id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15976	Crash in garbage collection	chimerax-bug-report@…	Eric Pettersen	"{{{
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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===== 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
}}}
"	defect	closed	normal		Core		duplicate		Tom Goddard				all	ChimeraX