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Opened 2 years ago
Closed 2 years ago
#9498 closed defect (limitation)
Restore new session in old ChimeraX
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/jng994/Desktop/paborra/lr4_fb123_02s.cxs
Opened map_b1_lr4_fb1_3o21_17k_locref_sh as #1, grid size 239,241,483, pixel
0.728, shown at level 0.1, step 1, values float32
Opened map_b1_cast_04Bb1_3o23_17k_nu_sh as #3, grid size 239,241,483, pixel
0.728, shown at level 0.08, step 1, values float32
Opened map_b2_lr4_fb2_3o74_20k_locref_sh as #4, grid size 239,241,483, pixel
0.728, shown at level 0.1, step 1, values float32
Opened map_b2_cast_04Bb2_3o27_20k_nus_sh as #6, grid size 239,241,483, pixel
0.728, shown at level 0.07, step 1, values float32
Opened map_b3_lr4_fb3_4o00_19k_locref_sh as #7, grid size 239,241,483, pixel
0.728, shown at level 0.05, step 1, values float32
Opened map_b3_cast_04Bb3_3o53_19k_nu_sh as #9, grid size 239,241,483, pixel
0.728, shown at level 0.06, step 1, values float32
Log from Tue Aug 1 12:56:49 2023UCSF ChimeraX version: 1.7.dev202305042315
(2023-05-04)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/pmesa/Desktop/lr4_fb123/lr4_fb123_02s.cxs
Opened map_b1_lr4_fb1_3o21_17k_locref_sh as #1, grid size 239,241,483, pixel
0.728, shown at level 0.1, step 1, values float32
Opened map_b1_cast_04Bb1_3o23_17k_nu_sh as #3, grid size 239,241,483, pixel
0.728, shown at level 0.08, step 1, values float32
Opened map_b2_lr4_fb2_3o74_20k_locref_sh as #4, grid size 239,241,483, pixel
0.728, shown at level 0.1, step 1, values float32
Opened map_b2_cast_04Bb2_3o27_20k_nus_sh as #6, grid size 239,241,483, pixel
0.728, shown at level 0.07, step 1, values float32
Opened map_b3_lr4_fb3_4o00_19k_locref_sh as #7, grid size 239,241,483, pixel
0.728, shown at level 0.05, step 1, values float32
Opened map_b3_cast_04Bb3_3o53_19k_nu_sh as #9, grid size 239,241,483, pixel
0.728, shown at level 0.06, step 1, values float32
Log from Mon Jul 31 20:30:42 2023UCSF ChimeraX version: 1.7.dev202305042315
(2023-05-04)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb1_3o21_17k_J1695/lr4_fb1_3o21_17k_J1695_005_sls_mb20.ccp4
Opened lr4_fb1_3o21_17k_J1695_005_sls_mb20.ccp4 as #1, grid size 239,241,483,
pixel 0.728, shown at level 0.0992, step 2, values float32
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb1_3o21_17k_J1695/lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb
Chain information for lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb #2
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb2_3o74_20k_J1693/lr4_fb2_3o74_20k_J1693_006_sls_mb20.ccp4
Opened lr4_fb2_3o74_20k_J1693_006_sls_mb20.ccp4 as #3, grid size 239,241,483,
pixel 0.728, shown at level 0.072, step 2, values float32
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb2_3o74_20k_J1693/lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb
Chain information for lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb #4
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb3_4o00_19k_J1694/lr4_fb3_4o00_19k_J1694_005_sls_mb20.ccp4
Opened lr4_fb3_4o00_19k_J1694_005_sls_mb20.ccp4 as #5, grid size 239,241,483,
pixel 0.728, shown at level 0.0639, step 2, values float32
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb3_4o00_19k_J1694/lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb
Chain information for lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb #6
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> close session
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb1_3o21_17k_J1695/lr4_fb1_3o21_17k_J1695_005_sls_mb20.ccp4
Opened lr4_fb1_3o21_17k_J1695_005_sls_mb20.ccp4 as #1, grid size 239,241,483,
pixel 0.728, shown at level 0.0992, step 2, values float32
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb1_3o21_17k_J1695/lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb
Chain information for lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb #2
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_nu/cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4
Opened cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4 as #3, grid size
239,241,483, pixel 0.728, shown at level 0.138, step 2, values float32
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb2_3o74_20k_J1693/lr4_fb2_3o74_20k_J1693_006_sls_mb20.ccp4
Opened lr4_fb2_3o74_20k_J1693_006_sls_mb20.ccp4 as #4, grid size 239,241,483,
pixel 0.728, shown at level 0.072, step 2, values float32
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb2_3o74_20k_J1693/lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb
Chain information for lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb #5
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_nu/cast_04Bb2_3o27_20k_J1629_007_nus_mb20.ccp4
Opened cast_04Bb2_3o27_20k_J1629_007_nus_mb20.ccp4 as #6, grid size
239,241,483, pixel 0.728, shown at level 0.133, step 2, values float32
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb3_4o00_19k_J1694/lr4_fb3_4o00_19k_J1694_005_sls_mb20.ccp4
Opened lr4_fb3_4o00_19k_J1694_005_sls_mb20.ccp4 as #7, grid size 239,241,483,
pixel 0.728, shown at level 0.0639, step 2, values float32
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb3_4o00_19k_J1694/lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb
Chain information for lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb #8
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_nu/cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4
Opened cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4 as #9, grid size
239,241,483, pixel 0.728, shown at level 0.11, step 2, values float32
> hide atoms
> show cartoons
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> volume step 1 level 0.1
> show #!3 models
> hide #!1 models
> volume #3 level 0.08
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!6 models
> open
> D:/Docs/phenix_projects/cast/L5_locref/L5_msLC_a258_2o35_258k/L5_msLC_a258_2o35_258k_r14.pdb
Chain information for L5_msLC_a258_2o35_258k_r14.pdb #10
---
Chain | Description
2 | No description available
3 | No description available
C | No description available
D E F G H I J K L M N O P Q | No description available
> hide #10 atoms
> show #10 cartoons
> hide #!6 models
> hide #10 models
> show #10 models
> combine #10 name C_b1
> combine #10 name C_b2
> combine #10 name C_b3
> hide #10 models
> hide #12 models
> hide #13 models
> show #11 cartoons
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> color #11 #5500ffff
> color #11 blue
> color #12 blue
> color #13 blue
> ui tool show "Fit in Map"
> fitmap #11 inMap #3
Fit molecule C_b1 (#11) to map cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4
(#3) using 30566 atoms
average map value = 0.1318, steps = 68
shifted from previous position = 0.451
rotated from previous position = 0.77 degrees
atoms outside contour = 8786, contour level = 0.08
Position of C_b1 (#11) relative to cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4
(#3) coordinates:
Matrix rotation and translation
0.99992867 0.00343305 -0.01143973 2.30076649
-0.00350360 0.99997493 -0.00615264 2.56653273
0.01141832 0.00619228 0.99991564 -5.83459619
Axis 0.45911096 -0.85009737 -0.25797595
Axis point 503.75729464 0.00000000 182.74156770
Rotation angle (degrees) 0.77032897
Shift along axis 0.37968987
> volume #3 style mesh
> volume #3 style surface
> fitmap #11 inMap #3
Fit molecule C_b1 (#11) to map cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4
(#3) using 30566 atoms
average map value = 0.1318, steps = 40
shifted from previous position = 0.0121
rotated from previous position = 0.00475 degrees
atoms outside contour = 8792, contour level = 0.08
Position of C_b1 (#11) relative to cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4
(#3) coordinates:
Matrix rotation and translation
0.99992807 0.00344207 -0.01148980 2.32341805
-0.00351218 0.99997531 -0.00608718 2.55526260
0.01146857 0.00612709 0.99991546 -5.83144971
Axis 0.45374019 -0.85286614 -0.25833928
Axis point 501.23696864 0.00000000 184.01488525
Rotation angle (degrees) 0.77119800
Shift along axis 0.38142373
> fitmap #11 inMap #3
Fit molecule C_b1 (#11) to map cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4
(#3) using 30566 atoms
average map value = 0.1318, steps = 40
shifted from previous position = 0.00454
rotated from previous position = 0.00552 degrees
atoms outside contour = 8794, contour level = 0.08
Position of C_b1 (#11) relative to cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4
(#3) coordinates:
Matrix rotation and translation
0.99992807 0.00343105 -0.01149296 2.32491120
-0.00350228 0.99997475 -0.00618304 2.57897148
0.01147146 0.00622284 0.99991484 -5.85975271
Axis 0.45936957 -0.85033484 -0.25672994
Axis point 503.68698321 0.00000000 183.97392030
Rotation angle (degrees) 0.77369760
Shift along axis 0.37937813
> show #!6 models
> hide #!3 models
> show #12 models
> hide #11 models
> fitmap #12 inMap #6
Fit molecule C_b2 (#12) to map cast_04Bb2_3o27_20k_J1629_007_nus_mb20.ccp4
(#6) using 30566 atoms
average map value = 0.1327, steps = 60
shifted from previous position = 0.827
rotated from previous position = 1.34 degrees
atoms outside contour = 11792, contour level = 0.1
Position of C_b2 (#12) relative to cast_04Bb2_3o27_20k_J1629_007_nus_mb20.ccp4
(#6) coordinates:
Matrix rotation and translation
0.99977296 -0.00203703 -0.02121028 7.72839573
0.00183604 0.99995327 -0.00949132 2.00530768
0.02122862 0.00945022 0.99972998 -9.86383697
Axis 0.40616404 -0.91001835 0.08305044
Axis point 471.03428505 0.00000000 349.85065127
Rotation angle (degrees) 1.33612135
Shift along axis 0.49493361
> volume #6 style mesh
> volume #6 style surface
> show #!9 models
> hide #!6 models
> show #13 models
> hide #12 models
> fitmap #13 inMap #9
Fit molecule C_b3 (#13) to map cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4
(#9) using 30566 atoms
average map value = 0.08978, steps = 48
shifted from previous position = 1.05
rotated from previous position = 0.21 degrees
atoms outside contour = 18459, contour level = 0.1
Position of C_b3 (#13) relative to cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4
(#9) coordinates:
Matrix rotation and translation
0.99999654 0.00239315 -0.00109287 -0.65765108
-0.00239594 0.99999387 -0.00255445 0.48262693
0.00108675 0.00255706 0.99999614 -1.21539230
Axis 0.69679116 -0.29712256 -0.65284015
Axis point 0.00000000 426.65509987 210.22243973
Rotation angle (degrees) 0.21015493
Shift along axis 0.19181208
> fitmap #13 inMap #9
Fit molecule C_b3 (#13) to map cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4
(#9) using 30566 atoms
average map value = 0.08978, steps = 40
shifted from previous position = 0.00866
rotated from previous position = 0.0104 degrees
atoms outside contour = 18462, contour level = 0.1
Position of C_b3 (#13) relative to cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4
(#9) coordinates:
Matrix rotation and translation
0.99999635 0.00240337 -0.00123210 -0.61668846
-0.00240665 0.99999354 -0.00267127 0.52291640
0.00122567 0.00267422 0.99999567 -1.30424488
Axis 0.70340716 -0.32341564 -0.63294604
Axis point 0.00000000 435.37955227 221.65489655
Rotation angle (degrees) 0.21770788
Shift along axis 0.22261421
> volume #9 style mesh
> volume #9 style surface
> volume #9 level 0.08
> volume #9 level 0.06
> show #!6 models
> hide #!9 models
> volume #6 level 0.06
> volume #6 level 0.07
> show #!9 models
> show #!3 models
> hide #!6 models
> hide #!9 models
> save
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb123/lr4_fb123_01.cxs
> includeMaps true
> set bgColor white
> set bgColor black
> hide #13 models
> show #11 models
> show #!6 models
> show #12 models
> hide #!3 models
> hide #!6 models
> show #13 models
> hide #13 models
> hide #12 models
> show #12 models
> show #13 models
> hide #13 models
> hide #12 models
> show #12 models
> show #13 models
> show #!3 models
> show #!6 models
> hide #13 models
> mmaker #12 to #11 bring #6 pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match C_b2 #12/2 to C_b1 #11/2
Using Nucleic matrix instead of BLOSUM-62 to match C_b2 #12/3 to C_b1 #11/3
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker C_b1, chain 2 (#11) with C_b2, chain 2 (#12), sequence alignment
score = 100
Matchmaker C_b1, chain 3 (#11) with C_b2, chain 3 (#12), sequence alignment
score = 104
Matchmaker C_b1, chain C (#11) with C_b2, chain C (#12), sequence alignment
score = 53.3
Matchmaker C_b1, chain D (#11) with C_b2, chain D (#12), sequence alignment
score = 1329.4
Matchmaker C_b1, chain E (#11) with C_b2, chain E (#12), sequence alignment
score = 1326.4
Matchmaker C_b1, chain F (#11) with C_b2, chain F (#12), sequence alignment
score = 1325.8
Matchmaker C_b1, chain G (#11) with C_b2, chain G (#12), sequence alignment
score = 1325.8
Matchmaker C_b1, chain H (#11) with C_b2, chain H (#12), sequence alignment
score = 1325.2
Matchmaker C_b1, chain I (#11) with C_b2, chain I (#12), sequence alignment
score = 1328.8
Matchmaker C_b1, chain J (#11) with C_b2, chain J (#12), sequence alignment
score = 1327.6
Matchmaker C_b1, chain K (#11) with C_b2, chain K (#12), sequence alignment
score = 1325.2
Matchmaker C_b1, chain L (#11) with C_b2, chain L (#12), sequence alignment
score = 1324
Matchmaker C_b1, chain M (#11) with C_b2, chain M (#12), sequence alignment
score = 1327
Matchmaker C_b1, chain N (#11) with C_b2, chain N (#12), sequence alignment
score = 1326.4
Matchmaker C_b1, chain O (#11) with C_b2, chain O (#12), sequence alignment
score = 1325.2
Matchmaker C_b1, chain P (#11) with C_b2, chain P (#12), sequence alignment
score = 1326.4
Matchmaker C_b1, chain Q (#11) with C_b2, chain Q (#12), sequence alignment
score = 1322.8
RMSD between 3659 pruned atom pairs is 0.000 angstroms; (across all 3659
pairs: 0.000)
> hide #!6 models
> hide #!3 models
> hide #12 models
> show #12 models
> show #!3 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!3 models
> show #!9 models
> hide #12 models
> show #13 models
> mmaker #13 to #11 bring #9 pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match C_b3 #13/2 to C_b1 #11/2
Using Nucleic matrix instead of BLOSUM-62 to match C_b3 #13/3 to C_b1 #11/3
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker C_b1, chain 2 (#11) with C_b3, chain 2 (#13), sequence alignment
score = 100
Matchmaker C_b1, chain 3 (#11) with C_b3, chain 3 (#13), sequence alignment
score = 104
Matchmaker C_b1, chain C (#11) with C_b3, chain C (#13), sequence alignment
score = 53.3
Matchmaker C_b1, chain D (#11) with C_b3, chain D (#13), sequence alignment
score = 1329.4
Matchmaker C_b1, chain E (#11) with C_b3, chain E (#13), sequence alignment
score = 1326.4
Matchmaker C_b1, chain F (#11) with C_b3, chain F (#13), sequence alignment
score = 1325.8
Matchmaker C_b1, chain G (#11) with C_b3, chain G (#13), sequence alignment
score = 1325.8
Matchmaker C_b1, chain H (#11) with C_b3, chain H (#13), sequence alignment
score = 1325.2
Matchmaker C_b1, chain I (#11) with C_b3, chain I (#13), sequence alignment
score = 1328.8
Matchmaker C_b1, chain J (#11) with C_b3, chain J (#13), sequence alignment
score = 1327.6
Matchmaker C_b1, chain K (#11) with C_b3, chain K (#13), sequence alignment
score = 1325.2
Matchmaker C_b1, chain L (#11) with C_b3, chain L (#13), sequence alignment
score = 1324
Matchmaker C_b1, chain M (#11) with C_b3, chain M (#13), sequence alignment
score = 1327
Matchmaker C_b1, chain N (#11) with C_b3, chain N (#13), sequence alignment
score = 1326.4
Matchmaker C_b1, chain O (#11) with C_b3, chain O (#13), sequence alignment
score = 1325.2
Matchmaker C_b1, chain P (#11) with C_b3, chain P (#13), sequence alignment
score = 1326.4
Matchmaker C_b1, chain Q (#11) with C_b3, chain Q (#13), sequence alignment
score = 1322.8
RMSD between 3659 pruned atom pairs is 0.000 angstroms; (across all 3659
pairs: 0.000)
> hide #!9 models
> hide #!3 models
> hide #13 models
> show #13 models
> show #12 models
> hide #12 models
> hide #13 models
> hide #11 models
> show #!3 models
> show #!6 models
> show #!9 models
> hide #!6 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #13 models
> hide #!3 models
> show #!6 models
> show #!3 models
> save
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb123/lr4_fb123_01.cxs
> includeMaps true
> hide #13 models
> combine #2 cast_b1
Expected a keyword
> combine #2 name cast_b1
> hide #!3 models
> hide #!6 models
> hide #!9 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!14 models
> combine #5 name cast_b2
> hide #!5 models
> show #!14 models
> hide #!15 models
> hide #!14 models
> show #!8 models
> combine #8 name cast_b3
> show #!15 models
> show #!14 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> hide #!8 models
> show #!1 models
> show #!14 models
> hide #!1 models
> show #!3 models
> ui tool show "Fit in Map"
> fitmap #14 inMap #3
Fit molecule cast_b1 (#14) to map cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4
(#3) using 16478 atoms
average map value = 0.07375, steps = 96
shifted from previous position = 1.04
rotated from previous position = 1.17 degrees
atoms outside contour = 10262, contour level = 0.08
Position of cast_b1 (#14) relative to
cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4 (#3) coordinates:
Matrix rotation and translation
0.99989265 -0.01181117 -0.00867129 5.74552132
0.01193361 0.99982788 0.01420595 -6.58777238
0.00850201 -0.01430790 0.99986149 0.64897185
Axis -0.69737573 -0.42001474 0.58073635
Axis point 0.00000000 75.63807843 490.16369044
Rotation angle (degrees) 1.17141827
Shift along axis -0.86294405
> hide #!3 models
> show #!3 models
> volume #3 style mesh
> volume #3 style surface
> volume #3 style mesh
> volume #3 style surface
> fitmap #14 inMap #3
Fit molecule cast_b1 (#14) to map cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4
(#3) using 16478 atoms
average map value = 0.07375, steps = 96
shifted from previous position = 0.0115
rotated from previous position = 0.0135 degrees
atoms outside contour = 10251, contour level = 0.08
Position of cast_b1 (#14) relative to
cast_04Bb1_3o23_17k_J1635_005_nus_mb20.ccp4 (#3) coordinates:
Matrix rotation and translation
0.99989392 -0.01186850 -0.00844366 5.70823268
0.01198789 0.99982685 0.01423251 -6.61263510
0.00827328 -0.01433222 0.99986306 0.73537635
Axis -0.70013949 -0.40974286 0.58473539
Axis point 0.00000000 81.59250741 490.28221746
Rotation angle (degrees) 1.16887543
Shift along axis -0.85707851
> show #!6 models
> hide #!3 models
> show #!15 models
> hide #!14 models
> fitmap #15 inMap #6
Fit molecule cast_b2 (#15) to map cast_04Bb2_3o27_20k_J1629_007_nus_mb20.ccp4
(#6) using 16478 atoms
average map value = 0.05601, steps = 280
shifted from previous position = 0.785
rotated from previous position = 0.764 degrees
atoms outside contour = 11840, contour level = 0.07
Position of cast_b2 (#15) relative to
cast_04Bb2_3o27_20k_J1629_007_nus_mb20.ccp4 (#6) coordinates:
Matrix rotation and translation
0.99995797 0.00631761 -0.00664451 1.80657751
-0.00630196 0.99997733 0.00237370 2.00470043
0.00665935 -0.00233173 0.99997511 -2.04051772
Axis -0.24855556 -0.70275080 -0.66660441
Axis point 357.16425178 -0.00000000 251.01614627
Rotation angle (degrees) 0.54234477
Shift along axis -0.49762159
> fitmap #15 inMap #6
Fit molecule cast_b2 (#15) to map cast_04Bb2_3o27_20k_J1629_007_nus_mb20.ccp4
(#6) using 16478 atoms
average map value = 0.05601, steps = 404
shifted from previous position = 0.0115
rotated from previous position = 0.00809 degrees
atoms outside contour = 11841, contour level = 0.07
Position of cast_b2 (#15) relative to
cast_04Bb2_3o27_20k_J1629_007_nus_mb20.ccp4 (#6) coordinates:
Matrix rotation and translation
0.99995697 0.00645046 -0.00666733 1.76752561
-0.00643447 0.99997638 0.00241690 2.04479333
0.00668276 -0.00237389 0.99997485 -2.04284256
Axis -0.25000995 -0.69668092 -0.67240667
Axis point 356.19725860 0.00000000 244.32306123
Rotation angle (degrees) 0.54897091
Shift along axis -0.49284651
> show #!16 models
> hide #!15 models
> show #!9 models
> hide #!6 models
> fitmap #16 inMap #9
Fit molecule cast_b3 (#16) to map cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4
(#9) using 16478 atoms
average map value = 0.04434, steps = 64
shifted from previous position = 0.868
rotated from previous position = 0.661 degrees
atoms outside contour = 12768, contour level = 0.06
Position of cast_b3 (#16) relative to
cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4 (#9) coordinates:
Matrix rotation and translation
0.99998801 0.00470175 0.00137058 -2.19367853
-0.00471260 0.99995672 0.00802163 -1.04617625
-0.00133281 -0.00802799 0.99996689 2.52285784
Axis -0.85359643 0.14377909 -0.50070021
Axis point 0.00000000 342.29948763 140.49150161
Rotation angle (degrees) 0.53865581
Shift along axis 0.45890244
> fitmap #16 inMap #9
Fit molecule cast_b3 (#16) to map cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4
(#9) using 16478 atoms
average map value = 0.04434, steps = 48
shifted from previous position = 0.017
rotated from previous position = 0.0056 degrees
atoms outside contour = 12761, contour level = 0.06
Position of cast_b3 (#16) relative to
cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4 (#9) coordinates:
Matrix rotation and translation
0.99998836 0.00464790 0.00129755 -2.16308617
-0.00465821 0.99995668 0.00805803 -1.07352143
-0.00126004 -0.00806398 0.99996669 2.49367790
Axis -0.85800998 0.13611450 -0.49526935
Axis point 0.00000000 337.80566638 143.05960704
Rotation angle (degrees) 0.53830211
Shift along axis 0.47478546
> fitmap #16 inMap #9
Fit molecule cast_b3 (#16) to map cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4
(#9) using 16478 atoms
average map value = 0.04434, steps = 44
shifted from previous position = 0.00808
rotated from previous position = 0.00483 degrees
atoms outside contour = 12760, contour level = 0.06
Position of cast_b3 (#16) relative to
cast_04Bb3_3o53_19k_J1632_006_nus_mb20.ccp4 (#9) coordinates:
Matrix rotation and translation
0.99998839 0.00465140 0.00125880 -2.15209095
-0.00466131 0.99995727 0.00798318 -1.05306286
-0.00122162 -0.00798895 0.99996734 2.46382593
Axis -0.85621085 0.13296664 -0.49922224
Axis point 0.00000000 337.35917213 141.58792703
Rotation angle (degrees) 0.53441801
Shift along axis 0.47262470
> save
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb123/lr4_fb123_01.cxs
> includeMaps true
> hide #!16 models
> hide #!9 models
> show #!14 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!3 models
> mmaker #2 to #14 bring #1 pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb #2/2 to cast_b1 #14/2
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb #2/3 to cast_b1 #14/3
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb #2/4 to cast_b1 #14/4
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb #2/5 to cast_b1 #14/5
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb #2/6 to cast_b1 #14/6
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb #2/7 to cast_b1 #14/7
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker cast_b1, chain 2 (#14) with
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb, chain 2 (#2), sequence alignment
score = 60
Matchmaker cast_b1, chain 3 (#14) with
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb, chain 3 (#2), sequence alignment
score = 184
Matchmaker cast_b1, chain 4 (#14) with
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb, chain 4 (#2), sequence alignment
score = 104
Matchmaker cast_b1, chain 5 (#14) with
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb, chain 5 (#2), sequence alignment
score = 104
Matchmaker cast_b1, chain 6 (#14) with
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb, chain 6 (#2), sequence alignment
score = 192
Matchmaker cast_b1, chain 7 (#14) with
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb, chain 7 (#2), sequence alignment
score = 60
Matchmaker cast_b1, chain R (#14) with
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb, chain R (#2), sequence alignment
score = 2593.5
Matchmaker cast_b1, chain S (#14) with
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb, chain S (#2), sequence alignment
score = 2578.9
Matchmaker cast_b1, chain T (#14) with
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb, chain T (#2), sequence alignment
score = 1548.3
Matchmaker cast_b1, chain U (#14) with
lr4_fb1_3o21_17k_J1695_005_sls_mb20_r02.pdb, chain U (#2), sequence alignment
score = 1556.5
RMSD between 1776 pruned atom pairs is 0.000 angstroms; (across all 1776
pairs: 0.000)
> hide #!1 models
> hide #!3 models
> hide #!14 models
> hide #!2 models
> show #!15 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!4 models
> hide #!6 models
> show #!4 models
> show #!6 models
> mmaker #5 to #15 bring #4 pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb #5/2 to cast_b2 #15/2
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb #5/3 to cast_b2 #15/3
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb #5/4 to cast_b2 #15/4
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb #5/5 to cast_b2 #15/5
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb #5/6 to cast_b2 #15/6
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb #5/7 to cast_b2 #15/7
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker cast_b2, chain 2 (#15) with
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb, chain 2 (#5), sequence alignment
score = 60
Matchmaker cast_b2, chain 3 (#15) with
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb, chain 3 (#5), sequence alignment
score = 184
Matchmaker cast_b2, chain 4 (#15) with
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb, chain 4 (#5), sequence alignment
score = 104
Matchmaker cast_b2, chain 5 (#15) with
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb, chain 5 (#5), sequence alignment
score = 104
Matchmaker cast_b2, chain 6 (#15) with
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb, chain 6 (#5), sequence alignment
score = 192
Matchmaker cast_b2, chain 7 (#15) with
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb, chain 7 (#5), sequence alignment
score = 60
Matchmaker cast_b2, chain R (#15) with
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb, chain R (#5), sequence alignment
score = 2588.7
Matchmaker cast_b2, chain S (#15) with
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb, chain S (#5), sequence alignment
score = 2572.9
Matchmaker cast_b2, chain T (#15) with
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb, chain T (#5), sequence alignment
score = 1548.9
Matchmaker cast_b2, chain U (#15) with
lr4_fb2_3o74_20k_J1693_006_sls_mb20_r02.pdb, chain U (#5), sequence alignment
score = 1551.7
RMSD between 1776 pruned atom pairs is 0.000 angstroms; (across all 1776
pairs: 0.000)
> hide #!4 models
> hide #!6 models
> hide #!15 models
> show #!4 models
> show #!6 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!6 models
> hide #!4 models
> show #!15 models
> show #!14 models
> hide #!14 models
> hide #!15 models
> show #!16 models
> hide #!5 models
> show #!8 models
> show #!7 models
> show #!9 models
> hide #!9 models
> volume #7 level 0.08
> volume #7 level 0.06
> hide #!16 models
> volume #7 level 0.04
> volume #7 level 0.05
> show #!16 models
> hide #!7 models
> show #!7 models
> show #!9 models
> hide #!7 models
> show #!7 models
> mmaker #8 to #16 bring #7 pairing ss
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb #8/2 to cast_b3 #16/2
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb #8/3 to cast_b3 #16/3
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb #8/4 to cast_b3 #16/4
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb #8/5 to cast_b3 #16/5
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb #8/6 to cast_b3 #16/6
Using Nucleic matrix instead of BLOSUM-62 to match
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb #8/7 to cast_b3 #16/7
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker cast_b3, chain 2 (#16) with
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb, chain 2 (#8), sequence alignment
score = 60
Matchmaker cast_b3, chain 3 (#16) with
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb, chain 3 (#8), sequence alignment
score = 184
Matchmaker cast_b3, chain 4 (#16) with
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb, chain 4 (#8), sequence alignment
score = 104
Matchmaker cast_b3, chain 5 (#16) with
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb, chain 5 (#8), sequence alignment
score = 104
Matchmaker cast_b3, chain 6 (#16) with
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb, chain 6 (#8), sequence alignment
score = 192
Matchmaker cast_b3, chain 7 (#16) with
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb, chain 7 (#8), sequence alignment
score = 60
Matchmaker cast_b3, chain R (#16) with
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb, chain R (#8), sequence alignment
score = 2591.7
Matchmaker cast_b3, chain S (#16) with
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb, chain S (#8), sequence alignment
score = 2573.5
Matchmaker cast_b3, chain T (#16) with
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb, chain T (#8), sequence alignment
score = 1544.7
Matchmaker cast_b3, chain U (#16) with
lr4_fb3_4o00_19k_J1694_005_sls_mb20_r01.pdb, chain U (#8), sequence alignment
score = 1555.9
RMSD between 1776 pruned atom pairs is 0.000 angstroms; (across all 1776
pairs: 0.000)
> hide #!7 models
> hide #!9 models
> hide #!16 models
> show #!7 models
> hide #!8 models
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!9 models
> show #!16 models
> hide #!16 models
> show #!9 models
> show #!7 models
> hide #!8 models
> hide #!9 models
> hide #!7 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!5 models
> show #!8 models
> hide #!8 models
> hide #!5 models
> hide #!2 models
> show #!1 models
> show #!3 models
> show #!4 models
> show #!6 models
> show #!7 models
> show #!9 models
> volume showOutlineBox true
> volume showOutlineBox false
> hide #!4 models
> hide #!6 models
> hide #!7 models
> hide #!9 models
> hide #!3 models
> show #!4 models
> show #!7 models
> color #4 yellow models
> save
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb123/lr4_fb123_01.cxs
> includeMaps true
> show #10 models
> show #!2 models
> hide #!1 models
> show #!5 models
> hide #!4 models
> show #!8 models
> hide #!7 models
> save
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb123/lr4_fb123_01.cxs
> includeMaps true
> save
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb123/lr4_fb123_02s.cxs
> includeMaps true
> hide #!4 models
> close #11-13#14-16
> rename #10 L5_TnsC
> rename #1 lr4_fb1_3o21_17k_locref_sharp
> rename #2 lr4_fb1_r02
> rename #3 cast_04Bb1_3o23_17k_nu_sharp
> rename #4 lr4_fb2_3o74_20k_locref_sharp
> rename #1 lr4_fb1_3o21_17k_locref_sh
> rename #3 cast_04Bb1_3o23_17k_nu_sh
> rename #4 lr4_fb2_3o74_20k_locref_sh
> rename #1 map_b1_lr4_fb1_3o21_17k_locref_sh
> rename #2 mod_b1_lr4_fb1_r02
> rename #3 map_b1_cast_04Bb1_3o23_17k_nu_sh
> rename #4 map_b2_lr4_fb2_3o74_20k_locref_sh
> rename #5 mod_b2_lr4_fb2_r02
> rename #6 map_b2_cast_04Bb2_3o27_20k_nus_sh
> rename #7 map_b3_lr4_fb3_4o00_19k_locref_sh
> rename #8 mod_b3_lr4_fb3_r01
> rename #9 map_b3_cast_04Bb3_3o53_19k_nu_sh
> show #!1 models
> show #!3 models
> hide #!5 models
> hide #!8 models
> hide #10 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #!4 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> color #1 #c6c6c6ff models
> color #3 #c6c6c6ff models
> color #3 #919191ff models
> color #3 #7e7e7eff models
> hide #!1 models
> show #!1 models
> volume #1 level 0.12
> hide #!3 models
> volume #1 level 0.1
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!4 models
> color #4 #0096ffff models
> show #!5 models
> hide #!4 models
> color #6 #0096ffff models
> color #6 blue models
> show #!4 models
> show #!6 models
> hide #!4 models
> hide #!6 models
> show #!2 models
> show #!8 models
> show #!1 models
> hide #!2 models
> show #!4 models
> hide #!5 models
> show #!7 models
> hide #!8 models
> show #!6 models
> hide #!4 models
> show #!3 models
> hide #!6 models
> hide #!7 models
> show #!4 models
> hide #!3 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!6 models
> color #6 #aa00ffff models
> color #6 #0055ffff models
> color #6 #aa55ffff models
> color #6 #0055ffff models
> color #6 #aa00ffff models
> color #6 #0055ffff models
> hide #!6 models
> hide #!4 models
> show #!7 models
> show #!9 models
> color #7 #ffaa00ff models
> color #9 #ffaa00ff models
> color #9 #cc8800ff models
> color #9 #ff5500ff models
> color #9 red models
> hide #!7 models
> show #!6 models
> show #!3 models
> show #!7 models
> hide #!6 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> hide #!9 models
> show #!4 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!4 models
> show #!5 models
> hide #!7 models
> show #!8 models
> show #10 models
> save
> D:/Docs/phenix_projects/cast/locref4L/lr4_cast_locref/lr4_fb123/lr4_fb123_02s.cxs
> includeMaps true
——— End of log from Mon Jul 31 20:30:42 2023 ———
opened ChimeraX session
> combine #2 name b1_fitR
> combine #5 name b2_fitR
> hide #!8 models
> show #!8 models
> combine #8 name b3_fitR
> hide #!2 models
> hide #!5 models
> hide #!8 models
> hide #10 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> show #!12 models
> select #11-13/R
12138 atoms, 12342 bonds, 3 pseudobonds, 1515 residues, 6 models selected
> hide #!12 models
> hide #!13 models
> select #11-13/R:182-999999
8502 atoms, 8652 bonds, 3 pseudobonds, 1062 residues, 6 models selected
> show #!12 models
> show #!13 models
> ui tool show Matchmaker
> matchmaker #!12-13 & sel to #11 & sel
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 b1_fitR, chain R (#11) with b2_fitR, chain R (#12), sequence
alignment score = 1764.8
RMSD between 342 pruned atom pairs is 0.771 angstroms; (across all 353 pairs:
0.949)
Matchmaker b1_fitR, chain R (#11) with b3_fitR, chain R (#13), sequence
alignment score = 1730.6
RMSD between 331 pruned atom pairs is 0.814 angstroms; (across all 353 pairs:
1.048)
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> hide #!11 models
> show #!11 models
> show #!12 models
> hide #!11 models
> select #11-13/R:411-999999
2988 atoms, 3006 bonds, 3 pseudobonds, 375 residues, 6 models selected
> ui tool show Matchmaker
> show #!11 models
> matchmaker #!12-13 & sel to #11 & sel
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 b1_fitR, chain R (#11) with b2_fitR, chain R (#12), sequence
alignment score = 584.7
RMSD between 117 pruned atom pairs is 0.952 angstroms; (across all 124 pairs:
1.248)
Matchmaker b1_fitR, chain R (#11) with b3_fitR, chain R (#13), sequence
alignment score = 582.9
RMSD between 107 pruned atom pairs is 0.869 angstroms; (across all 124 pairs:
1.357)
> hide #!12 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!11 models
> show #!11 models
> select #11-13/R:411-501
2196 atoms, 2220 bonds, 273 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #!12-13 & sel to #11 & sel
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 b1_fitR, chain R (#11) with b2_fitR, chain R (#12), sequence
alignment score = 429.5
RMSD between 85 pruned atom pairs is 0.851 angstroms; (across all 91 pairs:
1.073)
Matchmaker b1_fitR, chain R (#11) with b3_fitR, chain R (#13), sequence
alignment score = 439.1
RMSD between 87 pruned atom pairs is 0.845 angstroms; (across all 91 pairs:
0.985)
> rename #11 b1_fitR411-501
> rename #12 b2_fitR411-501
> rename #13 b3_fitR411-501
> hide #!12 models
> hide #!13 models
> show #!12 models
> show #!13 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> select clear
> show #!2 models
> show #!5 models
> show #!8 models
> show #10 models
> show #!11 models
> show #!12 models
> hide #!8 models
> hide #!5 models
> hide #10 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!5 models
> hide #!2 models
> hide #!11 models
> hide #!12 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #10 models
> hide #!2 models
> hide #!5 models
> hide #!8 models
> show #!11 models
> show #!12 models
> show #!13 models
> hide #10 models
> show #!2 models
> show #!5 models
> show #!8 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> show #10 models
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> save /Users/pmesa/Desktop/lr4_fb123/lr4_fb123_02s.cxs includeMaps true
——— End of log from Tue Aug 1 12:56:49 2023 ———
opened ChimeraX session
> open /Users/jng994/Desktop/paborra/L5_allmaps_locrefcomp_02s.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
Failed opening file
/Users/jng994/Desktop/paborra/L5_allmaps_locrefcomp_02s.cxs:
'list' object has no attribute 'values'
> open /Users/jng994/Desktop/paborra/L5_allmaps_locrefcomp_02s.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore
self.reset()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 458, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 1004, in open
session.restore(stream, path=path, resize_window=resize_window)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 742, in restore
self.reset()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state
self.clear()
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
AttributeError: 'list' object has no attribute 'values'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
See log for complete Python traceback.
OpenGL version: 4.1 ATI-4.12.7
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
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: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5060.0.0,0)
OS Loader Version: 577~170
Software:
System Software Overview:
System Version: macOS 13.4.1 (c) (22F770820d)
Kernel Version: Darwin 22.5.0
Time since boot: 19 days, 4 hours, 29 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
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: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Restore new session in old ChimeraX |
comment:2 by , 2 years ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
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