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Opened 20 months ago
Last modified 19 months ago
#14907 accepted defect
Clipper: 'SymmetryManager' object has no attribute 'spacegroup'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
This is probably a result of an earlier error in the session that I didn't report.
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH k.cxs"
Log from Thu Apr 4 00:01:16 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH k.pdb" format pdb
Chain information for RacGEF HH k.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
Q | No description available
> set bgColor white
> select /D
2553 atoms, 2573 bonds, 157 residues, 1 model selected
> select /Q
2665 atoms, 2685 bonds, 4 pseudobonds, 168 residues, 2 models selected
> color (#!1 & sel) forest green
> ui tool show "Color Actions"
> color sel lime green
> select /D
2553 atoms, 2573 bonds, 157 residues, 1 model selected
> color sel dark gray
> select /C
8002 atoms, 8101 bonds, 482 residues, 1 model selected
> color sel orange
> color N cornflowerblue atoms
> color O hotpink atoms
> color :arg,hic,his,lys & sidechain & N blue atoms
> color :asp,glu & sidechain & O red atoms
> color S yellow atoms
> color P purple atoms
> hide H atoms
> select clear
> hide atoms
> show cartoons
> graphics silhouettes true
> close session
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH j.pdb" format pdb
Chain information for RacGEF HH j.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
Q | No description available
> close session
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH i.pdb" format pdb
Chain information for RacGEF HH i.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
Q | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> sequence chain /C
Alignment identifier is 1/C
> sequence chain /D
Alignment identifier is 1/D
> select /B:13
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1-13
215 atoms, 218 bonds, 13 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected atoms"
> select /B:13
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:11
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /B:12
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:2
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /B:1-2
36 atoms, 35 bonds, 2 residues, 1 model selected
> select /B:5
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /B:2-5
61 atoms, 60 bonds, 4 residues, 1 model selected
> select /C:601
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select /B:6
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /B:7
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:7
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:6
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /B:1-6
99 atoms, 98 bonds, 6 residues, 1 model selected
> select /B:7
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:8
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:7
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:16-17
24 atoms, 24 bonds, 2 residues, 1 model selected
> select /B:1-17
268 atoms, 272 bonds, 17 residues, 1 model selected
> isolde sim start sel
> set selectionWidth 4
Done loading forcefield
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 27 residues in model #1 to IUPAC-IUB
standards.
Chain information for RacGEF HH i.pdb
---
Chain | Description
1.2/B | No description available
1.2/C | No description available
1.2/D | No description available
1.2/Q | No description available
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
Sim termination reason: None
ISOLDE: stopped sim
> select /D
1278 atoms, 1298 bonds, 157 residues, 1 model selected
> select clear
> select /B:17
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1-17
268 atoms, 272 bonds, 17 residues, 1 model selected
> addh
Summary of feedback from adding hydrogens to RacGEF HH i.pdb #1.2
---
notes | Termini for RacGEF HH i.pdb (#1.2) chain B determined from SEQRES
records
Termini for RacGEF HH i.pdb (#1.2) chain C determined from SEQRES records
Termini for RacGEF HH i.pdb (#1.2) chain D determined from SEQRES records
Termini for RacGEF HH i.pdb (#1.2) chain Q determined from SEQRES records
Chain-initial residues that are actual N termini: /B MET 1, /C GLN 566, /D TYR
408, /Q MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /B PHE 407, /C PRO 1047, /D
GLU 564, /Q HIS 166
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /B PHE 407
Missing OXT added to C-terminal residue /D GLU 564
1193 hydrogen bonds
1274 hydrogens added
> isolde sim start sel
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: started sim
> isolde sim pause
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> close #1.3
> select clear
> hide atoms
> show cartoons
> select /B:17
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1-17
268 atoms, 272 bonds, 17 residues, 1 model selected
> show sel atoms
> select /B:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /B:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right "isolde tug selection"
> isolde sim resume
> select
19802 atoms, 20007 bonds, 4 pseudobonds, 1214 residues, 17 models selected
> show sel atoms
> select clear
> ui mousemode right "isolde tug atom"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select /B
6582 atoms, 6648 bonds, 407 residues, 1 model selected
> select /B:1-2
36 atoms, 35 bonds, 2 residues, 1 model selected
> select /B:1-9
149 atoms, 150 bonds, 9 residues, 1 model selected
> select /B:10
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /B:1-10
169 atoms, 171 bonds, 10 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r phi -139
Assigning phi attribute to 10 items
Cannot set attribute 'phi' to '-139'
> setattr sel r psi 134
Assigning psi attribute to 10 items
> setattr sel r omega -179.4
Assigning omega attribute to 10 items
> select /B:7
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:7
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:6
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /B:1-6
99 atoms, 98 bonds, 6 residues, 1 model selected
> ui tool show "Selection Inspector"
> select /B:9
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:8-9
36 atoms, 36 bonds, 2 residues, 1 model selected
> setattr sel r phi -139
Assigning phi attribute to 2 items
> select /D
2553 atoms, 2573 bonds, 157 residues, 1 model selected
> ui tool show "Side View"
> roll y 2 180
> roll y 1 180
> roll y -1 90
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #1.2,1,0,0,-0.20126,0,1,0,0.058638,0,0,1,0.31919
> view matrix models #1.2,1,0,0,-0.30752,0,1,0,0.087404,0,0,1,0.66181
> ui mousemode right "translate selected atoms"
> select clear
> select /D:441
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:437-441
65 atoms, 64 bonds, 5 residues, 1 model selected
> select /D:427
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /D:415-427
235 atoms, 234 bonds, 13 residues, 1 model selected
> select /D:414
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:414
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:414
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:408-414
114 atoms, 114 bonds, 7 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r phi -57
Assigning phi attribute to 7 items
> setattr sel r psi -47
Assigning psi attribute to 7 items
> setattr sel r omega -180
Assigning omega attribute to 7 items
> select /B:367
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /B:367-407
655 atoms, 655 bonds, 41 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r phi -57
Assigning phi attribute to 41 items
> setattr sel r psi -47
Assigning psi attribute to 41 items
> isolde sim start sel
ISOLDE: started sim
> cofr sel
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select /D
2553 atoms, 2573 bonds, 157 residues, 1 model selected
> select clear
> select /B:407
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:407
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:364@C/B:365@N
2 atoms, 1 bond, 2 residues, 1 model selected
> ui tool show "Build Structure"
> ~bond sel
> split #1 connected
Split RacGEF HH i.pdb (#1.2) into 7 models
Deleting atomic symmetry model...
Deleting atomic symmetry model...
Chain information for RacGEF HH i.pdb 1 #1.2.1
---
Chain | Description
C | No description available
Chain information for RacGEF HH i.pdb 2 #1.2.2
---
Chain | Description
B | No description available
Chain information for RacGEF HH i.pdb 3 #1.2.3
---
Chain | Description
Q | No description available
Chain information for RacGEF HH i.pdb 4 #1.2.4
---
Chain | Description
D | No description available
Chain information for RacGEF HH i.pdb 5 #1.2.5
---
Chain | Description
B | No description available
> hide #1.2.1 models
> hide #1.2.3 models
> hide #1.2.6 models
> hide #1.2.7 models
> hide #1.2.2 models
> show #1.2.2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.5,0.9945,-0.067786,-0.079847,47.438,0.064742,0.9971,-0.040123,-9.7799,0.082334,0.034732,0.996,-38.386
> undo
> view matrix models
> #1.2.5,0.94205,0.33344,0.037007,-102.97,-0.056216,0.26564,-0.96243,544.49,-0.33074,0.90457,0.26899,22.559
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.5,0.94205,0.33344,0.037007,-102.7,-0.056216,0.26564,-0.96243,564.24,-0.33074,0.90457,0.26899,42.492
> show #1.2.1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.5,0.89307,0.39959,-0.20676,-37.519,-0.030974,-0.40385,-0.9143,766.57,-0.44885,0.82294,-0.34829,289.23
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2.2/B
Alignment identifier is 1.2.2/B
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2.2/B
Destroying pre-existing alignment with identifier 1.2.2/B
Alignment identifier is 1.2.2/B
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2.1/C
Alignment identifier is 1.2.1/C
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2.4/D
Alignment identifier is 1.2.4/D
> select #1.2.2/B:330
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.2.2/B:328-330
29 atoms, 28 bonds, 3 residues, 1 model selected
> ui mousemode right "translate selected models"
> select #1.2.5/B:367
17 atoms, 16 bonds, 1 residue, 1 model selected
> view matrix models
> #1.2.5,0.89307,0.39959,-0.20676,-42.062,-0.030974,-0.40385,-0.9143,755.09,-0.44885,0.82294,-0.34829,338.81
> view matrix models
> #1.2.5,0.89307,0.39959,-0.20676,-51.885,-0.030974,-0.40385,-0.9143,772.51,-0.44885,0.82294,-0.34829,338.44
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.5,0.86148,-0.50286,-0.070627,222.99,-0.11102,-0.050792,-0.99252,704.21,0.49551,0.86287,-0.099583,-74.109
> view matrix models
> #1.2.5,0.59249,-0.80007,-0.093974,422.83,-0.041682,0.086052,-0.99542,635.03,0.8045,0.5937,0.017636,-124.59
> view matrix models
> #1.2.5,-0.55241,-0.18832,-0.81202,821.52,0.81551,-0.32379,-0.47969,326.67,-0.17259,-0.9272,0.33245,634.12
> view matrix models
> #1.2.5,-0.48095,-0.28235,-0.83004,833.56,0.87151,-0.25732,-0.41744,266.94,-0.095723,-0.92415,0.36983,595.65
> view matrix models
> #1.2.5,-0.72086,-0.69185,0.041357,802.47,0.23193,-0.29702,-0.92628,648.97,0.65313,-0.65812,0.37457,245.38
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.5,-0.72086,-0.69185,0.041357,799.04,0.23193,-0.29702,-0.92628,664.97,0.65313,-0.65812,0.37457,231.9
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.5,-0.73967,-0.52841,-0.41674,883.03,0.59516,-0.22459,-0.77158,470.05,0.31411,-0.81875,0.48061,372.71
> select #1.2.2/B:332
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2.2/B:326-332
101 atoms, 101 bonds, 7 residues, 1 model selected
> select #1.2.2/B:340
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2.2/B:340-341
38 atoms, 38 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2.5/B
Alignment identifier is 1.2.5/B
> select #1.2.5/B:407
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2.5/B
682 atoms, 682 bonds, 43 residues, 1 model selected
> select #1.2.4/D:564
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2.4/D:562-564
53 atoms, 52 bonds, 3 residues, 1 model selected
> select #1.2.4/D:413
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2.4/D:408-413
107 atoms, 107 bonds, 6 residues, 1 model selected
> select #1.2.5/B:372-373
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #1.2.5/B:372-373
30 atoms, 29 bonds, 2 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.5,-0.73967,-0.52841,-0.41674,893.32,0.59516,-0.22459,-0.77158,455.25,0.31411,-0.81875,0.48061,358.19
> view matrix models
> #1.2.5,-0.73967,-0.52841,-0.41674,896.78,0.59516,-0.22459,-0.77158,456.87,0.31411,-0.81875,0.48061,360.1
> select #1.2.4/D:562
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2.4/D:562-564
53 atoms, 52 bonds, 3 residues, 1 model selected
> select #1.2.4/D:412-413
39 atoms, 38 bonds, 2 residues, 1 model selected
> select #1.2.4/D:408-413
107 atoms, 107 bonds, 6 residues, 1 model selected
> select #1.2.2/B:361
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2.2/B:361-364
63 atoms, 62 bonds, 4 residues, 1 model selected
> select #1.2.5/B:372
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.5,-0.94039,-0.31746,0.12203,739.75,-0.12718,-0.0045179,-0.99187,696.89,0.31543,-0.94826,-0.036127,552.5
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.5,-0.94039,-0.31746,0.12203,753.66,-0.12718,-0.0045179,-0.99187,698.21,0.31543,-0.94826,-0.036127,540.82
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.5,-0.86617,-0.35248,0.35427,672.59,-0.35868,-0.055147,-0.93183,778.09,0.34799,-0.93419,-0.07866,537.1
> view matrix models
> #1.2.5,-0.9425,-0.30605,0.13429,747.02,-0.17624,0.11373,-0.97775,671.39,0.28397,-0.9452,-0.16113,586.82
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.5,-0.9425,-0.30605,0.13429,749.34,-0.17624,0.11373,-0.97775,672.31,0.28397,-0.9452,-0.16113,587.61
> view matrix models
> #1.2.5,-0.9425,-0.30605,0.13429,756.4,-0.17624,0.11373,-0.97775,670.59,0.28397,-0.9452,-0.16113,587.17
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.5,-0.9692,-0.22494,-0.10024,806.18,0.036663,0.2707,-0.96197,539.5,0.24352,-0.93602,-0.25412,624.98
> view matrix models
> #1.2.5,-0.97098,-0.23183,-0.05872,797.11,-0.0090835,0.2811,-0.95963,551.18,0.23898,-0.93125,-0.27505,631
> undo
> view matrix models
> #1.2.5,-0.86702,-0.46698,-0.17381,873.37,0.016528,0.32167,-0.94671,524.94,0.498,-0.82369,-0.27118,503.97
> select #1.2.4/D:439
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2.4/D:428-439
175 atoms, 176 bonds, 12 residues, 1 model selected
> select sel @< 3.5
319 atoms, 280 bonds, 33 residues, 2 models selected
> select #1.2.4/D:433
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1.2.4/D:432-433
39 atoms, 40 bonds, 2 residues, 1 model selected
> select sel @< 3.5
93 atoms, 75 bonds, 14 residues, 1 model selected
> select #1.2.4/D:414
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.2.4/D:414-426
220 atoms, 219 bonds, 13 residues, 1 model selected
> select #1.2.4/D:427
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2.4/D:414-427
242 atoms, 241 bonds, 14 residues, 1 model selected
> select sel @< 3.5
475 atoms, 421 bonds, 53 residues, 4 models selected
> select #1.2.2/B:364
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2.2/B:364
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /D:442@C/D:443@N
2 atoms, 1 bond, 2 residues, 1 model selected
> ui tool show "Build Structure"
> ~bond sel
> select /D:442@C/D:443@N
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> split /D connected
Split RacGEF HH i.pdb 4 (#1.2.4) into 2 models
Deleting atomic symmetry model...
Chain information for RacGEF HH i.pdb 4 1 #1.2.4.1
---
Chain | Description
D | No description available
Chain information for RacGEF HH i.pdb 4 2 #1.2.4.2
---
Chain | Description
D | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2.4.1/D
Alignment identifier is 1.2.4.1/D
> sequence chain #1.2.4.2/D
Alignment identifier is 1.2.4.2/D
> hide #1.2.5 models
> show #1.2.5 models
> select #1.2.4.2/D:419
19 atoms, 18 bonds, 1 residue, 1 model selected
> view matrix models
> #1.2.4.2,0.20368,-0.69673,-0.68781,771.95,0.41196,0.6983,-0.58537,164.08,0.88815,-0.16412,0.42926,-59.654
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.4.2,0.20368,-0.69673,-0.68781,778.28,0.41196,0.6983,-0.58537,172.28,0.88815,-0.16412,0.42926,-50.4
> view matrix models
> #1.2.4.2,0.20368,-0.69673,-0.68781,778.79,0.41196,0.6983,-0.58537,173.04,0.88815,-0.16412,0.42926,-50.497
> select #1.2.4.1/D:444
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1.2.4.1/D:443-444
35 atoms, 35 bonds, 2 residues, 1 model selected
> select clear
> select #1.2.4.2/D:409
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.2.4.2/D:408-409
34 atoms, 34 bonds, 2 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.4.2,-0.45898,-0.74874,-0.47825,962.12,0.76013,-0.60961,0.2249,310.51,-0.45993,-0.2603,0.84894,320.76
> view matrix models
> #1.2.4.2,-0.48363,-0.028078,-0.87482,812.41,-0.70388,-0.5816,0.40779,748.64,-0.52024,0.81299,0.26151,104.96
> view matrix models
> #1.2.4.2,-0.44286,-0.01365,-0.89648,799.49,-0.76496,-0.51579,0.38574,750.84,-0.46766,0.85661,0.21798,83.394
> view matrix models
> #1.2.4.2,-0.47614,-0.024625,-0.87903,809.79,-0.72548,-0.55391,0.40849,744.95,-0.49696,0.83221,0.24587,94.281
> view matrix models
> #1.2.4.2,-0.62278,0.021537,-0.7821,811.34,-0.55737,-0.71373,0.42417,744.88,-0.54908,0.70008,0.4565,97.206
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.4.2,-0.62278,0.021537,-0.7821,804.06,-0.55737,-0.71373,0.42417,738.7,-0.54908,0.70008,0.4565,90.651
> view matrix models
> #1.2.4.2,-0.62278,0.021537,-0.7821,804.28,-0.55737,-0.71373,0.42417,738.76,-0.54908,0.70008,0.4565,91.499
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.4.2,-0.21322,-0.57032,-0.79327,900.07,0.61657,-0.70838,0.34356,355.27,-0.75788,-0.41585,0.50268,590.85
> view matrix models
> #1.2.4.2,-0.16577,-0.53152,-0.83066,880.23,0.21974,-0.84105,0.49432,497.15,-0.96137,-0.10059,0.25622,615.57
> view matrix models
> #1.2.4.2,-0.17634,-0.44199,-0.87952,864.1,0.18958,-0.89204,0.41027,554.7,-0.9659,-0.094394,0.2411,619.53
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.4.2,-0.17634,-0.44199,-0.87952,865.32,0.18958,-0.89204,0.41027,556.81,-0.9659,-0.094394,0.2411,617.61
> ui mousemode right "rotate selected models"
> select clear
> select #1.2.4.2/D:408
23 atoms, 23 bonds, 1 residue, 1 model selected
> view matrix models
> #1.2.4.2,-0.17424,-0.39982,-0.89988,854.42,0.18307,-0.91108,0.36935,579.71,-0.96754,-0.10038,0.23194,623.48
> view matrix models
> #1.2.4.2,0.0021206,-0.42828,-0.90364,805.72,-0.52015,-0.77225,0.36479,770.13,-0.85407,0.46926,-0.22441,504.79
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.4.2,0.0021206,-0.42828,-0.90364,806.59,-0.52015,-0.77225,0.36479,766.67,-0.85407,0.46926,-0.22441,505.53
> select #1.2.5/B:384
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.5,-0.0090154,-0.91265,-0.40865,793.68,-0.20673,0.40154,-0.8922,559.71,0.97836,0.076438,-0.19229,12.226
> view matrix models
> #1.2.5,0.1816,-0.88098,-0.43691,725.15,-0.25211,0.38774,-0.88662,578.46,0.95051,0.27116,-0.15169,-55.295
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.5,0.1816,-0.88098,-0.43691,724.08,-0.25211,0.38774,-0.88662,578.68,0.95051,0.27116,-0.15169,-53.972
> ui mousemode right "rotate selected models"
> ui mousemode right zoom
> select add #1.2.4
2570 atoms, 2588 bonds, 158 residues, 4 models selected
> select add #1.2.5
3235 atoms, 3254 bonds, 200 residues, 4 models selected
> show sel atoms
> ui mousemode right "translate selected atoms"
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.5,0.1816,-0.88098,-0.43691,727.32,-0.25211,0.38774,-0.88662,578.14,0.95051,0.27116,-0.15169,-57.05,#1.2.4,1,0,0,3.2366,0,1,0,-0.53605,0,0,1,-3.0779
> view matrix models
> #1.2.5,0.1816,-0.88098,-0.43691,727.75,-0.25211,0.38774,-0.88662,577.92,0.95051,0.27116,-0.15169,-56.371,#1.2.4,1,0,0,3.6643,0,1,0,-0.75418,0,0,1,-2.3982
> select clear
> ui mousemode right "rotate selected models"
Drag select of 1 atoms, 1 residues
> view matrix models
> #1.2.1,0.9999,0.014177,-0.00021564,-5.3904,-0.014178,0.99984,-0.010562,8.1624,6.5875e-05,0.010564,0.99994,-3.205,#1.2.5,0.1778,-0.87546,-0.44941,730.79,-0.26468,0.39731,-0.87869,576.19,0.9478,0.27518,-0.16107,-54.082
> view matrix models
> #1.2.1,0.99994,0.010864,-0.0020823,-3.631,-0.010894,0.99983,-0.014953,8.3649,0.0019195,0.014975,0.99989,-5.4342,#1.2.5,0.17687,-0.87728,-0.4462,730.78,-0.26825,0.39322,-0.87944,579.02,0.94697,0.27524,-0.16579,-52.41
> select clear
> select add #1.2.4.1
1993 atoms, 2010 bonds, 122 residues, 1 model selected
> select subtract #1.2.4.1
Nothing selected
> select add #1.2.4.2
560 atoms, 562 bonds, 35 residues, 1 model selected
> select subtract #1.2.4.2
Nothing selected
> hide #1.2.5 models
> show #1.2.5 models
> show #1.2.6 models
> hide #1.2.6 models
> show #1.2.7 models
> hide #1.2.7 models
> show #1.2.6 models
> hide #1.2.6 models
> hide #1.2.5 models
> show #1.2.5 models
> select add #1.2.5
682 atoms, 682 bonds, 43 residues, 1 model selected
> select clear
> select add #1.2.5
682 atoms, 682 bonds, 43 residues, 1 model selected
> view matrix models
> #1.2.5,0.18105,-0.86661,-0.46497,731.16,-0.19331,0.43221,-0.88081,540.34,0.96429,0.24936,-0.089269,-71.791
> undo
> view matrix models
> #1.2.5,0.18487,-0.85902,-0.4774,730.87,-0.14137,0.45747,-0.87791,513.02,0.97254,0.22979,-0.036867,-83.195
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.5,0.18487,-0.85902,-0.4774,729.8,-0.14137,0.45747,-0.87791,512.72,0.97254,0.22979,-0.036867,-78.952
> select #1.2.2/B:51
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
313 atoms, 313 bonds, 19 residues, 1 model selected
> select up
5900 atoms, 5965 bonds, 364 residues, 1 model selected
> style sel sphere
Changed 5900 atom styles
> select intersect C
1895 atoms, 1529 bonds, 364 residues, 1 model selected
> select clear
> color N cornflowerblue atoms
> color O hotpink atoms
> color :arg,hic,his,lys & sidechain & N blue atoms
> color :asp,glu & sidechain & O red atoms
> color S yellow atoms
> color P purple atoms
> hide H atoms
Drag select of 1 atoms, 5 residues
> select up
1780 atoms, 1799 bonds, 107 residues, 1 model selected
> select up
5900 atoms, 5965 bonds, 364 residues, 1 model selected
> select intersect C
1895 atoms, 1529 bonds, 364 residues, 1 model selected
> color (#1.2.2 & sel) orange
> select clear
Drag select of 6 atoms, 4 residues, 4 bonds
Drag select of 3 atoms, 2 residues
> select up
515 atoms, 518 bonds, 34 residues, 1 model selected
> select up
5900 atoms, 5965 bonds, 364 residues, 1 model selected
> hide sel cartoons
> select clear
> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH k.cxs"
——— End of log from Thu Apr 4 00:01:16 2024 ———
opened ChimeraX session
> select add #1.2.5
682 atoms, 682 bonds, 43 residues, 1 model selected
> select subtract #1.2.5
Nothing selected
> select add #1.2.4
2553 atoms, 2572 bonds, 157 residues, 3 models selected
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 1 time(s)]Coulombic values for RacGEF HH i.pdb 4 1_D SES surface
#1.2.4.1.1: minimum, -16.27, mean -0.08, maximum 17.11
Coulombic values for RacGEF HH i.pdb 4 2_D SES surface #1.2.4.2.1: minimum,
-11.14, mean 2.14, maximum 11.09
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2.2/B
Destroying pre-existing alignment with identifier 1.2.2/B
Alignment identifier is 1.2.2/B
> select /B:150@C
1 atom, 1 residue, 1 model selected
> select /B:80,84,85,97,100,150
135 atoms, 133 bonds, 6 residues, 1 model selected
> select #1.2.2/B:29@NZ
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:80,84,85,97,100,143,150,153
181 atoms, 177 bonds, 8 residues, 1 model selected
> style sel stick
Changed 181 atom styles
> select add #1.2.2
5900 atoms, 5965 bonds, 364 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select /B:80,84,85,97,100,143,150,153
181 atoms, 177 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 181 atom styles
> select clear
> select add #1.2.1
8002 atoms, 8101 bonds, 482 residues, 1 model selected
> style sel sphere
Changed 8002 atom styles
> select clear
> select add #1.2.2
5900 atoms, 5965 bonds, 364 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel surfaces
> hide sel atoms
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for RacGEF HH i.pdb 2_B SES surface #1.2.2.1: minimum,
-20.94, mean -2.42, maximum 11.99
To also show corresponding color key, enter the above coulombic command and
add key true
> select /B:80,84,85,97,100,143,150,153
181 atoms, 177 bonds, 8 residues, 1 model selected
> hide sel surfaces
> show sel atoms
> select #1.2.4.2/D:417@CB
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 2 models selected
> select up
242 atoms, 241 bonds, 14 residues, 2 models selected
> select up
560 atoms, 562 bonds, 35 residues, 2 models selected
> select up
560 atoms, 562 bonds, 35 residues, 2 models selected
> select up
2553 atoms, 2572 bonds, 157 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.4.1,1,0,0,-7.2763,0,1,0,-3.6842,0,0,1,-0.28209,#1.2.4.2,0.0021206,-0.42828,-0.90364,799.62,-0.52015,-0.77225,0.36479,762.9,-0.85407,0.46926,-0.22441,504.58
> select clear
> select add #1.2.1
8002 atoms, 8101 bonds, 482 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for RacGEF HH i.pdb 1_C SES surface #1.2.1.1: minimum,
-19.08, mean 0.18, maximum 21.66
To also show corresponding color key, enter the above coulombic command and
add key true
> select
19802 atoms, 20005 bonds, 1214 residues, 12 models selected
> show sel & #1.2.5#!1.2.1-2#!1.2.4.1-2 surfaces
> coulombic sel & #!1.2.1-2,5#!1.2.4.1-2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for RacGEF HH i.pdb 1_C SES surface #1.2.1.1: minimum,
-19.08, mean 0.18, maximum 21.66
Coulombic values for RacGEF HH i.pdb 2_B SES surface #1.2.2.1: minimum,
-20.94, mean -2.42, maximum 11.99
Coulombic values for RacGEF HH i.pdb 5_B SES surface #1.2.5.1: minimum,
-16.04, mean 0.55, maximum 11.51
Coulombic values for RacGEF HH i.pdb 4 1_D SES surface #1.2.4.1.1: minimum,
-16.27, mean -0.08, maximum 17.11
Coulombic values for RacGEF HH i.pdb 4 2_D SES surface #1.2.4.2.1: minimum,
-11.14, mean 2.14, maximum 11.09
To also show corresponding color key, enter the above coulombic command and
add key true
> view matrix models #1,1,0,0,1.4669,0,1,0,-0.77008,0,0,1,2.5333
> hide #!1.2.4 models
> show #1.2.3 models
> select clear
> select add #1.2.2
5900 atoms, 5965 bonds, 364 residues, 1 model selected
> show sel surfaces
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
89 atoms, 88 bonds, 6 residues, 1 model selected
> select up
2620 atoms, 2639 bonds, 166 residues, 1 model selected
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for RacGEF HH i.pdb 3_Q SES surface #1.2.3.1: minimum,
-14.78, mean -1.82, maximum 13.13
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!1.2.4 models
> select
19802 atoms, 20005 bonds, 1214 residues, 12 models selected
> select subtract #1.2.3
17182 atoms, 17366 bonds, 1048 residues, 17 models selected
> select add #1.2.3
19802 atoms, 20005 bonds, 1214 residues, 17 models selected
> select subtract #1.2.4
17249 atoms, 17433 bonds, 1057 residues, 15 models selected
> hide sel & #!1.2.1-3,5 surfaces
> select ~sel
2553 atoms, 2572 bonds, 157 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.4,0.99933,0.035643,0.0077973,-12.725,-0.035145,0.99777,-0.056694,30.887,-0.0098006,0.056382,0.99836,-20.713
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.4,0.99933,0.035643,0.0077973,-13.871,-0.035145,0.99777,-0.056694,28.267,-0.0098006,0.056382,0.99836,-20.572
> view matrix models
> #1.2.4,0.99933,0.035643,0.0077973,-13.283,-0.035145,0.99777,-0.056694,26.47,-0.0098006,0.056382,0.99836,-19.551
> view matrix models
> #1.2.4,0.99933,0.035643,0.0077973,-12.988,-0.035145,0.99777,-0.056694,25.363,-0.0098006,0.056382,0.99836,-19.388
> view matrix models
> #1.2.4,0.99933,0.035643,0.0077973,-13.241,-0.035145,0.99777,-0.056694,25.537,-0.0098006,0.056382,0.99836,-18.89
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.4,0.99877,0.025448,0.042611,-20.45,-0.020855,0.99426,-0.10495,37.802,-0.045037,0.10393,0.99356,-23.84
> view matrix models
> #1.2.4,0.99849,-0.0042037,0.054789,-12.682,0.01102,0.99213,-0.12472,34.081,-0.053834,0.12513,0.99068,-28.187
> view matrix models
> #1.2.4,0.99807,-0.045952,0.041784,8.1207,0.051791,0.98709,-0.15155,30.726,-0.03428,0.15342,0.98757,-45.051
> view matrix models
> #1.2.4,0.88728,-0.46122,0.0044742,221.63,0.46086,0.88689,0.032116,-132.86,-0.018781,-0.026434,0.99947,16.074
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.4,0.99807,-0.045952,0.041784,10.3,0.051791,0.98709,-0.15155,30.585,-0.03428,0.15342,0.98757,-47.988
> view matrix models
> #1.2.4,0.99807,-0.045952,0.041784,10.154,0.051791,0.98709,-0.15155,29.821,-0.03428,0.15342,0.98757,-48.064
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2.4,0.9957,-0.082638,0.041772,25.35,0.089008,0.97856,-0.18576,31.47,-0.025525,0.18868,0.98171,-62.992
> select
19802 atoms, 20005 bonds, 1214 residues, 12 models selected
> show sel & #!1.2.1-3,5#!1.2.4.1-2 cartoons
> show sel & #!1.2.1-3,5#!1.2.4.1-2 surfaces
> select clear
> select add #1.2.2
5900 atoms, 5965 bonds, 364 residues, 1 model selected
> select clear
> select /B:168@C/B:169@N
2 atoms, 1 bond, 2 residues, 1 model selected
> select add #1.2.2
5900 atoms, 5965 bonds, 364 residues, 2 models selected
> view matrix models
> #1.2.2,0.98592,0.008589,-0.16698,56.803,-0.0391,0.98283,-0.18031,79.031,0.16257,0.1843,0.96933,-108.22
> ui mousemode right "translate selected models"
> view matrix models
> #1.2.2,0.98592,0.008589,-0.16698,58.499,-0.0391,0.98283,-0.18031,81.35,0.16257,0.1843,0.96933,-111.28
> hide #!1.2.3 models
> select add #1.2.3
8520 atoms, 8604 bonds, 530 residues, 3 models selected
> select subtract #1.2.3
5900 atoms, 5965 bonds, 364 residues, 3 models selected
> show #!1.2.3 models
> hide #!1.2.3 models
> show #!1.2.3 models
> select clear
> select
19802 atoms, 20005 bonds, 1214 residues, 14 models selected
> hide sel & #!1.2.1-3,5#!1.2.4.1-2 surfaces
> select clear
> select #1.2.4.1/D:459
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2.4.1/D:459
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1.2.4.1/D:456
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2.4.1/D:456
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 22 atom styles
> select #1.2.3/Q
2620 atoms, 2639 bonds, 166 residues, 1 model selected
> show sel surfaces
> combine #1 name RacGEF
Remapping chain ID 'D' in RacGEF HH i.pdb 4 2 #1.2.4.2 to 'E'
Remapping chain ID 'B' in RacGEF HH i.pdb 5 #1.2.5 to 'F'
Remapping chain ID 'Q' in RacGEF HH i.pdb 6 #1.2.6 to 'R'
Remapping chain ID 'Q' in RacGEF HH i.pdb 7 #1.2.7 to 'S'
> hide #!1.2 models
> interfaces #2
10 buried areas: B D 1611, C D 1276, C B 1262, B Q 1147, C Q 1127, D E 985, C
E 848, B E 637, Q R 442, B F 313
> interfaces #2 areaCutoff 20
15 buried areas: B D 1611, C D 1276, C B 1262, B Q 1147, C Q 1127, D E 985, C
E 848, B E 637, Q R 442, B F 313, Q D 262, D F 171, Q E 70, Q S 25, R S 24
> ui tool show "Show Sequence Viewer"
[Repeated 1 time(s)]
> sequence chain #2/B
Alignment identifier is 2/B
> sequence chain #2/C
Alignment identifier is 2/C
> sequence chain #2/D
Alignment identifier is 2/D
> sequence chain #2/E
Alignment identifier is 2/E
> sequence chain #2/F
Alignment identifier is 2/F
> sequence chain #2/Q
Alignment identifier is 2/Q
> select /S
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> interfaces #2 areaCutoff 20
13 buried areas: B D 1611, C D 1276, C B 1262, B Q 1147, C Q 1127, D E 985, C
E 848, B E 637, Q R 442, B F 313, Q D 262, D F 171, Q E 70
> select /P
Nothing selected
> select /R
44 atoms, 46 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 44 atom styles
> delete atoms sel
> delete bonds sel
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH k.pdb"
Chain information for RacGEF HH k.pdb #3
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
Q | No description available
> hide #2#!3 atoms
> show #2#!3 cartoons
> ui tool show Matchmaker
> matchmaker #3/Q to #1.2.3/Q pairing ss
Parameters
---
Chain pairing | ss
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 RacGEF HH i.pdb 3, chain Q (#1.2.3) with RacGEF HH k.pdb, chain Q
(#3), sequence alignment score = 852.1
RMSD between 163 pruned atom pairs is 0.881 angstroms; (across all 166 pairs:
0.966)
> split #3 connected
Split RacGEF HH k.pdb (#3) into 14 models
Chain information for RacGEF HH k.pdb 1 #3.1
---
Chain | Description
C | No description available
Chain information for RacGEF HH k.pdb 2 #3.2
---
Chain | Description
B | No description available
Chain information for RacGEF HH k.pdb 3 #3.3
---
Chain | Description
E | No description available
Chain information for RacGEF HH k.pdb 4 #3.4
---
Chain | Description
Q | No description available
Chain information for RacGEF HH k.pdb 5 #3.5
---
Chain | Description
D | No description available
> select ::name="GTP"
88 atoms, 92 bonds, 2 residues, 2 models selected
> select ::name="MG"
2 atoms, 2 residues, 2 models selected
> select add #3.2
6584 atoms, 6648 bonds, 409 residues, 3 models selected
> select add ::name="GTP"
6672 atoms, 6740 bonds, 411 residues, 5 models selected
> select subtract #1.2.6
6628 atoms, 6694 bonds, 410 residues, 4 models selected
> select subtract #1.2.7
6627 atoms, 6694 bonds, 409 residues, 3 models selected
> select ~sel & ##selected
Nothing selected
> select add #3.3
2789 atoms, 2819 bonds, 177 residues, 1 model selected
> select add #3.7
2794 atoms, 2823 bonds, 178 residues, 2 models selected
> select add #3.14
2795 atoms, 2823 bonds, 179 residues, 3 models selected
> select ~sel & ##selected
Nothing selected
> select add #3.13
3 atoms, 2 bonds, 1 residue, 1 model selected
> select add #3.12
6 atoms, 4 bonds, 2 residues, 2 models selected
> select add #3.11
9 atoms, 6 bonds, 3 residues, 3 models selected
> select add #3.10
12 atoms, 8 bonds, 4 residues, 4 models selected
> select add #3.9
15 atoms, 10 bonds, 5 residues, 5 models selected
> select add #3
22614 atoms, 22842 bonds, 1398 residues, 15 models selected
> select subtract #3.3
19825 atoms, 20023 bonds, 1221 residues, 14 models selected
> select subtract #3.7
19820 atoms, 20019 bonds, 1220 residues, 13 models selected
> select subtract #3.14
19819 atoms, 20019 bonds, 1219 residues, 12 models selected
> hide sel cartoons
> delete atoms sel
> delete bonds sel
> Combine #3 close true name "Ras-GTP Q"
Unknown command: Combine #3 close true name "Ras-GTP Q"
> combine #3 close true name "Ras-GTP Q"
Remapping chain ID 'E' in RacGEF HH k.pdb 7 #3.7 to 'F'
> select ::name="GTP"
44 atoms, 46 bonds, 1 residue, 1 model selected
> show #2-3 atoms
> hide #2-3 atoms
> select clear
> select ::name="GTP"
44 atoms, 46 bonds, 1 residue, 1 model selected
> show #2-3 atoms
> show #1.2.6 models
> show #1.2.7 models
> hide #1.2.7 models
> hide #1.2.6 models
> show #1.2.6 models
> show #1.2.7 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.3 models
> hide #3 models
> show #3 models
> select ::name="GTP"
44 atoms, 46 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 44 atom styles
> show #!1.2.3 models
> ui tool show Matchmaker
> matchmaker #3/E to #1.2.3/Q pairing ss
Parameters
---
Chain pairing | ss
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 RacGEF HH i.pdb 3, chain Q (#1.2.3) with Ras-GTP Q, chain E (#3),
sequence alignment score = 338.2
RMSD between 110 pruned atom pairs is 1.092 angstroms; (across all 163 pairs:
2.867)
> select subtract #1.2.6
Nothing selected
> select add #3
2795 atoms, 2823 bonds, 179 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> select add #1.2.3
5415 atoms, 5462 bonds, 345 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> hide sel surfaces
> hide sel atoms
> select clear
> hide #3 models
> show #3 models
> hide #3 models
> select add #1.2.3
2620 atoms, 2639 bonds, 166 residues, 1 model selected
> hide (#!1.2.3 & sel) target a
> cartoon hide (#!1.2.3 & sel)
> delete atoms (#!1.2.3 & sel)
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/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 392, in _items_change
item_names = self._item_names()
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in <lambda>
filter_func=lambda c, ref=chain: c.structure != ref.structure)
^^^^^^^^^^^^^
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in
filter_func=lambda c, ref=chain: c.structure != ref.structure)
^^^^^^^^^^^^^
See log for complete Python traceback.
> delete bonds (#!1.2.3 & sel)
> show #3 models
> select add #3
2795 atoms, 2823 bonds, 179 residues, 1 model selected
> style sel sphere
Changed 2795 atom styles
> style sel sphere
Changed 2795 atom styles
> show sel atoms
> hide sel cartoons
> color sel forest green
> color N cornflowerblue atoms
> color O hotpink atoms
> color :arg,hic,his,lys & sidechain & N blue atoms
> color :asp,glu & sidechain & O red atoms
> color S yellow atoms
> color P purple atoms
> hide H atoms
> select clear
> hide #!1 models
> show #!1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2 models
> hide #!1.2.1 models
> hide #!1.2.2 models
> hide #!1.2.4 models
> hide #!1.2.5 models
> hide #1.2.6 models
> hide #1.2.7 models
> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH l.cxs"
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/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/tmckeithan/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/clipper/symmetry.py",
line 1170, in take_snapshot
'hall symbol': self.spacegroup.symbol_hall,
^^^^^^^^^^^^^^^
AttributeError: 'SymmetryManager' object has no attribute 'spacegroup'
The above exception was the direct cause of the following exception:
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/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x10bbe0310> ->
<chimerax.atomic.molobject.Residue object at 0x170778d10> 'GLU' ->
<chimerax.atomic.structure.AtomicStructure object at 0x17061d250> 'RacGEF HH
i.pdb 1' -> <chimerax.core.models.Model object at 0x1705e6ed0> 'RacGEF HH
i.pdb' -> <chimerax.clipper.symmetry.SymmetryManager object at 0x16ad14150>
'Data manager (RacGEF HH i.pdb)'
During handling of the above exception, another exception occurred:
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/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x10bbe0310> ->
<chimerax.atomic.molobject.Residue object at 0x170778d10> 'GLU' ->
<chimerax.atomic.structure.AtomicStructure object at 0x17061d250> 'RacGEF HH
i.pdb 1' -> <chimerax.core.models.Model object at 0x1705e6ed0> 'RacGEF HH
i.pdb' -> <chimerax.clipper.symmetry.SymmetryManager object at 0x16ad14150>
'Data manager (RacGEF HH i.pdb)': Error while saving session data for
'attribute registration' -> <chimerax.core.attributes.RegAttrManager object at
0x10bbe0310> -> <chimerax.atomic.molobject.Residue object at 0x170778d10>
'GLU' -> <chimerax.atomic.structure.AtomicStructure object at 0x17061d250>
'RacGEF HH i.pdb 1' -> <chimerax.core.models.Model object at 0x1705e6ed0>
'RacGEF HH i.pdb' -> <chimerax.clipper.symmetry.SymmetryManager object at
0x16ad14150> 'Data manager (RacGEF HH i.pdb)'
ValueError: error processing: 'attribute registration' -> -> 'GLU' -> 'RacGEF
HH i.pdb 1' -> 'RacGEF HH i.pdb' -> 'Data manager (RacGEF HH i.pdb)': Error
while saving session data for 'attribute registration' -> -> 'GLU' -> 'RacGEF
HH i.pdb 1' -> 'RacGEF HH i.pdb' -> 'Data manager (RacGEF HH i.pdb)'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
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/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/tmckeithan/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/clipper/symmetry.py",
line 1170, in take_snapshot
'hall symbol': self.spacegroup.symbol_hall,
^^^^^^^^^^^^^^^
AttributeError: 'SymmetryManager' object has no attribute 'spacegroup'
The above exception was the direct cause of the following exception:
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/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x10bbe0310> ->
<chimerax.atomic.molobject.Residue object at 0x170778d10> 'GLU' ->
<chimerax.atomic.structure.AtomicStructure object at 0x17061d250> 'RacGEF HH
i.pdb 1' -> <chimerax.core.models.Model object at 0x1705e6ed0> 'RacGEF HH
i.pdb' -> <chimerax.clipper.symmetry.SymmetryManager object at 0x16ad14150>
'Data manager (RacGEF HH i.pdb)'
During handling of the above exception, another exception occurred:
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/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x10bbe0310> ->
<chimerax.atomic.molobject.Residue object at 0x170778d10> 'GLU' ->
<chimerax.atomic.structure.AtomicStructure object at 0x17061d250> 'RacGEF HH
i.pdb 1' -> <chimerax.core.models.Model object at 0x1705e6ed0> 'RacGEF HH
i.pdb' -> <chimerax.clipper.symmetry.SymmetryManager object at 0x16ad14150>
'Data manager (RacGEF HH i.pdb)': Error while saving session data for
'attribute registration' -> <chimerax.core.attributes.RegAttrManager object at
0x10bbe0310> -> <chimerax.atomic.molobject.Residue object at 0x170778d10>
'GLU' -> <chimerax.atomic.structure.AtomicStructure object at 0x17061d250>
'RacGEF HH i.pdb 1' -> <chimerax.core.models.Model object at 0x1705e6ed0>
'RacGEF HH i.pdb' -> <chimerax.clipper.symmetry.SymmetryManager object at
0x16ad14150> 'Data manager (RacGEF HH i.pdb)'
ValueError: error processing: 'attribute registration' -> -> 'GLU' -> 'RacGEF
HH i.pdb 1' -> 'RacGEF HH i.pdb' -> 'Data manager (RacGEF HH i.pdb)': Error
while saving session data for 'attribute registration' -> -> 'GLU' -> 'RacGEF
HH i.pdb 1' -> 'RacGEF HH i.pdb' -> 'Data manager (RacGEF HH i.pdb)'
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGQ3LL/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 16 days, 3 hours, 51 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
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-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-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 (1)
comment:1 by , 19 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Clipper: 'SymmetryManager' object has no attribute 'spacegroup' |
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Reported by Tim McKeithan
I don't _think_ this is related to the earlier "'Sequence' object has no attribute 'structure'" error.