AllMetal3D: session save: 'AllMetal3D' object has no attribute 'line_edit'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-86-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/sandaru/CryoEM_Maps/Coot_Models/Final_Model_#1.pdb

Summary of feedback from opening
/home/sandaru/CryoEM_Maps/Coot_Models/Final_Model_#1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU a 21 TRP a 23 1 3  
Start residue of secondary structure not found: HELIX 2 2 TYR a 24 LEU a 34 1
11  
Start residue of secondary structure not found: HELIX 3 3 LEU a 53 VAL a 60 1
8  
Start residue of secondary structure not found: HELIX 4 4 TRP a 61 THR a 64 1
4  
Start residue of secondary structure not found: HELIX 5 5 PHE a 65 GLN a 85 1
21  
116 messages similar to the above omitted  
  
Chain information for Final_Model_#1.pdb #1  
---  
Chain | Description  
Aa | No description available  
Ba | No description available  
Ca | No description available  
Da | No description available  
Ea | No description available  
Fa | No description available  
  

> select

23472 atoms, 23735 bonds, 1 pseudobond, 1520 residues, 2 models selected  

> select B

Nothing selected  

> select Ba

Nothing selected  

> select #1/Ba

5935 atoms, 6027 bonds, 384 residues, 1 model selected  

> invert sel

Unknown command: invert sel  

> select invert

Expected an objects specifier or a keyword  

> select inv

Expected an objects specifier or a keyword  

> select ~sel & ##selected

17537 atoms, 17708 bonds, 1 pseudobond, 1136 residues, 2 models selected  

> hide sel atoms

> select #1/Ba

5935 atoms, 6027 bonds, 384 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

Computing secondary structure  

> open 8evu fromDatabase pdb format mmcif

8evu title:  
Cryo EM structure of Vibrio cholerae NQR [more info...]  
  
Chain information for 8evu #2  
---  
Chain | Description | UniProt  
A | Na(+)-translocating NADH-quinone reductase subunit A | NQRA_VIBCH 1-446  
B | Na(+)-translocating NADH-quinone reductase subunit B | NQRB_VIBCH 1-415  
C | Na(+)-translocating NADH-quinone reductase subunit C | NQRC_VIBCH 1-257  
D | Na(+)-translocating NADH-quinone reductase subunit D | NQRD_VIBCH 1-210  
E | Na(+)-translocating NADH-quinone reductase subunit E | NQRE_VIBCH 1-198  
F | Na(+)-translocating NADH-quinone reductase subunit F | NQRF_VIBCH 1-408  
  
Non-standard residues in 8evu #2  
---  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
RBF — riboflavin (riboflavine; vitamin B2)  
UQ1 — ubiquinone-1  
  

> matchmaker

Missing or invalid "matchAtoms" argument: empty atom specifier  

> matchmaker #2 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 Final_Model_#1.pdb, chain Aa (#1) with 8evu, chain A (#2), sequence
alignment score = 1441.1  
RMSD between 427 pruned atom pairs is 0.678 angstroms; (across all 443 pairs:
0.965)  
  

> select #1/Ba #2/B

9192 atoms, 9387 bonds, 799 residues, 2 models selected  

> select ~sel & ##selected

26182 atoms, 26520 bonds, 5 pseudobonds, 2266 residues, 4 models selected  

> hide sel atoms

> select #1/Ba #2/B

9192 atoms, 9387 bonds, 799 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/B:346

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select #1/Ba:336

12 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> show sel cartoons

> style sel stick

Changed 12 atom styles  

> select #1/Ba #2/B

9192 atoms, 9387 bonds, 799 residues, 2 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 1 time(s)]Coulombic values for Final_Model_#1.pdb_Ba SES surface
#1.2: minimum, -17.08, mean 1.03, maximum 20.26  
Coulombic values for 8evu_B SES surface #2.2: minimum, -20.24, mean -1.31,
maximum 12.96  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> select clear

> select #2/B:338,342

22 atoms, 22 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 22 atom styles  

> select clear

> select #1/Ba:332

20 atoms, 20 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 20 atom styles  

> show sel atoms

> select #1/Ba:328

20 atoms, 20 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 20 atom styles  

> show sel atoms

> select #2/B:164,165,168,64

31 atoms, 28 bonds, 4 residues, 1 model selected  

> style sel stick

Changed 31 atom styles  

> show sel atoms

> select #1/Ba:162

19 atoms, 18 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 19 atom styles  

> show sel atoms

> select #1/Ba

5935 atoms, 6027 bonds, 384 residues, 1 model selected  

> select H

11835 atoms, 1516 residues, 1 model selected  

> delete sel

> select #1/Ba:158

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 7 atom styles  

> select #1/Ba:64

7 atoms, 6 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 7 atom styles  

> show sel atoms

> select #1/Ba:159

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> show sel atoms

> select #2/B:342,164

19 atoms, 18 bonds, 2 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select #2/B:64

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/B:64

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color (#!2 & sel) byhetero

> select #2/B:64 #1/Ba:64

14 atoms, 12 bonds, 2 residues, 2 models selected  

> color (#!1-2 & sel) byhetero

> select #2/B #1/Ba

6233 atoms, 6428 bonds, 799 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select #1/Ba

2976 atoms, 3068 bonds, 384 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> select clear

> select #1/Ba

2976 atoms, 3068 bonds, 384 residues, 1 model selected  

> coulombic sel

Coulombic values for Final_Model_#1.pdb_Ba SES surface #1.2: minimum, -118.46,
mean -67.93, maximum -17.05  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> select clear

> select add #1

11637 atoms, 11900 bonds, 1 pseudobond, 1520 residues, 2 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen copy of Final_Model_#1.pdb #/Aa GLY 293 H bonded to atom that should
not have hydrogens (copy of Final_Model_#1.pdb #/Aa GLY 293 C)  

> show sel surfaces

> hide sel surfaces

> select clear

> select #1/Ba

2976 atoms, 3068 bonds, 384 residues, 1 model selected  

> show sel surfaces

> coulombic sel

Coulombic values for Final_Model_#1.pdb_Ba SES surface #1.2: minimum, -118.46,
mean -67.93, maximum -17.05  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> select clear

> select add #1

11637 atoms, 11900 bonds, 1 pseudobond, 1520 residues, 2 models selected  

> select add #2

23539 atoms, 24072 bonds, 5 pseudobonds, 3065 residues, 10 models selected  

> style sel stick

Changed 23539 atom styles  

> select subtract #1

11902 atoms, 12172 bonds, 4 pseudobonds, 1545 residues, 9 models selected  

> select subtract #2

1 model selected  

> select add #1

11637 atoms, 11900 bonds, 1 pseudobond, 1520 residues, 2 models selected  

> select add #2

23539 atoms, 24072 bonds, 5 pseudobonds, 3065 residues, 10 models selected  

> color (#!1-2 & sel) byhetero

> select clear

> select add #1.7

230 atoms, 31 residues, 1 model selected  

> select subtract #1.7

1 model selected  

> select #1/Aa

3384 atoms, 3450 bonds, 444 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> select #2/A

3416 atoms, 3480 bonds, 446 residues, 1 model selected  

> show sel cartoons

> select #2/A:62,61,85,84,40,445,443

67 atoms, 62 bonds, 7 residues, 1 model selected  

> show sel atoms

> select #1/Aa:442

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Aa:444

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #1/Aa:442

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select add #1/Aa:62

27 atoms, 24 bonds, 3 residues, 2 models selected  

> select add #1/Aa:61

36 atoms, 32 bonds, 4 residues, 2 models selected  

> select add #1/Aa:40

45 atoms, 40 bonds, 5 residues, 2 models selected  

> select add #1/Aa:84

54 atoms, 48 bonds, 6 residues, 2 models selected  

> select add #1/Aa:85

65 atoms, 58 bonds, 7 residues, 2 models selected  

> show sel atoms

> select #2/A #1/Aa

6800 atoms, 6930 bonds, 890 residues, 2 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 1 time(s)]Hydrogen copy of Final_Model_#1.pdb #/Aa GLY 293 H bonded
to atom that should not have hydrogens (copy of Final_Model_#1.pdb #/Aa GLY
293 C)  

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> select clear

> select add #1

11637 atoms, 11900 bonds, 1 pseudobond, 1520 residues, 2 models selected  

> show sel cartoons

> select clear

> open 7QU5 fromDatabase pdb format mmcif

Summary of feedback from opening 7QU5 fetched from pdb  
---  
notes | Fetching compressed mmCIF 7qu5 from http://files.rcsb.org/download/7qu5.cif  
Fetching CCD DMS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
Fetching CCD YVR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/YVR/YVR.cif  
  
7qu5 title:  
X-ray structure of FAD domain of NqrF of Pseudomonas aeruginosa [more info...]  
  
Chain information for 7qu5 #3  
---  
Chain | Description | UniProt  
A | Na(+)-translocating NADH-quinone reductase subunit F | NQRF_PSEAB 130-407  
  
Non-standard residues in 7qu5 #3  
---  
DMS — dimethyl sulfoxide  
FAD — flavin-adenine dinucleotide  
MG — magnesium ion  
YVR — gamma-Valerolactone  
  
83 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Drag select of 295 atoms, 280 residues, 6 pseudobonds, 244 bonds  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,90.499,0,1,0,232.45,0,0,1,181.51

> view matrix models #3,1,0,0,115.48,0,1,0,190.01,0,0,1,198.85

> view matrix models #3,1,0,0,215.17,0,1,0,201.7,0,0,1,200.36

> select #2/F

244 atoms, 247 bonds, 32 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> open 7XK3 fromDatabase pdb format mmcif

Summary of feedback from opening 7XK3 fetched from pdb  
---  
note | Fetching compressed mmCIF 7xk3 from http://files.rcsb.org/download/7xk3.cif  
  
7xk3 title:  
Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio
cholerae, state 1 [more info...]  
  
Chain information for 7xk3 #4  
---  
Chain | Description | UniProt  
A | Na(+)-translocating NADH-quinone reductase subunit A | NQRA_VIBC3 1-446  
B | Na(+)-translocating NADH-quinone reductase subunit B | NQRB_VIBC3 1-415  
C | Na(+)-translocating NADH-quinone reductase subunit C | NQRC_VIBC3 1-257  
D | Na(+)-translocating NADH-quinone reductase subunit D | NQRD_VIBC3 1-210  
E | Na(+)-translocating NADH-quinone reductase subunit E | NQRE_VIBC3 1-198  
F | Na(+)-translocating NADH-quinone reductase subunit F | NQRF_VIBC3 1-408  
  
Non-standard residues in 7xk3 #4  
---  
CA — calcium ion  
FAD — flavin-adenine dinucleotide  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
LMT — dodecyl-β-D-maltoside  
PEE — 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)  
RBF — riboflavin (riboflavine; vitamin B2)  
  
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> matchmaker #4 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 Final_Model_#1.pdb, chain Aa (#1) with 7xk3, chain A (#4), sequence
alignment score = 1435.1  
RMSD between 427 pruned atom pairs is 0.631 angstroms; (across all 443 pairs:
0.923)  
  

> matchmaker #3 to #4

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 7xk3, chain F (#4) with 7qu5, chain A (#3), sequence alignment
score = 1069.3  
RMSD between 273 pruned atom pairs is 0.668 angstroms; (across all 280 pairs:
0.834)  
  

> hide #4 models

> select up

11902 atoms, 12172 bonds, 1545 residues, 1 model selected  

> select down

244 atoms, 247 bonds, 32 residues, 3 models selected  

> show #4 models

> select add #4

15085 atoms, 15428 bonds, 1937 residues, 2 models selected  

> hide sel atoms

> show sel surfaces

> hide sel atoms

> show sel cartoons

> hide sel surfaces

> select subtract #4

244 atoms, 247 bonds, 32 residues, 8 models selected  

> select #4:368,371,372,399,104,100,397

233 atoms, 213 bonds, 27 residues, 1 model selected  

> select #4/F:368,371,372,399,104,100,397

64 atoms, 58 bonds, 7 residues, 1 model selected  

> style sel stick

Changed 64 atom styles  

> show sel atoms

> color (#!4 & sel) byhetero

> select #3/A:367

7 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select add #3/A:371

15 atoms, 14 bonds, 2 residues, 1 model selected  

> show sel atoms

> select add #3/A:370

24 atoms, 22 bonds, 3 residues, 1 model selected  

> show sel atoms

> select #1/Aa:84

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #3/A:396

18 atoms, 16 bonds, 2 residues, 3 models selected  

> select add #3/A:398

27 atoms, 24 bonds, 3 residues, 3 models selected  

> show sel atoms

> select clear

> select #4/F:368,371,372,399,104,100,397

64 atoms, 58 bonds, 7 residues, 1 model selected  

> select clear

> select add #3

2703 atoms, 2422 bonds, 6 pseudobonds, 639 residues, 2 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 7qu5_A SES surface #3.2: minimum, -18.75, mean -3.65,
maximum 7.73  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select add #4

17544 atoms, 17603 bonds, 6 pseudobonds, 2544 residues, 4 models selected  

> select subtract #3

14841 atoms, 15181 bonds, 1905 residues, 8 models selected  

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
7xk3 #4/D GLU 210 OXT  
7xk3 #4/E LEU 198 OXT  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 7xk3_A SES surface #4.1: minimum, -19.43, mean -2.06,
maximum 13.29  
Coulombic values for 7xk3_B SES surface #4.2: minimum, -16.85, mean -1.19,
maximum 15.55  
Coulombic values for 7xk3_C SES surface #4.3: minimum, -14.92, mean -1.28,
maximum 13.54  
Coulombic values for 7xk3_D SES surface #4.4: minimum, -12.54, mean -0.30,
maximum 10.05  
Coulombic values for 7xk3_E SES surface #4.5: minimum, -13.34, mean -0.67,
maximum 14.95  
Coulombic values for 7xk3_F SES surface #4.6: minimum, -21.05, mean -3.25,
maximum 11.24  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> select subtract #4

6 models selected  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> select add #1

11637 atoms, 11900 bonds, 1 pseudobond, 1520 residues, 2 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen copy of Final_Model_#1.pdb #/Aa GLY 293 H bonded to atom that should
not have hydrogens (copy of Final_Model_#1.pdb #/Aa GLY 293 C)  

> select #1/Aa:293

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> select H

12 atoms, 2 residues, 1 model selected  

> delete sel

> select add #1

11637 atoms, 11900 bonds, 1 pseudobond, 1520 residues, 2 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen copy of Final_Model_#1.pdb #/Aa GLY 293 H bonded to atom that should
not have hydrogens (copy of Final_Model_#1.pdb #/Aa GLY 293 C)  

> select #1/Aa:293

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide (#!1 & sel-residues & (protein|nucleic)) target a

> cartoon hide (#!1 & sel-residues)

> show (#!1 & sel-residues & backbone) target ab

> delete sel

> select add #1

11633 atoms, 11896 bonds, 1 pseudobond, 1519 residues, 2 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for Final_Model_#1.pdb_Aa SES surface #1.3: minimum, -15.47,
mean -0.61, maximum 16.98  
Coulombic values for Final_Model_#1.pdb_Ba SES surface #1.2: minimum, -118.46,
mean -67.93, maximum -17.05  
Coulombic values for Final_Model_#1.pdb_Ca SES surface #1.4: minimum, -12.40,
mean -0.86, maximum 12.26  
Coulombic values for Final_Model_#1.pdb_Da SES surface #1.5: minimum, -7.45,
mean 1.19, maximum 12.94  
Coulombic values for Final_Model_#1.pdb_Ea SES surface #1.6: minimum, -14.94,
mean -1.77, maximum 8.67  
Coulombic values for Final_Model_#1.pdb_Fa SES surface #1.7: minimum, -8.28,
mean 1.07, maximum 8.29  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1-3 surfaces

> show #!4 models

> hide surfaces

> select #1/Aa:84

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Aa:85

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/Aa:83

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:83

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show sel atoms

> open Q02PF8 fromDatabase alphafold format mmcif

Summary of feedback from opening Q02PF8 fetched from alphafold  
---  
notes | Fetching compressed AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold Q02PF8 from
https://alphafold.ebi.ac.uk/files/AF-Q02PF8-F1-model_v6.cif  
  
Chain information for AlphaFold Q02PF8 #5  
---  
Chain | Description | UniProt  
A | Na(+)-translocating NADH-quinone reductase subunit F | NQRF_PSEAB 1-407  
  
Color AlphaFold Q02PF8 by residue attribute pLDDT_score  

> matchmaker #5 to #3

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 7qu5, chain A (#3) with AlphaFold Q02PF8, chain A (#5), sequence
alignment score = 1480.9  
RMSD between 275 pruned atom pairs is 0.519 angstroms; (across all 279 pairs:
0.591)  
  

> select #5/A:1-32

238 atoms, 240 bonds, 32 residues, 1 model selected  

> delete sel

> close #3

> color #5 #ed333bff

> color #5 #b5835aff

> color #5 #986a44ff

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select add #5/A:367

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #5/A:371

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select add #5/A:370

24 atoms, 22 bonds, 3 residues, 1 model selected  

> show sel atoms

> select add #5

2962 atoms, 3042 bonds, 375 residues, 1 model selected  

> select subtract #5

Nothing selected  

> select add #5

2962 atoms, 3042 bonds, 375 residues, 1 model selected  

> color sel byhetero

> style sel stick

Changed 2962 atom styles  

> select subtract #5

Nothing selected  

> select #5/A:367

7 atoms, 7 bonds, 1 residue, 1 model selected  

> rename #5 PA_Fsubunit

> rename #4 VC

> select #4/F:371

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #5/A:396

18 atoms, 16 bonds, 2 residues, 3 models selected  

> select add #5/A:398

27 atoms, 24 bonds, 3 residues, 3 models selected  

> show sel atoms

> select add #4/F:394

35 atoms, 31 bonds, 4 residues, 3 models selected  

> select clear

> select #4/F:394

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #5/A:393

16 atoms, 14 bonds, 2 residues, 3 models selected  

> show sel atoms

> style sel stick

Changed 16 atom styles  

> hide sel atoms

> select #5/A:392

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #4/F:393

16 atoms, 14 bonds, 2 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 16 atom styles  

> select add #4/A:84

25 atoms, 22 bonds, 3 residues, 3 models selected  

> show sel atoms

> style sel stick

Changed 25 atom styles  

> select add #1

11658 atoms, 11918 bonds, 1 pseudobond, 1522 residues, 6 models selected  

> select add #2

23560 atoms, 24090 bonds, 5 pseudobonds, 3067 residues, 14 models selected  

> select add #4

38384 atoms, 39256 bonds, 5 pseudobonds, 4970 residues, 17 models selected  

> select add #5

41338 atoms, 42291 bonds, 5 pseudobonds, 5344 residues, 21 models selected  

> style sel & #5#!4 stick

Changed 17803 atom styles  

> color (#5#!4 & sel) byhetero

> select subtract #1

29705 atoms, 30395 bonds, 4 pseudobonds, 3825 residues, 19 models selected  

> select subtract #2

17803 atoms, 18223 bonds, 2280 residues, 11 models selected  

> select subtract #4

2962 atoms, 3042 bonds, 375 residues, 7 models selected  

> select subtract #5

Nothing selected  

> show #!1 models

> select add #4/A:85

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select add #4/A:84

20 atoms, 18 bonds, 2 residues, 2 models selected  

> select #4/F:397@OE1

1 atom, 1 residue, 1 model selected  

> select clear

> select add #4/A:83

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #4/A:46

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select subtract #4/A:46

1 model selected  

> select add #4/A:46

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #1/Aa:46

20 atoms, 18 bonds, 2 residues, 3 models selected  

> show sel atoms

> select clear

> select #5/A:367

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select add #5/A:100

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select add #5/A:99

18 atoms, 16 bonds, 2 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select clear

> select #5/A:100

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!2 models

> hide #!2 models

> hide #!4 models

> hide #5 models

> hide #1.1 models

> show #1.1 models

> hide #!1 models

> show #!1 models

> view matrix models
> #5,0.38064,-0.62915,0.67771,179.78,0.50955,0.75428,0.41404,167.53,-0.77167,0.18772,0.60769,143.34

> select #1/aRG,HIS

Nothing selected  

> select #1/ARG,HIS

Nothing selected  

> select #1:ARG,HIS

860 atoms, 806 bonds, 80 residues, 1 model selected  

> select #1/Ba:ARG,HIS

224 atoms, 213 bonds, 21 residues, 1 model selected  

> select #1/Ba:ARG,HIS,LYS,ASP,GLU,SER,THR,ASN,GLN

898 atoms, 829 bonds, 110 residues, 1 model selected  

> show sel atoms

> view matrix models #1,1,0,0,4.9326,0,1,0,3.952,0,0,1,0.8433

> select #1/Ba:AD

Nothing selected  

> select #1/Ba:D

Nothing selected  

> select #1/Ba:ARG,HIS,LYS,ASP,GLU,SER,THR,ASN,GLN

898 atoms, 829 bonds, 110 residues, 1 model selected  

> hide sel atoms

> select #1/Ba:TYR,SER,GLU,ASP,LYS,HIS,THR

676 atoms, 626 bonds, 84 residues, 1 model selected  

> show sel atoms

> select #1/Ba

2976 atoms, 3068 bonds, 384 residues, 1 model selected  

> combine sel

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> close #3

> select add #1

11633 atoms, 11896 bonds, 1 pseudobond, 1519 residues, 3 models selected  

> select subtract #1

6 models selected  

> select #1/Ba

2976 atoms, 3068 bonds, 384 residues, 1 model selected  

> show #!1 models

> combine

Remapping chain ID 'B' in 8evu #2 to 'G'  
Remapping chain ID 'C' in 8evu #2 to 'H'  
Remapping chain ID 'E' in 8evu #2 to 'I'  
Remapping chain ID 'A' in VC #4 to 'J'  
Remapping chain ID 'B' in VC #4 to 'K'  
Remapping chain ID 'C' in VC #4 to 'L'  
Remapping chain ID 'D' in VC #4 to 'M'  
Remapping chain ID 'E' in VC #4 to 'N'  
Remapping chain ID 'F' in VC #4 to 'O'  
Remapping chain ID 'A' in PA_Fsubunit #5 to 'P'  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> close #3

> select #1/Ba

2976 atoms, 3068 bonds, 384 residues, 1 model selected  

> combine sel

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> close #3

> show #!1 models

> combine sel

> hide #!1 models

> select add #1

11633 atoms, 11896 bonds, 1 pseudobond, 1519 residues, 3 models selected  

> select subtract #1

6 models selected  

> select add #3

11633 atoms, 11896 bonds, 1 pseudobond, 1519 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select #3/Aa,Ca,Da,Ea,Fa

8566 atoms, 8731 bonds, 1131 residues, 1 model selected  

> delete sel

> addh H

No structures specified  

> select add #3

3067 atoms, 3165 bonds, 1 pseudobond, 388 residues, 2 models selected  

> addh H

No structures specified  

> addh H sel

Expected a keyword  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Unknown hybridization for atom (P) of residue type FMN; not adding hydrogens to it  
Unknown hybridization for atom (P) of residue type FMN; not adding hydrogens
to it  
notes | No usable SEQRES records for Final_Model_#1.pdb (#1) chain Aa; guessing termini instead  
No usable SEQRES records for Final_Model_#1.pdb (#1) chain Ba; guessing
termini instead  
No usable SEQRES records for Final_Model_#1.pdb (#1) chain Ca; guessing
termini instead  
No usable SEQRES records for Final_Model_#1.pdb (#1) chain Da; guessing
termini instead  
No usable SEQRES records for Final_Model_#1.pdb (#1) chain Ea; guessing
termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: Final_Model_#1.pdb #1/Aa MET
1, Final_Model_#1.pdb #1/Ba GLU 21, Final_Model_#1.pdb #1/Ca ILE 8,
Final_Model_#1.pdb #1/Da ASN 20, Final_Model_#1.pdb #1/Ea MET 0,
Final_Model_#1.pdb #1/Fa ILE 2  
Chain-initial residues that are not actual N termini: Final_Model_#1.pdb #1/Aa
ASN 294  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: Final_Model_#1.pdb #1/Aa
GLU 444, Final_Model_#1.pdb #1/Aa PRO 292, Final_Model_#1.pdb #1/Ba GLY 403,
Final_Model_#1.pdb #1/Ca GLU 260, Final_Model_#1.pdb #1/Da SER 220,
Final_Model_#1.pdb #1/Ea LEU 202, Final_Model_#1.pdb #1/Fa VAL 32  
1414 hydrogen bonds  
Adding 'H' to Final_Model_#1.pdb #1/Aa ASN 294  
Final_Model_#1.pdb #1/Aa GLU 444 is not terminus, removing H atom from 'C'  
Final_Model_#1.pdb #1/Aa PRO 292 is not terminus, removing H atom from 'C'  
Final_Model_#1.pdb #1/Ba GLY 403 is not terminus, removing H atom from 'C'  
Final_Model_#1.pdb #1/Ca GLU 260 is not terminus, removing H atom from 'C'  
Final_Model_#1.pdb #1/Da SER 220 is not terminus, removing H atom from 'C'  
2 messages similar to the above omitted  
Termini for 8evu (#2) chain A determined from SEQRES records  
Termini for 8evu (#2) chain B determined from SEQRES records  
Termini for 8evu (#2) chain C determined from SEQRES records  
Termini for 8evu (#2) chain D determined from SEQRES records  
Termini for 8evu (#2) chain E determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: 8evu #2/A MET 1, 8evu #2/E
MET 1, 8evu #2/F MET 1  
Chain-initial residues that are not actual N termini: 8evu #2/B LEU 3, 8evu
#2/C SER 7, 8evu #2/D LYS 8  
Chain-final residues that are actual C termini: 8evu #2/A GLY 446, 8evu #2/E
LEU 198  
Chain-final residues that are not actual C termini: 8evu #2/B LYS 414, 8evu
#2/C LEU 256, 8evu #2/D LYS 209, 8evu #2/F THR 32  
1446 hydrogen bonds  
Adding 'H' to 8evu #2/B LEU 3  
Adding 'H' to 8evu #2/C SER 7  
Adding 'H' to 8evu #2/D LYS 8  
8evu #2/B LYS 414 is not terminus, removing H atom from 'C'  
8evu #2/C LEU 256 is not terminus, removing H atom from 'C'  
8evu #2/D LYS 209 is not terminus, removing H atom from 'C'  
8evu #2/F THR 32 is not terminus, removing H atom from 'C'  
Termini for VC (#4) chain A determined from SEQRES records  
Termini for VC (#4) chain B determined from SEQRES records  
Termini for VC (#4) chain C determined from SEQRES records  
Termini for VC (#4) chain D determined from SEQRES records  
Termini for VC (#4) chain E determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: VC #4/A MET 1, VC #4/E MET
1, VC #4/F MET 1  
Chain-initial residues that are not actual N termini: VC #4/B TYR 27, VC #4/C
ASP 6, VC #4/D LEU 7  
Chain-final residues that are actual C termini: VC #4/A GLY 446, VC #4/D GLU
210, VC #4/E LEU 198  
Chain-final residues that are not actual C termini: VC #4/B GLY 413, VC #4/C
LEU 256, VC #4/F GLY 408  
Missing OXT added to C-terminal residue VC #4/D GLU 210  
Missing OXT added to C-terminal residue VC #4/E LEU 198  
1401 hydrogen bonds  
Adding 'H' to VC #4/B TYR 27  
Adding 'H' to VC #4/C ASP 6  
Adding 'H' to VC #4/D LEU 7  
VC #4/B GLY 413 is not terminus, removing H atom from 'C'  
VC #4/C LEU 256 is not terminus, removing H atom from 'C'  
VC #4/F GLY 408 is not terminus, removing H atom from 'C'  
Termini for PA_Fsubunit (#5) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: PA_Fsubunit #5/A SER 33  
Chain-final residues that are actual C termini: PA_Fsubunit #5/A GLY 407  
Chain-final residues that are not actual C termini:  
332 hydrogen bonds  
Adding 'H' to PA_Fsubunit #5/A SER 33  
No usable SEQRES records for copy of Final_Model_#1.pdb (#3) chain Ba;
guessing termini instead  
Chain-initial residues that are actual N termini: copy of Final_Model_#1.pdb
#3/Ba GLU 21  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: copy of Final_Model_#1.pdb
#3/Ba GLY 403  
341 hydrogen bonds  
copy of Final_Model_#1.pdb #3/Ba GLY 403 is not terminus, removing H atom from
'C'  
44876 hydrogens added  
  

> delH

Unknown command: delH  

> delh

Unknown command: delh  

> removeh

Unknown command: removeh  

> remove h

Unknown command: remove h  

> delete H

> save /home/sandaru/Downloads/SubunitBPA.pdb models #3

> toolshed show

> ui tool show "Find Cavities"

> kvfinder #3

25 cavities found for copy of Final_Model_#1.pdb #3  
copy of Final_Model_#1.pdb Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
3.2.4 |  | 740.02 | 585.41 | 3426 | 13.3 | 4.94  
3.2.23 |  | 460.08 | 375.92 | 2130 | 5.94 | 2.04  
3.2.17 |  | 447.34 | 360.81 | 2071 | 8.36 | 3.68  
3.2.10 |  | 75.17 | 96.99 | 348 | 0 | 0  
3.2.15 |  | 60.48 | 79.56 | 280 | 5.09 | 2.31  
3.2.11 |  | 39.96 | 61.26 | 185 | 0 | 0  
3.2.9 |  | 33.26 | 63.46 | 154 | 0 | 0  
3.2.5 |  | 33.05 | 39.54 | 153 | 1.34 | 0.43  
3.2.16 |  | 30.67 | 48.51 | 142 | 0 | 0  
3.2.8 |  | 25.7 | 46.9 | 119 | 0 | 0  
3.2.1 |  | 25.27 | 45.33 | 117 | 3.7 | 1.85  
3.2.18 |  | 24.19 | 44.41 | 112 | 0 | 0  
3.2.3 |  | 22.25 | 44.42 | 103 | 0 | 0  
3.2.21 |  | 21.82 | 40.63 | 101 | 0 | 0  
3.2.12 |  | 17.28 | 36.68 | 80 | 0 | 0  
3.2.19 |  | 17.28 | 28.92 | 80 | 1.8 | 0.71  
3.2.7 |  | 15.55 | 21.93 | 72 | 1.2 | 0.31  
3.2.6 |  | 12.31 | 29.54 | 57 | 0 | 0  
3.2.13 |  | 12.31 | 29.54 | 57 | 0 | 0  
3.2.14 |  | 11.88 | 20.01 | 55 | 1.2 | 0.31  
3.2.2 |  | 11.45 | 19.33 | 53 | 1.2 | 0.38  
3.2.25 |  | 9.5 | 18.78 | 44 | 1.2 | 0.38  
3.2.22 |  | 8.64 | 16.79 | 40 | 1.2 | 0.34  
3.2.20 |  | 6.26 | 14.08 | 29 | 0.6 | 0.1  
3.2.24 |  | 6.26 | 14.77 | 29 | 1.04 | 0.34  
  

> view matrix models #3,1,0,0,9.4971,0,1,0,8.4809,0,0,1,5.7058

> select
> ::name="CA"::name="FAD"::name="FES"::name="FMN"::name="LIG"::name="LMT"::name="PEE"::name="RBF"::name="UQ1"

680 atoms, 714 bonds, 2 pseudobonds, 26 residues, 6 models selected  

> show sel & #!3 atoms

> select clear

Drag select of 4 atoms, 4 bonds, 1 pseudobonds  

> delete sel

> select add #3

13100 atoms, 3161 bonds, 412 residues, 27 models selected  

> toolshed show

Downloading bundle ChimeraX_AllMetal3D-0.8-py3-none-any.whl  
Installed ChimeraX-AllMetal3D (0.8)  

> ui tool show AllMetal3D/Water3D

Loaded as API: https://simonduerr-allmetal3d.hf.space ✔  

> select clear

> close #3

> select add #1

11633 atoms, 11896 bonds, 1 pseudobond, 1519 residues, 2 models selected  

> show #!1 models

> combine

Remapping chain ID 'B' in 8evu #2 to 'G'  
Remapping chain ID 'C' in 8evu #2 to 'H'  
Remapping chain ID 'E' in 8evu #2 to 'I'  
Remapping chain ID 'A' in VC #4 to 'J'  
Remapping chain ID 'B' in VC #4 to 'K'  
Remapping chain ID 'C' in VC #4 to 'L'  
Remapping chain ID 'D' in VC #4 to 'M'  
Remapping chain ID 'E' in VC #4 to 'N'  
Remapping chain ID 'F' in VC #4 to 'O'  
Remapping chain ID 'A' in PA_Fsubunit #5 to 'P'  

> select subtract #1

6 models selected  

> close #3

> select add #1

11633 atoms, 11896 bonds, 1 pseudobond, 1519 residues, 2 models selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select add #1

11633 atoms, 11896 bonds, 1 pseudobond, 1519 residues, 2 models selected  

> combine sel

> hide #!1 models

> select subtract #1

6 models selected  

> select #3/Aa,Ca,Da,Ea,Fa

8566 atoms, 8731 bonds, 1131 residues, 1 model selected  

> delete sle

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete sel

> ui tool show AllMetal3D/Water3D

> select add #3

3067 atoms, 3165 bonds, 1 pseudobond, 388 residues, 2 models selected  
Loaded as API: https://simonduerr-allmetal3d.hf.space ✔  

> ui tool show AllMetal3D/Water3D

No server URL given  

> ui tool show AllMetal3D/Water3D

Loaded as API: https://simonduerr-allmetal3d.hf.space ✔  

> ui tool show AllMetal3D/Water3D

Loaded as API: https://simonduerr-allmetal3d.hf.space ✔  

> show #!2 models

Drag select of 32 residues  

> delete sel

> select #2/A,C,D,E,F

8401 atoms, 8565 bonds, 4 pseudobonds, 1098 residues, 2 models selected  

> delete sel

> ui tool show AllMetal3D/Water3D

Loaded as API: https://simonduerr-allmetal3d.hf.space ✔  
No residues selected  

> select add #2

3257 atoms, 3360 bonds, 415 residues, 1 model selected  

> ui tool show AllMetal3D/Water3D

Loaded as API: https://simonduerr-allmetal3d.hf.space ✔  

> ui tool show AllMetal3D/Water3D

Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  

> view matrix models
> #2,0.76413,0.54921,-0.33834,-40.622,-0.044115,-0.47879,-0.87682,415.73,-0.64355,0.68493,-0.34163,201.07

Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  

> undo

Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "/home/sandaru/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/allmetal3d/tool.py", line 309, in update_animation  
self.label.setText(f"Loading {self.dots}")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 580.95.05
OpenGL renderer: NVIDIA GeForce RTX 5060 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_CA.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B760 GAMING X AX
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 28 Intel(R) Core(TM) i7-14700F
Cache Size: 33792 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        26Gi       265Mi       545Mi       5.4Gi       4.7Gi
	Swap:          2.0Gi       1.7Gi       286Mi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2d04] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:8a05]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.11.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AllMetal3D: 0.8
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.25.2
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.10.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    fsspec: 2025.10.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    gradio_client: 0.11.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.14.0
    hf-xet: 1.2.0
    html2text: 2024.2.26
    httpcore: 1.0.9
    httpx: 0.28.1
    huggingface_hub: 1.1.5
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    narwhals: 2.9.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 2.3.4
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    plotly: 6.3.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.8.3
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    PyYAML: 6.0.3
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    shellingham: 1.5.4
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tomlkit: 0.13.3
    tornado: 6.5.1
    tqdm: 4.67.1
    traitlets: 5.14.3
    typer-slim: 0.20.0
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    websockets: 11.0.3
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[Eric Pettersen]

Duplicate of #17193