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Opened 13 months ago
Closed 13 months ago
#16001 closed defect (fixed)
Selection history holding reference to dead PseudobondGroup
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-122-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_no-surface.cxs
> format session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Mon Sep 23 15:04:26 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/session 9-19-2024.cxs" format session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Thu Sep 19 16:51:19 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/figure-like-inspiation-
> article/mapview.cxs format session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Mon Sep 16 16:33:12 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/new-ribbon-
> display_intermediate-session2_Kchain-interactions_final_9-16-2024.cxs format
> session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Mon Sep 16 12:38:01 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v18_heavychainCDRs.cxs format session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Fri Sep 13 18:39:13 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v12_CDRs-lightchain-K.cxs format session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Fri Sep 13 15:03:30 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v10.cxs format session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Thu Sep 12 18:34:15 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60_v5.cxs format session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Wed Sep 11 11:34:53 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60_v4.cxs format session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Wed Sep 11 09:24:47 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60_v2.cxs format session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Tue Sep 10 16:25:29 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60_v1.cxs format session
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.229, step 1, values float32
Log from Mon Sep 9 17:52:25 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60.cxs
Log from Mon Sep 9 17:02:59 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Error running startup command 'volume defaultvalues limitVoxelCount false
voxelLimitForPlane 1000000000000000 voxelLimitForOpen 1000000000000000
saveSettings true': Expected a density maps specifier or a keyword
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/ana/Documents/__BajicLab/K1769_figures/k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
Summary of feedback from opening
/home/ana/Documents/__BajicLab/K1769_figures/k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
---
warnings | Ignored bad PDB record found on line 260
SSBOND *** CYS A 14 CYS A 466
Ignored bad PDB record found on line 261
SSBOND *** CYS A 64 CYS A 76
Ignored bad PDB record found on line 262
SSBOND *** CYS A 97 CYS A 139
Ignored bad PDB record found on line 263
SSBOND *** CYS A 281 CYS A 305
Ignored bad PDB record found on line 264
SSBOND *** CYS H 22 CYS H 96
11 messages similar to the above omitted
Chain information for
k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb #1
---
Chain | Description
A B C | No description available
H J L | No description available
I K M | No description available
> hide atoms
> show cartoons
> select ::name="BMA"::name="MAN"::name="NAG"
702 atoms, 735 bonds, 54 residues, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> view sel
> ui tool show "Side View"
[Repeated 1 time(s)]
> view
> select clear
> color bychain
> mlp
Map values for surface
"k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb_A SES surface":
minimum -27.7, mean -5.692, maximum 23.21
Map values for surface
"k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb_B SES surface":
minimum -27.94, mean -5.631, maximum 24.95
Map values for surface
"k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb_C SES surface":
minimum -27.83, mean -5.561, maximum 25.2
Map values for surface
"k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb_H SES surface":
minimum -27.31, mean -5.186, maximum 22.99
Map values for surface
"k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb_I SES surface":
minimum -25.74, mean -5.93, maximum 22.06
Map values for surface
"k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb_J SES surface":
minimum -27.22, mean -5.251, maximum 23.27
Map values for surface
"k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb_K SES surface":
minimum -26.46, mean -6.182, maximum 24.4
Map values for surface
"k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb_L SES surface":
minimum -25.44, mean -5.273, maximum 23.38
Map values for surface
"k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb_M SES surface":
minimum -27.04, mean -6.23, maximum 24.11
To also show corresponding color key, enter the above mlp command and add key
true
> show surfaces
> color bychain
> view orient
> ui tool show "Side View"
[Repeated 1 time(s)]
> view
> lighting simple
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> turn -x 90
[Repeated 3 time(s)]
> open /home/ana/Documents/__BajicLab/K1769_figures/example.bild
Opened BILD data containing 24 objects
> view orient
> select ::name="BMA"::name="MAN"::name="NAG"
702 atoms, 735 bonds, 54 residues, 1 model selected
> select /A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide #2 models
> show #2 models
> view orient
> turn -x 90
[Repeated 2 time(s)]
> turn -z 30
> undo
> turn -y 30
[Repeated 14 time(s)]
> hide #2 models
> turn -y 10
[Repeated 27 time(s)]
> view sel
> view orient
> turn -x 270
> ui tool show "Side View"
> view sel
> turn -y 10
[Repeated 5 time(s)]
> select clear
> select /A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> color (#!1 & sel) light gray
> select /C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> select ::name="BMA"::name="MAN"::name="NAG"
702 atoms, 735 bonds, 54 residues, 1 model selected
> color sel magenta
> color sel orange
> ui tool show "Color Actions"
> color sel brown
> color sel chocolate
> color sel sienna
> color sel goldenrod
> color sel sienna
> color sel chocolate
> select clear
> interfaces ~solvent
13 buried areas: B C 2143, A B 2125, A C 2115, L M 842, J K 833, H I 828, C H
549, A L 537, B J 536, B L 333, A M 330, A H 326, C J 309
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select /I,K,M:109
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /I,K,M
2505 atoms, 2559 bonds, 327 residues, 1 model selected
Alignment identifier is 1
> select /L
947 atoms, 974 bonds, 121 residues, 1 model selected
> ui tool show "Color Actions"
> color (#!1 & sel) #bf4747ff
> color (#!1 & sel) #3d1717ff
> color (#!1 & sel) #3d1111ff
> color (#!1 & sel) #792222ff
> color (#!1 & sel) #447922ff
> color (#!1 & sel) #40791bff
> color (#!1 & sel) #4d9221ff
[Repeated 4 time(s)]
> select /K
835 atoms, 853 bonds, 109 residues, 1 model selected
> color (#!1 & sel) #80bf40ff
> color (#!1 & sel) #8fbf5eff
> color (#!1 & sel) #a1d76aff
[Repeated 3 time(s)]
> select /H
947 atoms, 974 bonds, 121 residues, 1 model selected
> ui tool show "Color Actions"
> color (#!1 & sel) #4d9221ff
> select /J
947 atoms, 974 bonds, 121 residues, 1 model selected
> ui tool show "Color Actions"
> select clear
> select /J
947 atoms, 974 bonds, 121 residues, 1 model selected
> color (#!1 & sel) #71bf40ff
> color (#!1 & sel) #65bf2bff
> color (#!1 & sel) #4d9221ff
[Repeated 1 time(s)]
> select /I
835 atoms, 853 bonds, 109 residues, 1 model selected
> color (#!1 & sel) #a1d76aff
> select /K
835 atoms, 853 bonds, 109 residues, 1 model selected
> select /M
835 atoms, 853 bonds, 109 residues, 1 model selected
> ui tool show "Color Actions"
> color (#!1 & sel) #80bf40ff
> color (#!1 & sel) #8fbf5eff
> color (#!1 & sel) #a1d76aff
[Repeated 1 time(s)]
> view orient
> select clear
> turn -x 270
> turn -y 10
[Repeated 5 time(s)]
> select /C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> select /B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> color (#!1 & sel) #bf4085ff
> color (#!1 & sel) #bf86a5ff
> color (#!1 & sel) #e9a3c9ff
[Repeated 4 time(s)]
> select clear
> select ::name="BMA"::name="MAN"::name="NAG"
702 atoms, 735 bonds, 54 residues, 1 model selected
> color sel gray
> color sel black
> ui tool show "Color Actions"
> color sel #bf4089ff
> color sel #bf1a79ff
> color sel #c51b7dff
[Repeated 1 time(s)]
> color sel #c51b73ff
> color sel #c5aebaff
> color sel #fde0efff
[Repeated 4 time(s)]
> select clear
> turn -y 10
> view
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60.cxs
——— End of log from Mon Sep 9 17:02:59 2024 ———
opened ChimeraX session
> open
> /home/ana/Documents/__BajicLab/K1769_figures/volumes/cryosparc_P4_J137_008_volume_map.mrc
Opened cryosparc_P4_J137_008_volume_map.mrc as #3, grid size 420,420,420,
pixel 1.08, shown at level 0.0242, step 2, values float32
> volume #3 step 1
> volume #3 level 0.229
> hide #!1 models
> show #!1 models
> show cartoons
> hide surfaces
> show cartoons
> color zone #3 near #1 distance 6.46
> view orient
> turn -x 270
> turn -y 60
> select /A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> select /B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!1 & sel) 30
> transparency sel 0
> color zone #3 near sel & #1 distance 6.46
> undo
> transparency sel 50
> transparency (#!1 & sel) 80
> undo
> select add #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 3 models selected
> select subtract #1
9 models selected
> select add #3
2 models selected
> transparency sel 50
> undo
> redo
> volume sel style surface
> select clear
> transparency #1,3 0
> select ::name="BMA"::name="MAN"::name="NAG"
702 atoms, 735 bonds, 54 residues, 1 model selected
> transparency sel 70
> select add #3
702 atoms, 735 bonds, 54 residues, 3 models selected
> transparency (#!1 & sel) 30
> transparency (#!1 & sel) 70
> select add #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 4 models selected
> select subtract #1
11 models selected
> select ::name="BMA"::name="MAN"::name="NAG"
702 atoms, 735 bonds, 54 residues, 1 model selected
> transparency #1.2-10#3.1 50
> hide sel cartoons
[Repeated 1 time(s)]
> select add #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> hide sel cartoons
> select add #3
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 13 models selected
> select subtract #1
11 models selected
> transparency #3.1 40
> transparency #3.1 30
> select clear
> transparency #1,3 50
> view
[Repeated 1 time(s)]
> save
> /home/ana/Documents/__BajicLab/K1769_figures/pic1_rot-270plus-y60_map.tif
> width 1979 height 1191 supersample 3 transparentBackground true
> select /B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60_v1.cxs
——— End of log from Mon Sep 9 17:52:25 2024 ———
opened ChimeraX session
> hide #!3 models
> select add #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> show sel cartoons
> select subtract #1
9 models selected
> hide #!1 models
> show #2 models
> select add #2
1 model selected
> hide #2 target m
> select add #2
1 model selected
> select add #2
1 model selected
> select add #2
1 model selected
> close #2
> show #!1 models
> interfaces select #1/B contacting #1/J
10 contacting residues
> interfaces select #1/J contacting #1/B
12 contacting residues
> interfaces select #1/B contacting #1/J, interface select #1/J contacting
> #1/B
Expected a keyword
> interfaces select #1/B contacting #1/J, #1/J contacting #1/B
Invalid "contacting" argument: only initial part "#1/J" of atom specifier
valid
> ui tool show "Side View"
> select #1/B:45,25,27,33,315,313,312,310,308,498
91 atoms, 84 bonds, 10 residues, 1 model selected
> select #1/B:45,25,27,33,315,313,312,310,308,498
> #1/J:1,28,30,31,32,106,105,104,103,101
179 atoms, 171 bonds, 20 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 179 atom styles
> color (#!1 & sel) byhetero
> view sel
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> view sel
> hide #!1 models
> show #!1 models
> select add #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 4 models selected
> select subtract #1
9 models selected
> select add #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> transparency (#!1 & sel) 40
> transparency #1/J 50
> transparency #1/K 50
> transparency #1/K 50 ribbons
> transparency #1/KJ50 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #1/J 50 ribbons
> transparency #1/J 80 ribbons
> transparency #1/K 80 ribbons
> transparency #1/B 80 ribbons
> transparency #1 80 ribbons
> view sel
> select #1/B:45,25,27,33,315,313,312,310,308,498
> #1/J:1,28,30,31,32,106,105,104,103,101
179 atoms, 171 bonds, 20 residues, 1 model selected
> view sel
> hide #!1 models
> show #!1 models
> select add #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 4 models selected
> select subtract #1
9 models selected
> select add #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> select subtract #1
9 models selected
> select #1/B:45,25,27,33,315,313,312,310,308,498
> #1/J:1,28,30,31,32,106,105,104,103,101
179 atoms, 171 bonds, 20 residues, 1 model selected
> select add #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 4 models selected
> select subtract #1
9 models selected
> undo
> redo
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60_v2.cxs
——— End of log from Tue Sep 10 16:25:29 2024 ———
opened ChimeraX session
> select add #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> show #!3 models
> hide #!3 models
> open
> /home/ana/Documents/__BajicLab/K1769_figures/k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
Summary of feedback from opening
/home/ana/Documents/__BajicLab/K1769_figures/k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
---
warnings | Ignored bad PDB record found on line 260
SSBOND *** CYS A 14 CYS A 466
Ignored bad PDB record found on line 261
SSBOND *** CYS A 64 CYS A 76
Ignored bad PDB record found on line 262
SSBOND *** CYS A 97 CYS A 139
Ignored bad PDB record found on line 263
SSBOND *** CYS A 281 CYS A 305
Ignored bad PDB record found on line 264
SSBOND *** CYS H 22 CYS H 96
11 messages similar to the above omitted
Chain information for
k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb #2
---
Chain | Description
A B C | No description available
H J L | No description available
I K M | No description available
> select add #2
34464 atoms, 35304 bonds, 6 pseudobonds, 4320 residues, 13 models selected
> select subtract #1
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 11 models selected
> hide sel atoms
> show sel cartoons
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> color (#!2 & sel) light gray
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> color (#!2 & sel) light gray
> ui tool show "Color Actions"
> color (#!2 & sel) #e9a3c9ff
> hide #!1 models
> show #!1 models
> select add #2
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> select #2/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> color sel #4d9221ff
> select #1/B:45,25,27,33,315,313,312,310,308,498
> #1/J:1,28,30,31,32,106,105,104,103,101
179 atoms, 171 bonds, 20 residues, 1 model selected
> show (#!1 & sel-residues & sidechain) target ab
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & backbone) target ab
> show (#!1 & sel-residues & sidechain) target ab
> distance #1/j:103@N #1/b:33@OE1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#1/J SER 103 N and /B GLN 33 OE1: 3.007Å
> distance #1/j:103@OG #1/b:33@OE1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#1/J SER 103 OG and /B GLN 33 OE1: 3.544Å
> distance #1/j:103@OG #1/b:32@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#1/J SER 103 OG and /B ASP 32 O: 2.849Å
> ui mousemode right "resize markers"
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60_v3.cxs
> ui tool show "Show Sequence Viewer"
> sequence chain #1/J
Alignment identifier is 1/J
> select #1/J:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> save /home/ana/Documents/__BajicLab/K1769_figures/heavy format fasta
> alignment 1/J
> select #1/J:31
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/J:31-35
47 atoms, 49 bonds, 5 residues, 1 model selected
> color (#!1 & sel) light sea green
> select #1/J:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/J:1-32
236 atoms, 239 bonds, 32 residues, 1 model selected
> select #1/J:40
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/J:40-43
25 atoms, 25 bonds, 4 residues, 1 model selected
> select #1/J:47
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/J:47-48
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #1/J:50
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/J:50-58
74 atoms, 76 bonds, 9 residues, 1 model selected
> select #1/J:66
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/J:50-66
141 atoms, 145 bonds, 17 residues, 1 model selected
> color (#!1 & sel) light sea green
> select #1/J:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/J:99-110
96 atoms, 101 bonds, 12 residues, 1 model selected
> color (#!1 & sel) blue
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60_v4.cxs
——— End of log from Wed Sep 11 09:24:47 2024 ———
opened ChimeraX session
> open
> /home/ana/Documents/__BajicLab/K1769_figures/k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
Summary of feedback from opening
/home/ana/Documents/__BajicLab/K1769_figures/k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
---
warnings | Ignored bad PDB record found on line 260
SSBOND *** CYS A 14 CYS A 466
Ignored bad PDB record found on line 261
SSBOND *** CYS A 64 CYS A 76
Ignored bad PDB record found on line 262
SSBOND *** CYS A 97 CYS A 139
Ignored bad PDB record found on line 263
SSBOND *** CYS A 281 CYS A 305
Ignored bad PDB record found on line 264
SSBOND *** CYS H 22 CYS H 96
11 messages similar to the above omitted
Chain information for
k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb #5
---
Chain | Description
A B C | No description available
H J L | No description available
I K M | No description available
> select add #1
17232 atoms, 17652 bonds, 6 pseudobonds, 2160 residues, 3 models selected
> select subtract #1
9 models selected
> select add #5
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #4.1 models
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #5/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> show sel cartoons
> select #5/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> show sel cartoons
> color sel #a1d76aff
> select #5/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> color sel #4d9221ff
> hide #!5 models
> show #!5 models
> select add #5
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> select subtract #5
Nothing selected
> show #!1 models
> hide #!1 models
> select #5/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> color sel #40bf74ff
> color sel #00bf4eff
> color sel #005824ff
[Repeated 3 time(s)]
> select #5/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> color sel #40bfa1ff
> color sel #87bfb2ff
> color sel #99d8c9ff
[Repeated 3 time(s)]
> select add #5
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> select subtract #5
Nothing selected
> ui tool show "Show Sequence Viewer"
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #1/H,J,L:31 #2/H,J,L:31 #5/H,J,L:31
54 atoms, 45 bonds, 9 residues, 3 models selected
> select #1/H,J,L:31-35 #2/H,J,L:31-35 #5/H,J,L:31-35
423 atoms, 441 bonds, 45 residues, 3 models selected
> color (#!5 & sel) #bf9640ff
> color (#!5 & sel) #bf9e59ff
> color (#!5 & sel) #d8b365ff
[Repeated 4 time(s)]
> select #1/H,J,L:50 #2/H,J,L:50 #5/H,J,L:50
126 atoms, 135 bonds, 9 residues, 3 models selected
> select #1/H,J,L:50-59 #2/H,J,L:50-59 #5/H,J,L:50-59
738 atoms, 756 bonds, 90 residues, 3 models selected
> select #1/H,J,L:50 #2/H,J,L:50 #5/H,J,L:50
126 atoms, 135 bonds, 9 residues, 3 models selected
> select #1/H,J,L:50-66 #2/H,J,L:50-66 #5/H,J,L:50-66
1269 atoms, 1305 bonds, 153 residues, 3 models selected
> color (#!5 & sel) #bf9640ff
> color (#!5 & sel) #bf9e59ff
> color (#!5 & sel) #d8b365ff
[Repeated 1 time(s)]
> select #1/H,J,L:99 #2/H,J,L:99 #5/H,J,L:99
72 atoms, 63 bonds, 9 residues, 3 models selected
> select #1/H,J,L:99-110 #2/H,J,L:99-110 #5/H,J,L:99-110
864 atoms, 909 bonds, 108 residues, 3 models selected
> color (#!5 & sel) #bf9640ff
> color (#!5 & sel) #bf9e59ff
> color (#!5 & sel) #d8b365ff
[Repeated 1 time(s)]
> select #1/H,J,L:26 #2/H,J,L:26 #5/H,J,L:26
36 atoms, 27 bonds, 9 residues, 3 models selected
> select #1/H,J,L:26-32 #2/H,J,L:26-32 #5/H,J,L:26-32
531 atoms, 549 bonds, 63 residues, 3 models selected
> color (#!5 & sel) #bf9c40ff
> color (#!5 & sel) #bfb498ff
> color (#!5 & sel) #f6e8c3ff
[Repeated 3 time(s)]
> select #1/H,J,L:52 #2/H,J,L:52 #5/H,J,L:52
81 atoms, 72 bonds, 9 residues, 3 models selected
> select #1/H,J,L:52-57 #2/H,J,L:52-57 #5/H,J,L:52-57
405 atoms, 405 bonds, 54 residues, 3 models selected
> color (#!5 & sel) #d8b365ff
> color (#!5 & sel) #f6e8c3ff
> select #1/H,J,L:99 #2/H,J,L:99 #5/H,J,L:99
72 atoms, 63 bonds, 9 residues, 3 models selected
> select #1/H,J,L:99-110 #2/H,J,L:99-110 #5/H,J,L:99-110
864 atoms, 909 bonds, 108 residues, 3 models selected
> color (#!5 & sel) #d8b365ff
> color (#!5 & sel) #f6e8c3ff
> select #1/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show #!5 surfaces
> select add #1
17232 atoms, 17652 bonds, 6 pseudobonds, 2160 residues, 4 models selected
> select subtract #1
9 models selected
> select add #1
17232 atoms, 17652 bonds, 6 pseudobonds, 2160 residues, 3 models selected
> hide #!5 surfaces
> select #1/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show #!5 cartoons
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!5 & sel) #fde0efff
> color (#!5 & sel) #e9a3c9ff
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!5 & sel) light gray
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!5 & sel) light gray
> select clear
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #1/I,K,M:109 #2/I,K,M:109 #5/I,K,M:109
63 atoms, 54 bonds, 9 residues, 3 models selected
> select #1/I,K,M #2/I,K,M #5/I,K,M
7515 atoms, 7677 bonds, 981 residues, 3 models selected
> save "/home/ana/Documents/__BajicLab/K1769_figures/light chain" format fasta
> alignment 3
Alignment identifier is 1
> select #1/I,K,M:24 #2/I,K,M:24 #5/I,K,M:24
99 atoms, 90 bonds, 9 residues, 3 models selected
> select #1/I,K,M:24-34 #2/I,K,M:24-34 #5/I,K,M:24-34
864 atoms, 873 bonds, 99 residues, 3 models selected
> color (#!5 & sel) #bf8540ff
> color (#!5 & sel) #bf6f0eff
> color (#!5 & sel) #8c510aff
[Repeated 3 time(s)]
> select #1/I,K,M:50 #2/I,K,M:50 #5/I,K,M:50
36 atoms, 27 bonds, 9 residues, 3 models selected
> select #1/I,K,M:50-56 #2/I,K,M:50-56 #5/I,K,M:50-56
405 atoms, 396 bonds, 63 residues, 3 models selected
> color (#!5 & sel) #f6e8c3ff
> color (#!5 & sel) #8c510aff
> select #1/I,K,M:89 #2/I,K,M:89 #5/I,K,M:89
81 atoms, 72 bonds, 9 residues, 3 models selected
> select #1/I,K,M:89-97 #2/I,K,M:89-97 #5/I,K,M:89-97
630 atoms, 639 bonds, 81 residues, 3 models selected
> color (#!5 & sel) #f6e8c3ff
> color (#!5 & sel) #8c510aff
> select #1/I,K,M:1 #2/I,K,M:1 #5/I,K,M:1
72 atoms, 63 bonds, 9 residues, 3 models selected
> select #1/I,K,M:1-23 #2/I,K,M:1-23 #5/I,K,M:1-23
1476 atoms, 1476 bonds, 207 residues, 3 models selected
> color (#!5 & sel) #bf8940ff
> color (#!5 & sel) #bf812dff
[Repeated 4 time(s)]
> undo
[Repeated 5 time(s)]
> select #1/I,K,M:24 #2/I,K,M:24 #5/I,K,M:24
99 atoms, 90 bonds, 9 residues, 3 models selected
> select #1/I,K,M:24-34 #2/I,K,M:24-34 #5/I,K,M:24-34
864 atoms, 873 bonds, 99 residues, 3 models selected
> select #1/I,K,M:50 #2/I,K,M:50 #5/I,K,M:50
36 atoms, 27 bonds, 9 residues, 3 models selected
> select #1/I,K,M:50-56 #2/I,K,M:50-56 #5/I,K,M:50-56
405 atoms, 396 bonds, 63 residues, 3 models selected
> select #1/I,K,M:89 #2/I,K,M:89 #5/I,K,M:89
81 atoms, 72 bonds, 9 residues, 3 models selected
> select #1/I,K,M:89-97 #2/I,K,M:89-97 #5/I,K,M:89-97
630 atoms, 639 bonds, 81 residues, 3 models selected
> select clear
> select #5/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select #1/B:45,25,27,33,315,313,312,310,308,498
> #1/J:1,28,30,31,32,106,105,104,103,101
179 atoms, 171 bonds, 2 pseudobonds, 20 residues, 2 models selected
> view sel
> show #!1 models
> hide #!1 models
> show #!1 models
> style sel stick
Changed 179 atom styles
> style sel ball
Changed 179 atom styles
> color (#!1 & sel) byhetero
> hide #!1 models
> select add #1
17232 atoms, 17652 bonds, 6 pseudobonds, 2160 residues, 5 models selected
> select subtract #1
9 models selected
> select #5/B:45,25,27,33,315,313,312,310,308,498
> #5/J:1,28,30,31,32,106,105,104,103,101
179 atoms, 171 bonds, 20 residues, 1 model selected
> style sel ball
Changed 179 atom styles
> style sel ball
Changed 179 atom styles
> show sel atoms
> color (#!5 & sel) byhetero
> select #5/J:1,28,30,31,32,106,105,104,103,101
88 atoms, 87 bonds, 10 residues, 1 model selected
> show sel atoms
> select #5/B:45,25,27,33,315,313,312,310,308,498
91 atoms, 84 bonds, 10 residues, 1 model selected
> select add #5
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 13 models selected
> transparency #5 80 ribbons
> select subtract #5
9 models selected
> select #5/B:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> transparency #5 60 ribbons
> select #5/B:45,25,27,33,315,313,312,310,308,498
> #5/J:1,28,30,31,32,106,105,104,103,101
179 atoms, 171 bonds, 20 residues, 1 model selected
> view sel
> select add #5
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 14 models selected
> select subtract #5
9 models selected
> hide #!5.10 models
> hide #!5.9 models
> hide #!5.8 models
> hide #5.7 models
> hide #!5.6 models
> hide #5.5 models
> hide #!5.4 models
> hide #!5.3 models
> hide #!5.2 models
> hide #5.1 models
> hide #!5 models
> show #!5 models
> show #5.10 models
> hide #5.10 models
> show (#!5 & sidechain) target ab
> undo
> select #5/B:45,25,27,33,315,313,312,310,308,498
> #5/J:1,28,30,31,32,106,105,104,103,101
179 atoms, 171 bonds, 20 residues, 1 model selected
> show (#!5 & sel-residues & sidechain) target ab
> style (#!5 & sel) ringFill thin
Changed 20 residue ring styles
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> view sel
> show #!1 models
> hide #!1 models
> show #!2 models
> style sel stick
Changed 179 atom styles
> transparency #2 60 ribbons
> select clear
> transparency #2 60 ribbons
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot-x270plus-y60_v5.cxs
——— End of log from Wed Sep 11 11:34:53 2024 ———
opened ChimeraX session
> view orient
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel surfaces
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel surfaces
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel surfaces
Alignment identifier is 2/C
[Repeated 1 time(s)]
> select clear
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #1/I,K,M:27 #2/I,K,M:27 #5/I,K,M:27
81 atoms, 72 bonds, 9 residues, 3 models selected
> select #1/I,K,M:27-31 #2/I,K,M:27-31 #5/I,K,M:27-31
414 atoms, 414 bonds, 45 residues, 3 models selected
> select #1/I,K,M:27 #2/I,K,M:27 #5/I,K,M:27
81 atoms, 72 bonds, 9 residues, 3 models selected
> select #1/I,K,M:27-32 #2/I,K,M:27-32 #5/I,K,M:27-32
522 atoms, 531 bonds, 54 residues, 3 models selected
> select #1/I,K,M:89 #2/I,K,M:89 #5/I,K,M:89
81 atoms, 72 bonds, 9 residues, 3 models selected
> select #1/I,K,M:89-97 #2/I,K,M:89-97 #5/I,K,M:89-97
630 atoms, 639 bonds, 81 residues, 3 models selected
> select #1/I,K,M:4-7,9-14,18-25,32-38,44-47,61-66,70-76,83-91,101-107
> #2/I,K,M:4-7,9-14,18-25,32-38,44-47,61-66,70-76,83-91,101-107
> #5/I,K,M:4-7,9-14,18-25,32-38,44-47,61-66,70-76,83-91,101-107
4149 atoms, 4158 bonds, 522 residues, 3 models selected
> select #1/I,K,M:33 #2/I,K,M:33 #5/I,K,M:33
72 atoms, 63 bonds, 9 residues, 3 models selected
> select #1/I,K,M:33-49 #2/I,K,M:33-49 #5/I,K,M:33-49
1242 atoms, 1278 bonds, 153 residues, 3 models selected
> select #1/H,J,L:26 #2/H,J,L:26 #5/H,J,L:26
36 atoms, 27 bonds, 9 residues, 3 models selected
> select #1/H,J,L:26-33 #2/H,J,L:26-33 #5/H,J,L:26-33
639 atoms, 666 bonds, 72 residues, 3 models selected
> select #1/H,J,L:51 #2/H,J,L:51 #5/H,J,L:51
72 atoms, 63 bonds, 9 residues, 3 models selected
> select #1/H,J,L:51-58 #2/H,J,L:51-58 #5/H,J,L:51-58
540 atoms, 540 bonds, 72 residues, 3 models selected
> select #1/H,J,L:97 #2/H,J,L:97 #5/H,J,L:97
45 atoms, 36 bonds, 9 residues, 3 models selected
> select #1/H,J,L:97-110 #2/H,J,L:97-110 #5/H,J,L:97-110
1008 atoms, 1053 bonds, 126 residues, 3 models selected
> select
> #1/H,J,L:3-13,17-25,33-39,48-52,57-61,67-74,77-84,91-99,109-112,114-120
> #2/H,J,L:3-13,17-25,33-39,48-52,57-61,67-74,77-84,91-99,109-112,114-120
> #5/H,J,L:3-13,17-25,33-39,48-52,57-61,67-74,77-84,91-99,109-112,114-120
5265 atoms, 5292 bonds, 657 residues, 3 models selected
> select #1/H,J,L:34 #2/H,J,L:34 #5/H,J,L:34
72 atoms, 63 bonds, 9 residues, 3 models selected
> select #1/H,J,L:34-50 #2/H,J,L:34-50 #5/H,J,L:34-50
1305 atoms, 1368 bonds, 153 residues, 3 models selected
> select #1/H,J,L:101 #2/H,J,L:101 #5/H,J,L:101
126 atoms, 135 bonds, 9 residues, 3 models selected
> select #1/H,J,L:101-107 #2/H,J,L:101-107 #5/H,J,L:101-107
522 atoms, 549 bonds, 63 residues, 3 models selected
> select #1/H,J,L:111 #2/H,J,L:111 #5/H,J,L:111
126 atoms, 135 bonds, 9 residues, 3 models selected
> select #1/H,J,L:111-114 #2/H,J,L:111-114 #5/H,J,L:111-114
279 atoms, 288 bonds, 36 residues, 3 models selected
> select clear
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2 & sel) #ad40bfff
> color (#!2 & sel) #ac3dbfff
> color (#!2 & sel) #762a83ff
[Repeated 1 time(s)]
> color (#!2 & sel) #762a83e3
[Repeated 1 time(s)]
> color (#!2 & sel) #762a83d4
> color (#!2 & sel) #762a83c8
> color (#!2 & sel) #762a83bc
> color (#!2 & sel) #762a83aa
> color (#!2 & sel) #762a8392
> color (#!2 & sel) #762a837a
> color (#!2 & sel) #762a8366
> color (#!2 & sel) #762a835a
> color (#!2 & sel) #762a8347
> color (#!2 & sel) #762a833f
> color (#!2 & sel) #762a8339
> color (#!2 & sel) #762a832f
> color (#!2 & sel) #762a832e
> color (#!2 & sel) #762a832b
> color (#!2 & sel) #762a8329
> color (#!2 & sel) #762a8328
> color (#!2 & sel) #762a831f
> color (#!2 & sel) #762a8322
> color (#!2 & sel) #762a8352
> color (#!2 & sel) #762a8385
> color (#!2 & sel) #762a83ae
> color (#!2 & sel) #762a83fa
> color (#!2 & sel) #762a83ff
[Repeated 2 time(s)]
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2 & sel) #9840bfff
> color (#!2 & sel) #ab7dbfff
> color (#!2 & sel) #9970abff
[Repeated 4 time(s)]
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2 & sel) #9840bfff
> color (#!2 & sel) #b398bfff
> color (#!2 & sel) #c2a5cfff
[Repeated 3 time(s)]
> select clear
> select #1/H#2/H#5/H
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2 & sel) #bf8540ff
> color (#!2 & sel) #bf6f0eff
> color (#!2 & sel) #8c510aff
[Repeated 3 time(s)]
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> ui tool show "Color Actions"
> color (#!2 & sel) #bf8540ff
> color (#!2 & sel) #bf6f0eff
> color (#!2 & sel) #8c510aff
[Repeated 1 time(s)]
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2 & sel) #bf8540ff
> color (#!2 & sel) #bf6f0eff
> color (#!2 & sel) #8c510aff
[Repeated 1 time(s)]
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2 & sel) #71bf40ff
> color (#!2 & sel) #65bf2bff
> color (#!2 & sel) #4d9221ff
[Repeated 4 time(s)]
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2 & sel) #71bf40ff
> color (#!2 & sel) #65bf2bff
> color (#!2 & sel) #4d9221ff
[Repeated 1 time(s)]
> color (#!2 & sel) #71bf40ff
> color (#!2 & sel) #65bf2bff
> color (#!2 & sel) #4d9221ff
[Repeated 1 time(s)]
> select #1/M#2/M#5/M
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2 & sel) #71bf40ff
> color (#!2 & sel) #65bf2bff
> color (#!2 & sel) #4d9221ff
[Repeated 1 time(s)]
> select clear
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #1/H,J,L:26 #2/H,J,L:26 #5/H,J,L:26
36 atoms, 27 bonds, 9 residues, 3 models selected
> select #1/H,J,L:26-33 #2/H,J,L:26-33 #5/H,J,L:26-33
639 atoms, 666 bonds, 72 residues, 3 models selected
> color (#!2 & sel) #bf8940ff
> color (#!2 & sel) #bf812dff
[Repeated 2 time(s)]
> color (#!2 & sel) #bf942dff
> color (#!2 & sel) #bfa66bff
> color (#!2 & sel) #dfc27dff
[Repeated 3 time(s)]
> select #1/H,J,L:51 #2/H,J,L:51 #5/H,J,L:51
72 atoms, 63 bonds, 9 residues, 3 models selected
> select #1/H,J,L:51-58 #2/H,J,L:51-58 #5/H,J,L:51-58
540 atoms, 540 bonds, 72 residues, 3 models selected
> color (#!2 & sel) #bf9a40ff
> color (#!2 & sel) #bfa66bff
> color (#!2 & sel) #dfc27dff
[Repeated 1 time(s)]
> select #1/H,J,L:97 #2/H,J,L:97 #5/H,J,L:97
45 atoms, 36 bonds, 9 residues, 3 models selected
> select #1/H,J,L:97-110 #2/H,J,L:97-110 #5/H,J,L:97-110
1008 atoms, 1053 bonds, 126 residues, 3 models selected
> color (#!2 & sel) #bf9a40ff
> color (#!2 & sel) #bfa66bff
> color (#!2 & sel) #dfc27dff
[Repeated 1 time(s)]
> select clear
> select #1/I,K,M:27 #2/I,K,M:27 #5/I,K,M:27
81 atoms, 72 bonds, 9 residues, 3 models selected
> select #1/I,K,M:27-32 #2/I,K,M:27-32 #5/I,K,M:27-32
522 atoms, 531 bonds, 54 residues, 3 models selected
> color (#!2 & sel) #80bf40ff
> color (#!2 & sel) #81bf42ff
> color (#!2 & sel) #7fbc41ff
[Repeated 1 time(s)]
> color (#!2 & sel) #85bc41ff
> color (#!2 & sel) #9abc70ff
> color (#!2 & sel) #b8e186ff
[Repeated 3 time(s)]
> select #1/I,K,M:50 #2/I,K,M:50 #5/I,K,M:50
36 atoms, 27 bonds, 9 residues, 3 models selected
> select #1/I,K,M:50-52 #2/I,K,M:50-52 #5/I,K,M:50-52
135 atoms, 126 bonds, 27 residues, 3 models selected
> color (#!2 & sel) #86bf40ff
> color (#!2 & sel) #9cbf72ff
> color (#!2 & sel) #b8e186ff
[Repeated 1 time(s)]
> select #1/I,K,M:89 #2/I,K,M:89 #5/I,K,M:89
81 atoms, 72 bonds, 9 residues, 3 models selected
> select #1/I,K,M:89-97 #2/I,K,M:89-97 #5/I,K,M:89-97
630 atoms, 639 bonds, 81 residues, 3 models selected
> color (#!2 & sel) #86bf40ff
> color (#!2 & sel) #9cbf72ff
> color (#!2 & sel) #b8e186ff
[Repeated 1 time(s)]
> select clear
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #1/H,J,L:26 #2/H,J,L:26 #5/H,J,L:26
36 atoms, 27 bonds, 9 residues, 3 models selected
> select #1/H,J,L:26-33 #2/H,J,L:26-33 #5/H,J,L:26-33
639 atoms, 666 bonds, 72 residues, 3 models selected
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2 & sel) #bf9a40ff
> color (#!2 & sel) #bfa66bff
> color (#!2 & sel) #dfc27dff
[Repeated 3 time(s)]
> select #1/H,J,L:26 #2/H,J,L:26 #5/H,J,L:26
36 atoms, 27 bonds, 9 residues, 3 models selected
> select #1/H,J,L:26-33 #2/H,J,L:26-33 #5/H,J,L:26-33
639 atoms, 666 bonds, 72 residues, 3 models selected
> color (#!2 & sel) #bf8540ff
> color (#!2 & sel) #bf6f0eff
> color (#!2 & sel) #8c510aff
[Repeated 3 time(s)]
> select #1/H,J,L:51 #2/H,J,L:51 #5/H,J,L:51
72 atoms, 63 bonds, 9 residues, 3 models selected
> select #1/H,J,L:51-58 #2/H,J,L:51-58 #5/H,J,L:51-58
540 atoms, 540 bonds, 72 residues, 3 models selected
> color (#!2 & sel) #bf8540ff
> color (#!2 & sel) #bf6f0eff
> color (#!2 & sel) #8c510aff
[Repeated 1 time(s)]
> select #1/H,J,L:97 #2/H,J,L:97 #5/H,J,L:97
45 atoms, 36 bonds, 9 residues, 3 models selected
> select #1/H,J,L:97-110 #2/H,J,L:97-110 #5/H,J,L:97-110
1008 atoms, 1053 bonds, 126 residues, 3 models selected
> ui tool show "Color Actions"
> color (#!2 & sel) #bf8540ff
> color (#!2 & sel) #bf6f0eff
> color (#!2 & sel) #8c510aff
[Repeated 1 time(s)]
> select clear
> view orient
[Repeated 2 time(s)]
> turn -y 60
> view orient
> turn -y 60
> turn -z 60
> undo
> turn -y 10
[Repeated 7 time(s)]
> undo
[Repeated 8 time(s)]
> turn -y 60
> turn -x 60
[Repeated 5 time(s)]
> turn x 60
[Repeated 9 time(s)]
> turn x 10
[Repeated 51 time(s)]
> turn -x 10
[Repeated 2 time(s)]
> turn x 5
[Repeated 2 time(s)]
> turn y 5
> turn -y 5
[Repeated 9 time(s)]
> turn x 5
[Repeated 1 time(s)]
> turn -y 5
[Repeated 4 time(s)]
> turn -x 5
> turn x 5
[Repeated 1 time(s)]
> select
> #1/H,J,L:3-13,17-25,33-39,48-52,57-61,67-74,77-84,91-99,109-112,114-120
> #2/H,J,L:3-13,17-25,33-39,48-52,57-61,67-74,77-84,91-99,109-112,114-120
> #5/H,J,L:3-13,17-25,33-39,48-52,57-61,67-74,77-84,91-99,109-112,114-120
5265 atoms, 5292 bonds, 657 residues, 3 models selected
> select #1/H,J,L:72 #2/H,J,L:72 #5/H,J,L:72
99 atoms, 90 bonds, 9 residues, 3 models selected
> select #1/H,J,L:72-74 #2/H,J,L:72-74 #5/H,J,L:72-74
234 atoms, 225 bonds, 27 residues, 3 models selected
> view orient
> turn -y 60
> turn x 5
> turn -x 5
> turn x 45
> turn -y 5
[Repeated 7 time(s)]
> turn x 20
> turn y 15
[Repeated 2 time(s)]
> undo
[Repeated 2 time(s)]
> turn x 20
> turn x -20
[Repeated 1 time(s)]
> turn x 20
> turn x -20
> turn y -5
> turn y 5
[Repeated 5 time(s)]
> turn -y 5
[Repeated 9 time(s)]
> turn y 5
[Repeated 6 time(s)]
> turn x 5
[Repeated 2 time(s)]
> turn -x 5
[Repeated 4 time(s)]
> turn z 5
> turn -z 5
[Repeated 3 time(s)]
> view orient
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2 & sel) #dfc27dff
> select #1/H#2/H#5/H
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2 & sel) #b8e186ff
> color (#!2 & sel) #dfc27dff
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/normal-orientation.tif
> width 1979 height 1322 supersample 4 transparentBackground true
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> select ::name="BMA"::name="MAN"::name="NAG"
2106 atoms, 2205 bonds, 162 residues, 3 models selected
> show sel & #!2 atoms
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/normal-orientation2.tif
> width 1979 height 1322 supersample 4 transparentBackground true
> select #1/H,J,L:26 #2/H,J,L:26 #5/H,J,L:26
36 atoms, 27 bonds, 9 residues, 3 models selected
> select #1/H,J,L:26-33 #2/H,J,L:26-33 #5/H,J,L:26-33
639 atoms, 666 bonds, 72 residues, 3 models selected
> color (#!2 & sel) #bf8540ff
> color (#!2 & sel) #bf6f0eff
> color (#!2 & sel) #8c510aff
[Repeated 3 time(s)]
> select clear
> select #1/H,J,L:51 #2/H,J,L:51 #5/H,J,L:51
72 atoms, 63 bonds, 9 residues, 3 models selected
> select #1/H,J,L:51-58 #2/H,J,L:51-58 #5/H,J,L:51-58
540 atoms, 540 bonds, 72 residues, 3 models selected
> color (#!2 & sel) #bf8540ff
> color (#!2 & sel) #bf6f0eff
> color (#!2 & sel) #8c510aff
[Repeated 1 time(s)]
> select #1/H,J,L:97 #2/H,J,L:97 #5/H,J,L:97
45 atoms, 36 bonds, 9 residues, 3 models selected
> select #1/H,J,L:97-110 #2/H,J,L:97-110 #5/H,J,L:97-110
1008 atoms, 1053 bonds, 126 residues, 3 models selected
> color (#!2 & sel) #bf8540ff
> color (#!2 & sel) #bf6f0eff
> color (#!2 & sel) #8c510aff
[Repeated 1 time(s)]
> select clear
> transparency #2 60 surfaces
> transparency #2 30 surfaces
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/normal-orientation3.tif
> width 1979 height 1322 supersample 4 transparentBackground true
> turn -y 90
> turn -z 10
> turn z 10
[Repeated 1 time(s)]
> turn -z 10
> turn -x 10
[Repeated 34 time(s)]
> view orient
> turn -y 90
> save "/home/ana/Documents/__BajicLab/K1769_figures/normal-orientation turn
> -y90.tif" width 1979 height 1322 supersample 4 transparentBackground true
> turn x 10
[Repeated 1 time(s)]
> save "/home/ana/Documents/__BajicLab/K1769_figures/normal-orientation turn
> -y90plus x20.tif" width 1979 height 1322 supersample 4 transparentBackground
> true
> save "/home/ana/Documents/__BajicLab/K1769_figures/zoom normal-orientation
> turn -y90plus x20.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> turn x 5
[Repeated 1 time(s)]
> turn x -5
> lighting simple
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
[Repeated 1 time(s)]
> lighting full
[Repeated 2 time(s)]
> lighting simple
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2 cartoons
> show sel & #!2 cartoons
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2 cartoons
> save "/home/ana/Documents/__BajicLab/K1769_figures/normal-orientation turn
> -y90plus x15_zoom-good.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> show sel & #!2 cartoons
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/normal-orientation turn
> -y90plus x15_.tif" width 1979 height 1322 supersample 4
> transparentBackground true
[Repeated 1 time(s)]
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2 cartoons
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2 cartoons
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2 cartoons
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2 cartoons
> select #1/M#2/M#5/M
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2 cartoons
> select #2/J:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> 51-58; 97-110
Unknown command: 51-58; 97-110
> select #2/J:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> 51-58;97-110
Unknown command: 51-58;97-110
> select #2/J:26-33,51-58,797-110
131 atoms, 134 bonds, 16 residues, 1 model selected
> show sel cartoons
> select #2/J:26-33,51-58,97-110
243 atoms, 251 bonds, 30 residues, 1 model selected
> show sel cartoons
> select #2/J:70-74
41 atoms, 40 bonds, 5 residues, 1 model selected
> show sel cartoons
> select #2/J:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> show sel cartoons
> select #2/K:27-32,50-52,89-97,70-80
227 atoms, 229 bonds, 29 residues, 1 model selected
> show sel cartoons
> select #2/K:70-80
84 atoms, 85 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select #1/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> show #!2 cartoons
> undo
> select #1/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> show #!2 cartoons
> hide #!2 cartoons
> select clear
> transparency #2 0 surfaces
> select #2/K:27-32,50-52,89-97
143 atoms, 144 bonds, 18 residues, 1 model selected
> show sel cartoons
> select #2/J:26-33,51-58,97-110, 70-74
284 atoms, 291 bonds, 35 residues, 1 model selected
> show sel cartoons
> select clear
> select #2/J:26-33,51-58,97-110, 70-80
331 atoms, 340 bonds, 41 residues, 1 model selected
> show sel cartoons
> select clear
> select #2/J:26-33,51-58,97-110, 70-80
331 atoms, 340 bonds, 41 residues, 1 model selected
> view sel
> select clear
> select #5/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> show #!2 cartoons
> transparency #5 80 ribbons
> transparency #5 80 ribbons
> transparency #2 80 ribbons
> transparency #2 90 ribbons
> select #2/J:26-33,51-58,97-110, 70-80
331 atoms, 340 bonds, 41 residues, 1 model selected
> transparency sel 0
> transparency #2/J:26-33,51-58,97-110, 70-80 0 ribbons
> transparency #2/K:27-32,50-52,89-97 0 ribbons
> select #2/J:26-33,51-58,97-110, 70-80 #2/K:27-32,50-52,89-97
474 atoms, 484 bonds, 59 residues, 1 model selected
> view sel
> view orient
> turn -y 90
> turn x 15
> turn -z 90
> turn z 90
[Repeated 1 time(s)]
> turn -z 90
[Repeated 7 time(s)]
> view orient
> select up
912 atoms, 941 bonds, 110 residues, 1 model selected
> select up
1782 atoms, 1827 bonds, 230 residues, 1 model selected
> turn -z 90
> undo
> turn -y 90
> turn -z 90
> turn z 90
[Repeated 1 time(s)]
> turn x 90
> turn -x 90
> turn x 10
> turn x -10
> turn y -10
[Repeated 3 time(s)]
> turn y 30
[Repeated 4 time(s)]
> view orient
> turn y -90
> turn z 90
> turn y 90
> select #2/J:26-33,51-58,97-110, 70-80 #2/K:27-32,50-52,89-97
474 atoms, 484 bonds, 59 residues, 1 model selected
> view sel
> select clear
> select ::name="BMA"::name="MAN"::name="NAG"
2106 atoms, 2205 bonds, 162 residues, 3 models selected
> hide sel & #!2 atoms
> select #2/B:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> show sel atoms
> select #2/B:500
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:501
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:502
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:503
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:504
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:505
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:506
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:503
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:504
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:505
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> save "/home/ana/Documents/__BajicLab/K1769_figures/zoom normal-orientation
> turn -y90plus z 90 y90.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> select add #5
17243 atoms, 17663 bonds, 3 pseudobonds, 2161 residues, 3 models selected
> select add #2
34464 atoms, 35304 bonds, 6 pseudobonds, 4320 residues, 16 models selected
> select subtract #2
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 14 models selected
> show #!5 models
> hide sel atoms
> select #5/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> color (#!5 & sel) #dfc27dff
> select #5/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> color (#!5 & sel) #4d9221ff
> select #1/I,K,M:27 #2/I,K,M:27 #5/I,K,M:27
81 atoms, 72 bonds, 9 residues, 3 models selected
> select #1/I,K,M:27-32 #2/I,K,M:27-32 #5/I,K,M:27-32
522 atoms, 531 bonds, 54 residues, 3 models selected
> select #1/I,K,M:27-32,50-52 #2/I,K,M:27-32,50-52 #5/I,K,M:27-32,50-52
657 atoms, 657 bonds, 81 residues, 3 models selected
> select #1/I,K,M:27-32,50-52,89-97 #2/I,K,M:27-32,50-52,89-97
> #5/I,K,M:27-32,50-52,89-97
1287 atoms, 1296 bonds, 162 residues, 3 models selected
> color (#!2,5 & sel) #b8e186ff
> select #1/H,J,L:26 #2/H,J,L:26 #5/H,J,L:26
36 atoms, 27 bonds, 9 residues, 3 models selected
> select #1/H,J,L:26-33 #2/H,J,L:26-33 #5/H,J,L:26-33
639 atoms, 666 bonds, 72 residues, 3 models selected
> select #1/H,J,L:26-33,51-58 #2/H,J,L:26-33,51-58 #5/H,J,L:26-33,51-58
1179 atoms, 1206 bonds, 144 residues, 3 models selected
> select #1/H,J,L:26-33,51-58,97-110 #2/H,J,L:26-33,51-58,97-110
> #5/H,J,L:26-33,51-58,97-110
2187 atoms, 2259 bonds, 270 residues, 3 models selected
> color (#!2,5 & sel) #bf8540ff
> color (#!2,5 & sel) #bf6f0eff
> color (#!2,5 & sel) #8c510aff
[Repeated 3 time(s)]
> select clear
> select #1/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> transparency #2#!5 40
> undo
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> save "/home/ana/Documents/__BajicLab/K1769_figures/zoom normal-orientation
> turn -y90plus z 90 y90 zoom cdrs.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v6.cxs
> show #!5 models
> select add #5
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> transparency (#!5 & sel) 60
> transparency #5 80 ribbons
> transparency #5/J:26-33,51-58,97-110, 70-80 0 ribbons
> transparency #5/K:27-32,50-52,89-97 0 ribbons
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5/K:27-32,50-52,89-97 0 ribbon
Expected a keyword
> select clear
> select #5/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> select #5/K 80 ribbon
Expected a keyword
> select #5/K 80 ribbon
Expected a keyword
> transparency #5/K 80 ribbons
> transparency #5/K 90 ribbons
> select #5/K:27-32,50-52,89-97 0 ribbon
Expected a keyword
> transparency #5/K:27-32,50-52,89-97 0 ribbons
> select clear
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!5 models
> show #!2 models
> transparency #2 0 surfaces
> save "/home/ana/Documents/__BajicLab/K1769_figures/2nd normal-orientation
> turn -y90plus z 90 y90 zoom cdrs.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> transparency #5/J:31,103,104,105,106
Missing or invalid "percent" argument: Expected a number
> select #5/J:31,103,104,105,106
39 atoms, 38 bonds, 5 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> style sel ball
Changed 39 atom styles
> style sel stick
Changed 39 atom styles
> style sel ball
Changed 39 atom styles
> select clear
> turn z 5
> turn z -5
> turn y -5
[Repeated 1 time(s)]
> turn y 10
[Repeated 1 time(s)]
> undo
[Repeated 5 time(s)]
> select #5/B:27,32,33,45,312,315
49 atoms, 44 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 49 atom styles
> style sel stick
Changed 49 atom styles
> style sel stick
Changed 49 atom styles
> style sel stick
Changed 49 atom styles
> transparency #5/B:27,32,33,45,312,315 0 atoms
> hide #!2 models
> show #!2 models
> transparency (#!5 & sel) 60
> transparency #2 60 surfaces
> transparency #2 70 surfaces
> select #5/B:27,32,33,45,312,315
49 atoms, 44 bonds, 6 residues, 1 model selected
> color (#!5 & sel) byhetero
> select clear
> select #5/J:31,103,104,105,106
39 atoms, 38 bonds, 5 residues, 1 model selected
> style sel stick
Changed 39 atom styles
> select clear
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> select #5/k:28,30,31,32,92
53 atoms, 53 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 53 atom styles
> color (#!5 & sel) byhetero
> select clear
> select #5/B:21,23,24,25,35,315
44 atoms, 41 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 44 atom styles
> color (#!5 & sel) byhetero
> select clear
> select #2/L
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel cartoons
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #5/J:31,103,104,105,106
39 atoms, 38 bonds, 5 residues, 1 model selected
> style (#!5 & sel) ringFill off
Changed 5 residue ring styles
> select clear
> select #5/K:27-32,50-52,89-97
143 atoms, 144 bonds, 18 residues, 1 model selected
> color (#!5 & sel) #40bf66ff
> color (#!5 & sel) #2bbf58ff
> color (#!5 & sel) #1b7837ff
[Repeated 4 time(s)]
> color (#!5 & sel) byhetero
> select #2/K:27-32,50-52,89-97
143 atoms, 144 bonds, 18 residues, 1 model selected
> color sel #b8e186ff
> color sel #1b7837ff
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v7.cxs
> save "/home/ana/Documents/__BajicLab/K1769_figures/3nd turn -y90plus z 90
> y90 zoom cdrs.tif" width 1979 height 1322 supersample 3
> select #5/K:28@NH2 #5/B:21@O
2 atoms, 2 residues, 1 model selected
> distance #5/K:28@NH2 #5/B:21@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/K ARG 28 NH2 and /B PRO 21 O: 3.715Å
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> toolshed show
> ui tool show "Color Actions"
> distance #5/K:28@NH2 #5/B:21@O color gold
Distance already exists; modify distance properties with 'distance style'
> distance style #5/K:28@NH2 #5/B:21@O color gold
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #5/B:21,23,24,25,35,315
44 atoms, 41 bonds, 6 residues, 1 model selected
> show (#!5 & sel-residues & sidechain) target ab
[Repeated 1 time(s)]
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select #5/K:27-32,50-52,89-97
143 atoms, 144 bonds, 18 residues, 1 model selected
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> show sel atoms
> style sel stick
Changed 143 atom styles
> select clear
> select #5/B:21,23,24,25,35,315
44 atoms, 41 bonds, 6 residues, 1 model selected
> select #5/B:21,23,24,25,35,315
44 atoms, 41 bonds, 6 residues, 1 model selected
> select #5/J:31,103,104,105,106
39 atoms, 38 bonds, 5 residues, 1 model selected
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select #5/B:21,23,24,25,35,315
44 atoms, 41 bonds, 6 residues, 1 model selected
> select #5/B:27,32,33,45,312,315
49 atoms, 44 bonds, 6 residues, 1 model selected
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select #5/B:57,72,74
20 atoms, 18 bonds, 3 residues, 1 model selected
> show sel atoms
[Repeated 2 time(s)]
> hide #!2 models
> show #!2 models
> color (#!5 & sel) byhetero
> select #2/B:57,72,74
20 atoms, 18 bonds, 3 residues, 1 model selected
> select #5/B:57,72,74
20 atoms, 18 bonds, 3 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #5/J:57,72,74
29 atoms, 26 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 29 atom styles
> color (#!5 & sel) byhetero
> show (#!5 & sel-residues & sidechain) target ab
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select clear
> select #5/C:382,385,386,390
29 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 29 atom styles
> color (#!5 & sel) byhetero
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select clear
> distance #5/K:30@OG #5/B:23@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/K SER 30 OG and /B GLY 23 O: 2.613Å
> distance #5/K:31@OH #5/B:24@OG1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/K TYR 31 OH and /B THR 24 OG1: 3.279Å
> distance #5/K:92@OH #5/B:35@OE1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/K TYR 92 OH and /B GLU 35 OE1: 3.335Å
> distance #5/K:30@OG #5/B:23@N
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/K SER 30 OG and /B GLY 23 N: 2.416Å
> distance #5/K:32@OH #5/B:25@N
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/K TYR 32 OH and /B ILE 25 N: 3.177Å
> distance #5/K:32@OH #5/B:315@NZ
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/K TYR 32 OH and /B LYS 315 NZ: 3.850Å
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v8.cxs
> distance #5/J:103@N #5/B:33@OE1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J SER 103 N and /B GLN 33 OE1: 3.007Å
> distance #5/J:103@OG #5/B:32@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J SER 103 OG and /B ASP 32 O: 2.849Å
> distance #5/J:103@OG #5/B:33@OE1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J SER 103 OG and /B GLN 33 OE1: 3.544Å
> distance #5/J:106@ND2 #5/B:315@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ASN 106 ND2 and /B LYS 315 O: 13.262Å
> undo
> redo
> distance style #5/J:106@ND2 #5/B:315@O hide
Expected a keyword
> distance delete #5/J:106@ND2 #5/B:315@O
> distance delete #5/J:106@ND2 #5/B:312@O
> distance #5/J:106@ND2 #5/B:312@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ASN 106 ND2 and /B ASN 312 O: 3.872Å
> distance #5/J:106@ND2 #5/B:45@OG
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ASN 106 ND2 and /B SER 45 OG: 3.472Å
> distance #5/J:31@O #5/B:312@ND2
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J SER 31 O and /B ASN 312 ND2: 3.204Å
> distance #5/J:31@OG #5/B:312@N
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J SER 31 OG and /B ASN 312 N: 2.837Å
> distance #5/J:31@OG #5/B:312@ND2
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J SER 31 OG and /B ASN 312 ND2: 3.807Å
> distance #5/J:103@OG #5/B:27@N
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J SER 103 OG and /B LYS 27 N: 3.811Å
> distance #5/J:103@OG #5/B:27@NZ
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J SER 103 OG and /B LYS 27 NZ: 4.280Å
> distance delete #5/J:103@OG #5/B:27@NZ
> distance #5/J:104@OD1 #5/B:27@NZ
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ASP 104 OD1 and /B LYS 27 NZ: 2.387Å
> distance #5/J:104@OD2 #5/B:312@ND2
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ASP 104 OD2 and /B ASN 312 ND2: 2.883Å
> distance #5/J:105@O #5/B:315@NZ
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J PHE 105 O and /B LYS 315 NZ: 2.967Å
> distance style #5/J:104@OD1 #5/B:27@NZ color blue
> distance style color blue
> distance style #5/J:104@OD1 #5/B:27@NZ color gold
> distance style color gold
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> distance style #5/J:57@NH2 #5/C:382@O
> distance #5/J:57@NH2 #5/C:382@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ARG 57 NH2 and /C ASN 382 O: 3.596Å
> distance #5/J:57@NH2 #5/C:385@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ARG 57 NH2 and /C ILE 385 O: 3.561Å
> distance #5/J:57@NH2 #5/C:386@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ARG 57 NH2 and /C GLY 386 O: 3.147Å
> distance #5/J:72@NH1 #5/C:390@OE1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ARG 72 NH1 and /C GLU 390 OE1: 3.029Å
> distance #5/J:74@OG1 #5/C:390@OE2
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J THR 74 OG1 and /C GLU 390 OE2: 2.476Å
> distance #5/J:72@NH2 #5/C:390@OE1 color black
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ARG 72 NH2 and /C GLU 390 OE1: 3.417Å
> distance #5/J:72@NH1 #5/C:390@OE1 color blue
Distance already exists; modify distance properties with 'distance style'
> distance style #5/J:72@NH1 #5/C:390@OE1 color blue
> distance style color blue
> distance style #5/J:72@NH1 #5/C:390@OE1 color gold
> distance style color gold
> distance delete #5/J:72@NH1 #5/C:390@OE1 color
Expected fewer arguments
> distance delete #5/J:72@NH1 #5/C:390@OE1
> distance #5/J:72@NH1 #5/C:390@OE1 color blue
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ARG 72 NH1 and /C GLU 390 OE1: 3.029Å
> distance #5/J:72@NH2 #5/C:390@OE1 color black
Distance already exists; modify distance properties with 'distance style'
> distance delete #5/J:72@NH2 #5/C:390@OE1
> distance #5/J:72@NH2 #5/C:390@OE1 color black
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ARG 72 NH2 and /C GLU 390 OE1: 3.417Å
> distance #5/J:72@NH1 #5/C:390@OE2 color black
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ARG 72 NH1 and /C GLU 390 OE2: 3.229Å
> distance #5/J:72@NH2 #5/C:390@OE2 color black
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ARG 72 NH2 and /C GLU 390 OE2: 3.679Å
> distance delete #5/J:104@OD1 #5/B:27@NZ
> distance #5/J:104@OD1 #5/B:27@NZ color blue
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#5/J ASP 104 OD1 and /B LYS 27 NZ: 2.387Å
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v9.cxs
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5/K:27-32,50-52,89-97
143 atoms, 144 bonds, 18 residues, 1 model selected
> hide sel atoms
> select #5/K:28,30,31,32,92,
Expected an objects specifier or a keyword
> select #5/K:28,30,31,32,92
53 atoms, 53 bonds, 5 residues, 1 model selected
> show sel atoms
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v10.cxs
——— End of log from Thu Sep 12 18:34:15 2024 ———
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> select #2/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> hide sel & #!2,5 atoms
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2,5 cartoons
> hide sel & #!2,5 atoms
> select #5/K:28,30,31,32,92
53 atoms, 53 bonds, 5 residues, 1 model selected
> show sel atoms
> select #2/K:27-32,50-52,89-97
143 atoms, 144 bonds, 18 residues, 1 model selected
> show sel cartoons
> view sel
[Repeated 2 time(s)]
> transparency #2/K:27-32,50-52,89-97 60 ribbons
> transparency #2/K:27-32,50-52,89-97 80ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #2/K:27-32,50-52,89-97 80 ribbons
> select clear
> view
[Repeated 3 time(s)]
> select #2/K:27-32,50-52,89-97
143 atoms, 144 bonds, 18 residues, 1 model selected
> view sel
> select clear
> select #2/K:27-32,50-52,89-97
143 atoms, 144 bonds, 18 residues, 1 model selected
> view sel
> select #2/K:27-32,50-52,89-97
143 atoms, 144 bonds, 18 residues, 1 model selected
> transparency #2/K:27-32,50-52,89-97 65 ribbons
> select clear
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> hide sel & #!2,5 atoms
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> hide sel & #!2,5 atoms
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> hide sel & #!2,5 atoms
> select clear
> select #5/B:21,23,24,35,25,315
44 atoms, 41 bonds, 6 residues, 1 model selected
> show sel atoms
> select #5/B:499
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> transparency #2/K:27-32,50-52,89-97 40 ribbons
> transparency #2/K:27-32,50-52,89-97 30 ribbons
> view orient
[Repeated 1 time(s)]
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2,5 & sel) light gray
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2,5 & sel) gray
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2,5 & sel) dark gray
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2,5 & sel) dim gray
> transparency (#!2,5 & sel) 90
> transparency (#!2,5 & sel) 30
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2,5 & sel) 30
> transparency (#!2,5 & sel) 40
> transparency (#!2,5 & sel) 50
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2,5 & sel) 50
> transparency (#!2,5 & sel) 60
> transparency (#!2,5 & sel) 70
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2,5 & sel) 70
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2,5 & sel) blue
> transparency (#!2,5 & sel) 80
> color (#!2,5 & sel) cornflower blue
> transparency (#!2,5 & sel) 80
> select #5/B:21,23,24,35,25,315,499
58 atoms, 55 bonds, 7 residues, 1 model selected
> color (#!5 & sel) byhetero
> transparency #5/B:21,23,24,35,25,315,499 0 atoms
> select clear
> select #5/B:21,23,24,35,25,315,499
58 atoms, 55 bonds, 7 residues, 1 model selected
> style sel ball
Changed 58 atom styles
> style sel ball
Changed 58 atom styles
> style sel stick
Changed 58 atom styles
> style sel ball
Changed 58 atom styles
> style sel stick
Changed 58 atom styles
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2,5 & sel) 0
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2,5 & sel) 0
> select #2/K:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> color sel #bf40baff
> color sel #bf16b8ff
> color sel #810f7cff
[Repeated 3 time(s)]
> select #2/K:28,31,32
35 atoms, 35 bonds, 3 residues, 1 model selected
> select #5/K:28,31,32
35 atoms, 35 bonds, 3 residues, 1 model selected
> color (#!5 & sel) #bf40baff
> color (#!5 & sel) #bf16b8ff
> color (#!5 & sel) #810f7cff
[Repeated 1 time(s)]
> color (#!5 & sel) byhetero
> select #2/K:50-52
15 atoms, 14 bonds, 3 residues, 1 model selected
> color sel #7c40bfff
> color sel #9774bfff
> color sel #8c6bb1ff
[Repeated 4 time(s)]
> select #2/K:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> color sel #bf40bcff
> color sel #bf00baff
> color sel #4d004bff
[Repeated 3 time(s)]
> select #2/K:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> select #5/K:92
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!5 & sel) #bf40bcff
> color (#!5 & sel) #bf00baff
> color (#!5 & sel) #4d004bff
[Repeated 1 time(s)]
> color (#!5 & sel) byelement
> color (#!5 & sel) #bf40bcff
> color (#!5 & sel) #bf00baff
> color (#!5 & sel) #4d004bff
[Repeated 1 time(s)]
> color (#!5 & sel) byhetero
> select clear
> select #5/B:499
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel #dfc27dff
> color sel byhetero
> select #5/K:92.30
Expected an objects specifier or a keyword
> select #5/K:30
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!5 & sel) #4d004bff
> color (#!5 & sel) byhetero
> color (#!5 & sel) #810f7cff
> color (#!5 & sel) byhetero
> select clear
> select #5/K:32
12 atoms, 12 bonds, 1 residue, 1 model selected
> view orient
> select clear
> select #2/K:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> color sel #7b40bfff
> color sel #7637bfff
> color sel #542788ff
[Repeated 3 time(s)]
> select #2/K:92
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel #7b40bfff
> color sel #7637bfff
> color sel #542788ff
[Repeated 1 time(s)]
> select #5/K:92
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!5 & sel) #7b40bfff
> color (#!5 & sel) #7637bfff
> color (#!5 & sel) #542788ff
[Repeated 1 time(s)]
> color (#!5 & sel) byhetero
> select clear
> view orient
> turn -y 60
> view orient
> turn -y 60
> turn z 90
> turn x 45
[Repeated 16 time(s)]
> view orient
> turn -y 60
> turn z 90
> turn z 20
> turn -z 20
> turn -y 30
[Repeated 1 time(s)]
> turn y 30
[Repeated 3 time(s)]
> turn y -5
[Repeated 3 time(s)]
> turn y 5
[Repeated 22 time(s)]
> turn y -5
[Repeated 21 time(s)]
> select #1/H#2/H#5/H
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/M#2/M#5/M
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select clear
> select #2/K:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> transparency #2/K:27-32 30 ribbons
> transparency #2/K:27-32 40 ribbons
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v11.cxs
> save "/home/ana/Documents/__BajicLab/K1769_figures/K-B CDRs .tif" width 1979
> height 1322 supersample 4 transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v12.cxs
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v12_CDRs-lightchain-K.cxs
——— End of log from Fri Sep 13 15:03:30 2024 ———
opened ChimeraX session
> select #5/B:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color (#!5 & sel) byhetero
> transparency #5/B:22 30 atoms
> transparency #5/B:22 10 atoms
> transparency #5/B:22 5 atoms
> transparency #5/B:22 0 atoms
> select clear
> select #5/B:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> show (#!5 & sel-residues & sidechain) target ab
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> view orient
> turn z 90
> turn -y 20
> turn -z 20
> view orient
> turn -y 60
> turn z 90
> turn y 40
> turn -z 20
> select clear
> transparency #5/B:499 10 atoms
> transparency #5/B:499 0 atoms
> turn -z 20
> select #5/B:500
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel #b8e186ff
> color sel #dfc27dff
> color sel byhetero
> select #5/B:501
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #b8e186ff
> color sel #dfc27dff
> color sel byhetero
> select #5/B:502
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #b8e186ff
> color sel #dfc27dff
> color sel byhetero
> select #5/B:503
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/B:503
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/B:504
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/B:500-504
67 atoms, 70 bonds, 5 residues, 1 model selected
> hide sel atoms
> view orient
> turn -y 60
> turn z 90
> turn y 60
> turn -z 20
[Repeated 1 time(s)]
> turn z 20
> turn z 5
> turn -z 5
[Repeated 1 time(s)]
> turn -y 20
> turn y 20
> turn x 20
> turn x 10
> view orient
> turn -y 60
> turn z 90
> turn y 60
> turn y -20
> turn y -25
> undo
> turn z -25
> turn x 20
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v13_CDRs-lightchain-K.cxs
> save "/home/ana/Documents/__BajicLab/K1769_figures/K-B
> CDRs_best_modified.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> transparency #5/K:32, 31 30 atoms
> save "/home/ana/Documents/__BajicLab/K1769_figures/K-B
> CDRs_best_modified-2.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/K-B
> CDRs_best_modified-2_no-supersampling.tif" width 1979 height 1322
> supersample 1 transparentBackground true
> select #5/B:499
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/B:499
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel surfaces
> color (#!2 & sel) #b8e186ff
> color (#!2 & sel) #dfc27dff
> transparency (#!2 & sel) 80
> transparency (#!2 & sel) 90
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/K-B
> CDRs_best_modified-3.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v14_CDRs-lightchain-K.cxs
> save "/home/ana/Documents/__BajicLab/K1769_figures/full-HA_zoom-out_K-B
> CDRs_best_modified-3.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 80
> select clear
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 70
> select clear
> select #5/J:26-33,51-58,97-110,70-80
331 atoms, 340 bonds, 41 residues, 1 model selected
> show sel cartoons
> select #5/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> hide sel atoms
> select #5/J:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> color (#!5 & sel) #bf8a40ff
> color (#!5 & sel) #bfa989ff
> color (#!5 & sel) #fee0b6ff
[Repeated 3 time(s)]
> select #5/J:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> color (#!5 & sel) #bf7640ff
> color (#!5 & sel) #bf590cff
> color (#!5 & sel) #7f3b08ff
[Repeated 3 time(s)]
> select #5/J:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> color (#!5 & sel) #bf7c40ff
> color (#!5 & sel) #bf5e06ff
> color (#!5 & sel) #b35806ff
[Repeated 3 time(s)]
> select #5/J:97-110
112 atoms, 117 bonds, 14 residues, 1 model selected
> color (#!5 & sel) #bf8540ff
> color (#!5 & sel) #bf6f11ff
> color (#!5 & sel) #e08214ff
[Repeated 3 time(s)]
> select #5/J:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> color (#!5 & sel) #bf8640ff
> color (#!5 & sel) #bf8b4bff
> color (#!5 & sel) #fdb863ff
[Repeated 1 time(s)]
> color (#!5 & sel) #fd9412ff
> color (#!5 & sel) #f18d11ff
> color (#!5 & sel) #f18602ff
> color (#!5 & sel) #a95e01ff
> color (#!5 & sel) #a96715ff
> color (#!5 & sel) #c97b1aff
> color (#!5 & sel) #c98736ff
> color (#!5 & sel) #e89c3eff
> color (#!5 & sel) #e8a757ff
> color (#!5 & sel) #e9a857ff
> color (#!5 & sel) #e9ab5fff
> color (#!5 & sel) #d29a56ff
> color (#!5 & sel) #d29244ff
> color (#!5 & sel) #b37d3aff
> color (#!5 & sel) #b3701cff
> color (#!5 & sel) #a16419ff
> color (#!5 & sel) #a16215ff
> color (#!5 & sel) #8d5612ff
> color (#!5 & sel) #8d5c1fff
> color (#!5 & sel) #6d4718ff
> color (#!5 & sel) #6d4e28ff
> color (#!5 & sel) #634724ff
> color (#!5 & sel) #634827ff
> color (#!5 & sel) #fdb863ff
[Repeated 4 time(s)]
> select clear
> select #5/B:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ringFill off
Changed 1 residue ring style
> color sel byhetero
> select #5/B:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color (#!5 & sel) byhetero
> select #2/B:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel surfaces
> color (#!2 & sel) cornflower blue
> transparency (#!2 & sel) 80
> color (#!2 & sel) #fee0b6ff
> transparency (#!2 & sel) 80
> select #5/B:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel #7f3b08ff
> color sel #fee0b6ff
> color sel byhetero
> select clear
> select #5/B:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select clear
> select #5/B:33,32,312,45,27,315
49 atoms, 44 bonds, 6 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> select #5/C:390,382,385,386
29 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> select #5/J:57,72,74,31,103,104,106,105
68 atoms, 64 bonds, 8 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> hide #!5 models
> select #2/J:26-33,51-58,97-110,70-80
331 atoms, 340 bonds, 41 residues, 1 model selected
> show sel cartoons
> select #5/J:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> select #2/J:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> color sel #bf8640ff
> color sel #bf8b4bff
> color sel #fdb863ff
[Repeated 4 time(s)]
> select #2/J:97-110
112 atoms, 117 bonds, 14 residues, 1 model selected
> show #!5 models
> hide #!2 models
> show #!2 models
> color sel #bf8540ff
> color sel #bf6f11ff
> color sel #e08214ff
[Repeated 3 time(s)]
> hide #!2 models
> show #!2 models
> select #2/J:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> hide #!2 models
> show #!2 models
> color sel #bf7c40ff
> color sel #bf5e06ff
> color sel #b35806ff
[Repeated 3 time(s)]
> select #2/J:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> color sel byhetero
> undo
> color sel #bf7640ff
> color sel #bf590cff
> color sel #7f3b08ff
[Repeated 3 time(s)]
> select clear
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> save "/home/ana/Documents/__BajicLab/K1769_figures/CDRs only.tif" width 1979
> height 1322 supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/CDRs only zoom out.tif"
> width 1979 height 1322 supersample 4 transparentBackground true
> view orient
> turn -y 60
> turn z 90
> turn y 60
> turn y -20
> turn z -25
> turn x 20
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v15_allCDRS.cxs
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 0
> select #5/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency #2#!4 0
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 0
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2 & sel) 0
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/full HA with CDRs.tif"
> width 1979 height 1322 supersample 3
> save "/home/ana/Documents/__BajicLab/K1769_figures/full HA with CDRS.tif"
> width 1979 height 1322 supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/CDRs only zoom in no
> transparency.tif" width 1979 height 1322 supersample 4 transparentBackground
> true
> turn x 20
[Repeated 4 time(s)]
> undo
[Repeated 4 time(s)]
> turn y 20
[Repeated 2 time(s)]
> save "/home/ana/Documents/__BajicLab/K1769_figures/CDRs only zoom in no
> transparency plus y20.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/CDRs only zoom out no
> transparency plus y20.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> show #!5 models
> show #!3 models
> hide #!3 models
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2,5 & sel) 80
> show #4.1 models
> hide #4.1 models
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2,5 & sel) 80
> select clear
> select #5/B:1,26,26
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color (#!5 & sel) byhetero
> select #5/B:1,26,27
16 atoms, 15 bonds, 2 residues, 1 model selected
> select clear
> select #2/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> hide sel cartoons
> select #5/J:1,26,27
25 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 25 atom styles
> color (#!5 & sel) byhetero
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select clear
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> select #5/B:25,26,24-21,35,499
38 atoms, 36 bonds, 4 residues, 1 model selected
> hide sel atoms
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> select #5/B:23,22,21
19 atoms, 19 bonds, 3 residues, 1 model selected
> hide sel atoms
> select #5/B:23
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/B:23
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/B:24
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5/B:25
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/B:25
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:25
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v16_heavychainCDRs.cxs
> view orient
> turn -y 60
> turn z 90
> turn y 60
> turn y -20
> turn -z 25
> turn x 20
> turn y 20
> turn y 10
[Repeated 3 time(s)]
> select #2/J:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> transparency #2/J:70-80 50 ribbons
> undo
> transparency #2/J:70-80 70 ribbons
[Repeated 1 time(s)]
> undo
> redo
> transparency #5/J:70-80 70 ribbons
> transparency #5/J:70-80 80 ribbons
> transparency #5/J:97-110 80 ribbons
> transparency #2/J:97-110 80 ribbons
> undo
> select #5/J:103,106,31,104,105,57,74,72
68 atoms, 64 bonds, 8 residues, 1 model selected
> show (#!5 & sel-residues & sidechain) target ab
[Repeated 1 time(s)]
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v17_heavychainCDRs.cxs
> save "/home/ana/Documents/__BajicLab/K1769_figures/CDRs heavy chain
> interactions.tif" width 1979 height 1322 supersample 4 transparentBackground
> true
> turn y 10
[Repeated 2 time(s)]
> turn y -10
> select #2/J:103,106,31,104,105,57,74,72
68 atoms, 64 bonds, 8 residues, 1 model selected
> select clear
> transparency #2/J:26-33 80 ribbons
> transparency #2/J:26,27,28,29,30,31,32,33 80 ribbons
[Repeated 1 time(s)]
> transparency #5/J:26,27,28,29,30,31,32,33 80 ribbons
> transparency #5/J:26-33 80 ribbons
> transparency #2/J:26-33 80 ribbons
> transparency #2/J:26-33 50 ribbons
> transparency #2/J:26-33 40 ribbons
> transparency #2/J:51-58 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #2/J:51-58 80 ribbons
> transparency #5/J:51-58 80 ribbons
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/CDRs heavy chain
> interactions 2nd view plus y20.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/CDRs heavy chain
> interactions 2nd view plus y20.cxs"
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 60
> transparency (#!2 & sel) 0
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 60
> transparency (#!2 & sel) 70
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 70
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/CDRs heavy chain
> interactions 2nd view plus y20 less transparency-about70.tif" width 1979
> height 1322 supersample 4 transparentBackground true
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 50
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 50
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/CDRs heavy chain
> interactions 2nd view plus y20 less transparency-about50.tif" width 1979
> height 1322 supersample 4 transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/fist-
> pic_rot_Y-90Z90Y90_v18_heavychainCDRs.cxs
——— End of log from Fri Sep 13 18:39:13 2024 ———
opened ChimeraX session
> select add #2
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 48985 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> show sel surfaces
> hide #!2 models
> hide #!5 models
> show #!5 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #4.1 models
> hide #4.1 models
> hide #!2 models
> hide #!4 models
> show #4.1 models
> show #!2 models
> view orient
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> lighting flat
> lighting soft
> hide sel surfaces
> select clear
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel surfaces
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel surfaces
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel surfaces
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2,5 & sel) #5740bfff
> color (#!2,5 & sel) #a29cbfff
> color (#!2,5 & sel) #b2abd2ff
[Repeated 3 time(s)]
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> ui tool show "Color Actions"
> color (#!2,5 & sel) #5d40bfff
> color (#!2,5 & sel) #8e80bfff
> color (#!2,5 & sel) #8073acff
[Repeated 3 time(s)]
> color (#!2,5 & sel) #5740bfff
> color (#!2,5 & sel) #a29cbfff
> color (#!2,5 & sel) #b2abd2ff
[Repeated 3 time(s)]
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2,5 & sel) byelement
> color (#!2,5 & sel) #8c40bfff
> color (#!2,5 & sel) #7300bfff
> color (#!2,5 & sel) #2d004bff
[Repeated 3 time(s)]
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2,5 & sel) #7b40bfff
> color (#!2,5 & sel) #7637bfff
> color (#!2,5 & sel) #542788ff
[Repeated 3 time(s)]
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2,5 & sel) #5d40bfff
> color (#!2,5 & sel) #8e80bfff
> color (#!2,5 & sel) #8073acff
[Repeated 3 time(s)]
> select ::name="BMA"::name="MAN"::name="NAG"
2106 atoms, 2205 bonds, 162 residues, 3 models selected
> color (#!2,5 & sel) #bfbfbfff
> color (#!2,5 & sel) #f7f7f7ff
[Repeated 3 time(s)]
> select clear
> select ::name="BMA"::name="MAN"::name="NAG"
2106 atoms, 2205 bonds, 162 residues, 3 models selected
> color (#!2,5 & sel) #bfbfbfff
> color (#!2,5 & sel) #f7f7f7ff
[Repeated 1 time(s)]
> select #2/J:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #2/J:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> show sel cartoons
> select #2/J:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #2/J:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #2/J:97-110
112 atoms, 117 bonds, 14 residues, 1 model selected
> show sel cartoons
> select #2/k:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel cartoons
> select #2/k:50-52
15 atoms, 14 bonds, 3 residues, 1 model selected
> show sel cartoons
> select #2/k:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> show sel cartoons
Alignment identifier is 2/K
[Repeated 1 time(s)]
> select clear
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/B
> save /home/ana/Documents/__BajicLab/K1769_figures/HA format fasta alignment
> 2/B
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/B
> select #2/B:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:9-361
2678 atoms, 2740 bonds, 1 pseudobond, 342 residues, 2 models selected
> select #2/B:323
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color (#!2 & sel) #542788ff
> select #2/B:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> color (#!2 & sel) #b2abd2ff
> color (#!2 & sel) #8073acff
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/A
> select #2/A:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> select #2/A:323
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color (#!2 & sel) #542788ff
> select #2/A:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> color (#!2 & sel) #8073acff
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/C
> select #2/C:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> color (#!2 & sel) #b2abd2ff
> color (#!2 & sel) #8073acff
> select #2/C:323
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color (#!2 & sel) #542788ff
> select clear
> select ::name="BMA"::name="MAN"::name="NAG"
2106 atoms, 2205 bonds, 162 residues, 3 models selected
> show sel & #!2,5 surfaces
> select clear
> color #2,4#5.11-13#!5 #ad40bfff
> color #2,4#5.11-13#!5 #ac3dbfff
> color #2,4#5.11-13#!5 #762a83ff
[Repeated 1 time(s)]
> undo
[Repeated 3 time(s)]
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/B
> select #2/B:323
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color (#!2 & sel) #ad40bfff
> color (#!2 & sel) #ac3dbfff
> color (#!2 & sel) #762a83ff
[Repeated 1 time(s)]
> color (#!2 & sel) #682a83ff
> color (#!2 & sel) #755683ff
> color (#!2 & sel) #9970abff
[Repeated 1 time(s)]
> color (#!2 & sel) #a270abff
> color (#!2 & sel) #9a37abff
> color (#!2 & sel) #762a83ff
[Repeated 1 time(s)]
> color (#!2 & sel) #832a5dff
> color (#!2 & sel) #831253ff
> color (#!2 & sel) #c51b7dff
[Repeated 1 time(s)]
> select #2/B:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> color (#!2 & sel) #c51b76ff
> color (#!2 & sel) #c56a9aff
> color (#!2 & sel) #de77aeff
[Repeated 1 time(s)]
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/A
> select #2/A:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color (#!2 & sel) #cf77deff
> color (#!2 & sel) #c847deff
> color (#!2 & sel) #762a83ff
[Repeated 3 time(s)]
> select #2/A:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> color (#!2 & sel) #9840bfff
> color (#!2 & sel) #ab7dbfff
> color (#!2 & sel) #9970abff
[Repeated 4 time(s)]
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2,5 & sel) #58bf40ff
> color (#!2,5 & sel) #4bbf30ff
> color (#!2,5 & sel) #276419ff
[Repeated 3 time(s)]
> select #1/M#2/M#5/M
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2,5 & sel) #80bf40ff
> color (#!2,5 & sel) #81bf42ff
> color (#!2,5 & sel) #7fbc41ff
[Repeated 3 time(s)]
> select #1/H#2/H#5/H
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2,5 & sel) #40bf72ff
> color (#!2,5 & sel) #00bf4cff
> color (#!2,5 & sel) #00441bff
[Repeated 1 time(s)]
> color (#!2,5 & sel) #004414ff
> color (#!2,5 & sel) #0f441fff
> color (#!2,5 & sel) #1b7837ff
[Repeated 4 time(s)]
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2,5 & sel) #4dbf40ff
> color (#!2,5 & sel) #91bf8cff
> color (#!2,5 & sel) #a6dba0ff
[Repeated 5 time(s)]
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2,5 & sel) #58bf40ff
> color (#!2,5 & sel) #4bbf30ff
> color (#!2,5 & sel) #276419ff
[Repeated 3 time(s)]
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2,5 & sel) #80bf40ff
> color (#!2,5 & sel) #81bf42ff
> color (#!2,5 & sel) #7fbc41ff
[Repeated 3 time(s)]
> select clear
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2,5 & sel) #40bf72ff
> color (#!2,5 & sel) #00bf4cff
> color (#!2,5 & sel) #00441bff
[Repeated 3 time(s)]
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> select #1/M#2/M#5/M
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2,5 & sel) #40bf4aff
> color (#!2,5 & sel) #63bf6bff
> color (#!2,5 & sel) #5aae61ff
[Repeated 3 time(s)]
> select clear
> select #1/H#2/H#5/H
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2,5 & sel) #bf7640ff
> color (#!2,5 & sel) #bf590cff
> color (#!2,5 & sel) #7f3b08ff
[Repeated 3 time(s)]
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2,5 & sel) #bf8540ff
> color (#!2,5 & sel) #bf6f11ff
> color (#!2,5 & sel) #e08214ff
[Repeated 3 time(s)]
> undo
[Repeated 1 time(s)]
> select clear
> undo
[Repeated 4 time(s)]
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2,5 & sel) #bf8540ff
> color (#!2,5 & sel) #bf6f11ff
> color (#!2,5 & sel) #e08214ff
[Repeated 1 time(s)]
> select clear
> hide #!2 models
> show #!2 models
> select add #2
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> hide #!2 models
> show #!2 models
> show sel cartoons
> select add #5
34464 atoms, 35304 bonds, 33 pseudobonds, 4320 residues, 17 models selected
> select subtract #2
17232 atoms, 17652 bonds, 30 pseudobonds, 2160 residues, 27 models selected
> hide sel cartoons
> hide #!2 models
> show #!2 models
> select subtract #5
12 models selected
> select add #2
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> transparency (#!2 & sel) 70
> transparency (#!2 & sel) 60
> transparency (#!2 & sel) 0
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> hide #!2 models
> show #!2 models
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 50
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 50
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 50
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/H#2/H#5/H
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
[Repeated 1 time(s)]
> select #1/M#2/M#5/M
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #2/k:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> show sel cartoons
> select #2/k:50-52
15 atoms, 14 bonds, 3 residues, 1 model selected
> show sel cartoons
> select #2/k:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel cartoons
> select #2/i:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel cartoons
> select #2/i:50-52
15 atoms, 14 bonds, 3 residues, 1 model selected
> show sel cartoons
> select #2/i:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel cartoons
> select #2/i:50-52
15 atoms, 14 bonds, 3 residues, 1 model selected
> select #2/i:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> show sel cartoons
> select #2/m:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> show sel cartoons
> select #2/m:50-52
15 atoms, 14 bonds, 3 residues, 1 model selected
> show sel cartoons
> select #2/m:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel cartoons
> select #2/J:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #2/h:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #2/l:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #2/l:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #2/j:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #2/h:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #2/h:97-110
112 atoms, 117 bonds, 14 residues, 1 model selected
> show sel cartoons
> select #2/l:97-110
112 atoms, 117 bonds, 14 residues, 1 model selected
> show sel cartoons
> select #2/j:97-110
112 atoms, 117 bonds, 14 residues, 1 model selected
> show sel cartoons
> select #2/j:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> show sel cartoons
> select #2/l:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> show sel cartoons
> select #2/h:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> show sel cartoons
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/new-ribbon-
> display_intermediate-session.cxs
> select #1/H#2/H#5/H
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #1/M#2/M#5/M
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> hide sel & #!2,5 cartoons
> select #5/J:103,106,31,104,105,57,74,72
68 atoms, 64 bonds, 8 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select add #4.1
68 atoms, 64 bonds, 8 residues, 3 models selected
> select subtract #4.1
68 atoms, 64 bonds, 8 residues, 2 models selected
> select add #4
68 atoms, 64 bonds, 30 pseudobonds, 8 residues, 4 models selected
> select #5/K:28,30,31,92
41 atoms, 40 bonds, 4 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> select #5/B:21,23,24,35,25,315,27,33,32,312,45,315
84 atoms, 77 bonds, 11 residues, 1 model selected
> show sel atoms
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> color (#!5 & sel) byhetero
> hide #4.1 models
> select #5/c:382,385,386,390
29 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> color (#!5 & sel) byhetero
> select clear
> select #2/j:26-33,51-58,97-110,70-80
331 atoms, 340 bonds, 41 residues, 1 model selected
> transparency #2/j:26-33,51-58,97-110,70-80 50 ribbons
> transparency #2/k:27-32,50-52,89-97 50 ribbons
> transparency #5:498,499
Missing or invalid "percent" argument: Expected a number
> transparency #5/B:498,499
Missing or invalid "percent" argument: Expected a number
> select #5/B:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> transparency (#!5 & sel) 50
> style sel stick
Changed 28 atom styles
> style sel stick
Changed 28 atom styles
> undo
[Repeated 2 time(s)]
> style sel stick
Changed 28 atom styles
> select #2/B:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> transparency (#!2 & sel) 50
> select #2/B:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #5/B:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #2/B:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide sel surfaces
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select add #5
17260 atoms, 17680 bonds, 30 pseudobonds, 2162 residues, 5 models selected
> hide sel surfaces
> select subtract #5
28 atoms, 28 bonds, 2 residues, 14 models selected
> select add #4
28 atoms, 28 bonds, 30 pseudobonds, 2 residues, 4 models selected
> select subtract #4
28 atoms, 28 bonds, 2 residues, 2 models selected
> select add #2
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 3 models selected
> select subtract #2
12 models selected
> select add #2
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> select subtract #2
12 models selected
> hide #!2 models
> show #!2 models
> select #2/B:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> show sel surfaces
> select #5/B:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> color (#!5 & sel) byhetero
> select #5/B:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> select #5/B:500
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select #5/B:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> select #5/j:1,26,27
25 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> hide (#!5 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!5 & sel-residues)
> show (#!5 & sel-residues & backbone) target ab
> show (#!5 & sel-residues & sidechain) target ab
> color (#!5 & sel) byhetero
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 0
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/C
> select #2/C:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> transparency (#!2 & sel) 0
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/B
> select #2/B:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> transparency (#!2 & sel) 0
> select clear
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/A
> select clear
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/A
> select #2/A:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color (#!2 & sel) dim gray
> select #2/A:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> color (#!2 & sel) light gray
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/B
> select #2/B:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color (#!2 & sel) dim gray
> select #2/B:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> color (#!2 & sel) light gray
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/C
> select #2/C:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/C:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color (#!2 & sel) dim gray
> select #2/C:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:335-490
1255 atoms, 1276 bonds, 156 residues, 1 model selected
> color (#!2 & sel) light gray
> select clear
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 60
> select clear
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 2/C
> select #2/C:491
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/C:491
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!2 & sel) light gray
> select clear
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel cartoons
> transparency #2/b: 50 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #2/b 50 ribbons
> transparency #2/b 30 ribbons
> transparency #2/b 5 ribbons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
Alignment identifier is 4
> select #1/A:9 #2/A:9 #5/A:9
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/A:9-323 #2/A:9-323 #5/A:9-323
7383 atoms, 7548 bonds, 945 residues, 3 models selected
4 [ID: 4] region 3 chains [1-315] RMSD: 0.000
> color (#!2,5 & sel) dim gray
> select #1/A:335-336 #2/A:335-336 #5/A:335-336
39 atoms, 36 bonds, 6 residues, 3 models selected
> select #1/A:335-491 #2/A:335-491 #5/A:335-491
3801 atoms, 3867 bonds, 471 residues, 3 models selected
4 [ID: 4] region 3 chains [316-472] RMSD: 0.000
> color (#!2,5 & sel) light gray
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
Alignment identifier is 4
> select #1/B:9 #2/B:9 #5/B:9
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/B:9-323 #2/B:9-323 #5/B:9-323
7383 atoms, 7548 bonds, 945 residues, 3 models selected
4 [ID: 4] region 3 chains [1-315] RMSD: 0.000
> color (#!2,5 & sel) dim gray
> select #1/B:335 #2/B:335 #5/B:335
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/B:335-491 #2/B:335-491 #5/B:335-491
3801 atoms, 3867 bonds, 471 residues, 3 models selected
4 [ID: 4] region 3 chains [316-472] RMSD: 0.000
> color (#!2,5 & sel) light gray
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
Alignment identifier is 4
> select #1/C:9 #2/C:9 #5/C:9
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #1/C:9-323 #2/C:9-323 #5/C:9-323
7383 atoms, 7548 bonds, 945 residues, 3 models selected
4 [ID: 4] region 3 chains [1-315] RMSD: 0.000
> color (#!2,5 & sel) dim gray
> select #1/C:335 #2/C:335 #5/C:335
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/C:335-491 #2/C:335-491 #5/C:335-491
3801 atoms, 3867 bonds, 471 residues, 3 models selected
4 [ID: 4] region 3 chains [316-472] RMSD: 0.000
> color (#!2,5 & sel) light gray
> select #5/B:285,22
16 atoms, 14 bonds, 2 residues, 1 model selected
> color (#!5 & sel) byhetero
> select #5/B:21,23,24,35,25,315,27,33,32,312,45,315
84 atoms, 77 bonds, 11 residues, 1 model selected
> color (#!5 & sel) byhetero
> select #5/c:382,385,386,390
29 atoms, 26 bonds, 4 residues, 1 model selected
> color (#!5 & sel) byhetero
> select #2/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> color (#!2 & sel) #bf5140ff
> color (#!2 & sel) #bf5645ff
> color (#!2 & sel) #d6604dff
[Repeated 1 time(s)]
> color (#!2 & sel) #d6774dff
> color (#!2 & sel) #d69172ff
> color (#!2 & sel) #f4a582ff
[Repeated 1 time(s)]
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2,5 & sel) #bf6740ff
> color (#!2,5 & sel) #bf8166ff
> color (#!2,5 & sel) #f4a582ff
[Repeated 3 time(s)]
> transparency #2/k:27-32,50-52,89-97 50 ribbons
> select #5/K:28,30,31,92
41 atoms, 40 bonds, 4 residues, 1 model selected
> color (#!5 & sel) byhetero
> select #5/j:1,26,27
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!2,5 & sel) #4095bfff
> color (#!2,5 & sel) #7eaabfff
> color (#!2,5 & sel) #92c5deff
[Repeated 4 time(s)]
> select #5/j:1,26,27
25 atoms, 24 bonds, 3 residues, 1 model selected
> color (#!5 & sel) byhetero
> transparency #2/j:26-33,51-58,97-110,70-80 50 ribbons
> select #5/J:103,106,31,104,105,57,74,72
68 atoms, 64 bonds, 8 residues, 1 model selected
> color (#!5 & sel) byelement
> color (#!5 & sel) #f4a582ff
> color (#!5 & sel) #92c5deff
> color (#!5 & sel) byhetero
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/TEST-COLORS-FIGURE.tif
> width 1979 height 1322 supersample 3
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 50
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 50
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> transparency (#!2 & sel) 50
> select clear
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> save /home/ana/Documents/__BajicLab/K1769_figures/new-ribbon-
> display_intermediate-session2.cxs
> lighting full
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting soft
> lighting flat
> lighting soft
> lighting flat
> lighting soft
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 cartoons
> hide sel & #!2,5 atoms
> select #5/c:382,385,386,390
29 atoms, 26 bonds, 4 residues, 1 model selected
> hide sel atoms
> select #5/B:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5/B:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B:497
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/B:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5/B:27,33,32,312,45
40 atoms, 36 bonds, 5 residues, 1 model selected
> hide sel atoms
> select #5/k:32
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/new-ribbon-
> display_intermediate-session2_Kchain-interactions.cxs
> view orient
> select ::name="BMA"::name="MAN"::name="NAG"
2106 atoms, 2205 bonds, 162 residues, 3 models selected
> color (#!2,5 & sel) #bf9c40ff
> color (#!2,5 & sel) #bfa96cff
> color (#!2,5 & sel) #fee090ff
[Repeated 3 time(s)]
> color (#!2,5 & sel) byelement
> undo
> transparency (#!2,5 & sel) 50
> select #5/B:499
14 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!5 & sel) byhetero
> select clear
> view orient
> turn -y 60
> turn z 90
> turn y 40
> turn -z 25
> turn x 20
> turn y 20
> turn -y 20
> save /home/ana/Documents/__BajicLab/K1769_figures/new-ribbon-
> display_intermediate-session2_Kchain-interactions_final_9-16-2024.cxs
——— End of log from Mon Sep 16 12:38:01 2024 ———
opened ChimeraX session
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> hide sel & #!2,5 atoms
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #5/b:499
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/b:499
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/j:26-33,51-58,97-110,70-80
331 atoms, 340 bonds, 41 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2 & sel) 0
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2 & sel) 0
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> transparency (#!2 & sel) 0
> transparency #2/j:26-33,51-58,97-110,70-80 0 ribbons
> transparency #2/k:27-32,50-52,89-97 0 ribbons
> select clear
> view orient
> turn -y 60
> turn 90 z
Expected an axis vector or a keyword
> turn z 90
> turn y 40
> turn -z 25
> turn x 20
> turn y 20
> turn y -20
> turn y 20
[Repeated 2 time(s)]
> turn y -20
[Repeated 1 time(s)]
> turn y 40
> save /home/ana/Documents/__BajicLab/K1769_figures/new-ribbon-
> display_intermediate-session2_overall.cxs
> lighting soft
> lighting flat
> lighting soft
> save "/home/ana/Documents/__BajicLab/K1769_figures/overall new figure-
> grey.tif" width 1979 height 1322 supersample 3 transparentBackground true
> turn y -40
> turn y 40
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!2 & sel) orange
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> ui tool show "Color Actions"
> color sel gold
[Repeated 1 time(s)]
> color sel goldenrod
[Repeated 2 time(s)]
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> ui tool show "Color Actions"
> color sel dark orange
[Repeated 1 time(s)]
> color sel orange red
> color sel tomato
> select ::name="BMA"::name="MAN"::name="NAG"
2106 atoms, 2205 bonds, 162 residues, 3 models selected
> color (#!2 & sel) #bfbf40ff
> color (#!2 & sel) #bfbf8fff
> color (#!2 & sel) #ffffbfff
[Repeated 3 time(s)]
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color sel light gray
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color sel gray
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color sel dim gray
> color sel dark gray
> color sel slate gray
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color sel slate gray
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color sel gray
> color (#!2 & sel) #bfbfbfff
> color (#!2 & sel) #e9e9e9ff
[Repeated 3 time(s)]
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2 & sel) #bfbfbfff
> color (#!2 & sel) #d4d4d4ff
[Repeated 1 time(s)]
> color (#!2 & sel) #9a9a9aff
[Repeated 3 time(s)]
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!2 & sel) #bfbfbfff
> color (#!2 & sel) #707070ff
[Repeated 3 time(s)]
> select clear
> show #!3 models
> select add #3
2 models selected
> hide #!2 models
> show #!2 models
> color zone #3 near #2 distance 6.46
> select #1/H#2/H#5/H
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color sel tomato
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color sel goldenrod
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color sel tomato
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color sel goldenrod
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color sel tomato
> select #1/M#2/M#5/M
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color sel goldenrod
> color zone #3 near sel & #2 distance 6.46
> select add #2
18902 atoms, 19358 bonds, 3 pseudobonds, 2378 residues, 7 models selected
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!5 models
> hide #!5 models
> show #!1 models
> show #!3 models
> hide #!2 models
> color zone #3 near sel & #1 distance 6.46
[Repeated 1 time(s)]
> select add #1
35299 atoms, 36157 bonds, 9 pseudobonds, 4429 residues, 20 models selected
> show #!2 models
> hide #!2 models
> select subtract #2
18067 atoms, 18505 bonds, 6 pseudobonds, 2269 residues, 26 models selected
> select add #3
18067 atoms, 18505 bonds, 6 pseudobonds, 2269 residues, 16 models selected
> color zone #3 near sel & #1 distance 6.46
> show #!2 models
> hide #!2 models
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!1 & sel) #e9e9e9ff
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!1 & sel) #9a9a9aff
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
> color (#!1 & sel) #707070ff
> color zone #3 near sel & #1 distance 6.46
> hide #!3 models
> show #!3 models
> hide #!3 models
> select add #2
25156 atoms, 25766 bonds, 5 pseudobonds, 3140 residues, 11 models selected
> select subtract #2
7924 atoms, 8114 bonds, 2 pseudobonds, 980 residues, 19 models selected
> show #!2 models
> hide #!2 models
> show #!3 models
> select add #3
7924 atoms, 8114 bonds, 2 pseudobonds, 980 residues, 9 models selected
> color zone #3 near sel & #1 distance 6.46
[Repeated 1 time(s)]
> select add #1
21194 atoms, 21709 bonds, 7 pseudobonds, 2650 residues, 10 models selected
> select subtract #1
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 15 models selected
> color zone #3 near #1 distance 6.46
> select ::name="BMA"::name="MAN"::name="NAG"
2106 atoms, 2205 bonds, 162 residues, 3 models selected
> color (#!1 & sel) #ffffbfff
> color zone #3 near sel & #1 distance 6.46
> select clear
> select add #1
17232 atoms, 17652 bonds, 6 pseudobonds, 2160 residues, 3 models selected
> color zone #3 near sel & #1 distance 6.46
> hide #!1 models
> show #!1 models
> hide #!1 models
> view orient
> select add #4
17232 atoms, 17652 bonds, 33 pseudobonds, 2160 residues, 13 models selected
> select subtract #4
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 11 models selected
> hide #!4 models
> select subtract #1
9 models selected
> save "/home/ana/Documents/__BajicLab/K1769_figures/yop view map.tif" width
> 1979 height 1322 supersample 3 transparentBackground true
> turn -y 60
> turn z 90
> turn y 40
> turn -z 25
> turn x 20
> turn y 20
> turn y -60
> turn y 60
> turn x 35
> view orient
> turn y -60
> turn z 90
> turn y 40
> turn -z 25
> turn x 20
> turn y 20
> turn y -20
> turn x 35
> turn x 3-5
Expected a number or a keyword
> turn x -35
> turn y 10
> turn y -10
[Repeated 1 time(s)]
> save /home/ana/Documents/__BajicLab/K1769_figures/figure-like-inspiation-
> article/-Y60Z90Y40-Z25X20-Y20.tif width 1979 height 1322 supersample 3
> transparentBackground true
> turn y 20
[Repeated 1 time(s)]
> save /home/ana/Documents/__BajicLab/K1769_figures/figure-like-inspiation-
> article/-Y60Z90Y40-Z25X20Y20.tif width 1979 height 1322 supersample 3
> transparentBackground true
> turn y 10
[Repeated 1 time(s)]
> save /home/ana/Documents/__BajicLab/K1769_figures/figure-like-inspiation-
> article/-Y60Z90Y40-Z25X20Y40.tif width 1979 height 1322 supersample 3
> transparentBackground true
> turn y 10
[Repeated 5 time(s)]
> save /home/ana/Documents/__BajicLab/K1769_figures/figure-like-inspiation-
> article/-Y60Z90Y40-Z25X20Y40Y60.tif width 1979 height 1322 supersample 3
> transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/figure-like-inspiation-
> article/mapview.cxs
——— End of log from Mon Sep 16 16:33:12 2024 ———
opened ChimeraX session
> select #1/H#2/H#5/H
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> select add #2
19126 atoms, 19600 bonds, 3 pseudobonds, 2402 residues, 7 models selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!1 models
> hide #!3 models
> show #!3 models
> color zone #3 near sel & #1 distance 6.46
> color (#!1 & sel) #92c5deff
> color zone #3 near sel & #1 distance 6.46
> select #1/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> select #1/J#2/J#5/J
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!1 & sel) #fee090ff
> color (#!1 & sel) #92c5deff
> select #1/L
947 atoms, 974 bonds, 121 residues, 1 model selected
> select #1/L#2/L#5/L
2841 atoms, 2922 bonds, 363 residues, 3 models selected
> color (#!1 & sel) #fee090ff
> color (#!1 & sel) #92c5deff
> select clear
> color zone #3 near #1 distance 6.46
> volume zone #3 nearAtoms #1 range 6.46
> select #1/I#2/I#5/I
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> ui tool show "Color Actions"
> color sel salmon
> color zone #3 near sel & #1 distance 6.46
> color sel light salmon
> color zone #3 near sel & #1 distance 6.46
> color (#!1 & sel) #f4a582ff
> color zone #3 near sel & #1 distance 6.46
> select #1/K#2/K#5/K
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!1 & sel) #92c5deff
> color (#!1 & sel) #f4a582ff
> select #1/M#2/M#5/M
2505 atoms, 2559 bonds, 327 residues, 3 models selected
> color (#!1 & sel) #92c5deff
> color (#!1 & sel) #f4a582ff
> select add #1
18902 atoms, 19358 bonds, 6 pseudobonds, 2378 residues, 8 models selected
> color zone #3 near sel & #1 distance 6.46
> select #1/A#2/A#5/A
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
Alignment identifier is 1
> select #1/A:335 #2/A:335 #5/A:335
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:335-491 #2/A:335-491 #5/A:335-491
3801 atoms, 3867 bonds, 471 residues, 3 models selected
1 [ID: 1] region 3 chains [316-472] RMSD: 0.000
> color sel light gray
> select #1/A:323 #2/A:323 #5/A:323
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1/A:9-323 #2/A:9-323 #5/A:9-323
7383 atoms, 7548 bonds, 945 residues, 3 models selected
1 [ID: 1] region 3 chains [1-315] RMSD: 0.000
> color sel gray
> select #1/B#2/B#5/B
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
Alignment identifier is 1
> select #1/B:335 #2/B:335 #5/B:335
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/B:335-491 #2/B:335-491 #5/B:335-491
3801 atoms, 3867 bonds, 471 residues, 3 models selected
1 [ID: 1] region 3 chains [316-472] RMSD: 0.000
> color sel light gray
> select #1/B:323 #2/B:323 #5/B:323
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1/B:9-323 #2/B:9-323 #5/B:9-323
7383 atoms, 7548 bonds, 945 residues, 3 models selected
1 [ID: 1] region 3 chains [1-315] RMSD: 0.000
> color sel gray
> select #1/C#2/C#5/C
11886 atoms, 12171 bonds, 3 pseudobonds, 1470 residues, 6 models selected
Alignment identifier is 1
> select #1/C:335 #2/C:335 #5/C:335
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/C:335-491 #2/C:335-491 #5/C:335-491
3801 atoms, 3867 bonds, 471 residues, 3 models selected
1 [ID: 1] region 3 chains [316-472] RMSD: 0.000
> color sel light gray
> select #1/C:323 #2/C:323 #5/C:323
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #1/C:9-323 #2/C:9-323 #5/C:9-323
7383 atoms, 7548 bonds, 945 residues, 3 models selected
1 [ID: 1] region 3 chains [1-315] RMSD: 0.000
> color sel gray
> select add #1
22154 atoms, 22684 bonds, 6 pseudobonds, 2790 residues, 8 models selected
> color zone #3 near sel & #1 distance 6.46
> lighting soft
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!1 models
> show #!1 models
> select ::name="BMA"::name="MAN"::name="NAG"
2106 atoms, 2205 bonds, 162 residues, 3 models selected
> color (#!1-2 & sel) #fee090ff
> color (#!1-2 & sel) #ffffbfff
> color (#!1-2 & sel) #fee090ff
> hide #!2 models
> select clear
> show #!3 models
> hide #!1 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!1 models
> color zone #3 near #1 distance 6.46
> select add #1
17232 atoms, 17652 bonds, 6 pseudobonds, 2160 residues, 3 models selected
> color zone #3 near sel & #1 distance 6.46
> hide #!1 models
> vop gaussian #3 sdev 3.23
Opened cryosparc_P4_J137_008_volume_map.mrc gaussian as #6, grid size
420,420,420, pixel 1.08, shown at step 1, values float32
> vop gaussian #6 sdev 3.23
Opened cryosparc_P4_J137_008_volume_map.mrc gaussian as #7, grid size
420,420,420, pixel 1.08, shown at step 1, values float32
> undo
> vop gaussian #7 sdev 3.23
Opened cryosparc_P4_J137_008_volume_map.mrc gaussian as #8, grid size
420,420,420, pixel 1.08, shown at step 1, values float32
> close #7
> close #8
> close #6
> hide #!1 models
> lighting soft
> view orient
[Repeated 1 time(s)]
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> select #1/H
947 atoms, 974 bonds, 121 residues, 1 model selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!1 models
> select #1/H
947 atoms, 974 bonds, 121 residues, 1 model selected
> volume zone #3 nearAtoms sel & #1 range 6.46
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume zone #3 nearAtoms sel & #1 range 6.46
> select clear
> volume zone #3 nearAtoms #1 range 6.46
> view
> turn z 180
> turn -z 180
> turn y 180
> view orient
> turn y 180
[Repeated 2 time(s)]
> hide #!1 models
> lighting soft
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/top view new color.tif" width 1979 height 1322
> supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/top view new color white background.tif" width 1979
> height 1322 supersample 4
> turn y 180
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/bottom view new color.tif" width 1979 height 1322
> supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/bottom view new color white background.tif" width 1979
> height 1322 supersample 4
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/bottom view new color_fullmap.tif" width 1979 height 1322
> supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/bottom view new color full map white background.tif"
> width 1979 height 1322 supersample 4
> show #!1 models
> volume zone #3 nearAtoms #1 range 6.46
> hide #!1 models
> turn y 180
> turn y 90
> turn x 45
[Repeated 1 time(s)]
> turn -x 45
[Repeated 1 time(s)]
> turn z 45
[Repeated 1 time(s)]
> view orient
> turn y 180
> turn z 90
> undo
> turn z 45
> undo
> turn y 90
> turn z 90
> view orient
> turn y 180
> turn y 90
> turn z 90
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90.tif" width 1979 height 1322
> supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 white background.tif" width 1979
> height 1322 supersample 4
> turn x 10
> turn -x 10
> turn y 10
[Repeated 2 time(s)]
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y30 white background.tif" width
> 1979 height 1322 supersample 4
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y30.tif" width 1979 height 1322
> supersample 4 transparentBackground true
> show #!2 models
> hide #!3 models
> turn y 10
[Repeated 6 time(s)]
> show #!1 models
> hide #!1 models
> show #!3 models
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y90white background.tif" width
> 1979 height 1322 supersample 4
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y90.tif" width 1979 height 1322
> supersample 4 transparentBackground true
[Repeated 1 time(s)]
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y90white background.tif" width
> 1979 height 1322 supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y90.tif" width 1979 height 1322
> supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y90white background.tif" width
> 1979 height 1322 supersample 4
> turn y 30
> turn y 10
> turn y 5
> hide #!2 models
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y90 y45 white background.tif"
> width 1979 height 1322 supersample 4
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y90 y45.tif" width 1979 height
> 1322 supersample 4 transparentBackground true
> turn y 5
> turn y 20
[Repeated 1 time(s)]
> turn y -20
> turn y 10
> turn y -10
[Repeated 1 time(s)]
> view orient
> turn y 180
> turn y 90
> turn z 90
> turn y 45
> turn y -15
> turn y 90
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> turn y 30
> turn y 10
> hide #!2 models
> turn y -10
> view orient
> turn y 180
> turn y 90
> turn z 90
> turn y
[Repeated 2 time(s)]
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> view orient
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> turn y 180
> turn y 90
> turn z 90
> turn y 150
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y150.tif" width 1979 height 1322
> supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y150 white back.tif" width 1979
> height 1322 supersample 4
> hide #!3 models
> show #!2 models
> turn y -30
[Repeated 1 time(s)]
> hide #!2 models
> show #!3 models
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y90_.tif" width 1979 height 1322
> supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/side view y180 y90 z90 y90_ white background.tif" width
> 1979 height 1322 supersample 4
> hide #!3 models
> show #!2 models
> select #2/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> color (#!2 & sel) #92c5deff
> select #2/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> color (#!2 & sel) #f4a582ff
> select clear
> cartoon style #2/j:26-33,51-58,97-110,70-80 thickness 2
> cartoon style #2/j:26-33,51-58,97-110,70-80 thickness 2.5
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/thick CDRs.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/thick CDRs white background.tif" width 1979 height 1322
> supersample 4
> interfaces select #2/B & ::polymer_type>0 contacting #2/J & ::polymer_type>0
> areaCutoff 0
9 contacting residues
> interfaces select #2/B & ::polymer_type>0 contacting #2/J & ::polymer_type>0
> areaCutoff 0
9 contacting residues
> interfaces select #2/B & ::polymer_type>0 contacting #2/J & ::polymer_type>0
> areaCutoff 0
9 contacting residues
> select (#2/B & ::polymer_type>0 ) & ((#2/J & ::polymer_type>0 ) :<6)
135 atoms, 129 bonds, 16 residues, 1 model selected
> color (#!2 & sel) #92c5deff
> select (#2/C & ::polymer_type>0 ) & ((#2/J & ::polymer_type>0 ) :<6)
99 atoms, 95 bonds, 13 residues, 1 model selected
> color (#!2 & sel) #f4a582ff
> color (#!2 & sel) #92c5deff
> select (#2/B & ::polymer_type>0 ) & ((#2/K & ::polymer_type>0 ) :<6)
92 atoms, 87 bonds, 12 residues, 1 model selected
> color (#!2 & sel) #f4a582ff
> select #2/b:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> select #2/b:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/b:498,285
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #2/b:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!2 & sel) #92c5deff
> select #2/b:499
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/b:499,22
22 atoms, 22 bonds, 2 residues, 1 model selected
> color (#!2 & sel) #f4a582ff
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/thick CDRs colored footprint.tif" width 1979 height 1322
> supersample 4
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/thick CDRs colored footprint.tif" width 1979 height 1322
> supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/thick CDRs colored footprint transparent background.tif"
> width 1979 height 1322 supersample 4 transparentBackground true
> lighting soft
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/zoom thick CDRs colored footprint.tif" width 1979 height
> 1322 supersample 4
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/zoom thick CDRs colored footprint transparent
> background.tif" width 1979 height 1322 supersample 4 transparentBackground
> true
> select #2/b:499,22
22 atoms, 22 bonds, 2 residues, 1 model selected
> transparency (#!2 & sel) 80
> select #2/b:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> transparency (#!2 & sel) 80
> select (#2/B & ::polymer_type>0 ) & ((#2/K & ::polymer_type>0 ) :<6)
92 atoms, 87 bonds, 12 residues, 1 model selected
> transparency (#!2 & sel) 80
> select (#2/C & ::polymer_type>0 ) & ((#2/K & ::polymer_type>0 ) :<6)
Nothing selected
> select (#2/C & ::polymer_type>0 ) & ((#2/J & ::polymer_type>0 ) :<6)
99 atoms, 95 bonds, 13 residues, 1 model selected
> transparency (#!2 & sel) 80
> select (#2/B & ::polymer_type>0 ) & ((#2/J & ::polymer_type>0 ) :<6)
135 atoms, 129 bonds, 16 residues, 1 model selected
> transparency (#!2 & sel) 80
> select clear
> select #2/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel cartoons
> select #2/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> hide sel cartoons
> select #2/b:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency (#!2 & sel) 80
> select clear
> show #!5 models
> show #!4 models
> select #5/j:103,105,106,104,57,31,72,74,27,26,1
93 atoms, 88 bonds, 11 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) #92c5deff
> color (#!5 & sel) byhetero
> select clear
> select #5/k:28,30,31,92,30,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) #f4a582ff
> color (#!5 & sel) byhetero
> select clear
> select #5/B:21,23,24,35,25,315,45
50 atoms, 46 bonds, 7 residues, 1 model selected
> color (#!5 & sel) byhetero
> select #5/B:22,499
22 atoms, 22 bonds, 2 residues, 1 model selected
> color (#!5 & sel) byhetero
> select clear
> select #5/B:33,32,312,45,27,315
49 atoms, 44 bonds, 6 residues, 1 model selected
> select #5/C:382,385,386,390
29 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> select #5/C:382,385,386,390,285
37 atoms, 33 bonds, 5 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> select #5/C:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5/B:33,32,312,45,27,315
49 atoms, 44 bonds, 6 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> select #5/B:285,498
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> color (#!5 & sel) byhetero
> select clear
> select #5/B:27,33,32,312,45,315
49 atoms, 44 bonds, 6 residues, 1 model selected
> show sel atoms
> select #5/B:21,23,24,35,25,315
44 atoms, 41 bonds, 6 residues, 1 model selected
> show sel atoms
> select #5/j:103,105,106,104,57,31,72,74,27,26,1 #5/k:28,30,31,92,30,32
146 atoms, 141 bonds, 16 residues, 1 model selected
> view sel
[Repeated 1 time(s)]
> select clear
> select #5/b:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> color (#!5 & sel) #fee090ff
> color (#!5 & sel) byhetero
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details backg transp.tif" width 1979 height 1322
> supersample 4 transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details.tif width 1979 height 1322 supersample 4
> select #5/B:21,23,24,35,25,315,33,32,312,45,27,315
84 atoms, 77 bonds, 11 residues, 1 model selected
> select #5/B:21,23,24,35,25,315,33,32,312,45,27,315 #5/C:390,382,385,386
113 atoms, 103 bonds, 15 residues, 1 model selected
> view sel
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details_option2.tif width 1979 height 1322
> supersample 4
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details option2 backg transp.tif" width 1979 height
> 1322 supersample 4 transparentBackground true
> select #5/j:103,105,106,104,57,31,72,74,27,26,1
93 atoms, 88 bonds, 11 residues, 1 model selected
> view sel
> select #5/k:28,30,31,92,30,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> hide sel atoms
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details hevay chain .tif" width 1979 height 1322
> supersample 4
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details hevay chain trans back .tif" width 1979
> height 1322 supersample 4 transparentBackground true
> select #5/k:28,30,31,92,30,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> show sel atoms
> select #5/j:103,105,106,104,57,31,72,74,27,26,1
93 atoms, 88 bonds, 11 residues, 1 model selected
> hide sel atoms
> select #5/k:28,30,31,92,30,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> view sel
> undo
> view sel
> turn y 5
> turn y -5
[Repeated 2 time(s)]
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details light chain turn-y10 .tif" width 1979 height
> 1322 supersample 4
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details light chain turn-y10 .tif" width 1979 height
> 1322 supersample 4
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details light chain turn-y10 trans back.tif" width
> 1979 height 1322 supersample 4 transparentBackground true
> undo
[Repeated 5 time(s)]
> select #5/k:28,30,31,92,30,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> hide sel atoms
> select #5/j:103,105,106,104,57,31,72,74,27,26,1
93 atoms, 88 bonds, 11 residues, 1 model selected
> show sel atoms
> view sel
> turn y -10
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details lheavychain turn-y10 trans back.tif" width
> 1979 height 1322 supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details heavy chain turn-y10 .tif" width 1979 height
> 1322 supersample 4
> select #5/j:103,105,106,104,57,31,72,74,27,26,1
93 atoms, 88 bonds, 11 residues, 1 model selected
> stickRadius #5/j:103,105,106,104,57,31,72,74,27,26,1 +.5
Unknown command: stickRadius #5/j:103,105,106,104,57,31,72,74,27,26,1 +.5
> stickRadius #5/j +.5
Unknown command: stickRadius #5/j +.5
> size stickRadius #5/j:103,105,106,104,57,31,72,74,27,26,1 +.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #5/j:103,105,106,104,57,31,72,74,27,26,1 1
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #5/j 1
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #5/j +1
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #5/j +.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #5/j +0.5
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #5/j +1
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #5/j + 1
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> size stickRadius #5/j 1
Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
> ui tool show "Basic Actions"
> size #5/j:103,105,106,104,57,31,72,74,27,26,1 stickRadius +0.5
Changed 88 bond radii
> size #5/j:103,105,106,104,57,31,72,74,27,26,1 stickRadius -0.3
Changed 88 bond radii
> size #5/j:103,105,106,104,57,31,72,74,27,26,1 stickRadius -0.5
Cannot reduce stick radius to <= 0
> size #5/j:103,105,106,104,57,31,72,74,27,26,1 stickRadius -0.05
Changed 88 bond radii
> size #5/B:21,23,24,35,25,315,33,32,312,45,27,315 stickRadius +.05
Changed 77 bond radii
> size #5/B:21,23,24,35,25,315,33,32,312,45,27,315 stickRadius +.05
Changed 77 bond radii
> size #5/B:21,23,24,35,25,315,33,32,312,45,27,315 stickRadius -.05
Changed 77 bond radii
> size #5/B:21,23,24,35,25,315,33,32,312,45,27,315 stickRadius +.05
Changed 77 bond radii
> size #5/B:22,285,499,498 stickRadius +.05
Changed 44 bond radii
> size #5/B:22,285,499,498 stickRadius +.05
Changed 44 bond radii
> size #5/C:390,382,385,386 stickRadius +.05
Changed 26 bond radii
> size #5/C:390,382,385,386 stickRadius +.05
Changed 26 bond radii
> select clear
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details lheavychain turn-y10 radius change trans
> back.tif" width 1979 height 1322 supersample 4 transparentBackground true
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/view-details lheavychain turn-y10 radius change.tif"
> width 1979 height 1322 supersample 4
> save "/home/ana/Documents/__BajicLab/K1769_figures/figures-
> modified_9-18-2024/session 9-19-2024.cxs"
——— End of log from Thu Sep 19 16:51:19 2024 ———
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> open
> /home/ana/Documents/__BajicLab/K1769_figures/k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
Summary of feedback from opening
/home/ana/Documents/__BajicLab/K1769_figures/k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
---
warnings | Ignored bad PDB record found on line 260
SSBOND *** CYS A 14 CYS A 466
Ignored bad PDB record found on line 261
SSBOND *** CYS A 64 CYS A 76
Ignored bad PDB record found on line 262
SSBOND *** CYS A 97 CYS A 139
Ignored bad PDB record found on line 263
SSBOND *** CYS A 281 CYS A 305
Ignored bad PDB record found on line 264
SSBOND *** CYS H 22 CYS H 96
11 messages similar to the above omitted
Chain information for
k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb #6
---
Chain | Description
A B C | No description available
H J L | No description available
I K M | No description available
> hide #!4 models
> hide #!2 models
> hide #!5 models
> hide #!6 atoms
> show #!6 cartoons
> view
> select add #6
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #6/A-C:323
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #6/A-C:9-323
7383 atoms, 7548 bonds, 945 residues, 1 model selected
> color sel gray
> select #6/A-C:335
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #6/A-C:335-491
3801 atoms, 3867 bonds, 471 residues, 1 model selected
> color sel light gray
> select clear
> select #6/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #6/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> select #6/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> select #6/A-C:323
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #6/A-C:113-323
5013 atoms, 5130 bonds, 633 residues, 1 model selected
> select #6/A-C:323
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #6/A-C:9-323
7383 atoms, 7548 bonds, 945 residues, 1 model selected
> select #6/A-C:335
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #6/A-C:335-439
2538 atoms, 2583 bonds, 315 residues, 1 model selected
> color (#!6 & sel) light gray
> select #6/A-C:440
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #6/A-C:440-491
1263 atoms, 1281 bonds, 156 residues, 1 model selected
> color (#!6 & sel) light gray
> select clear
> select #6/H
947 atoms, 974 bonds, 121 residues, 1 model selected
> color sel medium blue
> ui tool show "Color Actions"
> color sel blue
> color sel dodger blue
> color sel blue
> color sel medium blue
> color sel royal blue
> color sel medium slate blue
> color sel deep sky blue
> color sel cornflower blue
> select #6/I
835 atoms, 853 bonds, 109 residues, 1 model selected
> color sel salmon
> color sel dark salmon
> color sel salmon
> color sel light salmon
> select #6/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel cartoons
> select #6/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> hide sel cartoons
> select #6/L
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel cartoons
> select #6/M
835 atoms, 853 bonds, 109 residues, 1 model selected
> hide sel cartoons
> select #6/H
947 atoms, 974 bonds, 121 residues, 1 model selected
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 16530 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select #6/A-C:323
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #6/A-C:69-323
6084 atoms, 6234 bonds, 765 residues, 1 model selected
> select #6/A-C:323
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #6/A-C:9-323
7383 atoms, 7548 bonds, 945 residues, 1 model selected
> color sel gray
> color sel dark gray
> color sel dim gray
> color sel gray
> color sel dim gray
> select clear
> select #6/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #6/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #6/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #6/A-C:9
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #6/A-C:9-323
7383 atoms, 7548 bonds, 945 residues, 1 model selected
> color sel gray
[Repeated 1 time(s)]
> select clear
> hide #!6 models
> show #!6 models
> select #6/H,J,L:12
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #6/H,J,L:12
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #6/A-C:9-323
7383 atoms, 7548 bonds, 945 residues, 1 model selected
> select clear
> select #6/J
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel cartoons
> select #6/K
835 atoms, 853 bonds, 109 residues, 1 model selected
> hide sel cartoons
> select #6/L
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel cartoons
> select #6/M
835 atoms, 853 bonds, 109 residues, 1 model selected
> hide sel cartoons
> select #6/H
947 atoms, 974 bonds, 121 residues, 1 model selected
> color sel #92c5deff
> select clear
> cartoon style #6/h thickness 2.5
> select #6/H
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel cartoons
> select #6/I
835 atoms, 853 bonds, 109 residues, 1 model selected
> hide sel cartoons
> select #6/h:27-32
55 atoms, 57 bonds, 6 residues, 1 model selected
> show sel cartoons
> select #6/h:50-52
31 atoms, 32 bonds, 3 residues, 1 model selected
> show sel cartoons
> select #6/h:89-70
Nothing selected
> show #!6 cartoons
> undo
> select #6/h:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> show sel cartoons
> select #6/h:27-32
55 atoms, 57 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #6/h:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select up
114 atoms, 115 bonds, 15 residues, 1 model selected
> select up
947 atoms, 974 bonds, 121 residues, 1 model selected
> select up
17232 atoms, 17652 bonds, 2160 residues, 1 model selected
> select up
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 5 models selected
> select #6/h:50-52
31 atoms, 32 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #6/h:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #6/h:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #6/h:97-110
112 atoms, 117 bonds, 14 residues, 1 model selected
> show sel cartoons
> select #6/h:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> show sel cartoons
> select clear
> select #6/i:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel cartoons
> select #6/i:50-52
15 atoms, 14 bonds, 3 residues, 1 model selected
> show sel cartoons
> select #6/i:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> show sel cartoons
> select clear
> select (#6/C & ::polymer_type>0 ) & ((#6/H & ::polymer_type>0 ) :<6)
143 atoms, 138 bonds, 17 residues, 1 model selected
> color (#!6 & sel) #fee090ff
> color (#!6 & sel) #92c5deff
> select (#6/C & ::polymer_type>0 ) & ((#6/I & ::polymer_type>0 ) :<6)
85 atoms, 80 bonds, 11 residues, 1 model selected
> color (#!6 & sel) #bf6440ff
> color (#!6 & sel) #bf785cff
> color (#!6 & sel) #ffa07aff
[Repeated 4 time(s)]
> select (#6/A & ::polymer_type>0 ) & ((#6/H & ::polymer_type>0 ) :<6)
110 atoms, 108 bonds, 14 residues, 1 model selected
> color #6 grey
> color #6 #92c5deff
> undo
[Repeated 1 time(s)]
> color (#!6 & sel) #4095bfff
> color (#!6 & sel) #7eaabfff
> color (#!6 & sel) #92c5deff
[Repeated 1 time(s)]
> select (#6/C & ::polymer_type>0 ) & ((#6/I & ::polymer_type>0 ) :<6)
85 atoms, 80 bonds, 11 residues, 1 model selected
> select (#6/C & ::polymer_type>0 ) & ((#6/H & ::polymer_type>0 ) :<6)
143 atoms, 138 bonds, 17 residues, 1 model selected
> color (#!6 & sel) #4095bfff
> color (#!6 & sel) #7eaabfff
> color (#!6 & sel) #92c5deff
[Repeated 4 time(s)]
> select clear
> select #6/i:28,30,31,92,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> style sel stick
Changed 53 atom styles
> show sel atoms
> color sel byhetero
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show (sel-residues & sidechain) target ab
> select #6/i:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #6/i:50-52
15 atoms, 14 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #6/i:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select clear
> select #6/h:103,106,104,105,57,72,54,74
70 atoms, 66 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #6/h:103,106,104,105,57,72,54,74,31
76 atoms, 71 bonds, 9 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #6/h:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> hide sel atoms
> select #6/h:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> hide sel cartoons
> undo
[Repeated 3 time(s)]
> select #6/h:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #6/h:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #6/h:97-110
112 atoms, 117 bonds, 14 residues, 1 model selected
> hide sel cartoons
> select #6/h:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select clear
> select #6/c:33,32,45,27,315,312,21,23,24,35,25
84 atoms, 77 bonds, 11 residues, 1 model selected
> show sel atoms
> color (#!6 & sel) byhetero
> transparency (#!6 & sel) 60
> undo
[Repeated 1 time(s)]
> select clear
> select (#6/C & ::polymer_type>0 ) & ((#6/H & ::polymer_type>0 ) :<6)
143 atoms, 138 bonds, 17 residues, 1 model selected
> transparency (#!6 & sel) 80
> transparency (#!6 & sel) 70
> select (#6/C & ::polymer_type>0 ) & ((#6/I & ::polymer_type>0 ) :<6)
85 atoms, 80 bonds, 11 residues, 1 model selected
> transparency (#!6 & sel) 70
> select (#6/A & ::polymer_type>0 ) & ((#6/H & ::polymer_type>0 ) :<6)
110 atoms, 108 bonds, 14 residues, 1 model selected
> transparency (#!6 & sel) 70
> select clear
> select #6/c:499,498
28 atoms, 28 bonds, 2 residues, 1 model selected
> transparency sel 70
> select #6/c:499,498
28 atoms, 28 bonds, 2 residues, 1 model selected
> transparency sel 70
> select #6/c:499,498
28 atoms, 28 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel surfaces
> hide sel atoms
> select #6/c:499
14 atoms, 14 bonds, 1 residue, 1 model selected
> select ::name="BMA"::name="MAN"::name="NAG"
2808 atoms, 2940 bonds, 216 residues, 4 models selected
> show sel & #!6 surfaces
> color (#!6 & sel) #ffffbfff
> select clear
> select #6/c:499
14 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!6 & sel) #ffa07aff
> transparency (#!6 & sel) 70
> select #6/c:298
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency (#!6 & sel) 70
> select #6/c:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> transparency (#!6 & sel) 70
> select clear
> open
> /home/ana/Documents/__BajicLab/K1769_figures/k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
Summary of feedback from opening
/home/ana/Documents/__BajicLab/K1769_figures/k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
---
warnings | Ignored bad PDB record found on line 260
SSBOND *** CYS A 14 CYS A 466
Ignored bad PDB record found on line 261
SSBOND *** CYS A 64 CYS A 76
Ignored bad PDB record found on line 262
SSBOND *** CYS A 97 CYS A 139
Ignored bad PDB record found on line 263
SSBOND *** CYS A 281 CYS A 305
Ignored bad PDB record found on line 264
SSBOND *** CYS H 22 CYS H 96
11 messages similar to the above omitted
Chain information for
k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb #7
---
Chain | Description
A B C | No description available
H J L | No description available
I K M | No description available
> select add #7
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> hide sel atoms
> select subtract #7
Nothing selected
> select #7/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 7/A
> select #7/A:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color sel gray
> select #7/A:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> color sel light gray
> select #7/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 7/B
> select #7/B:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/B:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color sel gray
> select #7/B:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/B:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> color sel light gray
> select #7/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
Alignment identifier is 7/C
> select #7/C:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/C:9-323
2461 atoms, 2516 bonds, 315 residues, 1 model selected
> color sel gray
> select #7/C:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/C:335-491
1267 atoms, 1289 bonds, 157 residues, 1 model selected
> color sel light gray
> select clear
> select #7/H
947 atoms, 974 bonds, 121 residues, 1 model selected
> color sel #92c5deff
> select #7/I
835 atoms, 853 bonds, 109 residues, 1 model selected
> color sel #ffa07aff
> select clear
> select #6/H
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel atoms
> select #6/I
835 atoms, 853 bonds, 109 residues, 1 model selected
> hide sel atoms
> select clear
> select #7/c:33,32,45,27,315,312,21,23,24,35,25
84 atoms, 77 bonds, 11 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 84 atom styles
> color sel byhetero
> select clear
> select #7/c:298
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #7/c:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> show sel atoms
> select #6/c:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> transparency (#!6 & sel) 70
> select #7/c:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #7/c:298
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/c:298
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency (#!6 & sel) 0
> select clear
> select #7/i:28,30,31,92,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 53 atom styles
> color sel byhetero
> select #7/h:1,26
13 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 13 atom styles
> color sel byhetero
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show (sel-residues & sidechain) target ab
> select clear
> select #7/h:103,106,104,105,57,72,54,74
70 atoms, 66 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 70 atom styles
> color sel byhetero
> select #7/a:382,285,386,390,389
37 atoms, 33 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 37 atom styles
> color sel byhetero
> select clear
> select #7/a:298
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> distance #7/h:103@N #7/c:33@OE1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H SER 103 N and /C GLN 33 OE1: 2.943Å
> select #7/h:103
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/c:103
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/c:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> distance #7/H:103@N #7/C:33@OE1
Distance already exists; modify distance properties with 'distance style'
> distance style #7/H:103@N #7/C:33@OE1 color goldenroad
Invalid "color" argument: Invalid color name or specifier
> ui tool show "Color Actions"
> distance style #7/H:103@N #7/C:33@OE1 color goldenrod
> distance style color goldenrod
> show #4.1 models
> hide #4.1 models
> distance #7/H:103@OG #7/C:33@OE1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H SER 103 OG and /C GLN 33 OE1: 3.516Å
> distance #7/H:103@OG #7/C:32@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H SER 103 OG and /C ASP 32 O: 3.089Å
> distance #7/H:106@ND2 #7/C:45@OG
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ASN 106 ND2 and /C SER 45 OG: 3.132Å
> distance #7/H:103@OG #7/C:27@N
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H SER 103 OG and /C LYS 27 N: 3.773Å
> distance #7/H:104@O #7/C:312@ND2
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ASP 104 O and /C ASN 312 ND2: 3.831Å
> distance #7/H:104@OD1 #7/C:27@NZ
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ASP 104 OD1 and /C LYS 27 NZ: 3.135Å
> distance #7/H:105@O #7/C:315@NZ
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H PHE 105 O and /C LYS 315 NZ: 3.232Å
> distance delete #7/H:104@OD1 #7/C:27@NZ
> distance #7/H:104@OD1 #7/C:27@NZ color navy
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ASP 104 OD1 and /C LYS 27 NZ: 3.135Å
> distance #7/H:104@OD2 #7/C:27@NZ color black
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ASP 104 OD2 and /C LYS 27 NZ: 3.385Å
> distance #7/i:28@NH2 #7/C:21@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/I ARG 28 NH2 and /C PRO 21 O: 3.773Å
> distance #7/i:30@OG #7/C:23@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/I SER 30 OG and /C GLY 23 O: 2.660Å
> distance #7/i:31@OH #7/C:24@OG1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/I TYR 31 OH and /C THR 24 OG1: 3.049Å
> distance #7/i:92@OH #7/C:35@OE1
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/I TYR 92 OH and /C GLU 35 OE1: 3.401Å
> distance #7/i:32@OH #7/C:315@NZ
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/I TYR 32 OH and /C LYS 315 NZ: 3.681Å
> distance #7/i:32@OH #7/C:25@N
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/I TYR 32 OH and /C ILE 25 N: 3.648Å
> distance #7/h:57@NH2 #7/a:382@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ARG 57 NH2 and /A ASN 382 O: 2.559Å
> distance #7/h:57@NH2 #7/a:385@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ARG 57 NH2 and /A ILE 385 O: 2.808Å
> select #7/a:385
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> distance #7/h:57@NE #7/a:386@O
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ARG 57 NE and /A GLY 386 O: 3.353Å
> distance #7/h:72@NH1 #7/a:390@OE2
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ARG 72 NH1 and /A GLU 390 OE2: 3.468Å
> distance #7/h:54@O #7/a:389@ND2
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ASN 54 O and /A ASN 389 ND2: 3.296Å
> distance delete #7/h:72@NH1 #7/a:390@OE2
> distance #7/h:72@NH1 #7/a:390@OE2 color navy
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ARG 72 NH1 and /A GLU 390 OE2: 3.468Å
> distance #7/h:72@NH1 #7/a:390@OE1 color black
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ARG 72 NH1 and /A GLU 390 OE1: 3.504Å
> distance #7/h:72@NH2 #7/a:390@OE2 color black
Distance between k1769_model_angelo_real_space_refined_011_reduced_ss_GB.pdb
#7/H ARG 72 NH2 and /A GLU 390 OE2: 3.786Å
> select #7/c:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024.cxs
> select #7/c:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #6/c:498
14 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!6 & sel) #92c5deff
> transparency (#!6 & sel) 70
> select clear
> view orient
> turn y 180
> turn y 90
> turn z 90
> turn y 90
[Repeated 1 time(s)]
> turn -y 90
[Repeated 1 time(s)]
> turn y 180
> turn -y 10
[Repeated 1 time(s)]
> turn y 10
[Repeated 4 time(s)]
> size #7 stickRadius +1
Changed 17652 bond radii
> size #7 stickRadius -1
Changed 17652 bond radii
> size #7 stickRadius +0.
Changed 17652 bond radii
> 3
Unknown command: 3
> size #7 stickRadius +0.3
Changed 17652 bond radii
> size #7 stickRadius -0.2
Changed 17652 bond radii
> size #7 stickRadius -0.2
Changed 17652 bond radii
> size #7 stickRadius 0.2
Changed 17652 bond radii
> undo
> redo
> view orient
> turn y 180
> turn y 90
> turn z 90
> turn y 180
> turn y 10
[Repeated 3 time(s)]
> turn y 5
> turn y -5
[Repeated 2 time(s)]
> turn y 5
[Repeated 1 time(s)]
> turn y -3
> lighting soft
> save "/home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/all footprint Fab HI.tif" width 1979 height 1322 supersample 4
> transparentBackground true
> select #7/c:33,32,45,27,315,312,21,23,24,35,25
84 atoms, 77 bonds, 11 residues, 1 model selected
> select #7/i:28,30,31,92,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> view sel
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024.cxs
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_LC-chain-i.cxs
> select #7/H
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel atoms
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_LC-chain-i.cxs
> lighting soft
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_LC-chain-i.tif width 1979
> height 1322 supersample 4 transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_LC-chain-i_white-
> background.tif width 1979 height 1322 supersample 4
> view
> select #7/i:28,30,31,92,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> hide sel atoms
> select #7/i:103,106,104,105,57,72,54,74
61 atoms, 56 bonds, 8 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #7/h:103,106,104,105,57,72,54,74
70 atoms, 66 bonds, 8 residues, 1 model selected
> show sel atoms
> select #7/h:1,26
13 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> select #7/h:103,106,104,105,57,72,54,74,1,26
83 atoms, 77 bonds, 10 residues, 1 model selected
> view sel
> select clear
> select #7/h:27,31
18 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> color sel byhetero
> select #7/h:57
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> turn -y 3
[Repeated 1 time(s)]
> turn y 3
[Repeated 1 time(s)]
> turn y 5
[Repeated 1 time(s)]
> turn -y 5
> turn -y 1
[Repeated 4 time(s)]
> select #7/c:28
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #7/h:28
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #7/c:498,499
28 atoms, 28 bonds, 2 residues, 1 model selected
> color sel #ffffbfff
> color sel byhetero
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H.tif width 1979
> height 1322 supersample 4 transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_whiteback.tif width
> 1979 height 1322 supersample 4
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H.cxs
> size #7 stickRadius +0.05
Changed 17652 bond radii
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H.cxs
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_whiteback.tif width
> 1979 height 1322 supersample 4
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H.tif width 1979
> height 1322 supersample 4 transparentBackground true
> turn y 3
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-
> H_whiteback_lastY40.tif width 1979 height 1322 supersample 4
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_lastY40.tif width
> 1979 height 1322 supersample 4 transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_2.cxs
> undo
> turn y -3
[Repeated 2 time(s)]
> turn y 3
> undo
> select add #6
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 8 models selected
> hide sel surfaces
> show sel cartoons
> undo
> select #6/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel cartoons
> select #6/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel cartoons
> select #6/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel cartoons
> select #6/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> show sel cartoons
> transparency #6 70 ribbons
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/HC-chainH-main-interactions_no-surfaceHA_fab-HI.tif width 1979
> height 1322 supersample 4
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/HC-chainH-main-interactions_no-surfaceHA_fab-HI_white-
> background.tif width 1979 height 1322 supersample 4 transparentBackground
> true
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_no-surface.cxs
——— End of log from Mon Sep 23 15:04:26 2024 ———
opened ChimeraX session
> select #6/h:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #6/h:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> show sel cartoons
> select #6/h:97-110
112 atoms, 117 bonds, 14 residues, 1 model selected
> show sel cartoons
> select #6/h:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> show sel cartoons
> select add #6
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 8 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #6/A-C:9
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #6/A-C:9-197
4464 atoms, 4575 bonds, 567 residues, 1 model selected
> select #6/A-C:323
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #6/A-C:299-323
594 atoms, 600 bonds, 75 residues, 1 model selected
> select #6/A-C:323
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #6/A-C:9-323
7383 atoms, 7548 bonds, 945 residues, 1 model selected
> color (#!6 & sel) gray
> select #6/A-C:335
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #6/A-C:335-491
3801 atoms, 3867 bonds, 471 residues, 1 model selected
> color (#!6 & sel) light gray
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_with-lycorice-
> cartoon.cxs
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/HC-chainH-main-interactions_cartoon-lycoriceHA_fab-HI_white-
> background.tif width 1979 height 1322 supersample 4
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/HC-chainH-main-interactions_cartoon-lycoriceHA_fab-HI.tif width
> 1979 height 1322 supersample 4 transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_with-lycorice-
> cartoon.cxs
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select add #2
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 2 models selected
> select subtract #2
12 models selected
> select #2/B
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #2/A
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #2/C
3962 atoms, 4057 bonds, 1 pseudobond, 490 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #2/H
947 atoms, 974 bonds, 121 residues, 1 model selected
> hide sel cartoons
> select #2/I
835 atoms, 853 bonds, 109 residues, 1 model selected
> hide sel cartoons
> select add #2
17232 atoms, 17652 bonds, 3 pseudobonds, 2160 residues, 8 models selected
> transparency (#!2 & sel) 60
> select clear
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_with-lycorice-
> cartoon-and-surface.cxs
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_with-lycorice-
> cartoon-and-surface.tif width 1979 height 1322 supersample 4
> transparentBackground true
> save /home/ana/Documents/__BajicLab/K1769_figures/chimera-session_Fab-H-
> I_interface/session-Fab-HI_09-23-2024_zoom-in_HC-chain-H_with-lycorice-
> cartoon-and-surface-whitebackground.tif width 1979 height 1322 supersample 4
> select #6/h:70-80
88 atoms, 89 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select #6/h:97-110
112 atoms, 117 bonds, 14 residues, 1 model selected
> hide sel cartoons
> select #6/h:51-58
60 atoms, 60 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select #6/h:26-33
71 atoms, 74 bonds, 8 residues, 1 model selected
> hide sel cartoons
> hide #!2 models
> select #7/h:103,106,104,105,57,72,54,74,1,26,27,31
101 atoms, 95 bonds, 12 residues, 1 model selected
> select #7/h:103,106,104,105,57,72,54,74,1,26,27,31,28
109 atoms, 103 bonds, 13 residues, 1 model selected
> hide sel atoms
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select #7/a:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #7/i:28,30,31,92,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> show sel atoms
> select #7/i:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> select #6/i:27-32
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel cartoons
> select #6/i:50-52
15 atoms, 14 bonds, 3 residues, 1 model selected
> show sel cartoons
> select #6/i:89-97
70 atoms, 71 bonds, 9 residues, 1 model selected
> show sel cartoons
> select #7/i:28,30,31,92,32
53 atoms, 53 bonds, 5 residues, 1 model selected
> view sel
> select clear
> turn y -3
[Repeated 4 time(s)]
> view orient
> select down
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2191, in
_forward_keystroke
self.tool_instance.session.ui.forward_keystroke(event)
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 297, in
forward_keystroke
run(self.session, 'select down')
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38,
in run
results = command.run(text, log=log, return_json=return_json)
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2897, in run
result = ci.function(session, **kw_args)
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/std_commands/select.py", line
138, in select_down
session.selection.demote(session)
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/selection.py", line 64, in
demote
self._promotion.demote_selection()
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/selection.py", line 200, in
demote_selection
p.demote()
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/selection.py", line 229, in
demote
m.selected = False # This may clear child drawing selections.
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 255,
in __setattr__
super(Drawing, self).__setattr__(key, value)
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/atomic/pbgroup.py", line 116, in
set_selected
self.pseudobonds.selected = sel
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 163, in
get_prop
vcount = getattr(self, value_count)
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 95, in
get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'
File "/programs/x86_64-linux/chimerax/1.6.1_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 95, in
get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) HD Graphics 530 (SKL GT2)
OpenGL vendor: Intel
Python: 3.9.11
Locale: pt_PT.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: ASUSTeK COMPUTER INC.
Model: GL552VX
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
Cache Size: 6144 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 7.3Gi 416Mi 1.5Gi 7.8Gi 6.4Gi
Swap: 3.7Gi 6.0Mi 3.7Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 530 [8086:191b] (rev 06)
Subsystem: ASUSTeK Computer Inc. HD Graphics 530 [1043:1060]
Kernel driver in use: i915
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
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
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: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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-Clipper: 0.21.0
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: 1.6.1
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: 1.1.1
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-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
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: 2.0.12
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: 1.3.7
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: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
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: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
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: 1.0.7
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: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
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: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
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: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
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: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 13 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Selection history holding reference to dead PseudobondGroup |
comment:2 by , 13 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Selection demotion and promotion for pseudobonds failed to check if the pseudobond group had been deleted. I added the check.
Note:
See TracTickets
for help on using tickets.
open 1gcn 1www
select one of the missing-structure pseudobonds in 1www
promote the selection with up arrow
close 1www
demote the selection with down arrow: error
Opening 1gcn isn't actually necessary, but is convenient to keep the graphics window shown when 1www is closed.