The following bug report has been submitted:
Platform: Linux-5.10.0-1050-oem-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202307052255 (2023-07-05 22:55:15 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
> lighting soft
UCSF ChimeraX version: 1.7.dev202307052255 (2023-07-05)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> 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
> 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 16189 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrixview matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
Expected an objects specifier or a view name or a keyword
> cartoon suppressBackboneDisplay false
> color #1/A #545454
> color #1/E #ebebeb
> view matrix camera
> -0.94092,0.044048,-0.33573,48.563,0.072396,0.99474,-0.07238,106.12,0.33078,-0.092409,-0.93917,-101.94
> color #1/A #545454
> color #1/E #ebebeb
> color #1/A #8a8a8a
> color #1/C #a3a3a3
> color #1/E #6d6d6d
> color #1/B #7ab497
> color #1/F #72a27e
> color #1/D #728f83
> select /J:26-33,53-57,99-110/I:48-56
280 atoms, 288 bonds, 34 residues, 1 model selected
> select ~sel
15909 atoms, 15964 bonds, 2283 residues, 1 model selected
> hide sel cartoons
> hide #1.1-8 models
> undo
[Repeated 1 time(s)]
> color #1/D #35433d
> delete ::name="HOH"
> select /A-F/J:99-110/I:48-56
10764 atoms, 10954 bonds, 1401 residues, 1 model selected
> select ~sel
5166 atoms, 5302 bonds, 657 residues, 1 model selected
> hide sel cartoons
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 0.8 angleSlop 25 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
7 hydrogen bonds found
> view matrix camera
> 0.92763,-0.34248,0.14898,251.06,-0.36172,-0.92317,0.13002,196.5,0.093006,-0.1745,-0.98025,-87.973
> select clear
> color byhetero
> 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
> 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 16189 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrixview matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
Expected an objects specifier or a view name or a keyword
> cartoon suppressBackboneDisplay false
> color #1/A #545454
> color #1/E #ebebeb
> view matrix camera
> -0.94092,0.044048,-0.33573,48.563,0.072396,0.99474,-0.07238,106.12,0.33078,-0.092409,-0.93917,-101.94
> color #1/A #545454
> color #1/E #ebebeb
> color #1/A #8a8a8a
> color #1/C #a3a3a3
> color #1/E #6d6d6d
> color #1/B #7ab497
> color #1/F #72a27e
> color #1/D #728f83
> surface #1/A-F resolution 6
6 Gaussian surfaces, threshold level 0.134 - 0.138
> color zone #1 near #1/I-J distance 5 sharpEdges true
> hide #1/G-L cartoons
> view matrix camera
> 0.47412,-0.026261,0.88006,435.33,-0.87993,0.020301,0.47466,309.84,-0.030334,-0.99944,-0.013483,163.37
> save
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/fecto2M_fab77_footprint.png
> supersample 8 transparentBackground true height 2500
> select /J:26-33,53-57,99-110/I:48-56
280 atoms, 288 bonds, 34 residues, 1 model selected
> select ~sel
15909 atoms, 15964 bonds, 2283 residues, 1 model selected
> hide sel cartoons
> hide #1.1-8 models
> save
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/fecto2M_fab77_CDRs_only.png
> supersample 8 transparentBackground true height 2500
> hide cartoons
> surface #1/A-F resolution 6
6 Gaussian surfaces, threshold level 0.134 - 0.138
> save
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/fecto2M_fab77_CDRS_Fonly.png
> supersample 8 transparentBackground true height 2500
> color #1/D #35433d
> delete ::name="HOH"
> select /A-F/J:99-110/I:48-56
10764 atoms, 10954 bonds, 1401 residues, 1 model selected
> select ~sel
5166 atoms, 5302 bonds, 657 residues, 1 model selected
> hide sel cartoons
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 0.8 angleSlop 25 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
7 hydrogen bonds found
> hide sel surfaces
> select clear
> hide surfaces
> 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
> 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 16189 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrixview matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
Expected an objects specifier or a view name or a keyword
> cartoon suppressBackboneDisplay false
> color #1/A #545454
> color #1/E #ebebeb
> view matrix camera
> -0.94092,0.044048,-0.33573,48.563,0.072396,0.99474,-0.07238,106.12,0.33078,-0.092409,-0.93917,-101.94
> color #1/A #545454
> color #1/E #ebebeb
> color #1/A #8a8a8a
> color #1/C #a3a3a3
> color #1/E #6d6d6d
> color #1/B #7ab497
> color #1/F #72a27e
> color #1/D #728f83
> color #1/D #35433d
> delete ::name="HOH"
> select /A-F/J:99-110/I:48-56
10764 atoms, 10954 bonds, 1401 residues, 1 model selected
> select ~sel
5166 atoms, 5302 bonds, 657 residues, 1 model selected
> hide sel cartoons
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 0.8 angleSlop 25 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
7 hydrogen bonds found
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> color sel byhetero
> select clear
> color byhetero
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 1 angleSlop 30 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
7 hydrogen bonds found
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 1.5 angleSlop 30 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
7 hydrogen bonds found
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 1.5 angleSlop 50 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
10 hydrogen bonds found
> view matrix camera
> 0.92763,-0.34248,0.14898,251.06,-0.36172,-0.92317,0.13002,196.5,0.093006,-0.1745,-0.98025,-87.973
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_fab77_VL_VH1.png
> supersample 8 transparentBackground true height 2500
> show cartoons
> hide atoms
> select /A-F/J:26-33,53-57
10690 atoms, 10874 bonds, 1393 residues, 1 model selected
> select ~sel
5240 atoms, 5382 bonds, 665 residues, 1 model selected
> hide sel cartoons
> hbonds (#1/A-F) restrict (/J:26-33,53-77) reveal true relax true distSlop
> 1.5 angleSlop 50 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions1.txt
12 hydrogen bonds found
> view matrix camera
> 0.19736,-0.53258,-0.82304,-13.655,-0.49186,-0.78003,0.38681,269.78,-0.848,0.32848,-0.41591,65.22
> select /A-F/J:26-33,53-57
10690 atoms, 10874 bonds, 11 pseudobonds, 1393 residues, 2 models selected
> select ~sel
5240 atoms, 5382 bonds, 665 residues, 1 model selected
> hide sel cartoons
> select /A-F/J:26-33,53-72
10808 atoms, 10994 bonds, 12 pseudobonds, 1408 residues, 2 models selected
> select ~sel
5122 atoms, 5262 bonds, 650 residues, 1 model selected
> hide sel cartoons
> select /A-F/J:26-33,53-72
10808 atoms, 10994 bonds, 12 pseudobonds, 1408 residues, 2 models selected
> hide sel cartoons
> select clear
> select /A-F/J:26-33,53-72
10808 atoms, 10994 bonds, 12 pseudobonds, 1408 residues, 2 models selected
> show cartoons
> show sel cartoons
> hide sel cartoons
> select clear
> hide cartoons
> select /A-F/J:26-33,53-72
10808 atoms, 10994 bonds, 12 pseudobonds, 1408 residues, 2 models selected
> show sel cartoons
> select clear
> view matrix camera
> 0.19736,-0.53258,-0.82304,-13.655,-0.49186,-0.78003,0.38681,269.78,-0.848,0.32848,-0.41591,65.22
> select clear
[Repeated 1 time(s)]
> hide cartoons
> select clear
> select /A-F/J:26-33,53-72
10808 atoms, 10994 bonds, 12 pseudobonds, 1408 residues, 2 models selected
> show sel cartoons
> select clear
> hide #1/B,A
> hide #1/B,A cartoons
> hide #1/B,A,F cartoons
> undo
> show cartoons
> hide atoms
> select /A-F/J:26-33,53-57
10690 atoms, 10874 bonds, 11 pseudobonds, 1393 residues, 2 models selected
> select ~sel
5240 atoms, 5382 bonds, 665 residues, 1 model selected
> hide sel cartoons
> show cartoons
> hide atoms
> select /A-F/J:26-33,53-72
10808 atoms, 10994 bonds, 12 pseudobonds, 1408 residues, 2 models selected
> select ~sel
5122 atoms, 5262 bonds, 650 residues, 1 model selected
> hide sel cartoons
> hbonds (#1/A-F) restrict (/J:26-33,53-77) reveal true relax true distSlop
> 1.5 angleSlop 50 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions1.txt
12 hydrogen bonds found
> view matrix camera
> 0.19736,-0.53258,-0.82304,-13.655,-0.49186,-0.78003,0.38681,269.78,-0.848,0.32848,-0.41591,65.22
> ui tool show "Side View"
> view matrix camera
> 0.19736,-0.53258,-0.82304,-13.655,-0.49186,-0.78003,0.38681,269.78,-0.848,0.32848,-0.41591,65.22
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_fab77_VH2_1.png
> supersample 8 transparentBackground true height 2500
> color #1/D #35433d
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> color byhetero
> delete ::name="HOH"
> select /A-F/J:99-110/I:48-56
10764 atoms, 10954 bonds, 1401 residues, 1 model selected
> select ~sel
5166 atoms, 5302 bonds, 657 residues, 1 model selected
> hide sel cartoons
> select clear
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 1.5 angleSlop 60 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
11 hydrogen bonds found
> show cartoons
> hide atoms
> select /A-F/J:99-110/I:48-56
10764 atoms, 10954 bonds, 11 pseudobonds, 1401 residues, 2 models selected
> select ~sel
5166 atoms, 5302 bonds, 657 residues, 1 model selected
> hide sel cartoons
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 1.5 angleSlop 60 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
11 hydrogen bonds found
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 2 angleSlop 60 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
17 hydrogen bonds found
> view matrix camera
> 0.92763,-0.34248,0.14898,251.06,-0.36172,-0.92317,0.13002,196.5,0.093006,-0.1745,-0.98025,-87.973
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_fab77_VL_VH1.png
> supersample 8 transparentBackground true height 2500
> hbonds (#1/A-F) restrict (/J-I:48) reveal true relax true distSlop 2
> angleSlop 60 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
'restrict' atom specifier selects no atoms
> hbonds (#1/A-F) restrict (/J-I) reveal true relax true distSlop 2 angleSlop
> 60 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
'restrict' atom specifier selects no atoms
> hbonds (#1/A-F) restrict (/J,I) reveal true relax true distSlop 2 angleSlop
> 60 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
40 hydrogen bonds found
> select clear
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/full_antibody_binding_interface.cxs
> close session
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/FectoFab_fecto2M_fab-
> coot-125.pdb format pdb
Chain information for FectoFab_fecto2M_fab-coot-125.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
> /media/dzyla/Data/Data_exchange/Phenix_linux/Fecto_post/Fecto2M_post_J772-coot-113.pdb
> format pdb
Chain information for Fecto2M_post_J772-coot-113.pdb #2
---
Chain | Description
A B C | No description available
a b | No description available
c | No description available
> lighting soft
> hide atoms
> show cartoons
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> lighting model #1,2 depthCue false
> cartoon style protein modeHelix default arrows false xsection oval width 3
> thickness 3
> view matrix camera
> 0.94842,0.053989,-0.3124,45.982,0.31564,-0.06871,0.94639,643.66,0.02963,-0.99617,-0.082207,120.06
> move x 50 models #2
> turn y 40 models #1
> hide #1/H,G,J,I,L,K cartoons
> open
> /media/dzyla/Data/Data_exchange/pycharm/Papers/Fecto2M_paper/F_variants/mev_all_protein_F_aligned.fasta
Summary of feedback from opening
/media/dzyla/Data/Data_exchange/pycharm/Papers/Fecto2M_paper/F_variants/mev_all_protein_F_aligned.fasta
---
notes | Alignment identifier is mev_all_protein_F_aligned.fasta
Associated FectoFab_fecto2M_fab-coot-125.pdb chain B to FFL2M <unknown
description> with 0 mismatches
Associated FectoFab_fecto2M_fab-coot-125.pdb chain D to FFL2M <unknown
description> with 0 mismatches
Associated FectoFab_fecto2M_fab-coot-125.pdb chain F to FFL2M <unknown
description> with 0 mismatches
Associated FectoFab_fecto2M_fab-coot-125.pdb chain A to ACU57150.1 <unknown
description> with 0 mismatches
Associated FectoFab_fecto2M_fab-coot-125.pdb chain C to ACU57150.1 <unknown
description> with 0 mismatches
1 messages similar to the above omitted
Associated Fecto2M_post_J772-coot-113.pdb chain a to FFL2M <unknown
description> with 0 mismatches
Associated Fecto2M_post_J772-coot-113.pdb chain b to FFL2M <unknown
description> with 0 mismatches
Associated Fecto2M_post_J772-coot-113.pdb chain c to FFL2M <unknown
description> with 0 mismatches
Associated Fecto2M_post_J772-coot-113.pdb chain A to CAA34568.1 <unknown
description> with 0 mismatches
Associated Fecto2M_post_J772-coot-113.pdb chain B to CAA34568.1 <unknown
description> with 0 mismatches
1 messages similar to the above omitted
Showing conservation header ("seq_conservation" residue attribute) for
alignment mev_all_protein_F_aligned.fasta
Opened 819 sequences from mev_all_protein_F_aligned.fasta
> color byattribute seq_conservation palette #ff2600:#ffc04d:#dedddaff
26053 atoms, 3686 residues, atom seq_conservation range -3.15 to 0.782
> hide #1/C,D,E,F cartoons
> hide #2/A,a,C,c cartoons
> move y 40 models #2
> show #1 cartoons
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> hbonds (#1/A-F) restrict (/H,G) reveal true relax true distSlop 0.8
> angleSlop 25
11 hydrogen bonds found
> style stick
Changed 26053 atom styles
> select #1/A-F:27:37:40:121:123:125:339:382:383:384:418:434:435:436:437
360 atoms, 339 bonds, 45 residues, 1 model selected
> hide sel cartoons
> show sel
> select ~sel
25693 atoms, 25780 bonds, 3641 residues, 2 models selected
> hide sel cartoons
> hide sel
> select #1/A-F:27:37:40:121:123:125:339:382:383:384:418:434:435:436:437
360 atoms, 339 bonds, 45 residues, 1 model selected
> hide sel cartoons
> show sel
> view matrix camera
> 0.7326,0.50057,0.46122,409.75,0.22623,-0.81815,0.52863,478.31,0.64197,-0.28293,-0.71262,-177.48
> select clear
> view matrix camera
> 0.8024,-0.13075,0.58228,441.47,0.3195,-0.72998,-0.60419,-63.085,0.50406,0.67084,-0.54397,-67.718
[Repeated 1 time(s)]
> hide #1.3 models
> hide #1.2 models
> select clear
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/conservation_residues_new.png
> supersample 8 transparentBackground true height 2500
> close session
> open
> /media/dzyla/Data/Data_exchange/pycharm/Papers/structure_comparison/figures_chimera/fig3c.cxs
Unable to restore session: either not a ChimeraX session file, or needs a
newer version of ChimeraX to restore
> open
> /media/dzyla/Data/Data_exchange/pycharm/Papers/structure_comparison/figures_chimera/fig5c.cxs
Unable to restore session: either not a ChimeraX session file, or needs a
newer version of ChimeraX to restore
> open
> /media/dzyla/Data/Data_exchange/pycharm/Papers/structure_comparison/figures_chimera/fig4a.cxc
> 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
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_post_side1.png
> supersample 8 transparentBackground true height 2500
executed fig4a.cxc
> close session
> open
> /media/dzyla/Data/Data_exchange/pycharm/Papers/structure_comparison/figures_chimera/fig3c.cxc
> 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
> 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 16189 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrixview matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
Expected an objects specifier or a view name or a keyword
> close session
> open
> /media/dzyla/Data/Data_exchange/pycharm/Papers/structure_comparison/figures_chimera/fig3c.cxc
> 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
> 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 16189 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrixview matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
Expected an objects specifier or a view name or a keyword
> close session
> open
> /media/dzyla/Data/Data_exchange/pycharm/Papers/structure_comparison/figures_chimera/fig3c.cxc
> 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
> 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 16189 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
> cartoon suppressBackboneDisplay false
> color #1/A #545454
> color #1/E #ebebeb
> view matrix camera
> -0.94092,0.044048,-0.33573,48.563,0.072396,0.99474,-0.07238,106.12,0.33078,-0.092409,-0.93917,-101.94
> color #1/A #545454
> color #1/E #ebebeb
> color #1/A #8a8a8a
> color #1/C #a3a3a3
> color #1/E #6d6d6d
> color #1/B #7ab497
> color #1/F #72a27e
> color #1/D #728f83
> color #1/D #35433d
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> color byhetero
> delete ::name="HOH"
> select /A-F/J:99-110/I:48-56
10764 atoms, 10954 bonds, 1401 residues, 1 model selected
> select ~sel
5166 atoms, 5302 bonds, 657 residues, 1 model selected
> hide sel cartoons
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 0.8 angleSlop 25 saveFile
> /home/dzyla/Documents/230404_Fecto2M_Fab_figures/HC_interactions.txt
7 hydrogen bonds found
> view matrix camera
> 0.92763,-0.34248,0.14898,251.06,-0.36172,-0.92317,0.13002,196.5,0.093006,-0.1745,-0.98025,-87.973
> zoom 2
[Repeated 2 time(s)]
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto2M_fab77_VL_VH1.png
> supersample 8 transparentBackground true height 2500
executed fig3c.cxc
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 1.5 angleSlop 40
8 hydrogen bonds found
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 2 angleSlop 40
11 hydrogen bonds found
> hbonds (#1/A-F) restrict (/J:99-110/I:48-56) reveal true relax true distSlop
> 2 angleSlop 50
14 hydrogen bonds found
> hbonds (#1/A-F) restrict (/J:99-110/I:48-73) reveal true relax true distSlop
> 2 angleSlop 50
14 hydrogen bonds found
> hbonds (#1/A-F) restrict (/J:70-110/I:48-73) reveal true relax true distSlop
> 2 angleSlop 50
18 hydrogen bonds found
> 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
> 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 16189 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
> cartoon suppressBackboneDisplay false
> color #1/A #545454
> color #1/E #ebebeb
> view matrix camera
> -0.94092,0.044048,-0.33573,48.563,0.072396,0.99474,-0.07238,106.12,0.33078,-0.092409,-0.93917,-101.94
> color #1/A #545454
> color #1/E #ebebeb
> color #1/A #8a8a8a
> color #1/C #a3a3a3
> color #1/E #6d6d6d
> color #1/B #7ab497
> color #1/F #72a27e
> color #1/D #728f83
> color #1/D #3a4741
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> color byhetero
> delete ::name="HOH"
> select /A-F/J:99-110/I:48-56
10764 atoms, 10954 bonds, 1401 residues, 1 model selected
> select ~sel
5166 atoms, 5302 bonds, 657 residues, 1 model selected
> hide sel cartoons
> view matrix camera
> 0.92763,-0.34248,0.14898,251.06,-0.36172,-0.92317,0.13002,196.5,0.093006,-0.1745,-0.98025,-87.973
> zoom 2
[Repeated 2 time(s)]
> show #1/I:55:49
> show #1/D:383:435:436
> show #1/J:101:107:105:109
> show #1/D:383:435:436:434
> 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
> transparency 50
[Repeated 1 time(s)]
> transparency 0
> 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
> 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
> 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 16189 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
> cartoon suppressBackboneDisplay false
> color #1/A #545454
> color #1/E #ebebeb
> view matrix camera
> -0.94092,0.044048,-0.33573,48.563,0.072396,0.99474,-0.07238,106.12,0.33078,-0.092409,-0.93917,-101.94
> color #1/A #545454
> color #1/E #ebebeb
> color #1/A #8a8a8a
> color #1/C #a3a3a3
> color #1/E #6d6d6d
> color #1/B #7ab497
> color #1/F #72a27e
> color #1/D #728f83
> color #1/D #3a4741
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> color byhetero
> delete ::name="HOH"
> select /A-F/J:99-110/I:48-56
10764 atoms, 10954 bonds, 1401 residues, 1 model selected
> select ~sel
5166 atoms, 5302 bonds, 657 residues, 1 model selected
> hide sel cartoons
> view matrix camera
> 0.92763,-0.34248,0.14898,251.06,-0.36172,-0.92317,0.13002,196.5,0.093006,-0.1745,-0.98025,-87.973
> zoom 2
[Repeated 2 time(s)]
> show #1/I:55:49
> show #1/D:383:435:436
> show #1/J:101:107:105:109
> show #1/D:383:435:436:434
> 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
> hide atoms
> color gray
> color #1 #9a9996ff
> color #1 #c0bfbcff
> color #1 #dedddaff
> color #1 #9a9996ff
> color gray
> select #1/B
565 atoms, 572 bonds, 72 residues, 1 model selected
> select clear
> select #1/a
2691 atoms, 2731 bonds, 350 residues, 1 model selected
> select clear
> select #1/A
565 atoms, 572 bonds, 72 residues, 1 model selected
> select clear
> select #1/a
2691 atoms, 2731 bonds, 350 residues, 1 model selected
> select clear
> select #1/b
2691 atoms, 2731 bonds, 350 residues, 1 model selected
> select #1/b,B
3256 atoms, 3306 bonds, 422 residues, 1 model selected
> select clear
> color #1/b:138-166 cyan
> select #1/B
565 atoms, 572 bonds, 72 residues, 1 model selected
> select #1/b
2691 atoms, 2731 bonds, 350 residues, 1 model selected
> select clear
> color white
> transparency #1-2 100
> transparency #1-2 1
> transparency #1-2 1 cartoons
> color #1/b:138-166 cyan
[Repeated 1 time(s)]
> transparency #1/b 0
> transparency #1/b 0 cartoons
[Repeated 1 time(s)]
> transparency #1/ 0 c
Missing or invalid "percent" argument: Expected a number
> transparency #1/ 0 c 100
Missing or invalid "percent" argument: Expected a number
> transparency #1/ 0 c
Missing or invalid "percent" argument: Expected a number
> transparency #1/ 0
Missing or invalid "percent" argument: Expected a number
> transparency #1/ 1
Missing or invalid "percent" argument: Expected a number
> transparency #1/
Missing or invalid "percent" argument: Expected a number
> transparency #1 1
> transparency #1 10
> transparency #1 100
> transparency #1 100 cartoons
> transparency #1/A 100 cartoons
> color #1/b:138-166 cyan
[Repeated 1 time(s)]
> transparency #1/b 100 cartoons
> transparency #1/b 0 cartoons
> color #1/D:138-166 cyan
> transparency #2/D 0 cartoons
> transparency #2 0 cartoons
> transparency #2 100 cartoons
> transparency #2/D 0 cartoons
> color #2/D:138-166 cyan
> color #2/D:462-487 magenta
> color #2/D:462-487 hot pink
> color #1/b:462-487 hot pink
> color #1/b gray
> color #2/D gray
> color #1/b:138-166 cyan
> color #2/D:138-166 cyan
> color #1/b:462-487 hot pink
> color #2/D:462-487 hot pink
> color #2/D:110-137 #ffd700
> color #2/D:110-137 #ffa500
> color #2/D:110-137 #ff4500
> color #2/D:110-137 #ff581a
> color #1/b #72a27e
> color #2/D #72a27e
> color #1/b:138-166 cyan
> color #2/D:138-166 cyan
> color #1/b:462-487 hot pink
> color #2/D:462-487 hot pink
> color #2/D:110-137 #ff581a
> color #1/b:378-473 hot pink
> color #2/D:378-473 hot pink
> transparency #1/C 0 cartoons
> undo
> transparency #1/C 0 cartoons
> color #2/D:378-473 hot pink
> transparency #1/C 0 cartoons
[Repeated 1 time(s)]
> color #1/b:1-110 gray
> transparency #1/C 0 cartoons
> color #1/b:1-110 gray
[Repeated 1 time(s)]
> color #2/C:1-110 gray
> transparency #1/C 0 cartoons
> color #2/C:1-110 gray
> transparency #2/C 0 cartoons
> transparency #1/B cartoons
Missing or invalid "percent" argument: Expected a number
> transparency #1/B 0 cartoons
[Repeated 1 time(s)]
> transparency #1-2 100 cartoons
> transparency #1/b,B 0 cartoons
> transparency #2/B,C 0 cartoons
> transparency #2/C,d 0 cartoons
> transparency #1-2 100 cartoons
> transparency #1/b,B 0 cartoons
> transparency #2/C,d 0 cartoons
> color #1/b #72a27e
> color #1/B gray
> color #2/D #72a27e
> color #2/C gray
> color #1/b:138-166 cyan
> color #2/D:138-166 cyan
> color #1/b:462-487 hot pink
> color #2/D:462-487 hot pink
> color #2/D:110-137 #ff581a
> color #1/b:378-473 hot pink
> color #2/D:378-473 hot pink
> color #1/b:378-473 light pink
> color #2/D:378-473 light pink
> color #1/b #72a27e
> color #1/B gray
> color #2/D #72a27e
> color #2/C gray
> color #1/b:138-166 cyan
> color #2/D:138-166 cyan
> color #1/b:462-487 hot pink
> color #2/D:462-487 hot pink
> color #2/D:110-137 #ff581a
> color #1/b:378-445 light pink
> color #2/D:378-445 light pink
> color #1/B #d3d3d3
> color #2/C #3b3b3b
> color #1/B #3b3b3b
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> color #1/b:168-228 #cda3cd
> color #2/D:168-228 #cda3cd
> color #1/b:167-288 #cda3cd
> color #2/D:167-288 #cda3cd
> color #2/D:167-288 #e888e8
> color #1/b:167-288 #e888e8
> color #1/b:167-288 #fd1c00
> color #1/b:167-288 #ff5e4b
> color #2/D:167-288 #ff5e4b
> color #2/D:167-288 #d77f70
> color #1/b:167-288 #d77f70
> color #2/D:110-137 #ff581a
> color #2/D:110-137 #0010ff
> color #1/b:138-166 cyan
> color #2/D:138-166 cyan
> color #1/b:138-166 #00a4ff
> color #2/D:138-166 #00a4ff
> color #1/b:167-288 #d77f70
> color #2/D:167-288 #d77f70
> color #1/b:167-288 #40ffb7
> color #2/D:167-288 #40ffb7
> color #1/b:229-377 #b7ff40
> color #2/D:229-377 #b7ff40
> color #1/b:378-445 light pink
> color #2/D:378-445 light pink
> color #1/b:378-445 #ffb900
> color #2/D:378-445 #ffb900
> color #1/b:462-487 hot pink
> color #2/D:462-487 hot pink
> color #1/b:462-487 #ff3000
> color #2/D:462-487 #ff3000
> color #1/B #000080
> color #2/C #000080
> color #1/B #7a4192
> color #2/C #7a4192
> color #1/B #7a4192
> color #2/C #7a4192
> color #2/D:110-137 #ff581a
> color #2/D:110-137 #0010ff
> color #1/b:138-166 cyan
> color #2/D:138-166 cyan
> color #1/b:138-166 #00a4ff
> color #2/D:138-166 #00a4ff
> color #1/b:167-288 #d77f70
> color #2/D:167-288 #d77f70
> color #1/b:167-288 #40ffb7
> color #2/D:167-288 #40ffb7
> color #1/b:229-377 #b7ff40
> color #2/D:229-377 #b7ff40
> color #1/b:378-445 light pink
> color #2/D:378-445 light pink
> color #1/b:378-445 #ffb900
> color #2/D:378-445 #ffb900
> color #1/b:462-487 hot pink
> color #2/D:462-487 hot pink
> color #1/b:462-487 #ff3000
> color #2/D:462-487 #ff3000
> color #1/b:167-288 #d77f70
> color #2/D:167-288 #d77f70
> color #1/b:167-288 #40ffb7
> color #2/D:167-288 #40ffb7
> color #1/b:229-377 #b7ff40
> color #2/D:229-377 #b7ff40
> color #1/b:378-445 light pink
> color #2/D:378-445 light pink
> color #1/b:378-461 #ffb900
> color #2/D:378-461 #ffb900
> color #1/b:462-487 hot pink
> color #2/D:462-487 hot pink
> color #1/b:462-487 #ff3000
> color #2/D:462-487 #ff3000
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto_pre_post_domains_1.png
> supersample 8 transparentBackground true height 2500
> hide ~#1,b,B cartoon
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~#1,b,B cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1,A,A,c,C cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1,a,A,c,C cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1,a,A,c,C
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1/a,A,c,C
> hide #1/a,A,c,C cartoons
> hide #2/A,B,E,F cartoons
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto_pre_post_domains_2.png
> supersample 8 transparentBackground true height 2500
> color #1/B #7a4192
> color #2/C #7a4192
> color #1/B #ff3000
> color #2/C #ff3000
> color #2/D:110-137 #ff581a
> color #2/D:110-137 #0010ff
> color #2/D:110-137 #ffb900
> color #1/b:138-166 cyan
> color #2/D:138-166 cyan
> color #1/b:138-166 #00a4ff
> color #2/D:138-166 #00a4ff
> color #1/b:138-166 #b7ff40
> color #2/D:138-166 #b7ff40
> color #1/b:167-288 #d77f70
> color #2/D:167-288 #d77f70
> color #1/b:167-288 #40ffb7
> color #2/D:167-288 #40ffb7
> color #1/b:229-377 #b7ff40
> color #2/D:229-377 #b7ff40
> color #1/b:378-445 light pink
> color #2/D:378-445 light pink
> color #1/b:378-461 #ffb900
> color #2/D:378-461 #ffb900
> color #1/b:462-487 hot pink
> color #2/D:462-487 hot pink
> color #1/b:462-487 #ff3000
> color #2/D:462-487 #ff3000
> color #1/b:462-487 #0010ff
> color #2/D:462-487 #0010ff
> color #1/B #7a4192
> color #2/C #7a4192
> color #1/B #ff3000
> color #2/C #ff3000
> color #2/D:110-137 #ff581a
> color #2/D:110-137 #0010ff
> color #2/D:110-137 #ffb900
> color #1/b:138-166 cyan
> color #2/D:138-166 cyan
> color #1/b:138-166 #00a4ff
> color #2/D:138-166 #00a4ff
> color #1/b:138-166 #b7ff40
> color #2/D:138-166 #b7ff40
> color #1/b:167-288 #d77f70
> color #2/D:167-288 #d77f70
> color #1/b:167-288 #40ffb7
> color #2/D:167-288 #40ffb7
> color #1/b:229-377 #b7ff40
> color #2/D:229-377 #b7ff40
> color #1/b:378-445 light pink
> color #2/D:378-445 light pink
> color #1/b:378-461 #ffb900
> color #2/D:378-461 #ffb900
> color #1/b:378-461 #0010ff
> color #2/D:378-461 #0010ff
> color #1/b:462-487 hot pink
> color #2/D:462-487 hot pink
> color #1/b:462-487 #ff3000
> color #2/D:462-487 #ff3000
> color #1/b:462-487 #7a4192
> color #2/D:462-487 #7a4192
> color #1/B #7a4192
> color #2/C #7a4192
> color #1/B #ff3000
> color #2/C #ff3000
> color #2/D:110-137 #ff581a
> color #2/D:110-137 #0010ff
> color #2/D:110-137 #ffb900
> color #1/b:138-166 cyan
> color #2/D:138-166 cyan
> color #1/b:138-166 #00a4ff
> color #2/D:138-166 #00a4ff
> color #1/b:138-166 #b7ff40
> color #2/D:138-166 #b7ff40
> color #1/b:167-288 #d77f70
> color #2/D:167-288 #d77f70
> color #1/b:167-288 #40ffb7
> color #2/D:167-288 #40ffb7
> color #1/b:229-377 #b7ff40
> color #2/D:229-377 #b7ff40
> color #1/b:229-377 #00a4ff
> color #2/D:229-377 #00a4ff
> color #1/b:378-445 light pink
> color #2/D:378-445 light pink
> color #1/b:378-461 #ffb900
> color #2/D:378-461 #ffb900
> color #1/b:378-461 #0010ff
> color #2/D:378-461 #0010ff
> color #1/b:462-487 hot pink
> color #2/D:462-487 hot pink
> color #1/b:462-487 #ff3000
> color #2/D:462-487 #ff3000
> color #1/b:462-487 #7a4192
> color #2/D:462-487 #7a4192
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto_pre_post_domains_2rev.png
> supersample 8 transparentBackground true height 2500
> show #1 cartoons
> show #2/A-F cartoons
> save
> /home/dzyla/OneDrive/PostDOC/papers/Fecto_mab_story/230404_Fecto2M_Fab_figures/fecto_pre_post_domains_1rev.png
> supersample 8 transparentBackground true height 2500
> save
> /media/dzyla/Data/Data_exchange/pycharm/Papers/structure_comparison/Fecto_pre_post_domains.cxs
> 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
> 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 16189 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrixview matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
Expected an objects specifier or a view name or a keyword
> cartoon suppressBackboneDisplay false
> open
> /media/dzyla/Data/Data_exchange/Phenix_linux/FectoFab/J1600__localfilter.mrc
Opened J1600__localfilter.mrc as #2, grid size 320,320,320, pixel 1.06, shown
at level 0.0816, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1742
> transparency 90
> color #1/A #545454
> color #1/E #ebebeb
> turn x 180
> turn z 30
> close #2
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/B ARG 485
/D ARG 485
/F ARG 485
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_A SES
surface #1.1: minimum, -9.62, mean 1.32, maximum 10.31
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_B SES
surface #1.2: minimum, -16.18, mean -1.84, maximum 9.27
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_C SES
surface #1.3: minimum, -9.37, mean 1.28, maximum 9.67
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_D SES
surface #1.4: minimum, -14.82, mean -1.91, maximum 13.26
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_E SES
surface #1.5: minimum, -9.86, mean 1.33, maximum 9.82
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_F SES
surface #1.6: minimum, -17.30, mean -1.86, maximum 10.14
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_G SES
surface #1.7: minimum, -14.09, mean -0.86, maximum 11.07
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_H SES
surface #1.8: minimum, -9.42, mean -0.52, maximum 8.37
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_I SES
surface #1.9: minimum, -15.06, mean -0.92, maximum 9.91
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_J SES
surface #1.10: minimum, -9.76, mean -0.57, maximum 8.66
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_K SES
surface #1.11: minimum, -14.09, mean -0.90, maximum 10.57
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_L SES
surface #1.12: minimum, -9.45, mean -0.55, maximum 8.28
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.12 models
> hide #1.11 models
> hide #1.10 models
> hide #1.9 models
> hide #1.8 models
> hide #1.7 models
> hide #1/H,G cartoons
> hide #1 cartoons
> view matrix camera
> 0.19736,-0.53258,-0.82304,-13.655,-0.49186,-0.78003,0.38681,269.78,-0.848,0.32848,-0.41591,65.22
> view matrix camera
> 0.92763,-0.34248,0.14898,251.06,-0.36172,-0.92317,0.13002,196.5,0.093006,-0.1745,-0.98025,-87.973
[Repeated 1 time(s)]
> select #1/A-F:27:37:40:123:125:383:384:434:435:436
240 atoms, 225 bonds, 30 residues, 1 model selected
> show sel atoms
> select clear
> transparency #1.1-12 50
> transparency #1.1-12 30
> color byhetero
> undo
> view matrix camera
> 0.53612,-0.040271,-0.84318,-86.671,0.84331,-0.018479,0.53709,334.75,-0.037213,-0.99901,0.024054,172.47
> transparency #1.1-12 0
> select clear
> 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
> 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 32378 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrixview matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
Expected an objects specifier or a view name or a keyword
> cartoon suppressBackboneDisplay false
> color #1/A #545454
> color #1/E #ebebeb
> turn x 180
> turn z 30
> turn x -90
> 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
> 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 16189 atom styles
> color #1/G,I,K #b188a7
> color #1/H,J,L #6a64a5
> color #1/B,D,F #72a27e
> color #1/A,C,E #a7a7a7
> view matrixview matrix camera
> 0.92096,-0.38965,0.00059709,158.95,-0.38959,-0.92083,-0.01701,147.38,0.0071806,0.015432,-0.99985,-110.27
Expected an objects specifier or a view name or a keyword
> cartoon suppressBackboneDisplay false
> color #1/A #545454
> color #1/E #ebebeb
> turn x 180
> turn z 30
> turn x -90
> hide #1/G-L
> hide #1/G-L cartoons
> view matrix
view matrix camera
0.48932,-0.011409,-0.87203,-241.38,0.87073,-0.049786,0.48924,418.33,-0.048996,-0.99869,-0.014427,159.97
view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix
view matrix camera
0.48932,-0.011409,-0.87203,-241.38,0.87073,-0.049786,0.48924,418.33,-0.048996,-0.99869,-0.014427,159.97
view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/B ARG 485
/D ARG 485
/F ARG 485
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_A SES
surface #1.1: minimum, -9.62, mean 1.32, maximum 10.31
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_B SES
surface #1.2: minimum, -16.18, mean -1.84, maximum 9.27
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_C SES
surface #1.3: minimum, -9.37, mean 1.28, maximum 9.67
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_D SES
surface #1.4: minimum, -14.82, mean -1.91, maximum 13.26
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_E SES
surface #1.5: minimum, -9.86, mean 1.33, maximum 9.82
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_F SES
surface #1.6: minimum, -17.30, mean -1.86, maximum 10.14
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_G SES
surface #1.7: minimum, -14.09, mean -0.86, maximum 11.07
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_H SES
surface #1.8: minimum, -9.42, mean -0.52, maximum 8.37
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_I SES
surface #1.9: minimum, -15.06, mean -0.92, maximum 9.91
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_J SES
surface #1.10: minimum, -9.76, mean -0.57, maximum 8.66
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_K SES
surface #1.11: minimum, -14.09, mean -0.90, maximum 10.57
Coulombic values for FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_L SES
surface #1.12: minimum, -9.45, mean -0.55, maximum 8.28
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.12 models
> hide #1.11 models
> hide #1.10 models
> hide #1.9 models
> hide #1.8 models
> hide #1.7 models
> hide #1.7-12 models
> mlp
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_A SES
surface": minimum -26.91, mean -3.396, maximum 21.14
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_B SES
surface": minimum -28.62, mean -4.108, maximum 25.24
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_C SES
surface": minimum -26.6, mean -3.432, maximum 21.93
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_D SES
surface": minimum -28.49, mean -4.029, maximum 24.18
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_E SES
surface": minimum -26.98, mean -3.318, maximum 22.84
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_F SES
surface": minimum -27.12, mean -4.093, maximum 24.45
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_G SES
surface": minimum -25.3, mean -5.79, maximum 21.74
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_H SES
surface": minimum -29.19, mean -4.473, maximum 24.08
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_I SES
surface": minimum -26.23, mean -5.791, maximum 21.2
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_J SES
surface": minimum -29.78, mean -4.626, maximum 24.12
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_K SES
surface": minimum -27.66, mean -5.391, maximum 22.4
Map values for surface "FectoFab_fecto2M_fab-coot-124_water_merged_F.pdb_L SES
surface": minimum -26.6, mean -4.587, maximum 25.01
To also show corresponding color key, enter the above mlp command and add key
true
> hide #1.7-12 models
> hide #1models
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 models
> show #!1 models
> swapaa #1/B:436 D
Using Dunbrack library
/B ARG 436: phi -108.6, psi 5.8 trans
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/swap_res/cmd.py", line 40, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 42, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params
return self._get_params(res_name, file_name, cache, archive)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> swapaa interactive #1/B:436 D
/B ARG 436: phi -108.6, psi 5.8 trans
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/swap_res/cmd.py", line 147, in rotamers
rotamers = swap_res.get_rotamers(session, r, res_type=r_type, rot_lib=rot_lib,
log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params
return self._get_params(res_name, file_name, cache, archive)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> swapaa interactive #1/B:436 ASD
/B ARG 436: phi -108.6, psi 5.8 trans
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/swap_res/cmd.py", line 147, in rotamers
rotamers = swap_res.get_rotamers(session, r, res_type=r_type, rot_lib=rot_lib,
log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params
return self._get_params(res_name, file_name, cache, archive)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> swapaa interactive #1/B:436 ASD rotLib Dynameomics
/B ARG 436: phi -108.6, psi 5.8 trans
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/swap_res/cmd.py", line 147, in rotamers
rotamers = swap_res.get_rotamers(session, r, res_type=r_type, rot_lib=rot_lib,
log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/dynameomics_rotamer_lib/lib.py", line 56, in rotamer_params
return self._get_params(res_name, res_name, _cache, "rotamerData.zip")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
AttributeError: 'DynameomicsRotamerLibrary' object has no attribute
'display_name'
AttributeError: 'DynameomicsRotamerLibrary' object has no attribute
'display_name'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> swapaa asd #1/B:436
Missing or invalid "residues" argument: invalid residues specifier
> swapaa asd #1/B:436.a
Missing or invalid "residues" argument: invalid residues specifier
> swapaa #1/B:436.a
Missing or invalid "residues" argument: only initial part "#1/B:436" of atom
specifier valid
> swapaa #1/B:436
Missing or invalid "resType" argument: Expected a text string
> swapaa #1/B:436 D
Using Dunbrack library
/B ARG 436: phi -108.6, psi 5.8 trans
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/swap_res/cmd.py", line 40, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 42, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params
return self._get_params(res_name, file_name, cache, archive)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> swapaa #1/B:436 D
Using Dunbrack library
/B ARG 436: phi -108.6, psi 5.8 trans
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
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/swap_res/cmd.py", line 40, in swap_aa
swap_res.swap_aa(session, residues, res_type, bfactor=bfactor,
clash_hbond_allowance=hbond_allowance,
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 42, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 236, in get_rotamers
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/dunbrack_rotamer_lib/lib.py", line 67, in rotamer_params
return self._get_params(res_name, file_name, cache, archive)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
AttributeError: 'DunbrackRotamerLibrary' object has no attribute
'display_name'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/rotamers/rot_lib.py", line 186, in _get_params
"%s library does not support residue type '%s'" % (self.display_name,
base_name))
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 535.86.10
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 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
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 35Gi 1.2Gi 1.3Gi 25Gi 25Gi
Swap: 2.0Gi 2.0Gi 0B
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: 2.2.1
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: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.46
ChimeraX-AtomicLibrary: 10.0.7
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: 2.10.3
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: 1.0.2
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: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202307052255
ChimeraX-CoreFormats: 1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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
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
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
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: 1.10.2
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: 1.1.1
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: 3.0
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: 2.9
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.1
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: 2.2.1
ChimeraX-TapeMeasure: 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: 1.30.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.2
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: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.40.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2023.3.16
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.7
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.8.0
prompt-toolkit: 3.0.39
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.6
PyOpenGL-accelerate: 3.1.6
pyparsing: 3.1.0
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.1.0
qtconsole: 5.4.3
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.8.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.3
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Dawid,
--Eric