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Opened 2 years ago
Closed 2 years ago
#9924 closed defect (fixed)
Unable to restore objects of NewerVersionQuery class
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | high | Milestone: | 1.7 |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.10.0-1050-oem-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202309300109 (2023-09-30 01:09:06 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.dev202309300109 (2023-09-30)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_updated.cxs
Log from Fri Oct 6 18:25:59 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\didny\\\OneDrive\\\Code\\\work\\\FectoFab_paper\\\figure_notebooks\\\F_mabs_session_comparison.cxs
Log from Fri Oct 6 16:48:39 2023
> lighting soft
> camera ortho
> ui mousemode right "translate selected models"
> lighting soft
> hide atoms
> set bgColor #ffffff00
> camera ortho
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
UCSF ChimeraX version: 1.7.dev202309300109 (2023-09-30)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> pen
> /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/RealSpaceRefine_7/Fecto2M_post_J772-coot-113_real_space_refined_007.pdb
Unknown command: pen
/media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/RealSpaceRefine_7/Fecto2M_post_J772-coot-113_real_space_refined_007.pdb
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/J783__localfilterZ.mrc
Opened J783__localfilterZ.mrc as #1, grid size 400,400,400, pixel 0.99, shown
at level 4.98e-05, step 2, values float32
> volume #2 step 1
No volumes specified
> volume #2 level 0.1124
No volumes specified
> transparency 90
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show cartoons
> style stick
Changed 0 atom styles
> view matrix camera
> -0.74823,0.042535,-0.66207,7.8769,0.66342,0.053621,-0.74632,-20.179,0.0037562,-0.99766,-0.06834,147.61
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
Invalid "models" argument: No models specified by "#2"
> zoom 0.45
> cartoon suppressBackboneDisplay false
> color #1/a #2e7fbd
> color #1/b #60a4d8
> color #1/c #9dc7e7
> color #1/A #c57e9e
> color #1/B #bc8ba7
> color #1/C #b094ab
> close #2
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #2
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> hide atoms
> lighting model #1,2 depthCue false
> hide #1/B,b,C,c cartoons
> show #2/A,B cartoons
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> matchmaker #2/B to #1/a:290-373
No 'to' model specified
> color #2/A #8a8a8a
> color #2/C #a3a3a3
> color #2/E #6d6d6d
> color #2/B #7ab497
> color #2/F #72a27e
> color #2/D #728f83
> view matrix camera
> -0.84574,0.026011,-0.53296,40.496,0.53352,0.025995,-0.84538,-47.511,-0.008135,-0.99933,-0.035864,165.23
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.039804,-0.96395,-0.2631,417.2,0.97181,0.023887,-0.23454,73.398,0.23237,-0.26502,0.93583,78.447
> zoom 0.9
> matchmaker #2/B to #1/a:290-373
No 'to' model specified
> show #1/A,a cartoons
> show #2/A,B cartoons
> hide ~:24-48,290-373 cartoons
> view matrix camera
> -0.76786,-0.36016,-0.52979,31.136,0.63944,-0.48073,-0.6,17.901,-0.038586,-0.7995,0.59944,405.36
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.039803,-0.96395,-0.2631,417.2,0.97181,0.023888,-0.23454,73.398,0.23237,-0.26502,0.93583,78.447
> zoom 2
[Repeated 1 time(s)]
> close session
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/RealSpaceRefine_7/Fecto2M_post_J772-coot-113_real_space_refined_007.pdb
Chain information for Fecto2M_post_J772-coot-113_real_space_refined_007.pdb #1
---
Chain | Description
A B C | No description available
a b | No description available
c | No description available
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/J783__localfilterZ.mrc
Opened J783__localfilterZ.mrc as #2, grid size 400,400,400, pixel 0.99, shown
at level 4.98e-05, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1124
> transparency 90
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show cartoons
> style stick
Changed 9894 atom styles
> view matrix camera
> -0.74823,0.042535,-0.66207,7.8769,0.66342,0.053621,-0.74632,-20.179,0.0037562,-0.99766,-0.06834,147.61
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
> zoom 0.45
> cartoon suppressBackboneDisplay false
> color #1/a #2e7fbd
> color #1/b #60a4d8
> color #1/c #9dc7e7
> color #1/A #c57e9e
> color #1/B #bc8ba7
> color #1/C #b094ab
> close #2
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #2
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> hide atoms
> lighting model #1,2 depthCue false
> hide #1/B,b,C,c cartoons
> show #2/A,B cartoons
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> matchmaker #2/B to #1/a:290-373
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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1)
with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence
alignment score = 372.7
RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs:
1.831)
> color #2/A #8a8a8a
> color #2/C #a3a3a3
> color #2/E #6d6d6d
> color #2/B #7ab497
> color #2/F #72a27e
> color #2/D #728f83
> view matrix camera
> -0.84574,0.026011,-0.53296,40.496,0.53352,0.025995,-0.84538,-47.511,-0.008135,-0.99933,-0.035864,165.23
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.039804,-0.96395,-0.2631,417.2,0.97181,0.023887,-0.23454,73.398,0.23237,-0.26502,0.93583,78.447
> zoom 0.9
> matchmaker #2/B to #1/a:290-373
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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1)
with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence
alignment score = 372.7
RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs:
1.831)
> color #2/C #9e0142
> color #2/D:110-137 #e95c47
> color #2/D:138-166 #fdbf6f
> color #2/D:167-288 #ffffbe
> color #2/D:229-377 #bfe5a0
> color #2/D:378-461 #54aead
> color #2/D:462-487 #5e4fa2
> color #1/B #9e0142
> color #1/b:110-137 #e95c47
> color #1/b:138-166 #fdbf6f
> color #1/b:167-288 #ffffbe
> color #1/b:229-377 #bfe5a0
> color #1/b:378-461 #54aead
> color #1/b:462-487 #5e4fa2
> close session
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/RealSpaceRefine_7/Fecto2M_post_J772-coot-113_real_space_refined_007.pdb
Chain information for Fecto2M_post_J772-coot-113_real_space_refined_007.pdb #1
---
Chain | Description
A B C | No description available
a b | No description available
c | No description available
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show cartoons
> style stick
Changed 9894 atom styles
> view matrix camera
> -0.74823,0.042535,-0.66207,7.8769,0.66342,0.053621,-0.74632,-20.179,0.0037562,-0.99766,-0.06834,147.61
> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0
Invalid "models" argument: No models specified by "#2"
> zoom 0.45
> cartoon suppressBackboneDisplay false
> color #1/a #2e7fbd
> color #1/b #60a4d8
> color #1/c #9dc7e7
> color #1/A #c57e9e
> color #1/B #bc8ba7
> color #1/C #b094ab
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #2
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> hide atoms
> lighting model #1,2 depthCue false
> hide #1/B,b,C,c cartoons
> show #2/A,B cartoons
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> matchmaker #2/B to #1/a:290-373
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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1)
with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence
alignment score = 372.7
RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs:
1.831)
> color #2/A #8a8a8a
> color #2/C #a3a3a3
> color #2/E #6d6d6d
> color #2/B #7ab497
> color #2/F #72a27e
> color #2/D #728f83
> view matrix camera
> -0.84574,0.026011,-0.53296,40.496,0.53352,0.025995,-0.84538,-47.511,-0.008135,-0.99933,-0.035864,165.23
> zoom 0.9
> matchmaker #2/B to #1/a:290-373
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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1)
with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence
alignment score = 372.7
RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs:
1.831)
> transparency #2/C-W 100 cartoons
> transparency #2 100 cartoons
> color #1/A #9e0142
> color #1/a:110-137 #e95c47
> color #1/a:138-166 #fdbf6f
> color #1/a:167-288 #ffffbe
> color #1/a:229-377 #bfe5a0
> color #1/a:378-461 #54aead
> color #1/a:462-487 #5e4fa2
> matchmaker #1/a:374-426 to #2/B:374-426
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 FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2) with
Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1), sequence
alignment score = 261.2
RMSD between 48 pruned atom pairs is 1.045 angstroms; (across all 53 pairs:
1.286)
> hide :24-48,290-373 cartoons
> hide :49-290 cartoons
> view matrix camera
> -0.98693,-0.058747,0.14997,233.46,-0.15529,0.099693,-0.98282,-136.45,0.042785,-0.99328,-0.10751,192.2
> matchmaker #2/B to #1/a:290-373
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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1)
with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence
alignment score = 372.7
RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs:
1.831)
> color #1/A #9e0142
> color #1/a:110-137 #e95c47
> color #1/a:138-166 #fdbf6f
> color #1/a:167-288 #ffffbe
> color #1/a:229-377 #bfe5a0
> color #1/a:374-461 #54aead
> color #1/a:462-487 #5e4fa2
> view matrix
view matrix camera
-0.90459,-0.41928,0.076824,206.19,0.006944,-0.19472,-0.98083,-135.96,0.4262,-0.88673,0.17907,288.7
view matrix models
#1,0.89496,0.093382,0.43626,-102.81,-0.22871,0.93562,0.26891,-9.4126,-0.38306,-0.34044,0.8587,169.45,#2,0.1565,-0.97608,0.1509,311.64,0.98083,0.17155,0.092386,-15.061,-0.11606,0.13355,0.98422,52.011
> close session
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/RealSpaceRefine_7/Fecto2M_post_J772-coot-113_real_space_refined_007.pdb
Chain information for Fecto2M_post_J772-coot-113_real_space_refined_007.pdb #1
---
Chain | Description
A B C | No description available
a b | No description available
c | No description available
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show cartoons
> style stick
Changed 9894 atom styles
> view matrix camera
> -0.74823,0.042535,-0.66207,7.8769,0.66342,0.053621,-0.74632,-20.179,0.0037562,-0.99766,-0.06834,147.61
> zoom 0.45
> cartoon suppressBackboneDisplay false
> color #1/a #2e7fbd
> color #1/b #60a4d8
> color #1/c #9dc7e7
> color #1/A #c57e9e
> color #1/B #bc8ba7
> color #1/C #b094ab
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #2
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> hide atoms
> lighting model #1,2 depthCue false
> hide #1/B,b,C,c cartoons
> show #2/A,B cartoons
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> matchmaker #2/B to #1/a:290-373
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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1)
with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence
alignment score = 372.7
RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs:
1.831)
> color #2/A #8a8a8a
> color #2/C #a3a3a3
> color #2/E #6d6d6d
> color #2/B #7ab497
> color #2/F #72a27e
> color #2/D #728f83
> view matrix camera
> -0.84574,0.026011,-0.53296,40.496,0.53352,0.025995,-0.84538,-47.511,-0.008135,-0.99933,-0.035864,165.23
> transparency #2 100 cartoons
> color #1/A #9e0142
> color #1/a:110-137 #e95c47
> color #1/a:138-166 #fdbf6f
> color #1/a:167-288 #ffffbe
> color #1/a:229-377 #bfe5a0
> color #1/a:374-461 #54aead
> color #1/a:462-487 #5e4fa2
> hide :24-48,290-373 cartoons
> hide :49-290 cartoons
> view matrix camera
> -0.90459,-0.41928,0.076824,206.19,0.006944,-0.19472,-0.98083,-135.96,0.4262,-0.88673,0.17907,288.7
> view matrix
view matrix camera
-0.99653,-0.031509,0.076824,202.17,-0.069875,-0.18189,-0.98083,-136.26,0.044881,-0.98281,0.17907,288.8
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.039804,-0.96395,-0.2631,417.2,0.97181,0.023887,-0.23454,73.398,0.23237,-0.26502,0.93583,78.447
> view matrix camera
> -0.99653,-0.031509,0.076824,202.17,-0.069875,-0.18189,-0.98083,-136.26,0.044881,-0.98281,0.17907,288.8
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_post_pre_trans_DII.png
> supersample 8 transparentBackground true height 2500
> matchmaker #1/a:374-426 to #2/B:374-426
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 FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2) with
Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1), sequence
alignment score = 261.2
RMSD between 48 pruned atom pairs is 1.045 angstroms; (across all 53 pairs:
1.286)
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_post_pre_trans_DII_local.png
> supersample 8 transparentBackground true height 2500
> show #1/A,a cartoons
> show #2/A,B
> show #2/A,B cartoons
> hide atoms
> matchmaker #2/B to #1/a:290-373
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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1)
with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence
alignment score = 372.7
RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs:
1.831)
> hide :24-48 cartoons
> hide :288-5000 cartoons
> view matrix camera
> -0.89502,-0.33808,0.29088,275.58,-0.3106,0.004444,-0.95052,-108.34,0.32006,-0.9411,-0.10898,160.67
[Repeated 1 time(s)]
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_post_pre_trans_DIII.png
> supersample 8 transparentBackground true height 2500
> matchmaker #2/B to #1/a:290-373
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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain a (#1)
with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain B (#2), sequence
alignment score = 372.7
RMSD between 71 pruned atom pairs is 0.782 angstroms; (across all 84 pairs:
1.831)
> matchmaker #2/A to #1/A
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 Fecto2M_post_J772-coot-113_real_space_refined_007.pdb, chain A (#1)
with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain A (#2), sequence
alignment score = 348.8
RMSD between 41 pruned atom pairs is 0.980 angstroms; (across all 72 pairs:
3.967)
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_post_pre_trans_DIII_aln.png
> supersample 8 transparentBackground true height 2500
> close session
> open
> /media/dzyla/Data/Data_exchange/pycharm/structures/structure_comparison/Fecto2M_post_super.pdb
Chain information for Fecto2M_post_super.pdb #1
---
Chain | Description
A B C | No description available
a b | No description available
c | No description available
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> open
> /media/dzyla/Data/Data_exchange/pycharm/structures/structure_comparison/Fecto2M_fab_super.pdb
Chain information for Fecto2M_fab_super.pdb #2
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> hide atoms
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show cartoons
> style stick
Changed 26083 atom styles
> zoom 0.45
> cartoon suppressBackboneDisplay false
> lighting model #1,2 depthCue false
> hide #2/G-L cartoons
> turn z -35 models #1-2
> move x 100 models #1
> color #1 #9dc7e7
> color #2 #7ab497
> select #2/ C:27,C:28,C:31,C:36,C:37,C:38,C:39,C:40,C:41
58 atoms, 57 bonds, 9 residues, 1 model selected
> select add #2/
> D:295,D:297,D:339,D:382,D:383,D:384,D:434,D:435,D:436,D:437,D:438,D:439
159 atoms, 156 bonds, 21 residues, 1 model selected
> select add #2/ F:121,F:122,F:123,F:124,F:125
188 atoms, 184 bonds, 26 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 188 atom styles
> select clear
> select #2/ D:418,D:434,D:435
25 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 25 atom styles
> select clear
> select add #1/ B:27,B:28,B:31,B:36,B:37,B:38,B:39,B:40,B:41
58 atoms, 57 bonds, 9 residues, 1 model selected
> select add #1/
> b:295,b:297,b:339,b:382,b:383,b:384,b:434,b:435,b:436,b:437,b:438,b:439
159 atoms, 156 bonds, 21 residues, 1 model selected
> select add #1/ c:121,c:122,c:123,c:124,c:125
159 atoms, 156 bonds, 21 residues, 1 model selected
> select add #1/ b:418,b:434,b:435
167 atoms, 163 bonds, 22 residues, 1 model selected
> color #2/ C:27,C:28,C:31,C:36,C:37,C:38,C:39,C:40,C:41 #6a64a5
> color #2/
> D:295,D:297,D:339,D:382,D:383,D:384,D:434,D:435,D:436,D:437,D:438,D:439
> #6a64a5
> color #2/ F:121,F:122,F:123,F:124,F:125 #6a64a5
> color #2/ D:418,D:434,D:435 #b188a7
> color #1/ B:27,B:28,B:31,B:36,B:37,B:38,B:39,B:40,B:41 #6a64a5
> color #1/
> b:295,b:297,b:339,b:382,b:383,b:384,b:434,b:435,b:436,b:437,b:438,b:439
> #6a64a5
> color #1/ c:121,c:122,c:123,c:124,c:125 #6a64a5
> color #1/ b:418,b:434,b:435 #b188a7
> show sel atoms
> style sel sphere
Changed 167 atom styles
> select clear
> view matrix camera
> 0.99309,-0.023442,0.115,291.87,-0.11595,-0.043809,0.99229,479.85,-0.018223,-0.99876,-0.046225,163.54
> transparancy 100 c
Unknown command: transparancy 100 c
> transparancy #1,2 100 c
Unknown command: transparancy #1,2 100 c
> transparency #1-2 100 cartoons
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/pre_post_epitope_trans.png
> supersample 8 transparentBackground true height 2500
> close session
> open 8DMJ
Summary of feedback from opening 8DMJ fetched from pdb
---
note | Fetching compressed mmCIF 8dmj from
http://files.rcsb.org/download/8dmj.cif
8dmj title:
Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...]
Chain information for 8dmj #1
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113
117-488
D H | antibody 1H1 heavy chain |
E L | antibody 1H1 light chain |
> open 8DMJ
8dmj title:
Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...]
Chain information for 8dmj #2
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113
117-488
D H | antibody 1H1 heavy chain |
E L | antibody 1H1 light chain |
> open 7UOP
Summary of feedback from opening 7UOP fetched from pdb
---
note | Fetching compressed mmCIF 7uop from
http://files.rcsb.org/download/7uop.cif
7uop title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more
info...]
Chain information for 7uop #3
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 4H3 heavy chain |
E F L | Fab 4H3 light chain |
Non-standard residues in 7uop #3
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPA
Summary of feedback from opening 7UPA fetched from pdb
---
note | Fetching compressed mmCIF 7upa from
http://files.rcsb.org/download/7upa.cif
7upa title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more
info...]
Chain information for 7upa #4
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480
B C H | Fab 1H8 heavy chain |
E F L | Fab 1H8 light chain |
Non-standard residues in 7upa #4
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPD
Summary of feedback from opening 7UPD fetched from pdb
---
note | Fetching compressed mmCIF 7upd from
http://files.rcsb.org/download/7upd.cif
7upd title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more
info...]
Chain information for 7upd #5
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474
B C H | Fab 2B12 heavy chain |
E F L | Fab 2B12 light chain |
Non-standard residues in 7upd #5
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPK
Summary of feedback from opening 7UPK fetched from pdb
---
note | Fetching compressed mmCIF 7upk from
http://files.rcsb.org/download/7upk.cif
7upk title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more
info...]
Chain information for 7upk #6
---
Chain | Description | UniProt
A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480
C E H | Fab 1A9 heavy chain |
F G L | Fab 1A9 light chain |
> open 7UP9
Summary of feedback from opening 7UP9 fetched from pdb
---
note | Fetching compressed mmCIF 7up9 from
http://files.rcsb.org/download/7up9.cif
7up9 title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more
info...]
Chain information for 7up9 #7
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
H | Fab 2D3 heavy chain |
L | Fab 2D3 light chain |
Non-standard residues in 7up9 #7
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPB
Summary of feedback from opening 7UPB fetched from pdb
---
note | Fetching compressed mmCIF 7upb from
http://files.rcsb.org/download/7upb.cif
7upb title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more
info...]
Chain information for 7upb #8
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 1H1 heavy chain |
E F L | Fab 1H1 light chain |
Non-standard residues in 7upb #8
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 8DG8
Summary of feedback from opening 8DG8 fetched from pdb
---
note | Fetching compressed mmCIF 8dg8 from
http://files.rcsb.org/download/8dg8.cif
8dg8 title:
Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more
info...]
Chain information for 8dg8 #9
---
Chain | Description
A B C | Fusion glycoprotein F0
H | 3x1 monoclonal antibody, VH region
L | 3x1 monoclonal antibody, VL region
Non-standard residues in 8dg8 #9
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 6T3F
Summary of feedback from opening 6T3F fetched from pdb
---
note | Fetching compressed mmCIF 6t3f from
http://files.rcsb.org/download/6t3f.cif
6t3f title:
Crystal structure Nipah virus fusion glycoprotein in complex with a
neutralising Fab fragment [more info...]
Chain information for 6t3f #10
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | FUS_NIPAV 26-482
H | Fab66 heavy chain |
L | Fab66 light chain |
Non-standard residues in 6t3f #10
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
6t3f mmCIF Assemblies
---
1| author_and_software_defined_assembly
> lighting soft
[Repeated 1 time(s)]
> hide atoms
> show cartoons
> close session
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> open 8DMJ
8dmj title:
Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...]
Chain information for 8dmj #2
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113
117-488
D H | antibody 1H1 heavy chain |
E L | antibody 1H1 light chain |
> open 8DMJ
8dmj title:
Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...]
Chain information for 8dmj #3
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113
117-488
D H | antibody 1H1 heavy chain |
E L | antibody 1H1 light chain |
> open 7UOP
7uop title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more
info...]
Chain information for 7uop #4
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 4H3 heavy chain |
E F L | Fab 4H3 light chain |
Non-standard residues in 7uop #4
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPA
7upa title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more
info...]
Chain information for 7upa #5
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480
B C H | Fab 1H8 heavy chain |
E F L | Fab 1H8 light chain |
Non-standard residues in 7upa #5
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPD
7upd title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more
info...]
Chain information for 7upd #6
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474
B C H | Fab 2B12 heavy chain |
E F L | Fab 2B12 light chain |
Non-standard residues in 7upd #6
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPK
7upk title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more
info...]
Chain information for 7upk #7
---
Chain | Description | UniProt
A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480
C E H | Fab 1A9 heavy chain |
F G L | Fab 1A9 light chain |
> open 7UP9
7up9 title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more
info...]
Chain information for 7up9 #8
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
H | Fab 2D3 heavy chain |
L | Fab 2D3 light chain |
Non-standard residues in 7up9 #8
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPB
7upb title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more
info...]
Chain information for 7upb #9
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 1H1 heavy chain |
E F L | Fab 1H1 light chain |
Non-standard residues in 7upb #9
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 8DG8
8dg8 title:
Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more
info...]
Chain information for 8dg8 #10
---
Chain | Description
A B C | Fusion glycoprotein F0
H | 3x1 monoclonal antibody, VH region
L | 3x1 monoclonal antibody, VL region
Non-standard residues in 8dg8 #10
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 6T3F
6t3f title:
Crystal structure Nipah virus fusion glycoprotein in complex with a
neutralising Fab fragment [more info...]
Chain information for 6t3f #11
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | FUS_NIPAV 26-482
H | Fab66 heavy chain |
L | Fab66 light chain |
Non-standard residues in 6t3f #11
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
6t3f mmCIF Assemblies
---
1| author_and_software_defined_assembly
> close session
> print('open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb')
Unknown command: print('open
/media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
coot-124_water_merged_F.pdb')
> print('open
> /home/dzyla/OneDrive/Code/F_fab/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009(1).pdb')
Unknown command: print('open
/home/dzyla/OneDrive/Code/F_fab/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009(1).pdb')
> force pdb_name in ['8DMJ', '8DMJ', '7UOP', '7UPA', '7UPD', '7UPK', '7UP9',
> '7UPB', '8DG8', '6T3F']:
force is provided by the uninstalled bundle SEQCROW versions 1.6.6 – 1.8.2
> print(f'open {pdb_name}')
Unknown command: print(f'open {pdb_name}')
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> open
> /home/dzyla/OneDrive/Code/F_fab/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009(1).pdb
No such file/path:
/home/dzyla/OneDrive/Code/F_fab/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009(1).pdb
> open 8DMJ
8dmj title:
Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...]
Chain information for 8dmj #2
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113
117-488
D H | antibody 1H1 heavy chain |
E L | antibody 1H1 light chain |
> open 8DMJ
8dmj title:
Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...]
Chain information for 8dmj #3
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113
117-488
D H | antibody 1H1 heavy chain |
E L | antibody 1H1 light chain |
> open 7UOP
7uop title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more
info...]
Chain information for 7uop #4
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 4H3 heavy chain |
E F L | Fab 4H3 light chain |
Non-standard residues in 7uop #4
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPA
7upa title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more
info...]
Chain information for 7upa #5
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480
B C H | Fab 1H8 heavy chain |
E F L | Fab 1H8 light chain |
Non-standard residues in 7upa #5
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPD
7upd title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more
info...]
Chain information for 7upd #6
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474
B C H | Fab 2B12 heavy chain |
E F L | Fab 2B12 light chain |
Non-standard residues in 7upd #6
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPK
7upk title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more
info...]
Chain information for 7upk #7
---
Chain | Description | UniProt
A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480
C E H | Fab 1A9 heavy chain |
F G L | Fab 1A9 light chain |
> open 7UP9
7up9 title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more
info...]
Chain information for 7up9 #8
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
H | Fab 2D3 heavy chain |
L | Fab 2D3 light chain |
Non-standard residues in 7up9 #8
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPB
7upb title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more
info...]
Chain information for 7upb #9
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 1H1 heavy chain |
E F L | Fab 1H1 light chain |
Non-standard residues in 7upb #9
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 8DG8
8dg8 title:
Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more
info...]
Chain information for 8dg8 #10
---
Chain | Description
A B C | Fusion glycoprotein F0
H | 3x1 monoclonal antibody, VH region
L | 3x1 monoclonal antibody, VL region
Non-standard residues in 8dg8 #10
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 6T3F
6t3f title:
Crystal structure Nipah virus fusion glycoprotein in complex with a
neutralising Fab fragment [more info...]
Chain information for 6t3f #11
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | FUS_NIPAV 26-482
H | Fab66 heavy chain |
L | Fab66 light chain |
Non-standard residues in 6t3f #11
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
6t3f mmCIF Assemblies
---
1| author_and_software_defined_assembly
> close session
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> open
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
Chain information for
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
#2
---
Chain | Description
A | No description available
C E G | No description available
D F | No description available
> open 8DMJ
8dmj title:
Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...]
Chain information for 8dmj #3
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113
117-488
D H | antibody 1H1 heavy chain |
E L | antibody 1H1 light chain |
> open 8DMJ
8dmj title:
Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...]
Chain information for 8dmj #4
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113
117-488
D H | antibody 1H1 heavy chain |
E L | antibody 1H1 light chain |
> open 7UOP
7uop title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more
info...]
Chain information for 7uop #5
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 4H3 heavy chain |
E F L | Fab 4H3 light chain |
Non-standard residues in 7uop #5
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPA
7upa title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more
info...]
Chain information for 7upa #6
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480
B C H | Fab 1H8 heavy chain |
E F L | Fab 1H8 light chain |
Non-standard residues in 7upa #6
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPD
7upd title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more
info...]
Chain information for 7upd #7
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474
B C H | Fab 2B12 heavy chain |
E F L | Fab 2B12 light chain |
Non-standard residues in 7upd #7
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPK
7upk title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more
info...]
Chain information for 7upk #8
---
Chain | Description | UniProt
A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480
C E H | Fab 1A9 heavy chain |
F G L | Fab 1A9 light chain |
> open 7UP9
7up9 title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more
info...]
Chain information for 7up9 #9
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
H | Fab 2D3 heavy chain |
L | Fab 2D3 light chain |
Non-standard residues in 7up9 #9
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPB
7upb title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more
info...]
Chain information for 7upb #10
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 1H1 heavy chain |
E F L | Fab 1H1 light chain |
Non-standard residues in 7upb #10
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 8DG8
8dg8 title:
Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more
info...]
Chain information for 8dg8 #11
---
Chain | Description
A B C | Fusion glycoprotein F0
H | 3x1 monoclonal antibody, VH region
L | 3x1 monoclonal antibody, VL region
Non-standard residues in 8dg8 #11
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 6T3F
6t3f title:
Crystal structure Nipah virus fusion glycoprotein in complex with a
neutralising Fab fragment [more info...]
Chain information for 6t3f #12
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | FUS_NIPAV 26-482
H | Fab66 heavy chain |
L | Fab66 light chain |
Non-standard residues in 6t3f #12
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
6t3f mmCIF Assemblies
---
1| author_and_software_defined_assembly
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> close session
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> open
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
Chain information for
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
#2
---
Chain | Description
A | No description available
C E G | No description available
D F | No description available
> open 8DMJ
8dmj title:
Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...]
Chain information for 8dmj #3
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113
117-488
D H | antibody 1H1 heavy chain |
E L | antibody 1H1 light chain |
> open 8DMJ
8dmj title:
Postfusion Nipah virus fusion protein in complex with Fab 1H1 [more info...]
Chain information for 8dmj #4
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0,Fusion glycoprotein F1 | FUS_NIPAV 26-113
117-488
D H | antibody 1H1 heavy chain |
E L | antibody 1H1 light chain |
> open 7UOP
7uop title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more
info...]
Chain information for 7uop #5
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 4H3 heavy chain |
E F L | Fab 4H3 light chain |
Non-standard residues in 7uop #5
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPA
7upa title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more
info...]
Chain information for 7upa #6
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480
B C H | Fab 1H8 heavy chain |
E F L | Fab 1H8 light chain |
Non-standard residues in 7upa #6
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPD
7upd title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more
info...]
Chain information for 7upd #7
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474
B C H | Fab 2B12 heavy chain |
E F L | Fab 2B12 light chain |
Non-standard residues in 7upd #7
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPK
7upk title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more
info...]
Chain information for 7upk #8
---
Chain | Description | UniProt
A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480
C E H | Fab 1A9 heavy chain |
F G L | Fab 1A9 light chain |
> open 7UP9
7up9 title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more
info...]
Chain information for 7up9 #9
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
H | Fab 2D3 heavy chain |
L | Fab 2D3 light chain |
Non-standard residues in 7up9 #9
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPB
7upb title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more
info...]
Chain information for 7upb #10
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 1H1 heavy chain |
E F L | Fab 1H1 light chain |
Non-standard residues in 7upb #10
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 8DG8
8dg8 title:
Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more
info...]
Chain information for 8dg8 #11
---
Chain | Description
A B C | Fusion glycoprotein F0
H | 3x1 monoclonal antibody, VH region
L | 3x1 monoclonal antibody, VL region
Non-standard residues in 8dg8 #11
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 6T3F
6t3f title:
Crystal structure Nipah virus fusion glycoprotein in complex with a
neutralising Fab fragment [more info...]
Chain information for 6t3f #12
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | FUS_NIPAV 26-482
H | Fab66 heavy chain |
L | Fab66 light chain |
Non-standard residues in 6t3f #12
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
6t3f mmCIF Assemblies
---
1| author_and_software_defined_assembly
> hide atoms
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show cartoons
> style stick
Changed 157624 atom styles
> zoom 0.45
> cartoon suppressBackboneDisplay false
> lighting model #1-100 depthCue false
> lighting soft
> mmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F
(#1), sequence alignment score = 1790.1
RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs:
0.837)
> mmaker #2 to #2
Must use different reference and match structures
> mmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain E (#2) with 8dmj, chain A (#3), sequence alignment score = 723.5
RMSD between 39 pruned atom pairs is 0.733 angstroms; (across all 252 pairs:
19.926)
> mmaker #4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain E (#2) with 8dmj, chain A (#4), sequence alignment score = 723.5
RMSD between 39 pruned atom pairs is 0.733 angstroms; (across all 252 pairs:
19.926)
> mmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7uop, chain G (#5), sequence alignment score = 900.1
RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs:
2.794)
> mmaker #6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upa, chain D (#6), sequence alignment score = 902.3
RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs:
3.175)
> mmaker #7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upd, chain A (#7), sequence alignment score = 885.6
RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs:
2.567)
> mmaker #8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upk, chain B (#8), sequence alignment score = 912.5
RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs:
2.604)
> mmaker #9 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7up9, chain G (#9), sequence alignment score = 902.5
RMSD between 269 pruned atom pairs is 1.254 angstroms; (across all 362 pairs:
2.596)
> mmaker #10 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upb, chain G (#10), sequence alignment score = 888.7
RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs:
2.541)
> mmaker #11 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 8dg8, chain C (#11), sequence alignment score = 578.5
RMSD between 93 pruned atom pairs is 0.983 angstroms; (across all 340 pairs:
5.826)
> mmaker #12 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 6t3f, chain F (#12), sequence alignment score = 911.4
RMSD between 263 pruned atom pairs is 1.279 angstroms; (across all 364 pairs:
2.713)
> hide #2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!8 models
> hide #!9 models
> hide #!11 models
> hide #!12 models
> hide #10 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!9 models
> show #10 models
> hide #10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!9 models
> show #!9 models
> show #2 models
> hide #1 models
> mmaker #9/G to #2/C
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
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7up9, chain G (#9), sequence alignment score = 898.3
RMSD between 265 pruned atom pairs is 1.251 angstroms; (across all 362 pairs:
2.613)
> hide #!12 models
> hide #!9 models
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> color #2/A,C,E #a7a7a7
> show #!9 models
> show #!11 models
> hide #!11 models
> show #10 models
> hide #10 models
> show #!12 models
> hide #!12 models
> hide #!9 models
> show #1 models
> hide #1 models
> color #2/A,B,C #a7a7a7
> color #2 bychain
> color #2/F,A,E #a7a7a7
> color #2/F,A,E #72a27e
> color #2 bychain
> color #2/F,A,E #72a27e
> color #2/G,D,C #a7a7a7
> color #2/F,A,E #72a27e
> color #2 bychain
> print('color #2/G,E,C #72a27e')
Unknown command: print('color #2/G,E,C #72a27e')
> color #2/G,E,C #72a27e
> color #2/F,D,A #a7a7a7
> color #2/G,E,C #72a27e
> show #1 models
> hide #1/A-F
> hide #1/A-F cartoons
> show #!3 models
> hide #2 models
> show #2 models
> hide #1/A-F,G,H,L,K cartoons
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #2 models
> hide #1 models
> hide #!3 models
> show #!3 models
> close session
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> open
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
Chain information for
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
#2
---
Chain | Description
A | No description available
C E G | No description available
D F | No description available
> open 7UOP
7uop title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more
info...]
Chain information for 7uop #3
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 4H3 heavy chain |
E F L | Fab 4H3 light chain |
Non-standard residues in 7uop #3
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPA
7upa title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more
info...]
Chain information for 7upa #4
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480
B C H | Fab 1H8 heavy chain |
E F L | Fab 1H8 light chain |
Non-standard residues in 7upa #4
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPD
7upd title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more
info...]
Chain information for 7upd #5
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474
B C H | Fab 2B12 heavy chain |
E F L | Fab 2B12 light chain |
Non-standard residues in 7upd #5
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPK
7upk title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more
info...]
Chain information for 7upk #6
---
Chain | Description | UniProt
A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480
C E H | Fab 1A9 heavy chain |
F G L | Fab 1A9 light chain |
> open 7UP9
7up9 title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more
info...]
Chain information for 7up9 #7
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
H | Fab 2D3 heavy chain |
L | Fab 2D3 light chain |
Non-standard residues in 7up9 #7
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPB
7upb title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more
info...]
Chain information for 7upb #8
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 1H1 heavy chain |
E F L | Fab 1H1 light chain |
Non-standard residues in 7upb #8
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 8DG8
8dg8 title:
Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more
info...]
Chain information for 8dg8 #9
---
Chain | Description
A B C | Fusion glycoprotein F0
H | 3x1 monoclonal antibody, VH region
L | 3x1 monoclonal antibody, VL region
Non-standard residues in 8dg8 #9
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 6T3F
6t3f title:
Crystal structure Nipah virus fusion glycoprotein in complex with a
neutralising Fab fragment [more info...]
Chain information for 6t3f #10
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | FUS_NIPAV 26-482
H | Fab66 heavy chain |
L | Fab66 light chain |
Non-standard residues in 6t3f #10
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
6t3f mmCIF Assemblies
---
1| author_and_software_defined_assembly
> hide atoms
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show cartoons
> style stick
Changed 135564 atom styles
> zoom 0.45
> cartoon suppressBackboneDisplay false
> lighting model #1-100 depthCue false
> lighting soft
> mmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F
(#1), sequence alignment score = 1790.1
RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs:
0.837)
> mmaker #2 to #2
Must use different reference and match structures
> mmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7uop, chain G (#3), sequence alignment score = 900.1
RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs:
2.794)
> mmaker #4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upa, chain D (#4), sequence alignment score = 902.3
RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs:
3.175)
> mmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upd, chain A (#5), sequence alignment score = 885.6
RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs:
2.567)
> mmaker #6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upk, chain B (#6), sequence alignment score = 912.5
RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs:
2.604)
> mmaker #7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7up9, chain G (#7), sequence alignment score = 902.5
RMSD between 269 pruned atom pairs is 1.254 angstroms; (across all 362 pairs:
2.596)
> mmaker #8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upb, chain G (#8), sequence alignment score = 888.7
RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs:
2.541)
> mmaker #9/G to #2/C
No molecules/chains to match specified
> color #2/F,D,A #a7a7a7
> color #2/G,E,C #72a27e
> hide #1/A-F,G,H,L,K cartoons
> hide #2,8#!3-7,9-10 target m
> hide #1 models
> show #1 models
> show #2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #8 models
> show #!9 models
> show #!10 models
> mmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F
(#1), sequence alignment score = 1790.1
RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs:
0.837)
> mmaker #2 to #2
Must use different reference and match structures
> mmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7uop, chain G (#3), sequence alignment score = 900.1
RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs:
2.794)
> mmaker #4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upa, chain D (#4), sequence alignment score = 902.3
RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs:
3.175)
> mmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upd, chain A (#5), sequence alignment score = 885.6
RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs:
2.567)
> mmaker #6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upk, chain B (#6), sequence alignment score = 912.5
RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs:
2.604)
> mmaker #7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7up9, chain G (#7), sequence alignment score = 902.5
RMSD between 269 pruned atom pairs is 1.254 angstroms; (across all 362 pairs:
2.596)
> mmaker #8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upb, chain G (#8), sequence alignment score = 888.7
RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs:
2.541)
> mmaker #9 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 8dg8, chain C (#9), sequence alignment score = 578.5
RMSD between 93 pruned atom pairs is 0.983 angstroms; (across all 340 pairs:
5.826)
> color #2/F,D,A #a7a7a7
> color #2/G,E,C #72a27e
> hide #1/A-F,G,H,L,K cartoons
> hide #8#!3-7,9-10 target m
> show #!10 models
> mmaker #10 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 6t3f, chain F (#10), sequence alignment score = 911.4
RMSD between 263 pruned atom pairs is 1.279 angstroms; (across all 364 pairs:
2.713)
> show #!9 models
> mmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F
(#1), sequence alignment score = 1790.1
RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs:
0.837)
> mmaker #2 to #2
Must use different reference and match structures
> mmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7uop, chain G (#3), sequence alignment score = 900.1
RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs:
2.794)
> mmaker #4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upa, chain D (#4), sequence alignment score = 902.3
RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs:
3.175)
> mmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upd, chain A (#5), sequence alignment score = 885.6
RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs:
2.567)
> mmaker #6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upk, chain B (#6), sequence alignment score = 912.5
RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs:
2.604)
> mmaker #7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7up9, chain G (#7), sequence alignment score = 902.5
RMSD between 269 pruned atom pairs is 1.254 angstroms; (across all 362 pairs:
2.596)
> mmaker #8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upb, chain G (#8), sequence alignment score = 888.7
RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs:
2.541)
> mmaker #9 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 8dg8, chain C (#9), sequence alignment score = 578.5
RMSD between 93 pruned atom pairs is 0.983 angstroms; (across all 340 pairs:
5.826)
> mmaker #9/G to #2/C
No molecules/chains to match specified
> color #2/F,D,A #a7a7a7
> color #2/G,E,C #72a27e
> hide #1/A-F,G,H,L,K cartoons
> hide #!9 models
> show #!9 models
> hide #!10 models
> mmaker #9/B to #2/C
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
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 8dg8, chain B (#9), sequence alignment score = 549.2
RMSD between 103 pruned atom pairs is 1.081 angstroms; (across all 335 pairs:
6.197)
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> show #!3 models
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> hide #1 models
> hide #!3 models
> hide #!9 models
> show #!3 models
> hide #2 models
> color #!3 bychain
> hide #3/G,A,D,C,F,B,E cartoons
> show #2 models
> show #1 models
> show #!4 models
> hide #!3 models
> hide #1 models
> hide #2 models
> show #1 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide ~#4/C,F cartoons
> show #!3 models
> show #2 models
> hide ~#4/A,B,D,E,G,H,I,J,K cartoons
> hide #4/A,B,D,E,G,H,I,J,K cartoons
> show #1-2#!3-4 cartoons
> hide #4/A,B,D,E,G,H,I,J,K cartoons
> hide #!3 models
> hide #2 models
> hide #1 models
> hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons
> show #1 models
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #2/F,D,A #a7a7a7
> color #2/G,E,C #72a27e
> hide #1/A-F,G,H,L,K cartoons
> hide #3/G,A,D,C,F,B,E cartoons
> hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons
[Repeated 1 time(s)]
> show #2 models
> show #!3 models
> show #!5 models
> show #1-2#!3-5 cartoons
> hide #!4 models
> hide #!3 models
> hide #2 models
> hide #1 models
> hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons
> show #2 models
> show #1 models
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #2/F,D,A #a7a7a7
> color #2/G,E,C #72a27e
> hide #1/A,C,D,F,G,H,K,L,M,N,O,P cartoons
> hide #3/G,A,D,C,F,B,E cartoons
> hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons
[Repeated 1 time(s)]
> hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons
> show #!3 models
> show #!4 models
> show #!6 models
> show #5-10 cartoons
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #1 models
> show #!5 models
> hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons
> show #!6 models
> hide #1/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons
> hide #6/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons
> hide #!5 models
> hide #!6 models
> show #!7 models
> show #1 models
> hide #1 models
> show #!3 models
> show #!4 models
> hide #!3 models
> mmaker #7/G to #2/C
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
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7up9, chain G (#7), sequence alignment score = 898.3
RMSD between 265 pruned atom pairs is 1.251 angstroms; (across all 362 pairs:
2.613)
> hide #7/A,B,C,D,F,I,J,K,M,N,O,P cartoons
> hide #7/A,B,C,D,F,G,I,J,K,M,N,O,P cartoons
> hide #!4 models
> hide #!7 models
> show #8 models
> hide #8/A,B,C,D,E,F,G,I,J,K,M,N,O,P cartoons
> hide #8 models
> show #!9 models
> hide #9/A,B,C,D,F,I,J,K,M,N,O,P cartoons
> hide #!9 models
> show #!10 models
> color #2#!10 bychain
> hide #2 models
> hide #10/A,B,C,D,F,I,J,K,M,N,O,P cartoons
> show #1 models
> hide #1 models
> show #2 models
> show #!3 models
> close session
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> open
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
Chain information for
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
#2
---
Chain | Description
A | No description available
C E G | No description available
D F | No description available
> open 7UOP
7uop title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more
info...]
Chain information for 7uop #3
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 4H3 heavy chain |
E F L | Fab 4H3 light chain |
Non-standard residues in 7uop #3
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPA
7upa title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more
info...]
Chain information for 7upa #4
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480
B C H | Fab 1H8 heavy chain |
E F L | Fab 1H8 light chain |
Non-standard residues in 7upa #4
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPD
7upd title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more
info...]
Chain information for 7upd #5
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474
B C H | Fab 2B12 heavy chain |
E F L | Fab 2B12 light chain |
Non-standard residues in 7upd #5
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPK
7upk title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more
info...]
Chain information for 7upk #6
---
Chain | Description | UniProt
A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480
C E H | Fab 1A9 heavy chain |
F G L | Fab 1A9 light chain |
> open 7UP9
7up9 title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more
info...]
Chain information for 7up9 #7
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
H | Fab 2D3 heavy chain |
L | Fab 2D3 light chain |
Non-standard residues in 7up9 #7
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPB
7upb title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more
info...]
Chain information for 7upb #8
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 1H1 heavy chain |
E F L | Fab 1H1 light chain |
Non-standard residues in 7upb #8
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 8DG8
8dg8 title:
Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more
info...]
Chain information for 8dg8 #9
---
Chain | Description
A B C | Fusion glycoprotein F0
H | 3x1 monoclonal antibody, VH region
L | 3x1 monoclonal antibody, VL region
Non-standard residues in 8dg8 #9
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 6T3F
6t3f title:
Crystal structure Nipah virus fusion glycoprotein in complex with a
neutralising Fab fragment [more info...]
Chain information for 6t3f #10
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | FUS_NIPAV 26-482
H | Fab66 heavy chain |
L | Fab66 light chain |
Non-standard residues in 6t3f #10
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
6t3f mmCIF Assemblies
---
1| author_and_software_defined_assembly
> hide atoms
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show cartoons
> style stick
Changed 135564 atom styles
> zoom 0.45
> cartoon suppressBackboneDisplay false
> lighting model #1-100 depthCue false
> lighting soft
> mmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F
(#1), sequence alignment score = 1790.1
RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs:
0.837)
> mmaker #2 to #2
Must use different reference and match structures
> mmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7uop, chain G (#3), sequence alignment score = 900.1
RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs:
2.794)
> mmaker #4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upa, chain D (#4), sequence alignment score = 902.3
RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs:
3.175)
> mmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upd, chain A (#5), sequence alignment score = 885.6
RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs:
2.567)
> mmaker #6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upk, chain B (#6), sequence alignment score = 912.5
RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs:
2.604)
> mmaker #7/G to #2/C
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
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7up9, chain G (#7), sequence alignment score = 898.3
RMSD between 265 pruned atom pairs is 1.251 angstroms; (across all 362 pairs:
2.613)
> mmaker #8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upb, chain G (#8), sequence alignment score = 888.7
RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs:
2.541)
> mmaker #9 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 8dg8, chain C (#9), sequence alignment score = 578.5
RMSD between 93 pruned atom pairs is 0.983 angstroms; (across all 340 pairs:
5.826)
> mmaker #9/B to #2/C
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
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 8dg8, chain B (#9), sequence alignment score = 549.2
RMSD between 103 pruned atom pairs is 1.081 angstroms; (across all 335 pairs:
6.197)
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #2/F,D,A #a7a7a7
> color #2/G,E,C #72a27e
> hide #1/A,C,D,F,G,H,K,L,M,N,O,P cartoons
> hide #3/G,A,D,C,F,B,E cartoons
> hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons
[Repeated 1 time(s)]
> hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons
> hide #6/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons
> hide #7/A,B,C,D,F,G,I,J,K,M,N,O,P cartoons
> hide #8/A,B,C,D,E,F,G,I,J,K,M,N,O,P cartoons
> hide #9/A,B,C,D,F,I,J,K,M,N,O,P cartoons
> hide #10/A,B,C,D,F,I,J,K,M,N,O,P cartoons
> close session
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-124_water_merged_F.pdb
Chain information for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
G I K | No description available
H J L | No description available
> open
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
Chain information for
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
#2
---
Chain | Description
A | No description available
C E G | No description available
D F | No description available
> open 7UOP
7uop title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 4H3 [more
info...]
Chain information for 7uop #3
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 4H3 heavy chain |
E F L | Fab 4H3 light chain |
Non-standard residues in 7uop #3
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPA
7upa title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H8 [more
info...]
Chain information for 7upa #4
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-480
B C H | Fab 1H8 heavy chain |
E F L | Fab 1H8 light chain |
Non-standard residues in 7upa #4
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPD
7upd title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12 [more
info...]
Chain information for 7upd #5
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-474
B C H | Fab 2B12 heavy chain |
E F L | Fab 2B12 light chain |
Non-standard residues in 7upd #5
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPK
7upk title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1A9 [more
info...]
Chain information for 7upk #6
---
Chain | Description | UniProt
A B D | Fusion glycoprotein F0 | FUS_NIPAV 1-480
C E H | Fab 1A9 heavy chain |
F G L | Fab 1A9 light chain |
> open 7UP9
7up9 title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3 [more
info...]
Chain information for 7up9 #7
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
H | Fab 2D3 heavy chain |
L | Fab 2D3 light chain |
Non-standard residues in 7up9 #7
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7UPB
7upb title:
Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 [more
info...]
Chain information for 7upb #8
---
Chain | Description | UniProt
A D G | Fusion glycoprotein F0 | FUS_NIPAV 1-475
B C H | Fab 1H1 heavy chain |
E F L | Fab 1H1 light chain |
Non-standard residues in 7upb #8
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 8DG8
8dg8 title:
Cryo-EM Structure of HPIV3 prefusion F trimer in complex with 3x1 Fab [more
info...]
Chain information for 8dg8 #9
---
Chain | Description
A B C | Fusion glycoprotein F0
H | 3x1 monoclonal antibody, VH region
L | 3x1 monoclonal antibody, VL region
Non-standard residues in 8dg8 #9
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 6T3F
6t3f title:
Crystal structure Nipah virus fusion glycoprotein in complex with a
neutralising Fab fragment [more info...]
Chain information for 6t3f #10
---
Chain | Description | UniProt
F | Fusion glycoprotein F0 | FUS_NIPAV 26-482
H | Fab66 heavy chain |
L | Fab66 light chain |
Non-standard residues in 6t3f #10
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
6t3f mmCIF Assemblies
---
1| author_and_software_defined_assembly
> hide atoms
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show cartoons
> style stick
Changed 135564 atom styles
> zoom 0.45
> cartoon suppressBackboneDisplay false
> lighting model #1-100 depthCue false
> lighting soft
> mmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain F
(#1), sequence alignment score = 1790.1
RMSD between 363 pruned atom pairs is 0.706 angstroms; (across all 372 pairs:
0.837)
> mmaker #2 to #2
Must use different reference and match structures
> mmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7uop, chain G (#3), sequence alignment score = 900.1
RMSD between 213 pruned atom pairs is 1.353 angstroms; (across all 362 pairs:
2.794)
> mmaker #4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upa, chain D (#4), sequence alignment score = 902.3
RMSD between 227 pruned atom pairs is 1.351 angstroms; (across all 367 pairs:
3.175)
> mmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upd, chain A (#5), sequence alignment score = 885.6
RMSD between 262 pruned atom pairs is 1.274 angstroms; (across all 361 pairs:
2.567)
> mmaker #6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7upk, chain B (#6), sequence alignment score = 912.5
RMSD between 227 pruned atom pairs is 1.243 angstroms; (across all 358 pairs:
2.604)
> mmaker #7/G to #2/C
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
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 7up9, chain G (#7), sequence alignment score = 898.3
RMSD between 265 pruned atom pairs is 1.251 angstroms; (across all 362 pairs:
2.613)
> mmaker #8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain G (#2) with 7upb, chain G (#8), sequence alignment score = 888.7
RMSD between 270 pruned atom pairs is 1.267 angstroms; (across all 362 pairs:
2.541)
> mmaker #9/B to #2/C
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
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 8dg8, chain B (#9), sequence alignment score = 549.2
RMSD between 103 pruned atom pairs is 1.081 angstroms; (across all 335 pairs:
6.197)
> mmaker #10 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 6t3f, chain F (#10), sequence alignment score = 911.4
RMSD between 263 pruned atom pairs is 1.279 angstroms; (across all 364 pairs:
2.713)
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #2/F,D,A #a7a7a7
> color #2/G,E,C #72a27e
> hide #1/A,C,D,F,G,H,K,L,M,N,O,P cartoons
> hide #3/G,A,D,C,F,B,E cartoons
> hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons
[Repeated 1 time(s)]
> hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons
> hide #6/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons
> hide #7/A,B,C,D,F,G,I,J,K,M,N,O,P cartoons
> hide #8/A,B,C,D,E,F,G,I,J,K,M,N,O,P cartoons
> hide #9/A,B,C,D,F,I,J,K,M,N,O,P cartoons
> hide #10/A,B,C,D,F,I,J,K,M,N,O,P cartoons
> hide #1 models
> show #1 models
> hide #1/A,B,C,D,E,F,G,H,K,L cartoons
> color #3 #d95847
> color #4 #3b4cc0
> color #5 #f18d6f
> color #6 #aac7fd
> color #7 #f7b89c
> color #8 #b40426
> color #9 #5d7ce6
> color #10 #82a6fb
> hide #!10 models
> hide #!9 models
> hide #8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #1 models
> show #!3 models
> show #!4 models
> define axis #2
Axis
'Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
#2/axis' centered at [132.07156997 131.9736923 125.48036225] with direction
[-0.00317055 -0.00116313 0.9999943 ], radius 23.6761, and length 107.201
> hide #!4 models
> hide #!3 models
> show #!3 models
> define axis #2 radius 5
Axis
'Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb
#2/axis' centered at [132.07156997 131.9736923 125.48036225] with direction
[-0.00317055 -0.00116313 0.9999943 ], radius 5, and length 107.201
> close #2.1
> define axis #3 @@display radius 5
Must specify a set of atoms or a plane
> define axis #3@@display radius 5
Must specify a set of atoms or a plane
> define axis #3 and @@display r 5
Expected a keyword
> define axis #3 radius 5
Axis '7uop #3/axis' centered at [132.58980133 132.06261726 141.02272846] with
direction [0.02033736 0.03261893 0.99926093], radius 5, and length 129.889
> close #3.2
> define axis #3/L,H radius 5
Axis '7uop #3/axis' centered at [134.19998443 171.79838611 174.79014516] with
direction [-0.54656499 0.54821979 -0.63302589], radius 5, and length 53.0916
> close #3.2
> define axis #3/H radius 5
Axis '7uop #3/axis' centered at [140.01239955 164.12249353 183.10141926] with
direction [0.6329338 0.59571875 0.49448354], radius 5, and length 52.3638
> show #!4 models
> define axis #4/C radius 5
Axis '7upa #4/axis' centered at [ 85.97369891 142.01804641 125.37514389] with
direction [-0.8230718 -0.56721815 -0.02857245], radius 5, and length 47.3939
> show #!5 models
> define axis #5/B radius 5
Axis '7upd #5/axis' centered at [ 95.87753356 155.20302377 87.46728033] with
direction [0.67325938 0.35084133 0.65087032], radius 5, and length 43.5673
> show #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> define axis #6/E radius 5
Axis '7upk #6/axis' centered at [ 88.49402984 115.34643043 136.2780465 ] with
direction [-0.75084234 -0.30557612 0.58554164], radius 5, and length 46.005
> close #3.2#4.2#5.2#6.2
axis to axis: distance: 21.887Å; angle: 81.6°
> open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb
Chain information for fab_af2.pdb #11
---
Chain | Description
A | No description available
B | No description available
> color #11 #dedddaff
> hide #!6 models
> show #1 models
> mmaker #11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain H (#1) with
fab_af2.pdb, chain A (#11), sequence alignment score = 608.4
RMSD between 117 pruned atom pairs is 0.513 angstroms; (across all 119 pairs:
0.605)
> mmaker #11 to #1/I
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 FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain I (#1) with
fab_af2.pdb, chain B (#11), sequence alignment score = 549.7
RMSD between 107 pruned atom pairs is 0.487 angstroms; (across all 107 pairs:
0.487)
> define axis #11 radius 5
Axis 'fab_af2.pdb #11/axis' centered at [134.92205552 199.21482183
116.20704463] with direction [0.29937749 0.93410689 0.19446706], radius 5, and
length 76.5755
> hide #1 models
> show #!3 models
> mmaker #11 to #3/L
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 7uop, chain L (#3) with fab_af2.pdb, chain B (#11), sequence
alignment score = 315.7
RMSD between 96 pruned atom pairs is 0.931 angstroms; (across all 106 pairs:
1.462)
> mmaker #11 to #1/I
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 FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb, chain I (#1) with
fab_af2.pdb, chain B (#11), sequence alignment score = 549.7
RMSD between 107 pruned atom pairs is 0.487 angstroms; (across all 107 pairs:
0.487)
> open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb
Chain information for fab_af2.pdb #12
---
Chain | Description
A | No description available
B | No description available
> mmaker #12 to #3/L
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 7uop, chain L (#3) with fab_af2.pdb, chain B (#12), sequence
alignment score = 315.7
RMSD between 96 pruned atom pairs is 0.931 angstroms; (across all 106 pairs:
1.462)
> define axis #12 radius 5
Axis 'fab_af2.pdb #12/axis' centered at [136.1808451 185.14787868
185.38873437] with direction [0.05507823 0.80887232 0.58539897], radius 5, and
length 76.5755
> open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb
Chain information for fab_af2.pdb #13
---
Chain | Description
A | No description available
B | No description available
> hide #!3 models
> show #!4 models
> mmaker #13 to #4/F
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 7upa, chain F (#4) with fab_af2.pdb, chain B (#13), sequence
alignment score = 367.3
RMSD between 104 pruned atom pairs is 0.737 angstroms; (across all 106 pairs:
0.883)
> define axis #13 radius 5
Axis 'fab_af2.pdb #13/axis' centered at [ 68.29352293 146.2888834
135.58720417] with direction [-0.99988945 -0.01085239 0.01016461], radius 5,
and length 76.5755
> hide #!4 models
> show #!5 models
> open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb
Chain information for fab_af2.pdb #14
---
Chain | Description
A | No description available
B | No description available
> mmaker #14 to #5/B
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 7upd, chain B (#5) with fab_af2.pdb, chain A (#14), sequence
alignment score = 330.8
RMSD between 102 pruned atom pairs is 0.943 angstroms; (across all 115 pairs:
1.567)
> define axis #14 radius 5
Axis 'fab_af2.pdb #14/axis' centered at [ 75.50786032 156.83255137
89.48139637] with direction [-0.8997972 0.17395918 -0.40012898], radius 5, and
length 76.5755
> open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb
Chain information for fab_af2.pdb #15
---
Chain | Description
A | No description available
B | No description available
> hide #!5 models
> show #!6 models
> mmaker #15 to #6/E
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 7upk, chain E (#6) with fab_af2.pdb, chain A (#15), sequence
alignment score = 334.2
RMSD between 105 pruned atom pairs is 0.880 angstroms; (across all 115 pairs:
1.604)
> define axis #15 radius 5
Axis 'fab_af2.pdb #15/axis' centered at [ 70.8730715 123.10044819
135.20212854] with direction [-0.98934821 -0.14290781 0.02770338], radius 5,
and length 76.5755
> hide #!6 models
> show #!7 models
> open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb
Chain information for fab_af2.pdb #16
---
Chain | Description
A | No description available
B | No description available
> mmaker #16 to #7/L
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 7up9, chain L (#7) with fab_af2.pdb, chain B (#16), sequence
alignment score = 351.5
RMSD between 104 pruned atom pairs is 0.765 angstroms; (across all 107 pairs:
1.035)
> define axis #16 radius 5
Axis 'fab_af2.pdb #16/axis' centered at [ 84.64639356 153.38938629
188.11426666] with direction [-0.61152451 0.06837696 0.78826542], radius 5,
and length 76.5755
> open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb
Chain information for fab_af2.pdb #17
---
Chain | Description
A | No description available
B | No description available
> hide #!7 models
> show #8 models
> mmaker #17 to #8/L
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 7upb, chain L (#8) with fab_af2.pdb, chain B (#17), sequence
alignment score = 379.7
RMSD between 102 pruned atom pairs is 0.747 angstroms; (across all 106 pairs:
1.014)
> define axis #17 radius 5
Axis 'fab_af2.pdb #17/axis' centered at [ 80.39113677 192.08979514
106.53048684] with direction [-0.57880148 0.81196359 -0.07552475], radius 5,
and length 76.5755
> open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb
Chain information for fab_af2.pdb #18
---
Chain | Description
A | No description available
B | No description available
> hide #8 models
> show #!9 models
> mmaker #18 to #9/L
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 8dg8, chain L (#9) with fab_af2.pdb, chain B (#18), sequence
alignment score = 199.7
RMSD between 72 pruned atom pairs is 1.058 angstroms; (across all 101 pairs:
2.403)
> define axis #18 radius 5
Axis 'fab_af2.pdb #18/axis' centered at [ 81.23556488 180.66688792
157.90592962] with direction [-0.6455834 0.76169205 0.05520224], radius 5, and
length 76.5755
> open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb
Chain information for fab_af2.pdb #19
---
Chain | Description
A | No description available
B | No description available
> hide #!9 models
> show #!10 models
> mmaker #19 to #10/L
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 6t3f, chain L (#10) with fab_af2.pdb, chain B (#19), sequence
alignment score = 637.6
RMSD between 89 pruned atom pairs is 0.827 angstroms; (across all 211 pairs:
7.541)
> define axis #19 radius 5
Axis 'fab_af2.pdb #19/axis' centered at [132.02301441 173.04240741
193.91243283] with direction [-0.34119941 -0.33010458 -0.88012154], radius 5,
and length 76.5755
> hide #!10 models
> hide #!11 models
> show #!11 models
> show #!10 models
> hide #!10 models
> hide #11-19 cartoons
axis #2.2 to axis #11.1: distance: 357.072Å; angle: 78.9°
axis #2.2 to axis #12.1: distance: 261.535Å; angle: 54.2°
axis #2.2 to axis #13.1: distance: 100.174Å; angle: 89.2°
axis #2.2 to axis #14.1: distance: 319.900Å; angle: 66.6°
axis #2.2 to axis #15.1: distance: 208.294Å; angle: 88.2°
axis #2.2 to axis #16.1: distance: 453.097Å; angle: 37.8°
axis #2.2 to axis #17.1: distance: 91.194Å; angle: 85.7°
axis #2.2 to axis #18.1: distance: 447.749Å; angle: 86.8°
axis #2.2 to axis #19.1: distance: 389.458Å; angle: 28.5°
> save
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_comaprison.pdb
> save
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison.cxs
> show #11-19 cartoons
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> hide #11-19 cartoons
> color #19.1 #dc8add
> color #11.1 #dc8add
> color #11.1 #c061cb
> color #11.1 #9141ac
> color #11.1 #813d9c
> color #19.1 #f66151
> color #12.1 #ffa348
> color #16.1 #f6d32d
> color #18.1 #f9f06b
> color #18.1 #e5a50a
> color #18.1 #c64600
> color #18.1 #a51d2d
> color #13.1 #99c1f1
> color #15.1 #1a5fb4
> color #14.1 #8ff0a4
> color #17.1 #26a269
> color #14.1 #bf5c40
> color #14.1 #4081bf
> color #14.1 #ab40bf
> color #14.1 #bf408d
> color #14.1 #bf4067
> color #19.1 #b340bf
> color #19.1 #b140bf
> color #19.1 #8a40bf
> color #19.1 #6d40bf
> color #19.1 #7040bf
> color #19.1 #b840bf
> color #19.1 #bf40aa
> color #19.1 #bf40a5
> color #19.1 #bf40a7
> color #19.1 #b640bf
> undo
[Repeated 3 time(s)]
> color #19.1 #f66151
> color #14.1 #8540bf
> color #14.1 #8745bf
> color #14.1 #773da9
> color #14.1 #8254a9
> color #14.1 #7d51a3
> color #14.1 #7e53a3
> color #14.1 #6f4990
> color #14.1 #704a90
> color #14.1 #4d3363
> color #14.1 #4d3263
> color #14.1 #4e3364
> color #14.1 #401564
> color #14.1 #541c84
> color #14.1 #551c85
> color #14.1 #572185
> color #14.1 #7c2fbe
> color #14.1 #8440be
> color #14.1 #974ad9
> color #14.1 #a262d9
> color #14.1 #ad69e7
> color #14.1 #b77ee7
> color #14.1 #c387f7
> color #14.1 #c488f7
> color #14.1 #c689f9
> color #14.1 #c68af9
> color #14.1 #cd9af9
> color #14.1 #d09cfc
> color #14.1 #d6a8fc
> color #14.1 #d8aaff
> color #14.1 #d7a9fe
> color #14.1 #cea2f4
> color #14.1 #cfa3f4
> color #14.1 #ca9fef
> color #17.1 #5640bf
> color #17.1 #8f40bf
> color #17.1 #a940bf
> color #17.1 #a640bf
> color #17.1 #7540bf
> color #17.1 #7340bf
> color #17.1 #7040bf
> color #17.1 #6d40bf
> color #17.1 #4140bf
> color #17.1 #4440bf
> color #17.1 #7840bf
> color #17.1 #9940bf
> color #17.1 #9f40bf
> color #17.1 #a440bf
> color #17.1 #ab40bf
> color #17.1 #b640bf
> color #17.1 #be40bf
> color #17.1 #bf40be
> color #17.1 #bf40bc
> color #17.1 #bf40b9
> color #17.1 #bf40af
> color #17.1 #bf40ac
> color #17.1 #bf409f
> color #17.1 #bf409a
> color #17.1 #bf4098
> color #17.1 #bf409a
> color #17.1 #bf499d
> color #17.1 #b24492
> color #17.1 #b22689
> color #17.1 #d02ca1
> color #17.1 #d0219d
> color #17.1 #d822a3
> color #17.1 #d81ba1
> color #17.1 #dd1ca5
> color #17.1 #dc1ca4
> color #17.1 #dc2aa8
> color #17.1 #d529a3
> color #17.1 #d52ba4
> color #17.1 #d32aa2
> save
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison.cxs
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_side.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top_angle.png
> supersample 8 transparentBackground true height 2500
> show #!3 models
> show #8 models
> show #!7 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #8 models
> hide #!7 models
> hide #!3 models
> show #!11 models
> show #!12 models
> show #!13 models
> show #!14 models
> show #!15 models
> show #!17 models
> show #!16 models
> show #!18 models
> show #!19 models
> show #!3 models
> hide #!3 models
> color #3 #ffbe6fff
> show #!3 models
> show #!10 models
> color #10 #d95847ff
> color #9 #c01c28ff
> show #!9 models
> show #!7 models
> color #7 #f8e45cff
> color #7 #f6d32dff
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top_noodle.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_side_noodle.png
> supersample 8 transparentBackground true height 2500
> hide #!7 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> show #!10 models
> show #!9 models
> hide #!9 models
> hide #!3 models
> hide #!10 models
> color #5 #99c1f1ff
> show #!5 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!5 models
> show #!4 models
> color #4 #99c1f1ff
> show #!6 models
> color #6 #1a5fb4ff
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top_face_noodle.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_side_face_noodle.png
> supersample 8 transparentBackground true height 2500
> hide #!6 models
> hide #!4 models
> show #1 models
> color #1 #813d9cff
> color #1 #613583ff
> color #1 #813d9cff
> color #1 #9141acff
> color #1 #6a64a5ff
> show #8 models
> color #8 #d32aa2ff
> show #!5 models
> color #5 #ca9fefff
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top_bottom_noodle.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_side_bottom_noodle.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison.cxs
——— End of log from Fri Oct 6 16:48:39 2023 ———
opened ChimeraX session
> show #!10 models
> show #!9 models
> show #!7 models
> show #!6 models
> show #!4 models
> show #!3 models
> open 7KI6
Summary of feedback from opening 7KI6 fetched from pdb
---
note | Fetching compressed mmCIF 7ki6 from
http://files.rcsb.org/download/7ki6.cif
7ki6 title:
Structure of the HeV F glycoprotein in complex with the 1F5 neutralizing
antibody [more info...]
Chain information for 7ki6 #20
---
Chain | Description | UniProt
A B E | Fusion glycoprotein F0 | F4YH70_9MONO
C F L | 1F5 Fab light chain |
D G H | 1F5 heavy chain |
Non-standard residues in 7ki6 #20
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> mmaker #20 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain E (#2) with 7ki6, chain A (#20), sequence alignment score = 869.1
RMSD between 267 pruned atom pairs is 1.325 angstroms; (across all 357 pairs:
2.520)
> hide atoms
> show cartoons
> hide #1/A,B,C,D,E,F,G,H,K,L cartoons
> hide #3/G,A,D,C,F,B,E cartoons
> hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons
[Repeated 1 time(s)]
> hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons
> hide #6/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons
> hide #7/A,B,C,D,F,G,I,J,K,M,N,O,P cartoons
> hide #8/A,B,C,D,E,F,G,I,J,K,M,N,O,P cartoons
> hide #9/A,B,C,D,F,I,J,K,M,N,O,P cartoons
> hide #10/A,B,C,D,F,I,J,K,M,N,O,P c\
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #8#!3-7,9-19 target m
> hide #1 target m
> show #1 models
> show #!6 models
> hide #!6 models
> hide #1/A,B,E,F,G,H,I,J,K,L,M,N,O,P cartoons
> hide #20/A,B,E,F,G,H,I,J,K,L,M,N,O,P cartoons
> open 7KI4
Summary of feedback from opening 7KI4 fetched from pdb
---
note | Fetching compressed mmCIF 7ki4 from
http://files.rcsb.org/download/7ki4.cif
7ki4 title:
Structure of the NiV F glycoprotein in complex with the 12B2 neutralizing
antibody [more info...]
Chain information for 7ki4 #21
---
Chain | Description | UniProt
A B E | Fusion glycoprotein F0 | FUS_NIPAV
C F L | 12B2 Fab light chain |
D G H | 12B2 heavy chain |
Non-standard residues in 7ki4 #21
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> hide #1#!2,20-21 atoms
> show #1#!2,20-21 cartoons
> mmaker #21 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain E (#2) with 7ki4, chain A (#21), sequence alignment score = 888.3
RMSD between 267 pruned atom pairs is 1.313 angstroms; (across all 368 pairs:
2.911)
> hide #1/A,B,C,D,E,F,G,H,K,L cartoons
> hide #3/G,A,D,C,F,B,E cartoons
> hide #4/A,B,D,E,G,H,I,J,K,L,M,N,O,P cartoons
[Repeated 1 time(s)]
> hide #5/A,C,D,F,G,H,I,J,K,L,M,N,O,P cartoons
> hide #6/A,B,C,D,F,H,I,J,K,L,M,N,O,P cartoons
> hide #7/A,B,C,D,F,G,I,J,K,M,N,O,P cartoons
> hide #8/A,B,C,D,E,F,G,I,J,K,M,N,O,P cartoons
> hide #9/A,B,C,D,F,I,J,K,M,N,O,P cartoons
> hide #10/A,B,C,D,F,I,J,K,M,N,O,P cartoons
> hide #20/A,B,E,F,G,H,I,J,K,L,M,N,O,P cartoons
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!15 models
> hide #!15 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #8 models
> hide #8 models
> show #!9 models
> hide #!9 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!3 models
> show #8 models
> hide #8 models
> show #!15 models
> hide #!15 models
> show #!10 models
> hide #21/A,B,E,F,G,H,I,J,K,L,M,N,O,P cartoons
> show #!9 models
> show #!7 models
> show #!15 models
> hide #!4 models
> hide #1 models
> hide #!15 models
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> color #21 #ff007fff
> color #21 #ff5500ff
> color #21 #d04500ff
> color #21 #c84300ff
> save
> C:/Users/didny/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_updated.cxs
> save
> C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_top_noodle.png
> supersample 8 transparentBackground true height 2500
> save
> C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_side_noodle.png
> supersample 8 transparentBackground true height 2500
> hide #!10 models
> hide #!9 models
> hide #!7 models
> hide #!3 models
> hide #!21 models
> show #!20 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!4 models
> color #20 #55ffffff
> color #20 #aaffffff
> color #20 #5555ffff
> color #20 #5500ffff
> color #20 #55007fff
> color #20 blue
> color #20 #00007fff
> color #20 #aaffffff
> color #20 cyan
> color #20 #aaffffff
> color #20 #8dd3d3ff
> save
> C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_top_noodle.png
> supersample 8 transparentBackground true height 2500
> save
> C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_side1_noodle.png
> supersample 8 transparentBackground true height 2500
> save
> C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_side2_noodle.png
> supersample 8 transparentBackground true height 2500
> save
> C:/Users/didny/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_top_noodle.png
> supersample 8 transparentBackground true height 2500
> hide #!6 models
> hide #!4 models
> open
> C:/Users/didny/OneDrive/Code/work/FectoFab_paper/figure_notebooks/structures_PDBs/fab_af2.pdb
Chain information for fab_af2.pdb #22
---
Chain | Description
A | No description available
B | No description available
> mmaker #22 to #20
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 7ki6, chain H (#20) with fab_af2.pdb, chain A (#22), sequence
alignment score = 800.3
RMSD between 113 pruned atom pairs is 0.602 angstroms; (across all 117 pairs:
1.363)
> mmaker #22 to #20/D
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 7ki6, chain D (#20) with fab_af2.pdb, chain A (#22), sequence
alignment score = 809.3
RMSD between 113 pruned atom pairs is 0.602 angstroms; (across all 117 pairs:
1.363)
> define axis #22 radius 5
Axis 'fab_af2.pdb #22/axis' centered at [ 73.44504807 134.30578164
152.24514275] with direction [-0.93683251 -0.18283826 0.29818623], radius 5,
and length 76.5755
> hide #!22 models
> show #!22 models
> close #22.1
> define axis #22/A-B radius 5
Axis 'fab_af2.pdb #22/axis' centered at [ 73.44504807 134.30578164
152.24514275] with direction [-0.93683251 -0.18283826 0.29818623], radius 5,
and length 76.5755
> close #22.1
> show #!21 models
> open E:/Downloads/fab_af2.pdb
Chain information for fab_af2.pdb #23
---
Chain | Description
A | No description available
B | No description available
> mmaker #23 to #21/D
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 7ki4, chain D (#21) with fab_af2.pdb, chain A (#23), sequence
alignment score = 682.2
RMSD between 112 pruned atom pairs is 0.745 angstroms; (across all 117 pairs:
1.608)
> define axis #23 radius 5
Axis 'fab_af2.pdb #23/axis' centered at [164.30463436 152.96821533
194.08491756] with direction [-0.57893742 -0.47128773 -0.66537158], radius 5,
and length 76.5755
> close #23.1
> save
> C:/Users/didny/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_updated.cxs
——— End of log from Fri Oct 6 18:25:59 2023 ———
opened ChimeraX session
> define axis #23 radius 5
Axis 'fab_af2.pdb #23/axis' centered at [164.30463499 152.96821592
194.08491844] with direction [-0.57893742 -0.47128773 -0.66537158], radius 5,
and length 76.5755
> color #23.1 #c84300
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #22 models
> show #22 models
> hide #!23 models
> show #!23 models
> hide #22 cartoons
> hide #21 cartoons
> hide #23 cartoons
> define axis #22 radius 5
Axis 'fab_af2.pdb #22/axis' centered at [ 73.44504695 134.30578133
152.24514318] with direction [-0.93683251 -0.18283825 0.29818622], radius 5,
and length 76.5755
> color #22.1 #8dd3d3
> hide #22 cartoons
> hide #20 cartoons
> show #!21 models
> show #!19 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #!13 models
> show #!12 models
> show #!11 models
> show #!10 models
> hide #!10 models
> hide #11-23 cartoons
> save
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_updated_linux.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x7f71a2b0a690>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, 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 "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x7f71a2b0a690>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_top.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_side1.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_side2.png
> supersample 8 transparentBackground true height 2500
> open 6TYS
6tys title:
A potent cross-neutralizing antibody targeting the fusion glycoprotein
inhibits Nipah virus and Hendra virus infection [more info...]
Chain information for 6tys #24
---
Chain | Description | UniProt
A B E | Fusion glycoprotein F0 | FUS_NIPAV 1-494
C F H | 5B3 antibody heavy chain |
D G L | 5B3 antibody light chain |
Non-standard residues in 6tys #24
---
BMA — beta-D-mannopyranose
MAN — alpha-D-mannopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> mmaker #24 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
Fecto2M_FIP_J1576_coot-1_real_space_refined_007-coot-4_real_space_refined_009.pdb,
chain C (#2) with 6tys, chain A (#24), sequence alignment score = 875.7
RMSD between 274 pruned atom pairs is 1.273 angstroms; (across all 367 pairs:
2.961)
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> hide #!2,11-24 atoms
> show #24 cartoons
> hide #24/A,B,C,D,E,F,G,I,J,K cartoons
> color #24 #3584e4ff
> color #24 #404ebfff
> color #24 #4050bfff
> color #24 #303763ff
> color #24 #313449ff
> color #24 #363a55ff
> open /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/fab_af2.pdb
Chain information for fab_af2.pdb #25
---
Chain | Description
A | No description available
B | No description available
> mmaker #25 to #24/L
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 6tys, chain L (#24) with fab_af2.pdb, chain B (#25), sequence
alignment score = 399
RMSD between 106 pruned atom pairs is 0.651 angstroms; (across all 107 pairs:
0.679)
> define axis #25 radius 5
Axis 'fab_af2.pdb #25/axis' centered at [ 70.29107461 138.97084878
150.75967364] with direction [-0.92877463 0.13498417 0.3451912 ], radius 5,
and length 76.5755
> color #25.1 #363a55
> hide #25 cartoons
> hide #!11-23,25 target m
> show #!6 models
> show #!4 models
> show #!21 models
> show #!20 models
> hide #!20 models
> hide #!21 models
> show #!20-21 target m
> hide #!21 models
> hide #!20 models
> show #!20 models
> show #!21 models
> show #21/C,D cartoons
> show #20/C,D cartoons
> hide #!21 models
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_top1.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_face_side1.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_updated_linux.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x7f71a2b0a690>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, 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 "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x7f71a2b0a690>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> hide #!24 models
> hide #!20 models
> hide #!6 models
> hide #!4 models
> show #!11-19 target m
> show #!22-23 target m
> show #!25 target m
> show #!22-23 target m
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_top.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_side1.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/Fecto_mabs_sticks_side2.png
> supersample 8 transparentBackground true height 2500
> save
> /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_linux.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x7f71a2b0a690>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, 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 "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x7f71a2b0a690>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 535.104.12
OpenGL renderer: Quadro T2000 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 20TJS07400
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) W-10855M CPU @ 2.80GHz
Cache Size: 12288 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 27Gi 1.0Gi 603Mi 33Gi 33Gi
Swap: 2.0Gi 1.3Gi 741Mi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117GLM [Quadro T2000 Mobile / Max-Q] [10de:1fb8] (rev a1)
Subsystem: Lenovo TU117GLM [Quadro T2000 Mobile / Max-Q] [17aa:22c0]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.0
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.7.22
cftime: 1.6.2
charset-normalizer: 3.3.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.11.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.48
ChimeraX-AtomicLibrary: 10.1
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: 1.0.3
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.4
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202309300109
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: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.1
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
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: 1.5.12
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: 1.11
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
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: 1.1.2
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: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.10
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: 1.12.2
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: 1.32.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.1
cxservices: 1.2.2
cycler: 0.12.0
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.0
filelock: 3.9.0
fonttools: 4.43.0
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
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: 5.3.2
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
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: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
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: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
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: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.0.5
wcwidth: 0.2.8
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Attachments (1)
Change History (9)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Milestone: | → 1.7 |
| Owner: | set to |
| Platform: | → all |
| Priority: | normal → high |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Unable to restore objects of NewerVersionQuery class |
comment:2 by , 2 years ago
I don't think we care if _this_ task is saved in sessions so it's probably enough to just add SESSION_SAVE = False to NewerVersionQuery's class attributes.
comment:3 by , 2 years ago
Hey, Thank you for your reply. Should I modify the ChimeraX code to enable the option of saving? I assume I won't be able to save the session that is currently open, correct? Thank you, Dawid On Mon, Oct 9, 2023 at 10:22 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > >
comment:4 by , 2 years ago
You may be able to modify the class at runtime.
In ChimeraX's command line:
ui tool show shell
Then in the shell:
from chimerax.core.toolshed import NewerVersionQuery NewerVersionQuery.SESSION_SAVE=False
I'm not sure if that will work. You can also change the code in path/to/ChimeraX.app/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py
comment:5 by , 2 years ago
Hey, Unfortunately, it does not work. I included the error log in the txt file. Thanks for the suggestion! Best, Dawid On Wed, Oct 11, 2023 at 10:18 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > > >
comment:6 by , 2 years ago
I see. Thanks for testing! We have a tasks object that handles saving things like NewerVersionQuery. It looks like when it's saving tasks, it doesn't check that attribute (but it should!). I'm going to commit both fixes, you might try the next daily build tomorrow and let us know if it works.
comment:7 by , 2 years ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
comment:8 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Starting in daily builds from today and in the release, ChimeraX will be able to restore sessions where I let it erroneously save NewerVersionQuery. No new sessions will save that class, but it's been added to the core class table and given a take/restore_snapshot pair so these sessions aren't lost.
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Reported by Dawid