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Opened 20 months ago
Closed 20 months ago
#14704 closed defect (can't reproduce)
Picking code: Singular matrix
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.3.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/antoninnourisson/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Thèse/Rédaction/Article/Figures/papierpolx.cxs format
> session
Log from Tue Feb 13 19:35:04 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/antoninnourisson/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Thèse/Manips/Structures/Polbetalike/refine.pdb
Summary of feedback from opening
/Users/antoninnourisson/Library/CloudStorage/OneDrive-
InstitutPasteurParis/Thèse/Manips/Structures/Polbetalike/refine.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK --------------------- added by autoBUSTER
---------------------------------START
Ignored bad PDB record found on line 2
REMARK run at = Mon Jan 8 14:08:44 CET 2024
Ignored bad PDB record found on line 13
REMARK Files used:
Ignored bad PDB record found on line 14
REMARK PDB = refine_6-4-notlsnoprunencs/pdbchk.pdb
Ignored bad PDB record found on line 15
REMARK MTZ =
/home/anouriss/Desktop/polbetalike/+nt/Antonin_20/Antonin_X2_1_staraniso.mtz
72 messages similar to the above omitted
Chain information for refine.pdb #1
---
Chain | Description
A C | No description available
E F | No description available
G I | No description available
H J | No description available
> open "/Users/antoninnourisson/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Thèse/Manips/Structures/mut K/refinemutk2.pdb"
Summary of feedback from opening
/Users/antoninnourisson/Library/CloudStorage/OneDrive-
InstitutPasteurParis/Thèse/Manips/Structures/mut K/refinemutk2.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK --------------------- added by autoBUSTER
---------------------------------START
Ignored bad PDB record found on line 2
REMARK run at = Thu Nov 16 16:26:10 CET 2023
Ignored bad PDB record found on line 9
REMARK Files used:
Ignored bad PDB record found on line 10
REMARK PDB = refine_X/pdbchk.pdb
Ignored bad PDB record found on line 11
REMARK MTZ = /home/anouriss/Desktop/mutK/6/PF6_007_Antonin_11_1.mtz
162 messages similar to the above omitted
Chain information for refinemutk2.pdb #2
---
Chain | Description
A | No description available
D | No description available
P | No description available
T | No description available
> open /Users/antoninnourisson/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Thèse/Manips/Structures/mutR/refinemutR.pdb
Summary of feedback from opening
/Users/antoninnourisson/Library/CloudStorage/OneDrive-
InstitutPasteurParis/Thèse/Manips/Structures/mutR/refinemutR.pdb
---
warnings | Ignored bad PDB record found on line 5
REMARK --------------------- added by autoBUSTER
-------------------------------
Ignored bad PDB record found on line 6
REMARK run at = Fri Jun 2 14:03:41 CEST 2023
Ignored bad PDB record found on line 13
REMARK Files used:
Ignored bad PDB record found on line 14
REMARK PDB = ./Buster/refine9.dir/pdbchk.pdb
Ignored bad PDB record found on line 15
REMARK MTZ = /data/Xtalo/COLLECT/2023/2023-05-27_SOLEIL_PX2A/Anto
76 messages similar to the above omitted
refinemutR.pdb title:
\--- [more info...]
Chain information for refinemutR.pdb #3
---
Chain | Description
A | No description available
F | No description available
G | No description available
H | No description available
Non-standard residues in refinemutR.pdb #3
---
CA — (CA)
EDO — (EDO)
TTP — (TTP)
> open "/Users/antoninnourisson/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Thèse/Manips/Structures/Ptet like/nt
> correct/refineptet.pdb"
Summary of feedback from opening
/Users/antoninnourisson/Library/CloudStorage/OneDrive-
InstitutPasteurParis/Thèse/Manips/Structures/Ptet like/nt
correct/refineptet.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK --------------------- added by autoBUSTER
---------------------------------START
Ignored bad PDB record found on line 2
REMARK run at = Fri Sep 15 12:00:22 CEST 2023
Ignored bad PDB record found on line 10
REMARK Files used:
Ignored bad PDB record found on line 11
REMARK PDB = refine_016/pdbchk.pdb
Ignored bad PDB record found on line 12
REMARK MTZ =
/home/anouriss/Desktop/Ptetlike/dataset-8/Antonin_PolD_PEG_220823_D6_EG_X16_1.mtz
123 messages similar to the above omitted
Chain information for refineptet.pdb #4
---
Chain | Description
A | No description available
D | No description available
P | No description available
T | No description available
> open "/Users/antoninnourisson/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Thèse/Manips/Structures/Ptet like/nt
> incorrect/refine.pdb"
Summary of feedback from opening
/Users/antoninnourisson/Library/CloudStorage/OneDrive-
InstitutPasteurParis/Thèse/Manips/Structures/Ptet like/nt incorrect/refine.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK --------------------- added by autoBUSTER
---------------------------------START
Ignored bad PDB record found on line 2
REMARK run at = Thu Dec 21 10:10:37 CET 2023
Ignored bad PDB record found on line 16
REMARK Files used:
Ignored bad PDB record found on line 17
REMARK PDB = refine_11/pdbchk.pdb
Ignored bad PDB record found on line 18
REMARK MTZ = /home/anouriss/Desktop/Ptetlike/nt-
incorrect/Antonin_21/ccp4if/Antonin_X6_1.mtz
82 messages similar to the above omitted
Chain information for refine.pdb #5
---
Chain | Description
A | No description available
D | No description available
P | No description available
T | No description available
> set bgColor white
> lighting soft
> graphics silhouettes true
> hide atoms
> show cartoons
> select add #1/C:277
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
126 atoms, 128 bonds, 16 residues, 1 model selected
> select up
2530 atoms, 2583 bonds, 321 residues, 1 model selected
> select clear
> select add #1/C:459
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select add #1/A:361
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select add #1/C:460
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
31 atoms, 30 bonds, 4 residues, 1 model selected
> select up
2530 atoms, 2583 bonds, 321 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #1/E:9
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
224 atoms, 251 bonds, 11 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 10 residues
> delete atoms sel
> delete bonds sel
> open /Users/antoninnourisson/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Thèse/Manips/Structures/Polbetalike/refine.pdb
Summary of feedback from opening
/Users/antoninnourisson/Library/CloudStorage/OneDrive-
InstitutPasteurParis/Thèse/Manips/Structures/Polbetalike/refine.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK --------------------- added by autoBUSTER
---------------------------------START
Ignored bad PDB record found on line 2
REMARK run at = Mon Jan 8 14:08:44 CET 2024
Ignored bad PDB record found on line 13
REMARK Files used:
Ignored bad PDB record found on line 14
REMARK PDB = refine_6-4-notlsnoprunencs/pdbchk.pdb
Ignored bad PDB record found on line 15
REMARK MTZ =
/home/anouriss/Desktop/polbetalike/+nt/Antonin_20/Antonin_X2_1_staraniso.mtz
72 messages similar to the above omitted
Chain information for refine.pdb #6
---
Chain | Description
A C | No description available
E F | No description available
G I | No description available
H J | No description available
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> hide #6 atoms
> show #6 cartoons
> select add #6/A:268
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
127 atoms, 128 bonds, 16 residues, 1 model selected
> select up
2530 atoms, 2583 bonds, 321 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #6/F:4
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
224 atoms, 251 bonds, 11 residues, 1 model selected
> select clear
Drag select of 21 residues
> delete atoms sel
> delete bonds sel
> show #5 models
> show #4 models
> show #3 models
> show #2 models
> show #1 models
> open /Users/antoninnourisson/Library/CloudStorage/OneDrive-
> InstitutPasteurParis/Thèse/Manips/Structures/7m43.pdb
7m43.pdb title:
Dna polymerase λ, TTP:At CA2+ ground state ternary complex [more info...]
Chain information for 7m43.pdb #7
---
Chain | Description | UniProt
A | DNA polymerase λ | DPOLL_HUMAN 242-575
D | DNA (5'-D(P*GP*CP*CP*G)-3') |
P | DNA (5'-D(*CP*ap*GP*TP*ap*C)-3') |
T | DNA (5'-D(*CP*GP*GP*CP*ap*GP*TP*ap*CP*TP*G)-3') |
Non-standard residues in 7m43.pdb #7
---
CA — calcium ion
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
NA — sodium ion
TTP — thymidine-5'-triphosphate
> show atoms
> hide atoms
> style stick
Changed 21980 atom styles
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> ui tool show Matchmaker
> matchmaker #1-6 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 7m43.pdb, chain A (#7) with refine.pdb, chain A (#1), sequence
alignment score = 1622.8
RMSD between 308 pruned atom pairs is 0.562 angstroms; (across all 320 pairs:
1.499)
Matchmaker 7m43.pdb, chain A (#7) with refinemutk2.pdb, chain A (#2), sequence
alignment score = 1587.5
RMSD between 320 pruned atom pairs is 0.389 angstroms; (across all 320 pairs:
0.389)
Matchmaker 7m43.pdb, chain A (#7) with refinemutR.pdb, chain A (#3), sequence
alignment score = 1576.3
RMSD between 320 pruned atom pairs is 0.380 angstroms; (across all 320 pairs:
0.380)
Matchmaker 7m43.pdb, chain A (#7) with refineptet.pdb, chain A (#4), sequence
alignment score = 1586
RMSD between 320 pruned atom pairs is 0.499 angstroms; (across all 320 pairs:
0.499)
Matchmaker 7m43.pdb, chain A (#7) with refine.pdb, chain A (#5), sequence
alignment score = 1580
RMSD between 320 pruned atom pairs is 0.422 angstroms; (across all 320 pairs:
0.422)
Matchmaker 7m43.pdb, chain A (#7) with refine.pdb, chain C (#6), sequence
alignment score = 1612.6
RMSD between 311 pruned atom pairs is 0.576 angstroms; (across all 320 pairs:
1.058)
> color #4 #90dcfdff
> color #7 #cdbea9ff
> color #2 #d195edff
> select add #1
3008 atoms, 3068 bonds, 385 residues, 1 model selected
> color #1 #ffd479ff
> select subtract #1
Nothing selected
> select add #6
3008 atoms, 3068 bonds, 385 residues, 1 model selected
> color #6 #a1e6caff
> color #3 #f4bff7ff
> color #6 #a2e8cbff
> color #6 #66d36aff
> select add #5
6075 atoms, 6154 bonds, 812 residues, 2 models selected
> select subtract #5
3008 atoms, 3068 bonds, 385 residues, 1 model selected
> select subtract #6
Nothing selected
> color #5 #73fa79ff
> select add #6
3008 atoms, 3068 bonds, 385 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
3008 atoms, 3068 bonds, 385 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #5
3067 atoms, 3086 bonds, 427 residues, 1 model selected
> select subtract #5
Nothing selected
> color #5 #e97668ff
> select add #6
3008 atoms, 3068 bonds, 385 residues, 1 model selected
> select subtract #6
Nothing selected
> color #4 #9afe9aff
> color #6 #008f00ff
> color #5 #76d6ffff
> color #7 #c3b7a7ff
> color #7 #c39f81ff
> color #7 #c39a6eff
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 2/A
Alignment identifier is 3/A
Alignment identifier is 5
Alignment identifier is 7/A
> select #1/F:1-2 #2/T:1-2 #3/F:1-2 #4/T:1-2 #5/T:1-2 #6/E:1-2 #7/T:1-2
266 atoms, 294 bonds, 14 residues, 7 models selected
> select #1/F #2/T #3/F:1-11 #4/T #5/T #6/E #7/T:1-11
1568 atoms, 1757 bonds, 77 residues, 7 models selected
2 [ID: 2] region 7 chains [1-11] RMSD: 1.433
> select #2/T:5
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/F:1 #2/T:1 #3/F:1 #4/T:1 #5/T:1 #6/E:1 #7/T:1
112 atoms, 119 bonds, 7 residues, 7 models selected
> select #1/F:1-6 #2/T:1-6 #3/F:1-6 #4/T:1-6 #5/T:1-6 #6/E:1-6 #7/T:1-6
854 atoms, 959 bonds, 42 residues, 7 models selected
2 [ID: 2] region 7 chains [1-6] RMSD: 1.511
> select #1/F:5 #2/T:5 #3/F:5 #4/T:5 #5/T:5 #6/E:5 #7/T:5
147 atoms, 161 bonds, 7 residues, 7 models selected
> select #1/F:5 #2/T:5 #3/F:5 #4/T:5 #5/T:5 #6/E:5 #7/T:5
147 atoms, 161 bonds, 7 residues, 7 models selected
2 [ID: 2] region 7 chains [5] RMSD: 2.123
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 147 atom styles
> select clear
> color byhetero
Alignment identifier is 2
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 3/A
Alignment identifier is 3/A
Alignment identifier is 9
Destroying pre-existing alignment with identifier 7/A
Alignment identifier is 7/A
> select #1/G:6 #2/P:6 #3/G:6 #4/P:6 #5/P:6 #6/I:6 #7/P:6
133 atoms, 140 bonds, 7 residues, 7 models selected
> select #1/G:6 #2/P:6 #3/G:6 #4/P:6 #5/P:6 #6/I:6 #7/P:6
133 atoms, 140 bonds, 7 residues, 7 models selected
7 [ID: 7] region 7 chains [6] RMSD: 0.711
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 133 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 133 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 133 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 133 atom styles
> select clear
> select #1/G:6 #2/P:6 #3/G:6 #4/P:6 #5/P:6 #6/I:6 #7/P:6
133 atoms, 140 bonds, 7 residues, 7 models selected
> select #1/G:6 #2/P:6 #3/G:6 #4/P:6 #5/P:6 #6/I:6 #7/P:6
133 atoms, 140 bonds, 7 residues, 7 models selected
7 [ID: 7] region 7 chains [6] RMSD: 0.711
> nucleotides sel fill
> style nucleic & sel stick
Changed 133 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 133 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 133 atom styles
> select clear
> select ::name="TTP"
116 atoms, 120 bonds, 4 residues, 4 models selected
> show sel atoms
> select clear
> select ::name="DCP"
40 atoms, 41 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select ::name="CA"
7 atoms, 7 residues, 5 models selected
> show sel atoms
> select clear
> select ::name="TTP"
116 atoms, 120 bonds, 4 residues, 4 models selected
> show sel atoms
> select clear
> select #1/A:528 #6/C:528
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/A:528-530 #6/C:528-530
58 atoms, 58 bonds, 6 residues, 2 models selected
1 [ID: 1] region chains A,C [274-276] RMSD: 0.114
> show sel atoms
> select #1/A:505 #6/C:505
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #1/A:505 #6/C:505
24 atoms, 24 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains A,C [251] RMSD: 0.081
> select #1/A:505 #6/C:505
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #1/A:505-506 #6/C:505-506
46 atoms, 48 bonds, 4 residues, 2 models selected
1 [ID: 1] region chains A,C [251-252] RMSD: 0.076
> show sel atoms
> select #1/A:492 #6/C:492
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/A:492 #6/C:492
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains A,C [238] RMSD: 0.049
> show sel atoms
> select #1/A:489-490 #6/C:489-490
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #1/A:489-490 #6/C:489-490
32 atoms, 30 bonds, 4 residues, 2 models selected
1 [ID: 1] region chains A,C [235-236] RMSD: 0.062
> select #1/A:490 #6/C:490
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/A:490 #6/C:490
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains A,C [236] RMSD: 0.038
> show sel atoms
> select #1/A:427 #6/C:427
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/A:427 #6/C:427
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains A,C [178] RMSD: 0.094
> show sel atoms
> select #1/A:429 #6/C:429
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/A:429 #6/C:429
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region chains A,C [180] RMSD: 0.030
> show sel atoms
> select #4/A:528 #5/A:528
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #4/A:528-530 #5/A:528-530
48 atoms, 48 bonds, 6 residues, 2 models selected
5 [ID: 5] region 2 chains [273-275] RMSD: 0.147
> show sel atoms
> select #4/A:505 #5/A:505
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #4/A:505-506 #5/A:505-506
46 atoms, 48 bonds, 4 residues, 2 models selected
5 [ID: 5] region 2 chains [250-251] RMSD: 0.287
> show sel atoms
> select #4/A:492 #5/A:492
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #4/A:492 #5/A:492
18 atoms, 16 bonds, 2 residues, 2 models selected
5 [ID: 5] region 2 chains [237] RMSD: 0.172
> show sel atoms
> select #4/A:490 #5/A:490
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #4/A:490 #5/A:490
16 atoms, 14 bonds, 2 residues, 2 models selected
5 [ID: 5] region 2 chains [235] RMSD: 0.234
> show sel atoms
> select #4/A:427 #5/A:427
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #4/A:427 #5/A:427
16 atoms, 14 bonds, 2 residues, 2 models selected
5 [ID: 5] region 2 chains [177] RMSD: 0.299
> show sel atoms
> select #4/A:429 #5/A:429
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #4/A:429-430 #5/A:429-430
30 atoms, 28 bonds, 4 residues, 2 models selected
5 [ID: 5] region 2 chains [179-180] RMSD: 0.187
> select #4/A:429 #5/A:429
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #4/A:429 #5/A:429
16 atoms, 14 bonds, 2 residues, 2 models selected
5 [ID: 5] region 2 chains [179] RMSD: 0.253
> show sel atoms
> select #1/A:528 #6/C:528
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/A:528-530 #6/C:528-530
58 atoms, 58 bonds, 6 residues, 2 models selected
2 [ID: 2] region chains A,C [274-276] RMSD: 0.114
> show sel atoms
> select #1/A:427 #6/C:427
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/A:427-429 #6/C:427-429
46 atoms, 44 bonds, 6 residues, 2 models selected
2 [ID: 2] region chains A,C [178-180] RMSD: 0.074
> select #2/A:505
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:505-506
23 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> select #2/A:492
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:492
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:490
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:490
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:379
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:379-429
392 atoms, 397 bonds, 51 residues, 1 model selected
> select #2/A:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:528
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:528-530
25 atoms, 25 bonds, 3 residues, 1 model selected
> show sel atoms
> select #3/A:505
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:505-506
23 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/A:528
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:528-530
25 atoms, 25 bonds, 3 residues, 1 model selected
> show sel atoms
> select #3/A:492
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:492
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:490
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:490
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:528 #5/A:528
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #4/A:528-530 #5/A:528-530
48 atoms, 48 bonds, 6 residues, 2 models selected
9 [ID: 9] region 2 chains [273-275] RMSD: 0.147
> show sel atoms
> select #4/A:505 #5/A:505
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #4/A:505-506 #5/A:505-506
46 atoms, 48 bonds, 4 residues, 2 models selected
9 [ID: 9] region 2 chains [250-251] RMSD: 0.287
> show sel atoms
> select #4/A:427 #5/A:427
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #4/A:427-429 #5/A:427-429
46 atoms, 44 bonds, 6 residues, 2 models selected
9 [ID: 9] region 2 chains [177-179] RMSD: 0.273
> select #7/A:528
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:528-530
25 atoms, 25 bonds, 3 residues, 1 model selected
> show sel atoms
> select #7/A:505
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/A:505-506
23 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> select #7/A:490
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:490
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:492
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:492
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7/A:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:429-430
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/A:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> transparency #1/P 50 cartoons
> transparency #1/F 50 cartoons
> transparency #4/T 50 cartoons
> transparency #2/T 50 cartoons
> transparency #6/E 50 cartoons
> transparency #7/T 50 cartoons
> transparency #5/T 50 cartoons
> hide #1 models
> hide #2 models
> hide #!7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> show #1 models
> hide #1 models
> show #2 models
> hide #2 models
> show #3 models
> transparency #3/F 50 cartoons
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #!7 models
> hide #!7 models
> show #5 models
> show #6 models
> show #!7 models
> show #4 models
> show #1 models
> show #2 models
> show #3 models
> select clear
> hide #6 models
> hide #5 models
> hide #3 models
> hide #2 models
> hide #1 models
> hide #4 models
> show #3 models
> show #2 models
> hide #3 models
> show #3 models
> hide #2 models
> hide #3 models
> show #1 models
> hide #1 models
> color #1 #fff76bff
> color #1 #fff463ff
> show #1 models
> select clear
> color #1#!7 byhetero
> select clear
> select add #1/F:8
21 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> transparency #1/F 50 cartoons
> select clear
[Repeated 1 time(s)]
> transparency #1/G 50 cartoons
> show #2 models
> hide #1 models
> transparency #2/P 50 cartoons
> hide #2 models
> show #3 models
> transparency #3/G 50 cartoons
> hide #3 models
> show #4 models
> transparency #4/P 50 cartoons
> hide #4 models
> show #5 models
> transparency #5/P 50 cartoons
> hide #5 models
> show #6 models
> transparency #6/I 50 cartoons
> hide #6 models
> select #1/G:1 #2/P:1 #3/G:1 #4/P:1 #5/P:1 #6/I:1 #7/P:1
112 atoms, 119 bonds, 7 residues, 7 models selected
> select #1/G #2/P #3/G #4/P #5/P #6/I #7/P:1-6
833 atoms, 931 bonds, 42 residues, 7 models selected
7 [ID: 7] region 7 chains [1-6] RMSD: 0.641
> show sel & #!7 cartoons
> select clear
> transparency #7/P 50 cartoons
> show #1 models
> hide #1 models
> show #3 models
> select #3/A:529@OE2
1 atom, 1 residue, 1 model selected
> select add #3/A:529@OE1
2 atoms, 1 residue, 1 model selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 7m43.pdb #7/A ARG 568 NE
26 hydrogen bonds found
> ~hbonds
> select clear
> undo
[Repeated 1 time(s)]
> select clear
> hide sel atoms
> select clear
> select add #7/T:6@N2
1 atom, 1 residue, 1 model selected
> select add #3/F:6@N2
2 atoms, 2 residues, 2 models selected
> show sel atoms
> select clear
> select #3/F:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select add #3/F:6@C3'
1 atom, 1 bond, 1 residue, 2 models selected
> show sel atoms
> select #3/A:543
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
7 atoms, 5 bonds, 2 residues, 2 models selected
> show sel atoms
> undo
> select clear
> select #3/F:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #7/T:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #7/A:701@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/W:142@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #7/A:610@C1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #7/A:517@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #3/A:517@CZ
12 atoms, 10 bonds, 2 residues, 2 models selected
> select up
22 atoms, 20 bonds, 2 residues, 2 models selected
> hide sel atoms
> select #7/A:610@O1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #7/A:610@C2
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #1 models
> show #2 models
> show #4 models
> show #5 models
> show #6 models
> select clear
> select add #5/A:502
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #2/W:214@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
44 atoms, 48 bonds, 2 residues, 2 models selected
> hide sel atoms
> select clear
> select #4/C:610@C1
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #6 models
> hide #5 models
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> select clear
> ui tool show "Side View"
> view orient
> view
> hide #!7 models
> show #1 models
> show #6 models
> show #!7 models
> color #6 #00af01ff
> color #6 #01b401ff
> transparency #7/E 50 cartoons
> transparency #6/E 50 cartoons
> transparency #6/I 50 cartoons
> select clear
> color #1 #ffc550ff
> color #1 #bdff5fff
> color #1 #42ffb4ff
> color #1 #4bffecff
> color #1 #a761ffff
> color #1 #9f5cf2ff
> color #1 #a761ffff
> color #1 #c193ffff
> select clear
> show #2 models
> hide #2 models
> color #2 #f188e7ff
> color #1 #ff81b9ff
> color #1 #ff6b75ff
> color #1 #ffa9a3ff
> color #1 #ff8e78ff
> select clear
> color #1,6#!7 byhetero
> transparency #1/G 50 cartoons
> transparency #1/F 50 cartoons
> hide #1 models
> show #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #5 models
> hide #!7 models
> show #!7 models
> show #6 models
> hide #6 models
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> show #1 models
> show #6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #6 models
> show #6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> size spec [ stickRadius [-2]rb ]
Expected a keyword
> size spec [stickRadius [-2]rb ]
Expected a keyword
> hide #6 models
> show #!7 models
> hide #1 models
> size #7/A [stickRadius [-2]rb ]
Expected a keyword
> size #7/A [stickRadius [-2]rb ]
Expected a keyword
> size #7/A stickRadius -2
Cannot reduce stick radius to <= 0
> size #7/A stickRadius -,1
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size #7/A stickRadius -.1
Changed 2430 bond radii
> size #7/A stickRadius +.5
Changed 2430 bond radii
> size #7/A stickRadius -.5
Changed 2430 bond radii
> size #7/A stickRadius +.005
Changed 2430 bond radii
> size #7/A stickRadius +.005
Changed 2430 bond radii
> size #7/A stickRadius +.005
Changed 2430 bond radii
> size #7/A stickRadius +.005
Changed 2430 bond radii
> size #7/A stickRadius +.005
Changed 2430 bond radii
> size #7/A stickRadius +.005
Changed 2430 bond radii
> size #7/A stickRadius +.005
Changed 2430 bond radii
> select clear
> size #7/P stickRadius +.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/P stickRadius -.005
Changed 133 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Changed 251 bond radii
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> size #7/T stickRadius -.005
Cannot reduce bond radius to <= 0
> show #6 models
> hide #6 models
> size #all stickRadius -.005
Expected a keyword
> size #all stickRadius -.005
Expected a keyword
> size #all stickRadius -.005
Expected a keyword
> size #all stickRadius -.005
Expected a keyword
> size #1,7ll stickRadius -.005
Expected a keyword
> size #1,7 stickRadius -.005
Cannot reduce bond radius to <= 0
> size #1,7 stickRadius -.0005
Cannot reduce bond radius to <= 0
> size #1-end stickRadius -.0005
Cannot reduce bond radius to <= 0
> size #1-end stickRadius +0.05
Changed 21387 bond radii
> size #1-end stickRadius +0.05
Changed 21387 bond radii
> show #5 models
> hide #5 models
> size #1-end stickRadius -0.05
Changed 21387 bond radii
> size #1-end stickRadius -0.05
Changed 21387 bond radii
> show #6 models
> hide #6 models
> size #7 stickRadius -0.05
Changed 2906 bond radii
> size #7 stickRadius +0.05
Changed 2906 bond radii
> size #7 stickRadius +0.05
Changed 2906 bond radii
> size #a1-end stickRadius -0.05
Expected a keyword
> size #1-end stickRadius -0.05
Changed 21387 bond radii
> size #1-end stickRadius -0.05
Changed 21387 bond radii
> size #1-end stickRadius -0.05
Cannot reduce bond radius to <= 0
> size #1-end stickRadius -0.005
Cannot reduce bond radius to <= 0
> size #1-end stickRadius -0.005
Cannot reduce bond radius to <= 0
> size #1-end stickRadius -0.005
Cannot reduce bond radius to <= 0
> size #1-end stickRadius -0.005
Cannot reduce bond radius to <= 0
> size #1-end stickRadius -0.005
Cannot reduce bond radius to <= 0
> size #1-end stickRadius -0.005
Cannot reduce bond radius to <= 0
> size #1-end stickRadius -0.005
Cannot reduce bond radius to <= 0
> show #5 models
> show #4 models
> show #3 models
> show #2 models
> show #1 models
> select clear
> hide #2 models
> hide #3 models
> hide #5 models
> hide #4 models
> hide #!7 models
> hide #6 models
> show #!7 models
> hide #1 models
> show #3 models
> hide #3 models
> show #2 models
> select clear
> select #2/T:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> transparency #2/T,P 50 cartoons
> select clear
> select add #2
3213 atoms, 3076 bonds, 583 residues, 1 model selected
> select subtract #2
Nothing selected
> select clear
> color #2#!7 byhetero
> show #4 models
> select #2/A:517
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
104 atoms, 105 bonds, 13 residues, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select #1/F:11 #2/T:11 #3/F:11 #4/T:11 #5/T:11 #6/E:11 #7/T:11
154 atoms, 168 bonds, 7 residues, 7 models selected
> select #1/F #2/T #3/F:1-11 #4/T #5/T #6/E #7/T:1-11
1568 atoms, 1757 bonds, 77 residues, 7 models selected
6 [ID: 6] region 7 chains [1-11] RMSD: 1.433
> select clear
> select nucleic-acid
2982 atoms, 3332 bonds, 147 residues, 7 models selected
> hide sel & #2,4#!7 cartoons
> hide sel & #2,4#!7 atoms
> select clear
> select ::name="TTP"
116 atoms, 120 bonds, 4 residues, 4 models selected
> hide sel & #2,4#!7 atoms
> select clear
> select ::name="DCP"
40 atoms, 41 bonds, 1 residue, 1 model selected
> hide #2,4#!7 atoms
> undo
> select ::name="DCP"
40 atoms, 41 bonds, 1 residue, 1 model selected
> hide #2,4#!7 atoms
> undo
> select clear
> hide #2,4#!7 atoms
> undo
> select clear
> show #5 models
> select add #5/A:601@C5
1 atom, 1 residue, 1 model selected
> select clear
> show #6 models
> select add #7
3062 atoms, 2906 bonds, 26 pseudobonds, 597 residues, 2 models selected
> select add #6
6070 atoms, 5974 bonds, 26 pseudobonds, 982 residues, 3 models selected
> select add #5
9137 atoms, 9060 bonds, 26 pseudobonds, 1409 residues, 4 models selected
> select add #4
12460 atoms, 12152 bonds, 26 pseudobonds, 2086 residues, 5 models selected
> select add #3
15759 atoms, 15243 bonds, 26 pseudobonds, 2741 residues, 6 models selected
> select add #2
18972 atoms, 18319 bonds, 26 pseudobonds, 3324 residues, 7 models selected
> select add #1
21980 atoms, 21387 bonds, 26 pseudobonds, 3709 residues, 8 models selected
> select nucleic-acid
2982 atoms, 3332 bonds, 147 residues, 7 models selected
> hide sel & #2,4-6#!7 cartoons
> hide sel & #2,4-6#!7 atoms
> select clear
> select add #5/A:601@C1'
1 atom, 1 residue, 1 model selected
> select up
40 atoms, 41 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #7/A:601@CA
1 atom, 1 residue, 1 model selected
> select clear
> select ::name="CA"
7 atoms, 7 residues, 5 models selected
> hide sel & #2,4-5#!7 atoms
> select clear
> show #1 models
> show #3 models
> select nucleic-acid
2982 atoms, 3332 bonds, 147 residues, 7 models selected
> hide sel atoms
> hide sel cartoons
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
29 atoms, 30 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #6/C:517@NE
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #5/A:517@CD
12 atoms, 10 bonds, 2 residues, 2 models selected
> select up
22 atoms, 20 bonds, 2 residues, 2 models selected
> hide sel atoms
> select clear
> hide #5 models
> show #5 models
> select clear
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> ui tool show Distances
> distance style color #88ce80
[Repeated 2 time(s)]Exactly two atoms must be selected!
> select add #4/A:492@NZ
1 atom, 1 residue, 1 model selected
> select add #4/A:529@OD1
2 atoms, 2 residues, 1 model selected
> select add #4/A:529@OD2
3 atoms, 2 residues, 1 model selected
> select subtract #4/A:529@OD2
2 atoms, 2 residues, 1 model selected
> distance #4/A:492@NZ #4/A:529@OD1
Distance between refineptet.pdb #4/A LYS 492 NZ (alt loc A) and ASP 529 OD1:
5.004Å
> select clear
> select #7/A:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:289-298
74 atoms, 76 bonds, 10 residues, 1 model selected
> ui dockable false "Sequence Viewer"
> ui dockable false Log
> ui windowfill toggle
[Repeated 1 time(s)]Alignment identifier is 7/A
> select clear
> hide #1 models
> hide #2 models
> hide #3 models
> hide #5 models
> hide #6 models
> hide #!7 models
> close #8
> ui tool show Distances
> hide #4 models
> show #1 models
> distance style color #ea8d77
[Repeated 2 time(s)]
> select #1/A:492@NH1
1 atom, 1 residue, 1 model selected
> select add #1/A:530@OH
2 atoms, 2 residues, 1 model selected
> distance #1/A:492@NH1 #1/A:530@OH
Distance between refine.pdb #1/A ARG 492 NH1 and TYR 530 OH: 3.885Å
> select clear
> select #1/A:492@NH2
1 atom, 1 residue, 1 model selected
> select add #1/A:529@OE1
2 atoms, 2 residues, 1 model selected
> distance #1/A:492@NH2 #1/A:529@OE1
Distance between refine.pdb #1/A ARG 492 NH2 and GLU 529 OE1: 3.580Å
> select clear
> distance style color #f063e5
[Repeated 2 time(s)]
> distance style color #f064e5
[Repeated 2 time(s)]
> distance style color #f0ab67
[Repeated 2 time(s)]
> distance style color #050302
[Repeated 2 time(s)]
> distance style color #040302
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> distance style color #010000
[Repeated 2 time(s)]
> distance style color #040302
[Repeated 2 time(s)]
> distance style color #070503
[Repeated 2 time(s)]
> distance style color #0a0704
[Repeated 2 time(s)]
> distance style color #0b0805
[Repeated 2 time(s)]
> distance style color #0c0905
[Repeated 2 time(s)]
> distance style color #0f0a06
[Repeated 2 time(s)]
> distance style color #110c07
[Repeated 2 time(s)]
> distance style color #1a130b
[Repeated 2 time(s)]
> distance style color #20170e
[Repeated 2 time(s)]
> distance style color #251a10
[Repeated 2 time(s)]
> distance style color #291d12
[Repeated 2 time(s)]
> distance style color #2e2114
[Repeated 2 time(s)]
> distance style color #2f2214
[Repeated 2 time(s)]
> distance style color #312315
[Repeated 2 time(s)]
> distance style color #322415
[Repeated 2 time(s)]
> distance style color #332416
[Repeated 2 time(s)]
> distance style color #342516
[Repeated 2 time(s)]
> distance style color #362617
[Repeated 2 time(s)]
> distance style color #3a2919
[Repeated 2 time(s)]
> distance style color #412e1c
[Repeated 2 time(s)]
> distance style color #4b3520
[Repeated 2 time(s)]
> distance style color #5d4228
[Repeated 2 time(s)]
> distance style color #684a2c
[Repeated 2 time(s)]
> distance style color #715030
[Repeated 2 time(s)]
> distance style color #7c5835
[Repeated 2 time(s)]
> distance style color #825c37
[Repeated 2 time(s)]
> distance style color #865f39
[Repeated 2 time(s)]
> distance style color #8a633b
[Repeated 2 time(s)]
> distance style color #8d643c
[Repeated 2 time(s)]
> distance style color #8e653d
[Repeated 2 time(s)]
> distance style color #8a623b
[Repeated 2 time(s)]
> distance style color #845e39
[Repeated 2 time(s)]
> distance style color #66492c
[Repeated 2 time(s)]
> distance style color #63472b
[Repeated 2 time(s)]
> distance style color #62462a
[Repeated 2 time(s)]
> distance style color #5e4328
[Repeated 2 time(s)]
> distance style color #5c4127
[Repeated 2 time(s)]
> distance style color #5a4027
[Repeated 2 time(s)]
> distance style color #503922
[Repeated 2 time(s)]
> distance style color #48331f
[Repeated 2 time(s)]
> distance style color #47331e
[Repeated 2 time(s)]
> distance style color #47331f
[Repeated 2 time(s)]
> distance style color #48341f
[Repeated 2 time(s)]
> select clear
[Repeated 1 time(s)]
> hide #1 models
> show #2 models
> select #2/A:492@NZ
1 atom, 1 residue, 1 model selected
> select add #2/A:529@OE1
2 atoms, 2 residues, 1 model selected
> distance #2/A:492@NZ #2/A:529@OE1
Distance between refinemutk2.pdb #2/A LYS 492 NZ and GLU 529 OE1: 4.728Å
> select clear
> select add #2/A:529@OE2
1 atom, 1 residue, 1 model selected
> select add #2/A:492@NZ
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> distance #2/A:529@OE2 #2/A:492@NZ
Distance between refinemutk2.pdb #2/A GLU 529 OE2 and LYS 492 NZ: 3.744Å
> select add #2/A:529@OE1
3 atoms, 2 residues, 1 model selected
> select subtract #2/A:529@OE2
2 atoms, 2 residues, 1 model selected
> select clear
> ~distance #2/A:492@NZ #2/A:529@OE1
> ~distance #2/A:529@OE2 #2/A:492@NZ
> ~distance #1/A:492@NH1 #1/A:530@OH
> ~distance #1/A:492@NH2 #1/A:529@OE1
Exactly two atoms must be selected!
> select add #2/A:529@OE2
1 atom, 1 residue, 1 model selected
> select add #2/A:492@NZ
2 atoms, 2 residues, 1 model selected
> distance #2/A:529@OE2 #2/A:492@NZ
Distance between refinemutk2.pdb #2/A GLU 529 OE2 and LYS 492 NZ: 3.744Å
> select clear
> distance style radius 0
> distance style radius 0.01
[Repeated 3 time(s)]
> select clear
> show #1 models
> select clear
> select #1/A:492@NH1
1 atom, 1 residue, 1 model selected
> select add #1/A:530@OH
2 atoms, 2 residues, 1 model selected
> distance #1/A:492@NH1 #1/A:530@OH
Distance between refine.pdb #1/A ARG 492 NH1 and TYR 530 OH: 3.885Å
> select clear
> select add #1/A:492@NH2
1 atom, 1 residue, 1 model selected
> select add #1/A:529@OE1
2 atoms, 2 residues, 1 model selected
> distance #1/A:492@NH2 #1/A:529@OE1
Distance between refine.pdb #1/A ARG 492 NH2 and GLU 529 OE1: 3.580Å
> select clear
[Repeated 1 time(s)]
> hide #1 models
> hide #2 models
> show #3 models
> select #3/A:492@NE
1 atom, 1 residue, 1 model selected
> select add #3/A:490@OD1
2 atoms, 2 residues, 1 model selected
> distance #3/A:492@NE #3/A:490@OD1
Distance between refinemutR.pdb #3/A ARG 492 NE and ASP 490 OD1: 2.816Å
> select clear
> select #3/A:492@NH2
1 atom, 1 residue, 1 model selected
> select add #3/A:490@OD2
2 atoms, 2 residues, 1 model selected
> distance #3/A:492@NH2 #3/A:490@OD2
Distance between refinemutR.pdb #3/A ARG 492 NH2 and ASP 490 OD2: 3.220Å
> select clear
> hide #3 models
> show #4 models
> select #4/A:492@NZ
1 atom, 1 residue, 1 model selected
> select clear
> show #5 models
> hide #4 models
> select add #5/A:492@NZ
1 atom, 1 residue, 1 model selected
> select add #5/A:429@OD1
2 atoms, 2 residues, 1 model selected
> distance #5/A:492@NZ #5/A:429@OD1
Distance between refine.pdb #5/A LYS 492 NZ and ASP 429 OD1: 2.743Å
> select clear
> hide #5 models
> show #6 models
> select clear
> select #6/C:492@NH2
1 atom, 1 residue, 1 model selected
> select add #6/C:529@OE1
2 atoms, 2 residues, 1 model selected
> distance #6/C:492@NH2 #6/C:529@OE1
Distance between refine.pdb #6/C ARG 492 NH2 and GLU 529 OE1: 3.525Å
> select clear
> select add #6/C:492@NH1
1 atom, 1 residue, 1 model selected
> select add #6/C:429@OD1
2 atoms, 2 residues, 1 model selected
> distance #6/C:492@NH1 #6/C:429@OD1
Distance between refine.pdb #6/C ARG 492 NH1 and ASP 429 OD1: 6.329Å
> select clear
> select add #6/C:492@NE
1 atom, 1 residue, 1 model selected
> select add #6/C:429@OD1
2 atoms, 2 residues, 1 model selected
> distance #6/C:492@NE #6/C:429@OD1
Distance between refine.pdb #6/C ARG 492 NE and ASP 429 OD1: 5.280Å
> ~distance #1/A:492@NH2 #1/A:529@OE1
> ~distance #3/A:492@NH2 #3/A:490@OD2
> ~distance #3/A:492@NE #3/A:490@OD1
> ~distance #6/C:492@NH1 #6/C:429@OD1
> ~distance #1/A:492@NH1 #1/A:530@OH
> show #1 models
> select add #1/A:492@NH1
3 atoms, 3 residues, 2 models selected
> select add #1/A:530@OH
4 atoms, 4 residues, 2 models selected
> select clear
> select add #1/A:492@NH1
1 atom, 1 residue, 1 model selected
> select add #6/C:530@OH
2 atoms, 2 residues, 2 models selected
> distance #1/A:492@NH1 #6/C:530@OH
Distance between refine.pdb #1/A ARG 492 NH1 and refine.pdb #6/C TYR 530 OH:
3.837Å
> select clear
> select add #1/A:492@NH2
1 atom, 1 residue, 1 model selected
> select add #1/A:529@OE1
2 atoms, 2 residues, 1 model selected
> distance #1/A:492@NH2 #1/A:529@OE1
Distance between refine.pdb #1/A ARG 492 NH2 and GLU 529 OE1: 3.580Å
> select clear
[Repeated 2 time(s)]
> ~distance #6/C:492@NE #6/C:429@OD1
> hide #1 models
> hide #6 models
> show #!7 models
> hide #!7 models
> show #1 models
> select clear
[Repeated 1 time(s)]
> select add #1/A:492@NH1
1 atom, 1 pseudobond, 1 residue, 2 models selected
> select clear
[Repeated 2 time(s)]
> hide #!8 models
> show #!8 models
> show #2 models
> select clear
> hide #2 models
> select add #1/A:530@OH
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select clear
> select add #1/A:492@NH1
1 atom, 1 residue, 1 model selected
> select add #1/A:530@OH
2 atoms, 2 residues, 1 model selected
> distance #1/A:492@NH1 #1/A:530@OH
Distance between refine.pdb #1/A ARG 492 NH1 and TYR 530 OH: 3.885Å
> select clear
[Repeated 1 time(s)]
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> distance style radius 0.01
> distance style symbol false
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #!7 models
> hide #1 models
> hide #2 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #!7 models
> select add #3/A:492@NE
1 atom, 1 residue, 1 model selected
> select add #3/A:490@OD1
2 atoms, 2 residues, 1 model selected
> distance #3/A:492@NE #3/A:490@OD1
Distance between refinemutR.pdb #3/A ARG 492 NE and ASP 490 OD1: 2.82Å
> select clear
> select add #3/A:492@NH2
1 atom, 1 residue, 1 model selected
> select add #3/A:490@OD2
2 atoms, 2 residues, 1 model selected
> distance #3/A:492@NH2 #3/A:490@OD2
Distance between refinemutR.pdb #3/A ARG 492 NH2 and ASP 490 OD2: 3.22Å
> select clear
> hide #3 models
> show #1 models
> hide #1 models
> show #6 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> select clear
> select add #6/C:492@NE
1 atom, 1 residue, 1 model selected
> select clear
> select add #6/C:492@NE
1 atom, 1 residue, 1 model selected
> select add #1/A:490@OD1
2 atoms, 2 residues, 2 models selected
> distance #6/C:492@NE #1/A:490@OD1
Distance between refine.pdb #6/C ARG 492 NE and refine.pdb #1/A ASP 490 OD1:
3.67Å
> select clear
> select add #6/C:492@NE
1 atom, 1 residue, 1 model selected
> select add #1/A:490@OD2
2 atoms, 2 residues, 2 models selected
> distance #6/C:492@NE #1/A:490@OD2
Distance between refine.pdb #6/C ARG 492 NE and refine.pdb #1/A ASP 490 OD2:
3.45Å
> select clear
> distance style dashes 5
> distance style radius 0.01
> distance style decimalPlaces 2
> select clear
> ~distance #6/C:492@NH2 #6/C:529@OE1
> select clear
> color #1 #50ff9eff
> color #1 #55ff65ff
> color #1 #50f260ff
> color #1 #4ff299ff
> color #1 #4ceb95ff
> color #1,6 byhetero
> select clear
> hide #1 models
> hide #6 models
> show #3 models
> hide #3 models
> show #1 models
> show #6 models
> select clear
> distance style color #5b4529
[Repeated 2 time(s)]
> distance style color #5b4223
[Repeated 2 time(s)]
> distance style color #5b4122
[Repeated 2 time(s)]
> distance style color #5b4121
[Repeated 2 time(s)]
> distance style color #5b4022
[Repeated 2 time(s)]
> distance style color #5b3f23
[Repeated 2 time(s)]
> distance style color #5b3d24
[Repeated 2 time(s)]
> distance style color #5b322b
[Repeated 2 time(s)]
> distance style color #5b312c
[Repeated 2 time(s)]
> distance style color #5b2f2c
[Repeated 2 time(s)]
> distance style color #5b2e2c
[Repeated 2 time(s)]
> distance style color #5b2c2e
[Repeated 2 time(s)]
> distance style color #5b2c32
[Repeated 2 time(s)]
> distance style color #5b2c34
[Repeated 2 time(s)]
> distance style color #5b2b39
[Repeated 2 time(s)]
> distance style color #5b2a3c
[Repeated 2 time(s)]
> distance style color #5b2a40
[Repeated 2 time(s)]
> distance style color #5b2843
[Repeated 2 time(s)]
> distance style color #5b2b3b
[Repeated 2 time(s)]
> distance style color #5b2c38
[Repeated 2 time(s)]
> distance style color #5b3a2a
[Repeated 2 time(s)]
> distance style color #5b3c29
[Repeated 2 time(s)]
> distance style color #5b3d29
[Repeated 2 time(s)]
> distance style color #5b3e28
[Repeated 2 time(s)]
> distance style color #5b4227
[Repeated 2 time(s)]
> distance style color #5b4327
[Repeated 2 time(s)]
> distance style color #5b4427
[Repeated 2 time(s)]
> distance style color #5b4426
[Repeated 2 time(s)]
> distance style color #5b4427
[Repeated 2 time(s)]
> select clear
> ~distance #1/A:492@NH1 #1/A:530@OH
> hide #1 models
> hide #6 models
> show #2 models
> select add #2/A:492@NZ
1 atom, 1 residue, 1 model selected
> select add #2/A:529@OE1
2 atoms, 2 residues, 1 model selected
> distance #2/A:492@NZ #2/A:529@OE1
Distance between refinemutk2.pdb #2/A LYS 492 NZ and GLU 529 OE1: 4.73Å
> select clear
> ~distance #2/A:492@NZ #2/A:529@OE1
> hide #2 models
> show #4 models
> show #5 models
> select clear
> select add #5/A:429@OD2
1 atom, 1 residue, 1 model selected
> select add #5/A:492@NZ
2 atoms, 2 residues, 1 model selected
> distance #5/A:429@OD2 #5/A:492@NZ
Distance between refine.pdb #5/A ASP 429 OD2 and LYS 492 NZ: 4.58Å
> select clear
[Repeated 1 time(s)]
> ~distance #5/A:429@OD2 #5/A:492@NZ
> distance style color #6f5635
[Repeated 2 time(s)]
> distance style color #785d39
[Repeated 2 time(s)]
> distance style color #d1a264
[Repeated 2 time(s)]
> distance style color #ffc67a
[Repeated 2 time(s)]
> distance style color #fff02d
[Repeated 2 time(s)]
> distance style color #fff12c
[Repeated 2 time(s)]
> distance style color #fff22c
[Repeated 2 time(s)]
> distance style color #fff32a
[Repeated 2 time(s)]
> distance style color #fff429
[Repeated 2 time(s)]
> distance style color #fffa17
[Repeated 2 time(s)]
> distance style color #fffa12
[Repeated 2 time(s)]
> distance style color #fffa0c
[Repeated 2 time(s)]
> distance style color #fff803
[Repeated 2 time(s)]
> distance style color #fff700
[Repeated 2 time(s)]
> hide #5 models
> hide #4 models
> show #1 models
> select clear
[Repeated 2 time(s)]
> distance style color #ff0207
[Repeated 2 time(s)]
> distance style color #ff0106
[Repeated 2 time(s)]
> distance style color #ff0002
[Repeated 2 time(s)]
> distance style color red
[Repeated 2 time(s)]
> select clear
> hide #1 models
> show #2 models
> show #1 models
> hide #1 models
> hide #2 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> show #4 models
> hide #4 models
> hide #5 models
> show #6 models
> show #1 models
> hide #6 models
> hide #1 models
> show #!7 models
> hide #!7 models
> show #4 models
> select add #4/A:492@NZ
1 atom, 1 residue, 1 model selected
> select add #4/A:529@OD1
2 atoms, 2 residues, 1 model selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 7m43.pdb #7/A ARG 568 NE
7 hydrogen bonds found
> select add #4/W:218@O
3 atoms, 3 residues, 1 model selected
> select clear
> size atomRadius #1-end +.5
Invalid "atomRadius" argument: Expected 'default' or a number >= 0 or a +/-
delta
> size atomRadius #1-end | default
Invalid "atomRadius" argument: Expected 'default' or a number >= 0 or a +/-
delta
> size atomRadius #1-end default
Invalid "atomRadius" argument: Expected 'default' or a number >= 0 or a +/-
delta
> size atomRadius #1-end default
Invalid "atomRadius" argument: Expected 'default' or a number >= 0 or a +/-
delta
> size atomRadius default #1-end
Expected a keyword
> show #1 models
> show #2 models
> show #3 models
> show #5 models
> show #6 models
> show #!7 models
> size atomRadius default #1
Expected a keyword
> size atomRadius #1 default
Invalid "atomRadius" argument: Expected 'default' or a number >= 0 or a +/-
delta
> size atomRadius default
Changed 21980 atom radii
> select clear
> size atomRadius default
Changed 21980 atom radii
> size atomRadius +0.5
Changed 21980 atom radii
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> size ballScale +0.5
Changed 7 ball scales
> select clear
> size stickRadius #3/W +.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W +5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W +.2
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3 +.2
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3 +.2
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3 +.2
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3 +.2
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W +.2
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W +.2
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickradius+.2 #3/W
Expected a keyword
> size stickRadius #3/W
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W .2
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W 2
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W 0.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W +0.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> toolshed show
> ui tool show "Basic Actions"
> size stickRadius #3/W +0.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W +0.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W -0.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W +1
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3/W 3
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3 3
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3 +,5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3 1
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3 +0.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3 +.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #3 +.005
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size ligand atomRadius +.5
Changed 1656 atom radii
> size #3/W atomRadius +.5
Changed 306 atom radii
> size #3/W stickRadius +.5
Changed 0 bond radii
> size #3/W stickRadius -.2
Changed 0 bond radii
> hide #1 models
> hide #2 models
> hide #3 models
> hide #5 models
> hide #6 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> size #4/W stickRadius +.2
Changed 0 bond radii
> select clear
> select #4/A:529
8 atoms, 7 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 7m43.pdb #7/A ARG 568 NE
13 hydrogen bonds found
> select clear
> select #4/W:8@O
1 atom, 1 residue, 1 model selected
> select add #4/W:218@O
2 atoms, 2 residues, 1 model selected
> select add #4/A:492@NZ
3 atoms, 3 residues, 1 model selected
> select add #4/W:295@O
4 atoms, 4 residues, 1 model selected
> select add #4/A:529@OD1
5 atoms, 5 residues, 1 model selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 7m43.pdb #7/A ARG 568 NE
87 hydrogen bonds found
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #4/A:498@CD
5 atoms, 3 bonds, 2 residues, 1 model selected
> select up
13 atoms, 11 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select #4/A:529@OD2
1 atom, 1 residue, 1 model selected
> select add #4/A:529@OD1
2 atoms, 1 residue, 1 model selected
> select add #4/W:218@O
3 atoms, 1 pseudobond, 2 residues, 2 models selected
> select add #4/W:295@O
4 atoms, 1 pseudobond, 3 residues, 2 models selected
> select add #4/A:492@NZ
5 atoms, 2 pseudobonds, 4 residues, 2 models selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 7m43.pdb #7/A ARG 568 NE
67 hydrogen bonds found
> select clear
> select add #4/C:610@O1
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
53 atoms, 47 bonds, 8 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> undo
[Repeated 8 time(s)]
> select clear
> select #4/A:529
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4/W:8@O
9 atoms, 7 bonds, 2 residues, 1 model selected
> select add #4/W:218@O
10 atoms, 7 bonds, 3 residues, 1 model selected
> select add #4/W:295@O
11 atoms, 7 bonds, 4 residues, 1 model selected
> select add #4/A:492@NZ
12 atoms, 7 bonds, 2 pseudobonds, 5 residues, 2 models selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 7m43.pdb #7/A ARG 568 NE
96 hydrogen bonds found
> select clear
> select add #4/A:530
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #4/A:529
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add #4/W:218@O
19 atoms, 17 bonds, 1 pseudobond, 3 residues, 2 models selected
> select add #4/W:295@O
20 atoms, 17 bonds, 2 pseudobonds, 4 residues, 2 models selected
> select add #4/A:492@NZ
21 atoms, 17 bonds, 3 pseudobonds, 5 residues, 2 models selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 7m43.pdb #7/A ARG 568 NE
99 hydrogen bonds found
> select clear
> select add #4/T:8@O5'
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
23 atoms, 24 bonds, 2 residues, 1 model selected
> hide sel atoms
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> hide sel atoms
> select add #4/A:498@OE2
26 atoms, 25 bonds, 3 residues, 1 model selected
> hide sel atoms
> select clear
> select add #4/W:93@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select add #4/A:528@OG
2 atoms, 2 residues, 1 model selected
> select up
7 atoms, 5 bonds, 2 residues, 1 model selected
> hide sel atoms
> select add #4/C:610@O1
8 atoms, 5 bonds, 1 pseudobond, 3 residues, 2 models selected
> select up
11 atoms, 8 bonds, 1 pseudobond, 3 residues, 2 models selected
> hide sel atoms
> select add #4/A:498
20 atoms, 16 bonds, 1 pseudobond, 4 residues, 2 models selected
> select up
267 atoms, 269 bonds, 1 pseudobond, 38 residues, 2 models selected
> select down
20 atoms, 16 bonds, 1 pseudobond, 4 residues, 2 models selected
> select clear
> select add #4/A:498
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
27 atoms, 27 bonds, 3 residues, 1 model selected
> hide sel atoms
> select clear
> show #1 models
> hide #1 models
> hide #4 models
> show #1 models
> hide #1 models
> show #2 models
> select add #2/T:8@O5'
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #2/A:498
30 atoms, 31 bonds, 2 residues, 1 model selected
> hide sel atoms
> select add #2/A:528
36 atoms, 36 bonds, 3 residues, 1 model selected
> hide sel atoms
Drag select of 1 atoms
Drag select of 2 atoms
Drag select of 1 atoms
[Repeated 2 time(s)]
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> show #3 models
> hide #2 models
> select add #3/W:85@O
1 atom, 1 residue, 1 model selected
> select #3/W:151@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 1 atoms
[Repeated 1 time(s)]
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
> select add #3/F:8@O5'
2 atoms, 2 residues, 1 model selected
> select up
22 atoms, 23 bonds, 2 residues, 1 model selected
> hide sel atoms
> select add #3/W:245@O
23 atoms, 23 bonds, 3 residues, 1 model selected
> select add #3/W:118@O
24 atoms, 23 bonds, 4 residues, 1 model selected
> select add #3/W:26@O
25 atoms, 23 bonds, 5 residues, 1 model selected
> hide sel atoms
> select add #3/F:7@C4'
26 atoms, 23 bonds, 6 residues, 1 model selected
> select up
45 atoms, 45 bonds, 6 residues, 1 model selected
> hide sel atoms
> select add #3/W:85@O
46 atoms, 45 bonds, 7 residues, 1 model selected
> hide sel atoms
> select add #3/A:528
52 atoms, 50 bonds, 8 residues, 1 model selected
> hide sel atoms
> select add #3/A:498
61 atoms, 58 bonds, 9 residues, 1 model selected
> hide sel atoms
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> select add #5/T:8@C5'
62 atoms, 58 bonds, 10 residues, 2 models selected
> select up
82 atoms, 81 bonds, 10 residues, 2 models selected
> hide sel & #5 atoms
> select add #5/A:498
91 atoms, 89 bonds, 11 residues, 2 models selected
> select add #5/A:528
97 atoms, 94 bonds, 12 residues, 2 models selected
> hide sel & #5 atoms
> select clear
> hide #5 models
> show #6 models
> select add #6/C:498
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/C:528
17 atoms, 15 bonds, 2 residues, 1 model selected
> hide sel atoms
> hide #6 models
> show #!7 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
224 atoms, 251 bonds, 11 residues, 1 model selected
> hide sel atoms
> select clear
Drag select of 1 atoms
[Repeated 3 time(s)]
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
> select #7/A:780@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select add #7/A:610@O1
2 atoms, 2 residues, 1 model selected
> select up
5 atoms, 3 bonds, 2 residues, 1 model selected
> hide sel atoms
> select add #7/A:517@CZ
6 atoms, 3 bonds, 3 residues, 1 model selected
> select clear
> select #7/A:517@NE
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 652, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Drag select of 1 residues
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 652, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Drag select of 3 residues
> select clear
> select add #7/A:498@CD
1 atom, 1 residue, 1 model selected
> select clear
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 652, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Drag select of 1 atoms, 1 residues, 1 bonds
> hide sel atoms
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 652, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Drag select of 11 residues, 1 bonds
> select clear
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 652, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 641, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 641, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 641, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 641, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 641, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 641, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
[deleted a _lot_ of these]
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_drag
self._rotate(axis, angle)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 403, in _rotate
self.view.rotate(saxis, angle, self.models())
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 1027, in rotate
center = self.center_of_rotation
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 708, in _get_cofr
cofr = self._compute_center_of_rotation()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 735, in _compute_center_of_rotation
p = self._front_center_cofr()
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 803, in _front_center_cofr
cr = self._front_center_point() # Can be None
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 812, in _front_center_point
p = self.picked_object(0.5 * w, 0.5 * h, max_transparent_layers = 0,
exclude=View.unpickable)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_drag
self._rotate(axis, angle)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 403, in _rotate
self.view.rotate(saxis, angle, self.models())
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 1027, in rotate
center = self.center_of_rotation
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 708, in _get_cofr
cofr = self._compute_center_of_rotation()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 735, in _compute_center_of_rotation
p = self._front_center_cofr()
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 803, in _front_center_cofr
cr = self._front_center_point() # Can be None
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 812, in _front_center_point
p = self.picked_object(0.5 * w, 0.5 * h, max_transparent_layers = 0,
exclude=View.unpickable)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_drag
self._rotate(axis, angle)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 403, in _rotate
self.view.rotate(saxis, angle, self.models())
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 1027, in rotate
center = self.center_of_rotation
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 708, in _get_cofr
cofr = self._compute_center_of_rotation()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 735, in _compute_center_of_rotation
p = self._front_center_cofr()
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 803, in _front_center_cofr
cr = self._front_center_point() # Can be None
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 812, in _front_center_point
p = self.picked_object(0.5 * w, 0.5 * h, max_transparent_layers = 0,
exclude=View.unpickable)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_drag
self._rotate(axis, angle)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 403, in _rotate
self.view.rotate(saxis, angle, self.models())
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 1027, in rotate
center = self.center_of_rotation
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 708, in _get_cofr
cofr = self._compute_center_of_rotation()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 735, in _compute_center_of_rotation
p = self._front_center_cofr()
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 803, in _front_center_cofr
cr = self._front_center_point() # Can be None
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 812, in _front_center_point
p = self.picked_object(0.5 * w, 0.5 * h, max_transparent_layers = 0,
exclude=View.unpickable)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_drag
self._rotate(axis, angle)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 403, in _rotate
self.view.rotate(saxis, angle, self.models())
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 1027, in rotate
center = self.center_of_rotation
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 708, in _get_cofr
cofr = self._compute_center_of_rotation()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 735, in _compute_center_of_rotation
p = self._front_center_cofr()
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 803, in _front_center_cofr
cr = self._front_center_point() # Can be None
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 812, in _front_center_point
p = self.picked_object(0.5 * w, 0.5 * h, max_transparent_layers = 0,
exclude=View.unpickable)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 651, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 550, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 311, in mouse_drag
self._rotate(axis, angle)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 403, in _rotate
self.view.rotate(saxis, angle, self.models())
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 1027, in rotate
center = self.center_of_rotation
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 708, in _get_cofr
cofr = self._compute_center_of_rotation()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 735, in _compute_center_of_rotation
p = self._front_center_cofr()
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 803, in _front_center_cofr
cr = self._front_center_point() # Can be None
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 812, in _front_center_point
p = self.picked_object(0.5 * w, 0.5 * h, max_transparent_layers = 0,
exclude=View.unpickable)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 831, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 863, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 685, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
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: MacBookPro17,1
Model Number: MYDA2FN/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 12 jours, 17 heures et 54 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
24P1X:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Main Display: Yes
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
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-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-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-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-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-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
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
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
openvr: 1.23.701
packaging: 21.3
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
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 20 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Picking code: Singular matrix |
comment:2 by , 20 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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User was trying to select with the mouse and some model has a singular position matrix. I did not see any commands suggesting how they got that singular position matrix. They had 7 PDB files opened from a session and had used matchmaker to align them, and the output from those alignments (320 atoms paired) looks fine.