12-13 atoms

> show #9#!12-13 cartoons

> hide #!12 models

> dssp

> delete #13/F,G:27-500

> show #11 models

> combine #13,9,11

Remapping chain ID 'D' in fold_armc5_cul3_dimer_model_0.cif #9 to 'I'  
Remapping chain ID 'D' in copy of fold_armc5_cul3_dimer_model_0.cif #11 to 'M'  

> hide #9 models

> hide #11 models

> hide #!13 models

> save /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-64_updated.pdb
> models #14

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-65.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-65.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 187 187 LYS I 28 GLN I 45 1 18  
Start residue of secondary structure not found: HELIX 188 188 PHE I 54 LEU I
66 1 13  
Start residue of secondary structure not found: HELIX 189 189 GLY I 70 LYS I
88 1 19  
Start residue of secondary structure not found: HELIX 190 190 VAL I 89 VAL I
93 1 5  
Start residue of secondary structure not found: HELIX 191 191 LEU I 94 SER I
96 1 3  
19 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-65.pdb #15  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!14-15 atoms

> show #!14-15 cartoons

> hide #!14 models

> dssp

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-66.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-66.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 187 187 LYS I 28 GLN I 45 1 18  
Start residue of secondary structure not found: HELIX 188 188 PHE I 54 LEU I
66 1 13  
Start residue of secondary structure not found: HELIX 189 189 GLY I 70 LYS I
88 1 19  
Start residue of secondary structure not found: HELIX 190 190 VAL I 89 VAL I
93 1 5  
Start residue of secondary structure not found: HELIX 191 191 LEU I 94 SER I
96 1 3  
19 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-66.pdb #16  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!15-16 atoms

> show #!15-16 cartoons

> hide #!15 models

> dssp

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-67.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-67.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 187 187 LYS I 28 GLN I 45 1 18  
Start residue of secondary structure not found: HELIX 188 188 PHE I 54 LEU I
66 1 13  
Start residue of secondary structure not found: HELIX 189 189 GLY I 70 LYS I
88 1 19  
Start residue of secondary structure not found: HELIX 190 190 VAL I 89 VAL I
93 1 5  
Start residue of secondary structure not found: HELIX 191 191 LEU I 94 SER I
96 1 3  
19 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-67.pdb #17  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!16-17 atoms

> show #!16-17 cartoons

> hide #!16 models

> dssp

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-68.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-68.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 187 187 LYS I 28 GLN I 45 1 18  
Start residue of secondary structure not found: HELIX 188 188 PHE I 54 LEU I
66 1 13  
Start residue of secondary structure not found: HELIX 189 189 GLY I 70 LYS I
88 1 19  
Start residue of secondary structure not found: HELIX 190 190 VAL I 89 VAL I
93 1 5  
Start residue of secondary structure not found: HELIX 191 191 LEU I 94 SER I
96 1 3  
19 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-68.pdb #18  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!17-18 atoms

> show #!17-18 cartoons

> hide #!17 models

> dssp

> open 8q7r

8q7r title:  
Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34:
NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide [more
info...]  
  
Chain information for 8q7r #19  
---  
Chain | Description | UniProt  
A | Cullin-2 | CUL2_HUMAN 1-745  
C | Ubiquitin-conjugating enzyme E2 R2 | UB2R2_HUMAN 1-238  
D | Elongin-C | ELOC_HUMAN 1-112  
F | Nucleotide exchange factor SIL1 | SIL1_HUMAN 442-461  
G | Elongin-B | ELOB_HUMAN 1-118  
H | Protein fem-1 homolog C | FEM1C_HUMAN 1-617  
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-108  
U | Ubiquitin | UBC_HUMAN 1-685  
  
Non-standard residues in 8q7r #19  
---  
U9O — 5-azanyl-1-oxidanyl-pentan-2-one  
ZN — zinc ion  
  
6 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!18-19 atoms

> show #!18-19 cartoons

> delete #19/A-C,F,H,R,U

> delete #19 ions

Expected a keyword  

> show #19 ions

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #19 IONS

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> delete #19 ZN

Expected a keyword  

> select :ZN

18 atoms, 18 residues, 9 models selected  

> show sel & #!18 atoms

> hide sel & #!18 atoms

> mmaker #19/D to #18.E

> matchmaker #19/D to #18.E

Invalid ""to"" argument: only initial part ""#18"" of atom specifier valid  

> mmaker #19/D to #18/E

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 JF1086_model2-coot-68.pdb, chain E (#18) with 8q7r, chain D (#19),
sequence alignment score = 441.9  
RMSD between 83 pruned atom pairs is 0.676 angstroms; (across all 90 pairs:
1.433)  
  

> select add #12

34521 atoms, 35252 bonds, 28 pseudobonds, 3644 residues, 11 models selected  

> select subtract #12

16 atoms, 16 residues, 8 models selected  

> select add #13

31829 atoms, 32525 bonds, 28 pseudobonds, 3316 residues, 10 models selected  

> select add #14

66352 atoms, 67798 bonds, 56 pseudobonds, 6942 residues, 12 models selected  

> select subtract #13

34537 atoms, 35273 bonds, 28 pseudobonds, 3640 residues, 9 models selected  

> select subtract #14

12 atoms, 12 residues, 6 models selected  

> select add #15

34535 atoms, 35273 bonds, 28 pseudobonds, 3638 residues, 8 models selected  

> select subtract #15

10 atoms, 10 residues, 5 models selected  

> select add #15

34535 atoms, 35273 bonds, 28 pseudobonds, 3638 residues, 8 models selected  

> select subtract #15

10 atoms, 10 residues, 5 models selected  

> select add #16

34533 atoms, 35273 bonds, 28 pseudobonds, 3636 residues, 7 models selected  

> select subtract #16

8 atoms, 8 residues, 4 models selected  

> select add #17

34531 atoms, 35273 bonds, 28 pseudobonds, 3634 residues, 6 models selected  

> select subtract #17

6 atoms, 6 residues, 3 models selected  

> select add #18

34521 atoms, 35267 bonds, 28 pseudobonds, 3632 residues, 5 models selected  

> select subtract #18

4 atoms, 4 residues, 2 models selected  

> combine #19

> mmaker #20/D to #18/D

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 JF1086_model2-coot-68.pdb, chain D (#18) with copy of 8q7r, chain D
(#20), sequence alignment score = 408.9  
RMSD between 80 pruned atom pairs is 0.698 angstroms; (across all 90 pairs:
1.542)  
  

> hide #!20 models

> hide #!19 models

> delete #18/B,C

> show #!19 models

> hide #!19 models

> show #!20 models

> delete #19,20/D:39-59

> delete #18/D,E:1-37,60-200

> show #!19 models

> dssp

> combine #18,19,20

Remapping chain ID 'D' in 8q7r #19 to 'I'  
Remapping chain ID 'G' in 8q7r #19 to 'M'  
Remapping chain ID 'D' in copy of 8q7r #20 to 'N'  
Remapping chain ID 'G' in copy of 8q7r #20 to 'O'  

> hide #!18 models

> hide #!19 models

> hide #!20 models

> save /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-68_updated.pdb
> models #21

> hide #!21 models

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-79.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-79.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-79.pdb #22  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!22 atoms

> show #!22 cartoons

> dssp

> open /Users/farnung/Downloads/cryosparc_P405_J92_005_volume_map.mrc

Opened cryosparc_P405_J92_005_volume_map.mrc as #23, grid size 616,616,616,
pixel 0.851, shown at level 0.00735, step 4, values float32  

> volume #23 step 1

> volume #23 level 0.01687

> color /A #C400F5

> color /J #d6d71d

> color /K #0496ff

> color /L #f94144

> color /H #ba83e7

> color /G,F #20b960

> color /B,C #edafd4

> color /E,D #6266c9

> hide #!23 models

> show #!23 models

> color zone #23 near #22 distance 5.11

> color zone #23 near #22 distance 12

> hide #!23 models

> color #23 #0496ffff models

> show #!23 models

> color zone #23 near #22 distance 5.11

> color zone #23 near #22 distance 12

> hide #!23 models

> show #22/A,H:1341,1344,1345,1348,1350

> color #22/A,H:1341,1344,1345,1348,1350 red

> style #!22 stick

Changed 33268 atom styles  

> open /Users/farnung/Downloads/cryosparc_P405_J180_006_volume_map.mrc

Opened cryosparc_P405_J180_006_volume_map.mrc as #24, grid size 616,616,616,
pixel 0.851, shown at level 0.00857, step 4, values float32  

> volume #24 step 1

> volume #24 level 0.021

> volume #24 level 0.02431

> select add #8

31797 atoms, 32504 bonds, 28 pseudobonds, 3304 residues, 4 models selected  

> select subtract #8

2 atoms, 2 residues, 1 model selected  

> hide #!24 models

> select #22:K:41-47 #22/L:7-13 #22/J:600-800

2562 atoms, 2635 bonds, 269 residues, 1 model selected  

> select #22:K:41-47 #22/L:7-13 #22/J:500-800

3326 atoms, 3413 bonds, 369 residues, 1 model selected  

> select #22:K:41-47 #22/L:7-13 #22/J:500-900

3693 atoms, 3790 bonds, 1 pseudobond, 413 residues, 2 models selected  

> molmap sel 12 onGrid #24

Opened JF1086_model2-coot-79.pdb map 12 as #25, grid size 616,616,616, pixel
0.851, shown at level 0.0338, step 1, values float32  

> hide #!25 models

> select add #22

33268 atoms, 34021 bonds, 28 pseudobonds, 3627 residues, 3 models selected  

> select subtract #22

Nothing selected  

> select #22:K:41-47 #22/L:7-13 #22/J:500-900

3693 atoms, 3790 bonds, 1 pseudobond, 413 residues, 2 models selected  

> show #!25 models

> ui mousemode right ""map eraser""

> volume erase #25 center 245.92,321.99,224.59 radius 31.654

> volume erase #25 center 243.68,327.78,255.75 radius 31.654

> volume erase #25 center 281.86,298.69,313.64 radius 31.654

> volume erase #25 center 273.15,295.63,339.39 radius 31.654

> volume erase #25 center 241.66,280.86,233.74 radius 31.654

> save /Users/farnung/Desktop/JF1086/Masks/JF1086_P405_J180_mask_bulge.mrc
> models #25

> select add #22

33268 atoms, 34021 bonds, 28 pseudobonds, 3627 residues, 3 models selected  

> select subtract #22

Nothing selected  

> hide #!22 models

> hide #!25 models

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-80.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-80.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-80.pdb #26  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!26 atoms

> show #!26 cartoons

> ui mousemode right translate

> dssp

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-81.pdb #27  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!26-27 atoms

> show #!26-27 cartoons

> dssp

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-81.pdb #28  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!26-28 atoms

> show #!26-28 cartoons

> hide #!26 models

> hide #!27 models

> show #!27 models

> hide #!28 models

> show #!28 models

> hide #!27 models

> show #!27 models

> hide #!27 models

> show #!27 models

> hide #!27 models

> dssp

> show #!27 models

> hide #!28 models

> show #!28 models

> hide #!27 models

> show #!27 models

> hide #!27 models

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-81_updated.pdb #29  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!28-29 atoms

> show #!28-29 cartoons

> hide #!28 models

> dssp

> show #!28 models

> hide #!29 models

> show #!29 models

> hide #!28 models

> hide #!29 models

> show #!29 models

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-81_updated.pdb #29  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb  
---  
warnings | Ignored bad PDB record found on line 336  
HELIX 211 211 SER H 1320 CYS H 1329 1 10  
  
Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I
36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-81_updated.pdb #29  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb  
---  
warnings | Ignored bad PDB record found on line 334  
HELIX 211 211 SER H 1320 CYS H 1329 1 10  
  
Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I
36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-81_updated.pdb #29  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-81_updated.pdb #29  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-81_updated.pdb #29  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-81_updated.pdb #29  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-81_updated.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-81_updated.pdb #29  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> dssp

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> save /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb models
> #29

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb

Chain information for JF1086_model2-coot-82.pdb #29  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb

Chain information for JF1086_model2-coot-82.pdb #29  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb

Chain information for JF1086_model2-coot-82.pdb #29  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb

Chain information for JF1086_model2-coot-82.pdb #29  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb

Chain information for JF1086_model2-coot-82.pdb #29  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-79.pdb

Summary of feedback from opening
/Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-79.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 201 201 ARG I 33 ALA I 36 1 4  
Start residue of secondary structure not found: HELIX 202 202 SER I 67 TYR I
76 1 10  
Start residue of secondary structure not found: HELIX 203 203 PHE I 77 TYR I
79 1 3  
Start residue of secondary structure not found: HELIX 204 204 ALA I 100 LEU I
110 1 11  
Start residue of secondary structure not found: HELIX 205 205 VAL M 24 ILE M
34 1 11  
13 messages similar to the above omitted  
  
Chain information for JF1086_model2-coot-79.pdb #29  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb

Chain information for JF1086_model2-coot-82.pdb #30  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 models

> hide #!30 cartoons

> hide #!30 atoms

> show #!30 cartoons

> delete #29

> delete #30

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb

Chain information for JF1086_model2-coot-82.pdb #29  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> delete #30

> delete #29

> open /Users/farnung/Desktop/JF1086/Krios/JF1086_model2-coot-82.pdb

Chain information for JF1086_model2-coot-82.pdb #29  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide #!29 atoms

> show #!29 cartoons

> hide #!29 models

> show #!23 models

> ui mousemode right ""map eraser""

> volume erase #23 center 319.23,124.31,190.65 radius 58.778

Opened cryosparc_P405_J92_005_volume_map.mrc copy as #31, grid size
616,616,616, pixel 0.851, shown at step 1, values float32  

> volume erase #31 center 265.85,205.46,171.57 radius 58.726

> volume erase #31 center 276.48,272.42,198.28 radius 58.726

> volume erase #31 center 227.59,338.41,226.57 radius 58.726

> volume erase #31 center 166.46,314.02,245.24 radius 58.726

> volume erase #31 center 214.68,257.02,173.13 radius 58.726

> volume erase #31 center 334.76,283.93,292.18 radius 58.726

> volume erase #31 center 282.69,311.6,324.95 radius 58.726

> volume erase #31 center 276.56,294.15,260 radius 58.726

> volume erase #31 center 259.07,260.49,212.55 radius 58.726

> volume erase #31 center 336.54,206.91,210.46 radius 58.726

> volume erase #31 center 322.07,204.83,218.59 radius 58.726

> volume #31 level 0.01947

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> save /Users/farnung/Desktop/JF1086/Masks/JF1086_P405_J180_mask_3prime.mrc
> models #31

> volume erase #31 center 221.09,249.61,304.52 radius 58.726

> volume erase #31 center 261.8,248.61,340.15 radius 58.726

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> save
> /Users/farnung/Desktop/JF1086/Masks/JF1086_P405_J180_mask_3prime_truncated.mrc
> models #31

> hide #!31 models

> show #!29 models

> open /Users/farnung/Downloads/cryosparc_P405_J210_003_volume_map_sharp.mrc

Opened cryosparc_P405_J210_003_volume_map_sharp.mrc as #30, grid size
616,616,616, pixel 0.851, shown at level 0.026, step 4, values float32  

> ui mousemode right translate

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #30 step 1

> volume #30 level 0.06938

> volume #30 level 0.1214

> hide #!30 models

> color /A #C400F5

> color /J #d6d71d

> color /K #0496ff

> color /L #f94144

> color /H #ba83e7

> color /G,F #20b960

> color /B,C #edafd4

> color /E,D #6266c9

> color /J #fe711a

> color /J #F49E4C

> color /J #FFD166

> color /J #5BA0FC

> color /J #FFD166

> lighting soft

> graphics silhouettes true

> set bgColor white

> color /A #C400F5

> color /J #d6d71d

> color /K #0496ff

> color /L #f94144

> color /H #ba83e7

> color /G,F #20b960

> color /B,C #edafd4

> color /E,D #6266c9

> show #!3 models

> color zone #3 near #29 distance 5.11

> ui tool show ""Side View""

> show #!23 models

> hide #!3 models

> volume #31 level 0.04155

> hide #!31 models

> hide #!23 models

> show #!23 models

> volume #23 level 0.02856

> volume #23 level 0.01687

> open /Users/farnung/Downloads/cryosparc_P405_J221_map.mrc

Opened cryosparc_P405_J221_map.mrc as #32, grid size 616,616,616, pixel 0.851,
shown at level 0.00592, step 4, values float32  

> hide #!23 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #32 step 1

> volume #32 level 0.01543

> open /Users/farnung/Downloads/cryosparc_P405_J200_map.mrc

Opened cryosparc_P405_J200_map.mrc as #33, grid size 616,616,616, pixel 0.851,
shown at level 0.00574, step 4, values float32  

> hide #!32 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #33 step 1

> volume #33 level 0.01189

> color zone #33 near #29 distance 5.11

> color zone #33 near #29 distance 12

> color zone #33 near #29 distance 14

> open /Users/farnung/Downloads/cryosparc_P405_J215_004_volume_map.mrc

Opened cryosparc_P405_J215_004_volume_map.mrc as #34, grid size 616,616,616,
pixel 0.851, shown at level 0.00901, step 4, values float32  

> hide #!33 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #34 step 1

> volume #34 level 0.04074

> volume #34 level 0.02604

> open /Users/farnung/Downloads/cryosparc_P405_J219_003_volume_map.mrc

Opened cryosparc_P405_J219_003_volume_map.mrc as #35, grid size 616,616,616,
pixel 0.851, shown at level 0.00682, step 4, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #35 step 1

> volume #35 level 0.01956

> hide #!34 models

> volume #35 level 0.03039

> hide #!35 models

> show #!34 models

> show #!35 models

> hide #!34 models

> volume #35 level 0.03167

> hide #!35 models

> hide #!29 models

> show #!23 models

> ui mousemode right ""map eraser""

> volume erase #23 center 270.6,282.28,324.2 radius 53.362

Opened cryosparc_P405_J92_005_volume_map.mrc copy as #37, grid size
616,616,616, pixel 0.851, shown at step 1, values float32  

> volume erase #37 center 337.99,307.06,297.83 radius 53.22

> volume erase #37 center 352.14,291.25,298.12 radius 53.22

> volume erase #37 center 239.3,226.67,312.65 radius 53.22

> volume erase #37 center 253.92,167.56,285.34 radius 53.22

> volume erase #37 center 314.51,107.88,245.37 radius 53.22

> volume erase #37 center 317.08,114.39,195.11 radius 53.22

> volume erase #37 center 288.81,84.875,221.55 radius 53.22

> volume erase #37 center 179.67,328.25,256.52 radius 53.22

> volume erase #37 center 250.25,339.41,239.2 radius 53.22

> volume erase #37 center 265.23,291.28,286.65 radius 53.22

> volume erase #37 center 231.86,164.46,237.69 radius 53.22

> volume erase #37 center 240.06,295.29,272.49 radius 53.22

> ui mousemode right translate

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> save /Users/farnung/Desktop/JF1086/Masks/JF1086_P405_J180_mask_5prime.mrc
> models #37

> show #!35 models

> hide #!35 models

> show #!35 models

> show #!34 models

> hide #!37 models

> hide #!34 models

> hide #!35 models

> show #!29 models

> open /Users/farnung/Downloads/cryosparc_P405_J211_map_sharp.mrc

Opened cryosparc_P405_J211_map_sharp.mrc as #36, grid size 616,616,616, pixel
0.851, shown at level 0.000367, step 4, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #36 step 1

> volume #36 level 0.0482

> ui tool show ""Side View""

> volume #36 level 0.05298

> hide #!36 models

> open /Users/farnung/Downloads/cryosparc_P405_J219_006_volume_map_sharp.mrc

Opened cryosparc_P405_J219_006_volume_map_sharp.mrc as #38, grid size
616,616,616, pixel 0.851, shown at level 0.0365, step 4, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #38 step 1

> volume #38 level 0.06092

> volume #38 level 0.08809

> volume #38 level 0.08266

> hide #!38 models

> open 8tqw

Summary of feedback from opening 8tqw fetched from pdb  
---  
note | Fetching compressed mmCIF 8tqw from http://files.rcsb.org/download/8tqw.cif  
  
8tqw title:  
Structure of human transcriptional Mediator complex [more info...]  
  
Chain information for 8tqw #39  
---  
Chain | Description | UniProt  
0 | Mediator of RNA polymerase II transcription subunit 27 | MED27_HUMAN 1-311  
1 | Mediator of RNA polymerase II transcription subunit 28 | MED28_HUMAN 1-178  
2 | Mediator of RNA polymerase II transcription subunit 29 | MED29_HUMAN 1-200  
3 | Mediator of RNA polymerase II transcription subunit 30 | MED30_HUMAN 1-178  
4 | Mediator of RNA polymerase II transcription subunit 31 | MED31_HUMAN 1-131  
A | Mediator of RNA polymerase II transcription subunit 1 | MED1_HUMAN 1-1581  
B | Unknown Chain |   
D | Mediator of RNA polymerase II transcription subunit 4 | MED4_HUMAN 1-270  
F | Mediator of RNA polymerase II transcription subunit 6 | MED6_HUMAN 1-246  
G | Mediator of RNA polymerase II transcription subunit 7 | MED7_HUMAN 1-233  
H | Mediator of RNA polymerase II transcription subunit 8 | MED8_HUMAN 1-268  
I | Mediator of RNA polymerase II transcription subunit 9 | MED9_HUMAN 1-146  
J | Mediator of RNA polymerase II transcription subunit 10 | MED10_HUMAN 1-135  
K | Mediator of RNA polymerase II transcription subunit 11 | MED11_HUMAN 1-117  
N | Mediator of RNA polymerase II transcription subunit 14 | MED14_HUMAN 1-1454  
O | Mediator of RNA polymerase II transcription subunit 15 | MED15_HUMAN 1-788  
P | Mediator of RNA polymerase II transcription subunit 16 | MED16_HUMAN 1-877  
Q | Mediator of RNA polymerase II transcription subunit 17 | MED17_HUMAN 1-651  
R | Mediator of RNA polymerase II transcription subunit 18 | MED18_HUMAN 1-208  
S | Mediator of RNA polymerase II transcription subunit 19 | MED19_HUMAN 1-244  
T | Mediator of RNA polymerase II transcription subunit 20 | MED20_HUMAN 1-212  
U | Mediator of RNA polymerase II transcription subunit 21 | MED21_HUMAN 1-144  
V | Mediator of RNA polymerase II transcription subunit 22 | MED22_HUMAN 1-200  
W | Mediator of RNA polymerase II transcription subunit 23 | MED23_HUMAN 1-1368  
X | Mediator of RNA polymerase II transcription subunit 24 | MED24_HUMAN 1-989  
a | Cyclin-dependent kinase 8 | CDK8_HUMAN 1-464  
b | Cyclin-C | CCNC_HUMAN 1-283  
c | Mediator of RNA polymerase II transcription subunit 12 | MED12_HUMAN 1-2177  
d | Mediator of RNA polymerase II transcription subunit 13 | MED13_HUMAN 1-2174  
  
Non-standard residues in 8tqw #39  
---  
ZN — zinc ion  
  
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac15,3
      Model Number: Z1C8000TMD/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 11881.41.5

Software:

    System Software Overview:

      System Version: macOS 15.1.1 (24B91)
      Kernel Version: Darwin 24.1.0
      Time since boot: 7 days, 2 hours, 46 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    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: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 2.2.4
    ChimeraX-Clipper: 0.23.1
    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: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX