![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#15976 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.0-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 1300000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 213858,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-09-13 09:35:41.3761 +0800",
"codeSigningMonitor" : 1,
"incident" : "7CB70439-C2D7-412C-895C-19D015E4D299",
"pid" : 76031,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-09 17:19:04.5537 +0800",
"procStartAbsTime" : 28711680788866,
"procExitAbsTime" : 33462426091219,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3EAC0DD1-9F72-5289-AE22-5F091527EFE7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "32525C7F-93DA-C799-A39F-3423ED9CAD6D",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 4399,
"sleepWakeUUID" : "04281BD5-6DA6-4A0C-9364-FDFE932201E2",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":76031},
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===== Log before crash start =====
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/T1-D233A-Met-
> SAM/SAM-pocket/SAM-pocket-5A.cxs
Opened cryosparc_P13_J106_003_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.526, shown at level 0.248, step 1, values float32
opened ChimeraX session
> close #1-2
> open
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/predict-
> tRNA-structure/predict-Ala-mt-tRNA.pdb
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/predict-
> tRNA-structure/predict-Gln-mt-tRNA.pdb
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/predict-
> tRNA-structure/predict-Met-methylation-tRNA-model.pdb
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/predict-
> tRNA-structure/predict-Met-tRNA-G26out-model.pdb
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/predict-
> tRNA-structure/predict-Met-tRNA-model.pdb
Summary of feedback from opening
/Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/predict-
tRNA-structure/predict-Ala-mt-tRNA.pdb
---
warnings | Ignored bad PDB record found on line 2314
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 2315
#BEGIN_POSE_ENERGIES_TABLE /tmp/yangserver/RNA005806_0.45_2/pose_0.45_2.pdb
Ignored bad PDB record found on line 2316
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
fa_dun p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 2317
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 2318
pose -616.855 17.7272 706.679 2.6011 140.065 -99.0366 -74.4341 0 0 0 -15.406
-72.3739 0 0 0 0 0 0 0 -11.034
74 messages similar to the above omitted
Summary of feedback from opening
/Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/predict-
tRNA-structure/predict-Gln-mt-tRNA.pdb
---
warnings | Ignored bad PDB record found on line 2424
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 2425
#BEGIN_POSE_ENERGIES_TABLE /tmp/yangserver/RNA005807_0.45_3/pose_0.45_3.pdb
Ignored bad PDB record found on line 2426
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
fa_dun p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 2427
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 2428
pose -677.488 21.0075 786.596 2.61176 149.337 -110.619 -92.578 0 0 0 -18.8148
-82.6629 0 0 0 0 0 0 0 -22.6107
77 messages similar to the above omitted
Summary of feedback from opening
/Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/predict-
tRNA-structure/predict-Met-tRNA-model.pdb
---
warnings | Ignored bad PDB record found on line 2454
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 2455
#BEGIN_POSE_ENERGIES_TABLE /tmp/yangserver/RNA005805_0.45_1/pose_0.45_1.pdb
Ignored bad PDB record found on line 2456
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
fa_dun p_aa_pp yhh_planarity ref rama_prepro total
Ignored bad PDB record found on line 2457
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA
Ignored bad PDB record found on line 2458
pose -676.241 19.2699 805.681 2.73489 147.438 -111.04 -103.42 0 0 0 -17.9861
-84.8118 0 0 0 0 0 0 0 -18.3769
78 messages similar to the above omitted
Chain information for predict-Ala-mt-tRNA.pdb #1
---
Chain | Description
A | No description available
Chain information for predict-Gln-mt-tRNA.pdb #2
---
Chain | Description
A | No description available
Chain information for predict-Met-methylation-tRNA-model.pdb #3
---
Chain | Description
D | No description available
Chain information for predict-Met-tRNA-G26out-model.pdb #4
---
Chain | Description
T | No description available
Chain information for predict-Met-tRNA-model.pdb #5
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 predict-Ala-mt-tRNA.pdb, chain A (#1) with predict-Gln-mt-tRNA.pdb,
chain A (#2), sequence alignment score = 96.5
RMSD between 30 pruned atom pairs is 1.080 angstroms; (across all 67 pairs:
10.396)
Matchmaker predict-Ala-mt-tRNA.pdb, chain A (#1) with predict-Met-methylation-
tRNA-model.pdb, chain D (#3), sequence alignment score = 80.5
RMSD between 24 pruned atom pairs is 1.232 angstroms; (across all 72 pairs:
9.167)
Matchmaker predict-Ala-mt-tRNA.pdb, chain A (#1) with predict-Met-tRNA-G26out-
model.pdb, chain T (#4), sequence alignment score = 76.4
RMSD between 4 pruned atom pairs is 1.219 angstroms; (across all 54 pairs:
31.862)
Matchmaker predict-Ala-mt-tRNA.pdb, chain A (#1) with predict-Met-tRNA-
model.pdb, chain A (#5), sequence alignment score = 79.8
RMSD between 26 pruned atom pairs is 0.995 angstroms; (across all 72 pairs:
12.196)
> hide #5 models
> hide #3 models
> hide #2 models
> hide #1 models
> hide #4 models
> show #5 models
> hide #5 models
> show #3 models
> show #2 models
> show #1 models
> hide #2 models
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_methylated/fold_t1_ala_methylated_model_0.cif
Chain information for fold_t1_ala_methylated_model_0.cif #6
---
Chain | Description
A | .
B | .
> hide #3 models
> hide #1 models
> color #6 #607cdbff
> select up
24 atoms, 26 bonds, 1 residue, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 24 atom styles
> select add #6
6606 atoms, 6891 bonds, 731 residues, 1 model selected
> select subtract #6
Nothing selected
> close #6
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_2_m2g/fold_t1_ala_2_m2g_model_0.cif
Chain information for fold_t1_ala_2_m2g_model_0.cif #6
---
Chain | Description
A B | .
C D | .
> color #6 #5d8cdbff
> select add #6
13212 atoms, 13782 bonds, 1462 residues, 1 model selected
> color sel bychain
> select subtract #6
Nothing selected
> open /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/TRMT-
> RNA-Met-SAH/model&map/TRMT1-tRNA-met-coot-14.pdb
Chain information for TRMT1-tRNA-met-coot-14.pdb #7
---
Chain | Description
A | No description available
B | No description available
T | No description available
> select add #7
16258 atoms, 16581 bonds, 9 pseudobonds, 982 residues, 3 models selected
> select subtract #7
Nothing selected
> ui tool show Matchmaker
> matchmaker #1-6 to #7
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 TRMT1-tRNA-met-coot-14.pdb, chain T (#7) with predict-Ala-mt-
tRNA.pdb, chain A (#1), sequence alignment score = 76.4
RMSD between 4 pruned atom pairs is 1.446 angstroms; (across all 54 pairs:
40.789)
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain B (#7) with predict-Gln-mt-
tRNA.pdb, chain A (#2), sequence alignment score = 2.21433e+253
Fewer than 3 residues aligned; cannot match TRMT1-tRNA-met-coot-14.pdb, chain
B with predict-Gln-mt-tRNA.pdb, chain A
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with predict-Met-
methylation-tRNA-model.pdb, chain D (#3), sequence alignment score =
2.24385e+253
Fewer than 3 residues aligned; cannot match TRMT1-tRNA-met-coot-14.pdb, chain
A with predict-Met-methylation-tRNA-model.pdb, chain D
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain B (#7) with predict-Met-
tRNA-G26out-model.pdb, chain T (#4), sequence alignment score = 2.05873e+08
Fewer than 3 residues aligned; cannot match TRMT1-tRNA-met-coot-14.pdb, chain
B with predict-Met-tRNA-G26out-model.pdb, chain T
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain T (#7) with predict-Met-tRNA-
model.pdb, chain A (#5), sequence alignment score = 296
RMSD between 48 pruned atom pairs is 1.138 angstroms; (across all 74 pairs:
2.410)
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_2_m2g_model_0.cif, chain A (#6), sequence alignment score = 907.8
RMSD between 450 pruned atom pairs is 0.945 angstroms; (across all 485 pairs:
5.001)
> hide #6 models
> show #6 models
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_methylated/fold_t1_ala_methylated_model_1.cif
Chain information for fold_t1_ala_methylated_model_1.cif #8
---
Chain | Description
A | .
B | .
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_methylated/fold_t1_ala_methylated_model_2.cif
Chain information for fold_t1_ala_methylated_model_2.cif #9
---
Chain | Description
A | .
B | .
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_methylated/fold_t1_ala_methylated_model_3.cif
Chain information for fold_t1_ala_methylated_model_3.cif #10
---
Chain | Description
A | .
B | .
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_methylated/fold_t1_ala_methylated_model_4.cif
Chain information for fold_t1_ala_methylated_model_4.cif #11
---
Chain | Description
A | .
B | .
> ui tool show Matchmaker
> matchmaker #6,8-11 to #7
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 TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_2_m2g_model_0.cif, chain A (#6), sequence alignment score = 2316.1
RMSD between 461 pruned atom pairs is 0.946 angstroms; (across all 485 pairs:
1.384)
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_methylated_model_1.cif, chain A (#8), sequence alignment score =
2296.3
RMSD between 470 pruned atom pairs is 0.912 angstroms; (across all 485 pairs:
1.077)
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_methylated_model_2.cif, chain A (#9), sequence alignment score =
2308.3
RMSD between 467 pruned atom pairs is 0.952 angstroms; (across all 485 pairs:
1.072)
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_methylated_model_3.cif, chain A (#10), sequence alignment score =
2315.5
RMSD between 470 pruned atom pairs is 0.924 angstroms; (across all 485 pairs:
1.091)
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_methylated_model_4.cif, chain A (#11), sequence alignment score =
2309.5
RMSD between 472 pruned atom pairs is 0.989 angstroms; (across all 485 pairs:
1.086)
> hide #6 models
> hide #!7 models
> show #!7 models
> hide #8 models
> hide #10 models
> hide #11 models
> select add #9
6606 atoms, 6891 bonds, 731 residues, 1 model selected
> color sel bychain
> select subtract #9
Nothing selected
> select #9/B:23
24 atoms, 26 bonds, 1 residue, 1 model selected
> select up
1537 atoms, 1717 bonds, 72 residues, 1 model selected
> select down
24 atoms, 26 bonds, 1 residue, 1 model selected
> color sel red
> nucleotides sel atoms
> style nucleic & sel stick
Changed 24 atom styles
> select #7/T:26
34 atoms, 36 bonds, 1 residue, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 34 atom styles
> color sel red
> select add #7
16258 atoms, 16581 bonds, 9 pseudobonds, 982 residues, 3 models selected
> select subtract #7
Nothing selected
> hide #!7 models
> hide #9 models
> show #8 models
> hide #8 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #11 models
> hide #11 models
> show #!7 models
> hide #!7 models
> show #9 models
> show #!7 models
> select add #7
16258 atoms, 16581 bonds, 9 pseudobonds, 982 residues, 3 models selected
> select subtract #7
Nothing selected
> hide #!7 models
> show #!7 models
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_2_m2g/fold_t1_ala_2_m2g_model_0.cif
Chain information for fold_t1_ala_2_m2g_model_0.cif #12
---
Chain | Description
A B | .
C D | .
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_2_m2g/fold_t1_ala_2_m2g_model_1.cif
Chain information for fold_t1_ala_2_m2g_model_1.cif #13
---
Chain | Description
A B | .
C D | .
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_2_m2g/fold_t1_ala_2_m2g_model_2.cif
Chain information for fold_t1_ala_2_m2g_model_2.cif #14
---
Chain | Description
A B | .
C D | .
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_2_m2g/fold_t1_ala_2_m2g_model_3.cif
Chain information for fold_t1_ala_2_m2g_model_3.cif #15
---
Chain | Description
A B | .
C D | .
> open
> /Users/LaymanXUE/Downloads/fold_t1_ala_2_m2g/fold_t1_ala_2_m2g_model_4.cif
Chain information for fold_t1_ala_2_m2g_model_4.cif #16
---
Chain | Description
A B | .
C D | .
> ui tool show Matchmaker
> matchmaker #12-16 to #7
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 TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_2_m2g_model_0.cif, chain A (#12), sequence alignment score =
2316.1
RMSD between 461 pruned atom pairs is 0.946 angstroms; (across all 485 pairs:
1.384)
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_2_m2g_model_1.cif, chain A (#13), sequence alignment score =
2326.9
RMSD between 458 pruned atom pairs is 0.943 angstroms; (across all 485 pairs:
1.377)
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_2_m2g_model_2.cif, chain B (#14), sequence alignment score =
2321.5
RMSD between 460 pruned atom pairs is 0.983 angstroms; (across all 485 pairs:
1.358)
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_2_m2g_model_3.cif, chain A (#15), sequence alignment score =
2332.9
RMSD between 462 pruned atom pairs is 0.944 angstroms; (across all 485 pairs:
1.157)
Matchmaker TRMT1-tRNA-met-coot-14.pdb, chain A (#7) with
fold_t1_ala_2_m2g_model_4.cif, chain A (#16), sequence alignment score =
2325.1
RMSD between 461 pruned atom pairs is 0.931 angstroms; (across all 485 pairs:
1.311)
> hide #9 models
> show #9 models
> close #8
> close #6
> close #10
> close #11
> hide #9 models
> hide #16 models
> hide #15 models
> hide #14 models
> hide #13 models
> hide #12 models
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #16 models
> hide #16 models
> show #9 models
> close #12-16
> rename #9 id #8
> hide #!7 models
> show #!7 models
> hide #8 models
> select add #7
16258 atoms, 16581 bonds, 9 pseudobonds, 982 residues, 3 models selected
> show sel atoms
> select H
10920 atoms, 1276 residues, 5 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> hbonds #!7 reveal true
1888 hydrogen bonds found
> select ::name="CYS"
312 atoms, 261 bonds, 1 pseudobond, 52 residues, 3 models selected
> select add #7/T:73
334 atoms, 285 bonds, 1 pseudobond, 53 residues, 3 models selected
> select up
5001 atoms, 5236 bonds, 1 pseudobond, 530 residues, 3 models selected
> select down
334 atoms, 285 bonds, 1 pseudobond, 53 residues, 3 models selected
> select #7/T:33
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
1579 atoms, 1764 bonds, 74 residues, 1 model selected
> color sel cyan
> select ::name="CYS"
312 atoms, 261 bonds, 1 pseudobond, 52 residues, 3 models selected
> select #7/B:410
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
96 atoms, 96 bonds, 13 residues, 1 model selected
> select up
2775 atoms, 2830 bonds, 364 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select ::name="CYS"
312 atoms, 261 bonds, 1 pseudobond, 52 residues, 3 models selected
> ui mousemode right "tape measure"
> marker segment #9 position 147.2,125.4,94.03 toPosition 151.5,139.6,98.59
> color yellow radius 0.1 label 15.5 labelHeight 1.55 labelColor yellow
> close #1-6,8#7,9
> open
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/paper/figure/pocket-
> compare/pocket-compare.cxs
opened ChimeraX session
> hide #!4 models
> hide #1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/A:235@CB
22 atoms, 21 bonds, 2 residues, 2 models selected
> select up
42 atoms, 42 bonds, 2 residues, 2 models selected
> color sel purple
> select add #3
16279 atoms, 16602 bonds, 9 pseudobonds, 983 residues, 4 models selected
> select subtract #3
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2
16255 atoms, 16578 bonds, 10 pseudobonds, 982 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #5
16285 atoms, 16608 bonds, 10 pseudobonds, 1000 residues, 3 models selected
> select subtract #5
Nothing selected
> hide #!3 models
> hide #!2 models
> select #5/A:235
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel purple
> select H
23076 atoms, 2923 residues, 3 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select add #3
23986 atoms, 16581 bonds, 9 pseudobonds, 1961 residues, 4 models selected
> select subtract #3
7728 atoms, 979 residues, 1 model selected
> select add #2
16255 atoms, 16578 bonds, 10 pseudobonds, 982 residues, 3 models selected
> select subtract #2
Nothing selected
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> hide #!5 models
> show #!5 models
> show #!3 models
> show #!2 models
> open
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/D233A-apo/T1-D233A-apo-
> coot-1.pdb
Chain information for T1-D233A-apo-coot-1.pdb #6
---
Chain | Description
A B | No description available
> open
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/T1-apo-
> map-model/final/TRMT-Dimer-1-coot-0.pdb
Chain information for TRMT-Dimer-1-coot-0.pdb #7
---
Chain | Description
A B | No description available
> color #6 #7b7adbff
> ui tool show Matchmaker
> matchmaker #!2-7 to #1
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 TRMT1-2tRNA-predict.pdb, chain A (#1) with TRMT1-D233A-Met-SAM-
coot-7.pdb, chain A (#2), sequence alignment score = 2308.7
RMSD between 474 pruned atom pairs is 0.950 angstroms; (across all 485 pairs:
1.084)
Matchmaker TRMT1-2tRNA-predict.pdb, chain A (#1) with TRMT1-tRNA-met-
coot-14.pdb, chain A (#3), sequence alignment score = 2316.1
RMSD between 473 pruned atom pairs is 0.972 angstroms; (across all 485 pairs:
1.096)
Matchmaker TRMT1-2tRNA-predict.pdb, chain A (#1) with T1-2tRNA-1-coot-1.pdb,
chain A (#4), sequence alignment score = 2331.1
RMSD between 473 pruned atom pairs is 0.972 angstroms; (across all 485 pairs:
1.096)
Matchmaker TRMT1-2tRNA-predict.pdb, chain A (#1) with D233A-Met-coot-1.pdb,
chain D (#5), sequence alignment score = 2456.5
RMSD between 33 pruned atom pairs is 0.000 angstroms; (across all 33 pairs:
0.000)
Matchmaker TRMT1-2tRNA-predict.pdb, chain A (#1) with T1-D233A-apo-coot-1.pdb,
chain B (#6), sequence alignment score = 2057.5
RMSD between 416 pruned atom pairs is 0.847 angstroms; (across all 423 pairs:
0.939)
Matchmaker TRMT1-2tRNA-predict.pdb, chain A (#1) with TRMT-Dimer-1-coot-0.pdb,
chain B (#7), sequence alignment score = 2049.9
RMSD between 417 pruned atom pairs is 0.786 angstroms; (across all 423 pairs:
0.880)
> hide #!5 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #!2-7 to #1
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 TRMT1-2tRNA-predict.pdb, chain A (#1) with TRMT1-D233A-Met-SAM-
coot-7.pdb, chain A (#2), sequence alignment score = 2308.7
RMSD between 474 pruned atom pairs is 0.950 angstroms; (across all 485 pairs:
1.084)
Matchmaker TRMT1-2tRNA-predict.pdb, chain A (#1) with TRMT1-tRNA-met-
coot-14.pdb, chain A (#3), sequence alignment score = 2316.1
RMSD between 473 pruned atom pairs is 0.972 angstroms; (across all 485 pairs:
1.096)
Matchmaker TRMT1-2tRNA-predict.pdb, chain A (#1) with T1-2tRNA-1-coot-1.pdb,
chain A (#4), sequence alignment score = 2331.1
RMSD between 473 pruned atom pairs is 0.972 angstroms; (across all 485 pairs:
1.096)
Matchmaker TRMT1-2tRNA-predict.pdb, chain A (#1) with D233A-Met-coot-1.pdb,
chain D (#5), sequence alignment score = 2456.5
RMSD between 33 pruned atom pairs is 0.000 angstroms; (across all 33 pairs:
0.000)
Matchmaker TRMT1-2tRNA-predict.pdb, chain A (#1) with T1-D233A-apo-coot-1.pdb,
chain B (#6), sequence alignment score = 2057.5
RMSD between 416 pruned atom pairs is 0.847 angstroms; (across all 423 pairs:
0.939)
Matchmaker TRMT1-2tRNA-predict.pdb, chain A (#1) with TRMT-Dimer-1-coot-0.pdb,
chain B (#7), sequence alignment score = 2049.9
RMSD between 417 pruned atom pairs is 0.786 angstroms; (across all 423 pairs:
0.880)
> matchmaker #!5 to #1
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 TRMT1-2tRNA-predict.pdb, chain A (#1) with D233A-Met-coot-1.pdb,
chain D (#5), sequence alignment score = 2456.5
RMSD between 33 pruned atom pairs is 0.000 angstroms; (across all 33 pairs:
0.000)
> matchmaker #!5 to #2
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 TRMT1-D233A-Met-SAM-coot-7.pdb, chain A (#2) with D233A-Met-
coot-1.pdb, chain A (#5), sequence alignment score = 2307.6
RMSD between 462 pruned atom pairs is 0.395 angstroms; (across all 471 pairs:
0.556)
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #6/B:235
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #7/B:235
24 atoms, 24 bonds, 2 residues, 2 models selected
> show sel atoms
> color sel medium blue
> select add #6
6462 atoms, 6586 bonds, 10 pseudobonds, 849 residues, 4 models selected
> select subtract #6
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #7
6456 atoms, 6580 bonds, 10 pseudobonds, 848 residues, 3 models selected
> select subtract #7
Nothing selected
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!7 models
> open /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/TRMT-
> RNA-Met-SAH/model&map/cryosparc_P11_J98_004_volume_map_sharp.mrc
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/TRMT-RNA-
> Met-SAH/model&map/TRMT1-tRNA-met-coot-14.pdb
Opened cryosparc_P11_J98_004_volume_map_sharp.mrc as #8, grid size
320,320,320, pixel 0.838, shown at level 0.0953, step 2, values float32
Chain information for TRMT1-tRNA-met-coot-14.pdb #9
---
Chain | Description
A | No description available
B | No description available
T | No description available
> hide #!6 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> volume #8 step 1
> volume #8 level 0.2462
> surface dust #8 size 8.38
> transparency 50
> volume #8 level 0.2537
> hide #!8 models
> select #9/A:235@CA
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> select add #9
16258 atoms, 16581 bonds, 9 pseudobonds, 982 residues, 3 models selected
> select subtract #9
Nothing selected
> select #9/T:26
34 atoms, 36 bonds, 1 residue, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 34 atom styles
> color sel hot pink
> select add #9
16258 atoms, 16581 bonds, 9 pseudobonds, 982 residues, 3 models selected
> select subtract #9
Nothing selected
> show #!8 models
> ui tool show "Side View"
> volume #8 level 0.216
> hide #!9 models
> hide #!8 models
> open
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/T1-D233A-Met-
> SAM/cryosparc_P13_J106_003_volume_map_sharp.mrc
> /Users/LaymanXUE/Documents/XUE/sustech/projects/TRMT1/T-model&map/T1-D233A-Met-
> SAM/TRMT1-D233A-Met-SAM-coot-7.pdb
Opened cryosparc_P13_J106_003_volume_map_sharp.mrc as #10, grid size
400,400,400, pixel 0.526, shown at level 0.0838, step 2, values float32
Chain information for TRMT1-D233A-Met-SAM-coot-7.pdb #11
---
Chain | Description
A | No description available
B | No description available
T | No description available
> surface dust #10 size 5.26
> volume #10 step 1
> hide #!10 models
> select #11/T:47
30 atoms, 31 bonds, 1 residue, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 30 atom styles
> color sel hot pink
> select add #11
16255 atoms, 16578 bonds, 10 pseudobonds, 982 residues, 3 models selected
> select subtract #11
Nothing selected
> select #11/T:26
34 atoms, 36 bonds, 1 residue, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 34 atom styles
> color sel hot pink
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel medium blue
> select add #11
16255 atoms, 16578 bonds, 10 pseudobonds, 982 residues, 3 models selected
> select subtract #11
Nothing selected
> show #!10 models
> surface dust #10 size 5.26
> transparency #10.1 50
> volume #10 level 0.1454
> volume #10 level 0.2192
> volume #10 level 0.2685
> hide #!11 models
> hide #!10 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> show #!4 models
> show #!3 models
> hide #!4 models
> select add #3/T:14
33 atoms, 35 bonds, 1 residue, 1 model selected
> select add #3/T:15
67 atoms, 71 bonds, 2 residues, 1 model selected
> select add #3/T:16
98 atoms, 103 bonds, 3 residues, 1 model selected
> select add #3/T:17
132 atoms, 139 bonds, 4 residues, 1 model selected
> select add #3/T:18
166 atoms, 175 bonds, 5 residues, 1 model selected
> select add #3/T:19
200 atoms, 211 bonds, 6 residues, 1 model selected
> select add #3/T:20
231 atoms, 243 bonds, 7 residues, 1 model selected
> select add #3/T:21
264 atoms, 278 bonds, 8 residues, 1 model selected
> color sel light sea green
> select add #3
16258 atoms, 16581 bonds, 9 pseudobonds, 982 residues, 3 models selected
> select subtract #3
Nothing selected
> show #1 models
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3CH/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.1.1
OS Loader Version: 11881.1.1
Software:
System Software Overview:
System Version: macOS 15.0 (24A335)
Kernel Version: Darwin 24.0.0
Time since boot: 34分钟36秒
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
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
DELL P2719H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
biopython: 1.83
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
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: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
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: 1.1.3
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: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBImages: 1.2
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.2
ChimeraX-PickBlobs: 1.0.1
ChimeraX-PICKLUSTER: 0.5
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RIBFIND: 0.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StarMap: 1.2.15
ChimeraX-StdCommands: 1.12.4
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: 2.2.2
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: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
et-xmlfile: 1.1.0
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 21.3
pandas: 2.2.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
pyqtgraph: 0.13.3
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.31.0
ribfind: 2.0.2
scipy: 1.11.1
seaborn: 0.13.2
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: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 13 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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