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Opened 2 years ago
Closed 2 years ago
#10005 closed defect (duplicate)
Render by attribute: TypeError: object of type 'function' has no len()
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.5.2-arm64-arm-64bit
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
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/a-b-
> E-site_lateral.cxs format session
Opened PF1.mrc as #1.1, grid size 568,568,568, pixel 1.06, shown at level
0.128, step 1, values float32
Opened PF2.mrc as #1.2, grid size 568,568,568, pixel 1.06, shown at level
0.194, step 1, values float32
Log from Tue Oct 17 11:39:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/a-b-
> E-site_lateral.cxs format session
Opened PF1.mrc as #1.1, grid size 568,568,568, pixel 1.06, shown at level
0.128, step 1, values float32
Opened PF2.mrc as #1.2, grid size 568,568,568, pixel 1.06, shown at level
0.194, step 1, values float32
Log from Tue Oct 17 11:36:42 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Nucleotide_sensing/Mloop_Nucleotide_sensing.cxs
> format session
Opened PF1.mrc as #1.1, grid size 568,568,568, pixel 1.06, shown at level
0.128, step 1, values float32
Opened PF2.mrc as #1.2, grid size 568,568,568, pixel 1.06, shown at level
0.194, step 1, values float32
Log from Tue Oct 3 17:12:51 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Nucleotide_sensing/Mloop_Nucleotide_sensing.cxs
> format session
Opened PF1.mrc as #1.1, grid size 568,568,568, pixel 1.06, shown at level
0.128, step 1, values float32
Opened PF2.mrc as #1.2, grid size 568,568,568, pixel 1.06, shown at level
0.194, step 1, values float32
Log from Tue Oct 3 17:01:46 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Nucleotide_sensing/Mloop_Nucleotide_sensing.cxs
Opened PF1.mrc as #1.1, grid size 568,568,568, pixel 1.06, shown at level
0.128, step 1, values float32
Opened PF2.mrc as #1.2, grid size 568,568,568, pixel 1.06, shown at level
0.194, step 1, values float32
Log from Mon Oct 2 14:31:26 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/lateral_interface_obBeta.cxs
> format session
Opened PF1.mrc as #1.1, grid size 568,568,568, pixel 1.06, shown at level
0.128, step 1, values float32
Opened PF2.mrc as #1.2, grid size 568,568,568, pixel 1.06, shown at level
0.0439, step 1, values float32
Log from Mon Oct 2 13:45:49 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/lateral_interface.cxs
> format session
Log from Mon Oct 2 12:53:18 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_interface/lateral_Interface_substitutions_TSA_bII_bIII.cxs
Opened TSA_GMPCPP_PF1-3.mrc as #1, grid size 568,568,568, pixel 1.06, shown at
level 0.00759, step 1, values float32
Log from Thu May 25 06:47:12 2023UCSF ChimeraX version: 1.5rc202210140205
(2022-10-14)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/Tyr271_Lys58.cxs format
> session
Opened TSA_GMPCPP_PF1-3.mrc as #1, grid size 568,568,568, pixel 1.06, shown at
level 0.00759, step 1, values float32
Log from Wed May 24 14:59:33 2023UCSF ChimeraX version: 1.5rc202210140205
(2022-10-14)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/Tyr271_Lys58.cxs format
> session
Opened TSA_GMPCPP_PF1-3.mrc as #1, grid size 568,568,568, pixel 1.06, shown at
level 0.00759, step 1, values float32
Log from Wed May 24 14:53:47 2023UCSF ChimeraX version: 1.5rc202210140205
(2022-10-14)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_3PF.cxs
> format session
Opened TSA_GMPCPP_PF1-3.mrc as #1, grid size 568,568,568, pixel 1.06, shown at
level 0.00531, step 1, values float32
Log from Wed May 24 09:54:31 2023UCSF ChimeraX version: 1.5rc202210140205
(2022-10-14)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/PanelB.cxs format
> session
Opened TSA_GMPCPP_PF1.mrc as #1, grid size 568,568,568, pixel 1.06, shown at
level 0.0063, step 1, values float32
Opened TSA_GMPCPP_PF2.mrc as #2, grid size 568,568,568, pixel 1.06, shown at
level 0.00693, step 1, values float32
Log from Tue May 23 15:07:19 2023UCSF ChimeraX version: 1.5rc202210140205
(2022-10-14)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_vs_6DPU_Brain_GMPCPP_lateral.cxs
> format session
Opened TSA_GMPCPP_PF1.mrc as #1, grid size 77,79,347, pixel 1.06,1.06,1.06,
shown at level 0.00669, step 1, values float32
Opened TSA_GMPCPP_PF2.mrc as #2, grid size 568,568,568, pixel 1.06, shown at
level 0.00568, step 1, values float32
Log from Tue May 23 14:25:49 2023UCSF ChimeraX version: 1.5rc202210140205
(2022-10-14)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_PF1.mrc
Opened TSA_GMPCPP_PF1.mrc as #1, grid size 77,79,347, pixel 1.06,1.06,1.06,
shown at level 0.0139, step 1, values float32
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_PF2.mrc
Opened TSA_GMPCPP_PF2.mrc as #2, grid size 568,568,568, pixel 1.06, shown at
level 1.45e-06, step 4, values float32
> volume #2 level 0.005683
> volume #2 step 1
> volume #2 color #919191
> volume #2 color #929292
> volume #2 color darkgrey
> volume #1 level 0.006689
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_MT_GMPCPP_lateral.pdb
Chain information for TSA_MT_GMPCPP_lateral.pdb #3
---
Chain | Description
A C | No description available
B D | No description available
E I | No description available
F Q | No description available
> show cartoons
> hide atoms
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> select add #3
27454 atoms, 28070 bonds, 4 pseudobonds, 3494 residues, 2 models selected
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,-0.19729,0,1,0,0.056511,0,0,1,-3.0901
> undo
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> ui mousemode right "translate selected models"
> ui mousemode right translate
> select subtract #3
Nothing selected
> select add #3
27454 atoms, 28070 bonds, 4 pseudobonds, 3494 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,0.76103,0,1,0,-0.43294,0,0,1,-11.312
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule TSA_MT_GMPCPP_lateral.pdb (#3) to map TSA_GMPCPP_PF1.mrc (#1)
using 27454 atoms
average map value = 0.003732, steps = 108
shifted from previous position = 5.8
rotated from previous position = 1.62 degrees
atoms outside contour = 23109, contour level = 0.0066889
Position of TSA_MT_GMPCPP_lateral.pdb (#3) relative to TSA_GMPCPP_PF1.mrc (#1)
coordinates:
Matrix rotation and translation
0.99960521 -0.02655655 -0.00917509 10.01654679
0.02658562 0.99964186 0.00306039 -7.64507912
0.00909053 -0.00330311 0.99995322 -11.53764874
Axis -0.11252318 -0.32298365 0.93969149
Axis point 407.43165422 330.86973272 0.00000000
Rotation angle (degrees) 1.62033397
Shift along axis -9.49968841
> fitmap #3 inMap #2
Fit molecule TSA_MT_GMPCPP_lateral.pdb (#3) to map TSA_GMPCPP_PF2.mrc (#2)
using 27454 atoms
average map value = 0.00256, steps = 68
shifted from previous position = 1.02
rotated from previous position = 1.1 degrees
atoms outside contour = 22335, contour level = 0.0056826
Position of TSA_MT_GMPCPP_lateral.pdb (#3) relative to TSA_GMPCPP_PF2.mrc (#2)
coordinates:
Matrix rotation and translation
0.99901792 -0.04192552 -0.01433365 18.19464041
0.04211364 0.99902714 0.01308481 -16.77500024
0.01377111 -0.01367560 0.99981165 -10.02922102
Axis -0.28909354 -0.30361662 0.90787768
Axis point 473.46579213 358.94981175 0.00000000
Rotation angle (degrees) 2.65278567
Shift along axis -9.27209000
> view matrix models
> #3,0.99902,-0.041926,-0.014334,17.849,0.042114,0.99903,0.013085,-18.525,0.013771,-0.013676,0.99981,11.637
> fitmap #3 inMap #2
Fit molecule TSA_MT_GMPCPP_lateral.pdb (#3) to map TSA_GMPCPP_PF2.mrc (#2)
using 27454 atoms
average map value = 0.005045, steps = 132
shifted from previous position = 11.9
rotated from previous position = 2.22 degrees
atoms outside contour = 16421, contour level = 0.0056826
Position of TSA_MT_GMPCPP_lateral.pdb (#3) relative to TSA_GMPCPP_PF2.mrc (#2)
coordinates:
Matrix rotation and translation
0.99995379 -0.00957059 0.00090707 2.95136463
0.00957188 0.99995317 -0.00142652 -2.82581641
-0.00089338 0.00143513 0.99999857 0.56110777
Axis 0.14721381 0.09262167 0.98475851
Axis point 303.68598391 295.75564535 0.00000000
Rotation angle (degrees) 0.55688778
Shift along axis 0.72530546
> view matrix models
> #3,0.99995,-0.0095706,0.00090707,1.2561,0.0095719,0.99995,-0.0014265,-3.8884,-0.00089338,0.0014351,1,42.971
> fitmap #3 inMap #2
Fit molecule TSA_MT_GMPCPP_lateral.pdb (#3) to map TSA_GMPCPP_PF2.mrc (#2)
using 27454 atoms
average map value = 0.005021, steps = 68
shifted from previous position = 1.97
rotated from previous position = 0.145 degrees
atoms outside contour = 15967, contour level = 0.0056826
Position of TSA_MT_GMPCPP_lateral.pdb (#3) relative to TSA_GMPCPP_PF2.mrc (#2)
coordinates:
Matrix rotation and translation
0.99997457 -0.00708860 0.00077809 2.24313067
0.00709008 0.99997303 -0.00191416 -2.01306388
-0.00076450 0.00191962 0.99999787 42.59154694
Axis 0.25958945 0.10445059 0.96005385
Axis point 887.24374126 -1197.79179185 0.00000000
Rotation angle (degrees) 0.42309368
Shift along axis 41.26220587
> volume #1 color #b2b2b280
> volume #2 level 0.005683
> volume #2 color #a9a9a980
> select clear
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/6dpu_lateral.pdb
Chain information for 6dpu_lateral.pdb #4
---
Chain | Description
A C | No description available
B D | No description available
E I | No description available
F Q | No description available
> show cartoons
> hide atoms
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_vs_6DPU_Brain_GMPCPP_lateral.cxs
——— End of log from Tue May 23 14:25:49 2023 ———
opened ChimeraX session
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> close #4
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/6dpu_lateral.pdb
Chain information for 6dpu_lateral.pdb #4
---
Chain | Description
A C | No description available
B D | No description available
E I | No description available
F Q | No description available
> show #!4 cartoons
> hide #!4 atoms
> close #3
> close #4
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_MT_GMPCPP_lateral.pdb
Chain information for TSA_MT_GMPCPP_lateral.pdb #3
---
Chain | Description
A C | No description available
B D | No description available
E I | No description available
F Q | No description available
> hide atoms
> show cartoons
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/6dpu_lateral.pdb
Summary of feedback from opening /Users/zehrea/Documents/Roll-
Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/6dpu_lateral.pdb
---
warnings | Cannot find LINK/SSBOND residue GTP (501 )
Cannot find LINK/SSBOND residue GTP (501 )
Cannot find LINK/SSBOND residue G2P (501 )
Cannot find LINK/SSBOND residue G2P (501 )
Cannot find LINK/SSBOND residue G2P (501 )
3 messages similar to the above omitted
6dpu_lateral.pdb title:
Undecorated gmpcpp microtubule [more info...]
Chain information for 6dpu_lateral.pdb #4
---
Chain | Description | UniProt
A C K L | tubulin α-1B chain | TBA1B_PIG
B D H I | β-tubulin | TBB_PIG
Non-standard residues in 6dpu_lateral.pdb #4
---
G2P — phosphomethylphosphonic acid guanylate ester
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> hide cartoons
> show cartoons
> hide atoms
> select add #3
27454 atoms, 28070 bonds, 4 pseudobonds, 3494 residues, 2 models selected
> select add #4
54554 atoms, 55786 bonds, 24 pseudobonds, 6938 residues, 5 models selected
> view matrix models
> #3,1,0,0,2.4913,0,1,0,0.66877,0,0,1,35.386,#4,1,0,0,2.4913,0,1,0,0.66877,0,0,1,35.386
> view matrix models
> #3,1,0,0,2.3896,0,1,0,1.9598,0,0,1,42.175,#4,1,0,0,2.3896,0,1,0,1.9598,0,0,1,42.175
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule TSA_MT_GMPCPP_lateral.pdb (#3) to map TSA_GMPCPP_PF2.mrc (#2)
using 27454 atoms
average map value = 0.005021, steps = 92
shifted from previous position = 3.03
rotated from previous position = 0.423 degrees
atoms outside contour = 15966, contour level = 0.0056826
Position of TSA_MT_GMPCPP_lateral.pdb (#3) relative to TSA_GMPCPP_PF2.mrc (#2)
coordinates:
Matrix rotation and translation
0.99997468 -0.00707015 0.00080825 2.22868092
0.00707173 0.99997307 -0.00195999 -1.99135203
-0.00079438 0.00196566 0.99999775 42.58847191
Axis 0.26589559 0.10855084 0.95787069
Axis point 908.85498086 -1236.38547081 0.00000000
Rotation angle (degrees) 0.42295759
Shift along axis 41.17068227
> fitmap #4 inMap #2
Fit molecule 6dpu_lateral.pdb (#4) to map TSA_GMPCPP_PF2.mrc (#2) using 27100
atoms
average map value = 0.004991, steps = 92
shifted from previous position = 2.48
rotated from previous position = 0.501 degrees
atoms outside contour = 15788, contour level = 0.0056826
Position of 6dpu_lateral.pdb (#4) relative to TSA_GMPCPP_PF2.mrc (#2)
coordinates:
Matrix rotation and translation
0.99997525 -0.00077730 0.00699292 -1.34039794
0.00074104 0.99998628 0.00518644 -1.06213630
-0.00699686 -0.00518113 0.99996210 47.98063166
Axis -0.59315404 0.80038877 0.08686836
Axis point 6807.11424310 0.00000000 -133.09360188
Rotation angle (degrees) 0.50073494
Shift along axis 4.11293905
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_vs_6DPU_Brain_GMPCPP_lateral.cxs
Drag select of 152 residues
> select clear
> select add #4
27100 atoms, 27716 bonds, 20 pseudobonds, 3444 residues, 3 models selected
> color (#!4 & sel) purple
> hide #!4 models
> select #3/B,D,Q,F
13658 atoms, 13962 bonds, 1736 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark sea green
> select ~sel
40896 atoms, 41824 bonds, 24 pseudobonds, 5202 residues, 9 models selected
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> select ~sel
13658 atoms, 13962 bonds, 1736 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light blue
> select #3/C,A,E,I
13796 atoms, 14108 bonds, 4 pseudobonds, 1758 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark sea green
> select clear
> show #!2 models
> show #!1 models
> show #!4 models
> hide #!4 models
> volume #1 color #b2b2b24d
> volume #2 color #a9a9a94d
> hide #3.1 models
> ui tool show "Side View"
> graphics silhouettes true
> select :G2P
256 atoms, 272 bonds, 8 residues, 2 models selected
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/PanelA.cxs
> show sel & #!3 atoms
> color (#!3 & sel) byhetero
> select :Mg
16 atoms, 16 residues, 2 models selected
> color (#!3 & sel) byhetero
> select :GTP
256 atoms, 272 bonds, 8 residues, 2 models selected
> color (#!3 & sel) byhetero
> volume #1 level 0.007923
> volume #1 level 0.008442
> volume #1 level 0.006299
> volume #2 level 0.006931
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/PanelA.cxs
> cd /Users/zehrea/Documents/Roll-Mecak_lab/PAPERS/JMB_TSApaper/Figure1/
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd /Users/zehrea/Documents/Roll-Mecak_lab/PAPERS/JMB_TSApaper/Fig1/
Current working directory is: /Users/zehrea/Documents/Roll-
Mecak_lab/PAPERS/JMB_TSApaper/Fig1
> save PanelA.tif supersample 4 transparentBackground true
[Repeated 1 time(s)]
> save PanelA.tif supersample 4 transparentBackground false
> select #3/C,A,E,I
13796 atoms, 14108 bonds, 4 pseudobonds, 1758 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium aquamarine
> color sel medium sea green
> color sel sea green
> select #3/B,D,Q,F
13658 atoms, 13962 bonds, 1736 residues, 1 model selected
> select #3/C,A,E,I
13796 atoms, 14108 bonds, 4 pseudobonds, 1758 residues, 2 models selected
> color sel medium sea green
> color sel dark sea green
> graphics silhouettes false
> graphics silhouettes true
> select clear
> ui tool show "Hide Dust"
> surface dust #1 size 6.36
> surface dust #2 size 6.36
> select clear
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/PanelA.cxs
> save PanelA.tif supersample 4 transparentBackground false
> hide #!2 models
> hide #!1 models
> select :GTP
256 atoms, 272 bonds, 8 residues, 2 models selected
> show sel & #!3 cartoons
> show sel & #!3 atoms
> color (#!3 & sel) byhetero
> select clear
> save PanelB.tif supersample 4 transparentBackground false
> cd /Users/zehrea/Documents/Roll-Mecak_lab/PAPERS/JMB_TSApaper/Fig1/
Current working directory is: /Users/zehrea/Documents/Roll-
Mecak_lab/PAPERS/JMB_TSApaper/Fig1
> save PanelB.tif supersample 4 transparentBackground false
[Repeated 1 time(s)]
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/PanelB.cxs
> save PanelB.tif supersample 4 transparentBackground false
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/PanelB.cxs
——— End of log from Tue May 23 15:07:19 2023 ———
opened ChimeraX session
> close #2
> close #1
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_PF1-3.mrc
Opened TSA_GMPCPP_PF1-3.mrc as #1, grid size 568,568,568, pixel 1.06, shown at
level 0.00121, step 4, values float32
> volume #1 level 0.004255
> volume #1 step 1
> volume #1 level 0.005313
> hide #!3 models
> show #!3 models
> close #4
> select add #3
27454 atoms, 28070 bonds, 4 pseudobonds, 3494 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99997,-0.0070702,0.00080825,16.472,0.0070717,0.99997,-0.00196,-116.13,-0.00079438,0.0019657,1,-74.368
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.48722,0.86679,0.10628,-114.84,-0.87326,0.48273,0.066302,399.72,0.0061653,-0.12511,0.99212,-30.253
> view matrix models
> #3,0.5962,0.78398,0.17298,-150.2,-0.79862,0.60119,0.027812,339.83,-0.082191,-0.15473,0.98453,18.12
> view matrix models
> #3,0.47869,0.84102,0.25207,-146.89,-0.87409,0.48353,0.046624,405.78,-0.082669,-0.24265,0.96659,54.595
> view matrix models
> #3,0.5221,0.83576,0.17005,-137.53,-0.85284,0.51354,0.094532,372.06,-0.0083214,-0.19438,0.98089,3.2948
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.5221,0.83576,0.17005,-133.31,-0.85284,0.51354,0.094532,377.87,-0.0083214,-0.19438,0.98089,7.7574
> view matrix models
> #3,0.5221,0.83576,0.17005,-129.96,-0.85284,0.51354,0.094532,385.17,-0.0083214,-0.19438,0.98089,3.9906
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.556,0.8181,0.14689,-130.39,-0.83117,0.54644,0.10275,362.38,0.0037968,-0.17922,0.9838,-7.1033
> view matrix models
> #3,0.67704,0.73584,0.012731,-109.47,-0.72951,0.66872,0.14361,266.01,0.097162,-0.10652,0.98955,-72.031
> view matrix models
> #3,0.42066,0.90114,0.10484,-91.984,-0.90106,0.40157,0.16378,422.72,0.10549,-0.16336,0.98091,-52.839
> view matrix models
> #3,0.9019,0.43045,-0.035886,-78.428,-0.43059,0.90254,0.0042189,105.96,0.034204,0.011647,0.99935,-90.998
> view matrix models
> #3,0.86221,0.50219,-0.066334,-78.232,-0.49635,0.86372,0.08733,120.73,0.10115,-0.042372,0.99397,-97.463
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.86221,0.50219,-0.066334,-62.832,-0.49635,0.86372,0.08733,123.6,0.10115,-0.042372,0.99397,-105.95
> view matrix models
> #3,0.86221,0.50219,-0.066334,-94.814,-0.49635,0.86372,0.08733,116.59,0.10115,-0.042372,0.99397,-94.397
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule TSA_MT_GMPCPP_lateral.pdb (#3) to map TSA_GMPCPP_PF1-3.mrc (#1)
using 27454 atoms
average map value = 0.01017, steps = 152
shifted from previous position = 9.58
rotated from previous position = 21.6 degrees
atoms outside contour = 4683, contour level = 0.0053131
Position of TSA_MT_GMPCPP_lateral.pdb (#3) relative to TSA_GMPCPP_PF1-3.mrc
(#1) coordinates:
Matrix rotation and translation
0.63262637 0.77445622 0.00119925 -122.99885644
-0.77445621 0.63262726 -0.00057600 343.63460587
-0.00120477 -0.00056438 0.99999912 -64.91381952
Axis 0.00000750 0.00155207 -0.99999880
Axis point 300.60025950 301.41401110 0.00000000
Rotation angle (degrees) 50.75584145
Shift along axis 65.44616329
> volume #1 color #b2b2b280
> select add #1
27454 atoms, 28070 bonds, 4 pseudobonds, 3494 residues, 4 models selected
> view matrix models
> #3,0.63263,0.77446,0.0011993,-95.454,-0.77446,0.63263,-0.000576,396.88,-0.0012048,-0.00056438,1,-64.23,#1,1,0,0,27.545,0,1,0,53.244,0,0,1,0.68403
> ui mousemode right zoom
> open /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_MT_GMPCPP_FINAL-
> coot-1.pdb
Chain information for TSA_MT_GMPCPP_FINAL-coot-1.pdb #2
---
Chain | Description
A | No description available
B | No description available
I | No description available
Q | No description available
> select subtract #1
27454 atoms, 28070 bonds, 4 pseudobonds, 3494 residues, 2 models selected
> select add #1
27454 atoms, 28070 bonds, 4 pseudobonds, 3494 residues, 4 models selected
> hide #!2 models
> show #!2 models
> hide #!3 models
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.63263,0.77446,0.0011993,-103.36,-0.77446,0.63263,-0.000576,386.98,-0.0012048,-0.00056438,1,-62.866,#1,1,0,0,19.642,0,1,0,43.348,0,0,1,2.0479
> undo
> select subtract #3
2 models selected
> select add #2
13727 atoms, 14035 bonds, 2 pseudobonds, 1747 residues, 4 models selected
> view matrix models
> #1,1,0,0,30.425,0,1,0,56.923,0,0,1,-0.19123,#2,1,0,0,2.8805,0,1,0,3.6788,0,0,1,-0.87525
> undo
> show #!3 models
> select subtract #1
13727 atoms, 14035 bonds, 2 pseudobonds, 1747 residues, 2 models selected
> view matrix models #2,1,0,0,-72.579,0,1,0,-88.692,0,0,1,0.93481
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule TSA_MT_GMPCPP_FINAL-coot-1.pdb (#2) to map TSA_GMPCPP_PF1-3.mrc
(#1) using 13727 atoms
average map value = 0, steps = 36
shifted from previous position = 2.62
rotated from previous position = 0.869 degrees
atoms outside contour = 13727, contour level = 0.0053131
Position of TSA_MT_GMPCPP_FINAL-coot-1.pdb (#2) relative to
TSA_GMPCPP_PF1-3.mrc (#1) coordinates:
Matrix rotation and translation
0.99996889 0.00665364 -0.00423550 -103.93252220
-0.00659819 0.99989406 0.01297417 -141.70837803
0.00432137 -0.01294582 0.99990686 3.77997777
Axis -0.85424270 -0.28200795 -0.43673897
Axis point 0.00000000 4520.69776293 8196.69196654
Rotation angle (degrees) 0.86928667
Shift along axis 127.09562417
> fitmap #2 inMap #1
Fit molecule TSA_MT_GMPCPP_FINAL-coot-1.pdb (#2) to map TSA_GMPCPP_PF1-3.mrc
(#1) using 13727 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 13727, contour level = 0.0053131
Position of TSA_MT_GMPCPP_FINAL-coot-1.pdb (#2) relative to
TSA_GMPCPP_PF1-3.mrc (#1) coordinates:
Matrix rotation and translation
0.99996889 0.00665364 -0.00423550 -103.93252220
-0.00659819 0.99989406 0.01297417 -141.70837803
0.00432137 -0.01294582 0.99990686 3.77997777
Axis -0.85424270 -0.28200795 -0.43673897
Axis point 0.00000000 4520.69776293 8196.69196654
Rotation angle (degrees) 0.86928667
Shift along axis 127.09562417
> view matrix models
> #2,0.99997,0.0066536,-0.0042355,-75.927,-0.0065982,0.99989,0.012974,-87.356,0.0043214,-0.012946,0.99991,1.5818
> view matrix models
> #2,0.99997,0.0066536,-0.0042355,-9.7173,-0.0065982,0.99989,0.012974,-119.99,0.0043214,-0.012946,0.99991,-10.199
> fitmap #2 inMap #1
Fit molecule TSA_MT_GMPCPP_FINAL-coot-1.pdb (#2) to map TSA_GMPCPP_PF1-3.mrc
(#1) using 13727 atoms
average map value = 0.005199, steps = 148
shifted from previous position = 15.3
rotated from previous position = 1.78 degrees
atoms outside contour = 8136, contour level = 0.0053131
Position of TSA_MT_GMPCPP_FINAL-coot-1.pdb (#2) relative to
TSA_GMPCPP_PF1-3.mrc (#1) coordinates:
Matrix rotation and translation
0.99964393 0.02273577 -0.01396782 -49.01553980
-0.02289784 0.99967103 -0.01155474 -167.43970134
0.01370052 0.01187046 0.99983568 -13.22151620
Axis 0.40193381 -0.47473825 -0.78298965
Axis point -5905.69414710 3303.37940015 0.00000000
Rotation angle (degrees) 1.66987085
Shift along axis 70.14133913
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.23637,0.96807,-0.083515,-56.332,-0.97002,0.24009,0.037656,526.8,0.056505,0.072111,0.99579,-50.681
> fitmap #2 inMap #1
Fit molecule TSA_MT_GMPCPP_FINAL-coot-1.pdb (#2) to map TSA_GMPCPP_PF1-3.mrc
(#1) using 13727 atoms
average map value = 0.009965, steps = 152
shifted from previous position = 4.79
rotated from previous position = 27 degrees
atoms outside contour = 2418, contour level = 0.0053131
Position of TSA_MT_GMPCPP_FINAL-coot-1.pdb (#2) relative to
TSA_GMPCPP_PF1-3.mrc (#1) coordinates:
Matrix rotation and translation
-0.22021066 0.97545222 -0.00047535 73.54812073
-0.97545169 -0.22021105 -0.00104893 662.23478712
-0.00112786 0.00023270 0.99999934 -4.54032169
Axis 0.00065694 0.00033446 -0.99999973
Axis point 301.47142033 301.72024148 0.00000000
Rotation angle (degrees) 102.72143734
Shift along axis 4.81012972
> select add #3
41181 atoms, 42105 bonds, 6 pseudobonds, 5241 residues, 4 models selected
> select add #1
41181 atoms, 42105 bonds, 6 pseudobonds, 5241 residues, 6 models selected
> select subtract #1
41181 atoms, 42105 bonds, 6 pseudobonds, 5241 residues, 4 models selected
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms sel distance 10
> surface zone #1 nearAtoms sel distance 8
[Repeated 1 time(s)]
> surface zone #1 nearAtoms sel distance 7
[Repeated 1 time(s)]
> surface zone #1 nearAtoms sel distance 6
[Repeated 1 time(s)]
> view matrix models
> #3,0.60678,0.40965,0.68118,-174.55,-0.40491,0.89674,-0.1786,212.33,-0.68401,-0.16745,0.71,359.19,#2,0.050632,0.73137,0.6801,-62.791,-0.95564,0.23331,-0.17975,568.34,-0.29014,-0.64083,0.71074,426.64
> undo
> select add #1
41181 atoms, 42105 bonds, 6 pseudobonds, 5241 residues, 6 models selected
> view matrix models
> #3,0.52817,0.82772,-0.18952,-11.422,-0.84688,0.52976,-0.046409,473.43,0.061989,0.18501,0.98078,-142.57,#1,0.97494,0.11471,-0.19063,56.703,-0.12553,0.99104,-0.045687,114.47,0.18368,0.068472,0.9806,-79.857,#2,-0.32637,0.9257,-0.19121,205.24,-0.93901,-0.3407,-0.046667,761.74,-0.10835,0.16432,0.98044,-25.455
> surface zone #1 nearAtoms sel distance 5
[Repeated 1 time(s)]
> select clear
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_3PF.cxs
> hide #!1 models
> select /Q,F
10242 atoms, 10470 bonds, 1302 residues, 2 models selected
> select /Q,F,B,D
20487 atoms, 20943 bonds, 2604 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select /F,D
6829 atoms, 6981 bonds, 868 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium blue
> select /A,I
13796 atoms, 14108 bonds, 4 pseudobonds, 1758 residues, 4 models selected
> ui tool show "Color Actions"
> color sel dark sea green
> select /C,E
6898 atoms, 7054 bonds, 2 pseudobonds, 879 residues, 2 models selected
> ui tool show "Color Actions"
> color sel green
> color sel forest green
> color sel green
> select clear
> show #!1 models
> ui mousemode right "translate selected models"
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_3PF.cxs
> volume #1 level 0.004839
> volume #1 level 0.005313
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_3PF.cxs
——— End of log from Wed May 24 09:54:31 2023 ———
opened ChimeraX session
> ui tool show "Side View"
> ui tool show "Volume Viewer"
> volume #1 level 0.0063
> volume #1 level 0.005774
> color #1 #b2b2b233 models
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_3PF.cxs
> save TSA_GMPCPP_3PFs.tif supersample 4 transparentBackground false
> volume #1 level 0.006366
> volume #1 level 0.006827
> volume #1 level 0.007551
> hide atoms
> select :G2P
192 atoms, 204 bonds, 6 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select :GTP
192 atoms, 204 bonds, 6 residues, 2 models selected
> color sel byhetero
> select :MG
12 atoms, 12 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select :GTP
192 atoms, 204 bonds, 6 residues, 2 models selected
> show sel atoms
> select clear
> select #3/F:57
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel magenta
> select #3/F:35
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select clear
> volume #1 level 0.008604
> select #2/Q:281
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show #!1 models
> save "/Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_with_resibue_changesbetween
> BII.cxs"
> show sel atoms
> select #3/F:53
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/F:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #2/Q:281
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel byhetero
> hide #!1 models
> hide sel atoms
> select #3/F:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> hide #!1 models
> select #2/Q:281
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> select #3/F:53
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> show #!1 models
> hide #!1 models
> select #3/F:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> show #!1 models
> hide #!1 models
> select #2/Q:281
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #2/Q:280
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> color sel byhetero
> show #!1 models
> hide #!1 models
> select #3/F:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> color sel byhetero
> select #3/F:87
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #2/Q:277
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/F:60
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #3/F:54
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> color sel byhetero
> save "/Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_with_resibue_changesbetween
> BII_residues_shown.cxs"
> select #3/F:53
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/Q:283
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/Q:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> hide sel atoms
> select #2/Q:291
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #3/F:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #2/Q:294
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select /Q:367
22 atoms, 22 bonds, 2 residues, 2 models selected
> show sel atoms
> select /K:310
Nothing selected
> show atoms
> undo
> select /K:310
Nothing selected
> select #2/Q:310
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #2/Q:305
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 26 atoms, 55 residues, 28 bonds
> hide sel atoms
Drag select of 15 atoms, 22 residues, 15 bonds
> hide sel atoms
Drag select of 8 atoms, 48 residues, 8 bonds
> hide sel atoms
> select clear
Drag select of 11 atoms, 36 residues, 10 bonds
> hide sel atoms
> select clear
> select #2/Q:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select /K:325
Nothing selected
> select /K :325
Nothing selected
> select /K
Nothing selected
> select :221
108 atoms, 96 bonds, 12 residues, 2 models selected
> select :221
108 atoms, 96 bonds, 12 residues, 2 models selected
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select #2/Q:278
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/Q:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> hide sel atoms
> select #3/F:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> hide #!1 models
> select #2/Q:283@CA
1 atom, 1 residue, 1 model selected
> select #2/Q:283
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/Q:284
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select ?B
Expected an objects specifier or a keyword
> select /B
6830 atoms, 6982 bonds, 868 residues, 2 models selected
> select #2/Q:284
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel LEU rotLib Dunbrack
TSA_MT_GMPCPP_FINAL-coot-1.pdb #2/Q LEU 284: phi -90.7, psi 85.1 trans
Changed 45 bond radii
> swapaa #!2/Q:284 LEU criteria 7 rotLib Dunbrack retain false
Using Dunbrack library
TSA_MT_GMPCPP_FINAL-coot-1.pdb #!2/Q LEU 284: phi -90.7, psi 85.1 trans
Applying LEU rotamer (chi angles: 70.6 164.8) to TSA_MT_GMPCPP_FINAL-
coot-1.pdb #!2/Q LEU 284
> select #3/F:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #2/Q:284
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> select #3/F:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byhetero
> save "/Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_with_resibue_changesbetween
> BII_residues_shown.cxs"
> ui tool show Distances
> select #3/F:55@CG2
1 atom, 1 residue, 1 model selected
> select add #2/Q:284@CD2
2 atoms, 2 residues, 2 models selected
> distance #3/F:55@CG2 #2/Q:284@CD2
Distance between TSA_MT_GMPCPP_lateral.pdb #3/F THR 55 CG2 and
TSA_MT_GMPCPP_FINAL-coot-1.pdb #2/Q LEU 284 CD2: 2.981Å
> ~distance #3/F:55@CG2 #2/Q:284@CD2
> select #3/F:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2/Q:288
18 atoms, 16 bonds, 2 residues, 2 models selected
> show sel target ab
> style sel stick
Changed 18 atom styles
> color sel byhetero
> select #3/F:122@NZ
1 atom, 1 residue, 1 model selected
> select add #2/A:289
6 atoms, 4 bonds, 2 residues, 2 models selected
> select #2/Q:288@OE1
1 atom, 1 residue, 1 model selected
> select add #3/F:122@NZ
2 atoms, 2 residues, 2 models selected
> distance #2/Q:288@OE1 #3/F:122@NZ
Distance between TSA_MT_GMPCPP_FINAL-coot-1.pdb #2/Q GLU 288 OE1 and
TSA_MT_GMPCPP_lateral.pdb #3/F LYS 122 NZ: 6.346Å
> show #!1 models
> volume #1 level 0.007588
> hide #!1 models
> select #2/Q:292
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> hide sel atoms
> select add #2/Q:291@OE1
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #3/F:122@NZ
11 atoms, 8 bonds, 1 pseudobond, 3 residues, 3 models selected
Exactly two atoms must be selected!
> select #3/F:122@NZ
1 atom, 1 residue, 1 model selected
> select add #2/Q:291@OE1
2 atoms, 2 residues, 2 models selected
> distance #3/F:122@NZ #2/Q:291@OE1
Distance between TSA_MT_GMPCPP_lateral.pdb #3/F LYS 122 NZ and
TSA_MT_GMPCPP_FINAL-coot-1.pdb #2/Q GLN 291 OE1: 6.106Å
> ~distance #2/Q:288@OE1 #3/F:122@NZ
> select #2/Q:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/F:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/Q:280
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> ~distance #3/F:122@NZ #2/Q:291@OE1
> select #2/Q:284
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/Q:283
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> save "/Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_with_resibue_changesbetween
> BII_residues_shown.cxs"
> select #2/Q:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/F:122@NZ
1 atom, 1 residue, 1 model selected
> select add #2/Q:288@OE1
2 atoms, 2 residues, 2 models selected
> distance #3/F:122@NZ #2/Q:288@OE1
Distance between TSA_MT_GMPCPP_lateral.pdb #3/F LYS 122 NZ and
TSA_MT_GMPCPP_FINAL-coot-1.pdb #2/Q GLU 288 OE1: 6.346Å
> ~distance #3/F:122@NZ #2/Q:288@OE1
> select #3/F:58@NZ
1 atom, 1 residue, 1 model selected
> select add #2/Q:281@OH
2 atoms, 2 residues, 2 models selected
> distance #3/F:58@NZ #2/Q:281@OH
Distance between TSA_MT_GMPCPP_lateral.pdb #3/F LYS 58 NZ and
TSA_MT_GMPCPP_FINAL-coot-1.pdb #2/Q TYR 281 OH: 4.187Å
> select #3/F:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/Q:280
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/F:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/Q:280
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> distance style symbol false
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> select #3/F:33@CG2
1 atom, 1 residue, 1 model selected
> select add #3/F:60
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #3/F:58@NZ
1 atom, 1 residue, 1 model selected
> select add #3/F:33@CG2
2 atoms, 2 residues, 1 model selected
> distance #3/F:58@NZ #3/F:33@CG2
Distance between TSA_MT_GMPCPP_lateral.pdb #3/F LYS 58 NZ and THR 33 CG2:
4.317Å
> select #3/F:237
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/F:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style decimalPlaces 0
[Repeated 2 time(s)]
> distance style decimalPlaces -1
Invalid "decimalPlaces" argument: Must be greater than or equal to 0
> distance style symbol false
[Repeated 2 time(s)]
> distance style decimalPlaces 0
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> select #3/F:83@NE2
1 atom, 1 residue, 1 model selected
> select add #2/Q:281@OH
2 atoms, 2 residues, 2 models selected
> distance #3/F:83@NE2 #2/Q:281@OH
Distance between TSA_MT_GMPCPP_lateral.pdb #3/F GLN 83 NE2 and
TSA_MT_GMPCPP_FINAL-coot-1.pdb #2/Q TYR 281 OH: 3.2
> select add #3/F:60
9 atoms, 6 bonds, 3 residues, 2 models selected
> select #2/Q:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #3/F:60
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add #3/F:54
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/Q:283
10 atoms, 8 bonds, 2 residues, 2 models selected
> select add #2/Q:288
19 atoms, 16 bonds, 3 residues, 2 models selected
> select clear
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/Tyr271_Lys58.cxs
Drag select of 6 atoms, 2 residues, 5 bonds
> hide sel atoms
Drag select of 2 atoms, 1 residues, 1 bonds
> hide sel atoms
Drag select of 2 atoms, 1 residues, 1 bonds
> hide sel atoms
> select #3/F:86
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> hide sel atoms
> select clear
> select #3/F:85
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> hide sel atoms
> select #2/Q:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/Q:284
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #2/Q:283
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/F:54
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/Q:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/Q:284
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/Q:280
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/Tyr271_Lys58.cxs
> select #3/F:53
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> hide sel atoms
> lighting simple
> lighting soft
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/Tyr271_Lys58.cxs
——— End of log from Wed May 24 14:53:47 2023 ———
opened ChimeraX session
> select #3/F:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> swapaa interactive sel THR rotLib Dunbrack
TSA_MT_GMPCPP_lateral.pdb #3/F THR 33: phi -98.4, psi -9.3 trans
Changed 12 bond radii
> swapaa #!3/F:33 THR criteria 3 rotLib Dunbrack retain false
Using Dunbrack library
TSA_MT_GMPCPP_lateral.pdb #!3/F THR 33: phi -98.4, psi -9.3 trans
Applying THR rotamer (chi angles: -168.8) to TSA_MT_GMPCPP_lateral.pdb #!3/F
THR 33
> select #3/F:33@OG1
1 atom, 1 residue, 1 model selected
> select add #3/F:58@NZ
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #3/F:33@OG1 #3/F:58@NZ
Distance between TSA_MT_GMPCPP_lateral.pdb #3/F THR 33 OG1 and LYS 58 NZ: 4.2
> select clear
> ui tool show "Side View"
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/Tyr271_Lys58.cxs
——— End of log from Wed May 24 14:59:33 2023 ———
opened ChimeraX session
> ui tool show "Side View"
> select /F,Q
10242 atoms, 10470 bonds, 3 pseudobonds, 1302 residues, 3 models selected
> select /F,Q :33,35,37,55
93 atoms, 84 bonds, 12 residues, 2 models selected
> select /F,Q :33,35,37,55,56
105 atoms, 96 bonds, 15 residues, 2 models selected
> select /F,Q :33,35,37,55,56,57
117 atoms, 108 bonds, 18 residues, 2 models selected
> select /F,Q :33,35,37,55,56,57,80
138 atoms, 129 bonds, 21 residues, 2 models selected
> select /F,Q :33,35,37,55,56,57,80,83,84,124,126
222 atoms, 204 bonds, 33 residues, 2 models selected
> select /F,Q :33,35,37,55,56,57,80,83,84,124,126,155
246 atoms, 225 bonds, 36 residues, 2 models selected
> select /F,Q :33,35,37,55,56,57,80,83,84,124,126,155,170
267 atoms, 243 bonds, 39 residues, 2 models selected
> select /F,Q :33,35,37,55,56,57,80,83,84,124,126,155,170,189
288 atoms, 261 bonds, 42 residues, 2 models selected
> select /F,Q :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201
306 atoms, 276 bonds, 45 residues, 2 models selected
> select /F,Q :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218
327 atoms, 294 bonds, 48 residues, 2 models selected
> select /F,Q :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239
345 atoms, 309 bonds, 51 residues, 2 models selected
> select /F,Q :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275
363 atoms, 324 bonds, 54 residues, 2 models selected
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296
378 atoms, 336 bonds, 57 residues, 2 models selected
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296,315,316
414 atoms, 369 bonds, 63 residues, 2 models selected
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296,315,316,332
438 atoms, 390 bonds, 66 residues, 2 models selected
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296,315,316,332,333,335,351
504 atoms, 450 bonds, 75 residues, 2 models selected
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296,315,316,332,333,335,351,365
525 atoms, 468 bonds, 78 residues, 2 models selected
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296,315,316,332,333,335,351,365,431
540 atoms, 480 bonds, 81 residues, 2 models selected
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296,315,316,332,333,335,351,365,431,433
540 atoms, 480 bonds, 81 residues, 2 models selected
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296,315,316,332,333,335,351,365,431
540 atoms, 480 bonds, 81 residues, 2 models selected
> color sel magenta
> ui tool show Distances
> ~distance #3/F:33@OG1 #3/F:58@NZ
> ~distance #3/F:58@NZ #2/Q:281@OH
> ~distance #3/F:83@NE2 #2/Q:281@OH
> style sel ball
Changed 540 atom styles
> hide sel atoms
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296,315,316,332,333,335,351,365,431@CA
81 atoms, 81 residues, 2 models selected
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_vs_bIIandbIII_mutations.cxs
> select /F,Q
> :33@CA,35@CA,37@CA,55@CA,56@CA,57@CA,80@CA,83@CA,84@CA,124@CA,126@CA,155@CA,170@CA,189@CA,201@CA,218@CA,239@CA,275@CA,296@CA,315@CA,316@CA,332@CA,333@CA,335@CA,351@CA,365@CA,431@CA
3 atoms, 3 residues, 2 models selected
> style sel ball
Changed 3 atom styles
> show sel atoms
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296,315,316,332,333,335,351,365,431@CA
81 atoms, 81 residues, 2 models selected
> color sel magenta
> select
41181 atoms, 42105 bonds, 6 pseudobonds, 5241 residues, 6 models selected
> hide (#!2-3 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!2-3 & sel-residues)
> show (#!2-3 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> hide sel cartoons
> hide sel atoms
> show sel atoms
> select
41181 atoms, 42105 bonds, 6 pseudobonds, 5241 residues, 6 models selected
> hide (#!2-3 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!2-3 & sel-residues)
> show (#!2-3 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> style sel stick
Changed 41181 atom styles
> select /F,Q
> :33,35,37,55,56,57,80,83,84,124,126,155,170,189,201,218,239,275,296,315,316,332,333,335,351,365,431@CA
81 atoms, 15 pseudobonds, 81 residues, 4 models selected
> style sel ball
Changed 81 atom styles
> select clear
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/TSA_GMPCPP_vs_bIIandbIII_mutations.cxs
> save TSA_vs_BIIandBIII.tif supersample 4 transparentBackground false
> show cartoons
> save TSA_vs_BIIandBIII.tif supersample 4 transparentBackground false
> select #3/F:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #3/F:35
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 7 atom styles
> select #3/F:33@CA
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> select #3/F:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #2/Q:280
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #2/Q:281
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #3/F:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 9 atom styles
> select #3/F:67
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/F:87
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/F:54
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/Q:283
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/lateral_Interface_substitutions_TSA_bII_bIII.cxs
> save TSA_vs_BIIandBIII_lateral_interfcae.tif supersample 4
> transparentBackground false
[Repeated 1 time(s)]
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/lateral_Interface_substitutions_TSA_bII_bIII.cxs
> select #3/F:55
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #2/Q:275
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 6 atom styles
> select #3/F:80
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #3/F:37
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel byhetero
> style sel stick
Changed 10 atom styles
> save /Users/zehrea/Documents/Roll-
> Mecak_lab/PAPERS/JMB_TSApaper/Fig1/Lateral_interface/lateral_Interface_substitutions_TSA_bII_bIII.cxs
——— End of log from Thu May 25 06:47:12 2023 ———
opened ChimeraX session
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/models/TSA_MT_GMPCP_FINAL.pdb
Chain information for TSA_MT_GMPCP_FINAL.pdb #4
---
Chain | Description
A | No description available
B Q | No description available
I | No description available
> ui tool show Matchmaker
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TSA_MT_GMPCPP_FINAL-coot-1.pdb, chain I (#2) with
TSA_MT_GMPCP_FINAL.pdb, chain A (#4), sequence alignment score = 2257.8
RMSD between 436 pruned atom pairs is 0.456 angstroms; (across all 437 pairs:
0.482)
> view sel
> ui tool show "Side View"
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/models/TSA_MT_GMPCP_FINAL.pdb
> format pdb
Chain information for TSA_MT_GMPCP_FINAL.pdb #5
---
Chain | Description
A | No description available
B Q | No description available
I | No description available
Drag select of 25 atoms, 235 residues, 28 bonds
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> matchmaker #!5 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TSA_MT_GMPCPP_lateral.pdb, chain F (#3) with
TSA_MT_GMPCP_FINAL.pdb, chain Q (#5), sequence alignment score = 848.3
RMSD between 160 pruned atom pairs is 0.296 angstroms; (across all 160 pairs:
0.296)
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/models/TSA_MT_GMPCP_FINAL.pdb
> format pdb
Chain information for TSA_MT_GMPCP_FINAL.pdb #6
---
Chain | Description
A | No description available
B Q | No description available
I | No description available
> select clear
Drag select of 65 atoms, 720 residues, 68 bonds
> matchmaker #!6 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TSA_MT_GMPCPP_lateral.pdb, chain A (#3) with
TSA_MT_GMPCP_FINAL.pdb, chain I (#6), sequence alignment score = 1555.8
RMSD between 298 pruned atom pairs is 0.479 angstroms; (across all 300 pairs:
0.524)
> hide #!5 models
> hide #!6 models
> hide #!4 models
Drag select of 99 atoms, 1180 residues, 102 bonds
> select clear
Drag select of 123 atoms, 1167 residues, 134 bonds
> matchmaker #!6 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TSA_MT_GMPCPP_lateral.pdb, chain I (#3) with
TSA_MT_GMPCP_FINAL.pdb, chain I (#6), sequence alignment score = 1551.4
RMSD between 298 pruned atom pairs is 0.452 angstroms; (across all 300 pairs:
0.489)
> show #!6 models
> hide #!6 models
> select clear
Drag select of 132 atoms, 1319 residues, 1 pseudobonds, 136 bonds
> matchmaker #!4 to #2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TSA_MT_GMPCPP_FINAL-coot-1.pdb, chain B (#2) with
TSA_MT_GMPCP_FINAL.pdb, chain Q (#4), sequence alignment score = 1786.2
RMSD between 344 pruned atom pairs is 0.380 angstroms; (across all 347 pairs:
0.464)
> show #!4 models
> hide #!4 models
> close #1
> hide #!2 models
> show #!2 models
> close #2
> close #3
> show #!4 models
> show #!5 models
> show #!6 models
> close #4
> save
> "/Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/New
> Folder/lateral_interface.cxs"
> select #5 /B,Q
6825 atoms, 6977 bonds, 868 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light blue
> select #6 /B,Q
6825 atoms, 6977 bonds, 868 residues, 1 model selected
> color sel dodger blue
> color sel royal blue
> color sel deep sky blue
> select #5 /A,I
6898 atoms, 7054 bonds, 2 pseudobonds, 879 residues, 2 models selected
> color sel dark sea green
> select #6 /A,I
6898 atoms, 7054 bonds, 2 pseudobonds, 879 residues, 2 models selected
> color sel medium spring green
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/Lateral_panelA.cxs
> hide #5.1 models
> hide #6.1 models
> select /GTP,G2P,Mg
Nothing selected
> select :GTP,G2P,Mg
264 atoms, 272 bonds, 16 residues, 2 models selected
> color sel byhetero
> select clear
> cd
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New
Current working directory is:
/Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New
> save PanelA.tif supersample 4 TransparentBackground True
Expected a keyword
> save PanelA.tif supersample 4 Transparentbackground True
Expected a keyword
No help found for 'help:user/commands/save.htmlback'
> save PanelA.tif supersample 4 transparentBackground true
> ui mousemode right zoom
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/lateral_interface.cxs
——— End of log from Mon Oct 2 12:53:18 2023 ———
opened ChimeraX session
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_interface/TSA_GMPCPP_PF1-3.mrc
> format mrc
Opened TSA_GMPCPP_PF1-3.mrc as #1, grid size 568,568,568, pixel 1.06, shown at
level 0.00121, step 4, values float32
> volume #1 level 0.004139
> volume #1 step 1
> volume #1 level 0.004859
> volume #1 color #b2b2b286
> hide #!1 models
> show #!1 models
> select add #5
13723 atoms, 14031 bonds, 2 pseudobonds, 1747 residues, 2 models selected
> select add #6
27446 atoms, 28062 bonds, 4 pseudobonds, 3494 residues, 4 models selected
> hide #!5 models
> show #!5 models
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.11535,0.97462,-0.19185,-4.5057,-0.99298,0.10806,-0.04809,549.55,-0.026139,0.19605,0.98025,-62.085,#6,0.5255,0.82936,-0.18979,-82.76,-0.84856,0.52707,-0.046288,380.01,0.061645,0.18537,0.98073,-94.305
> view matrix models
> #5,0.11535,0.97462,-0.19185,-3.8803,-0.99298,0.10806,-0.04809,548.57,-0.026139,0.19605,0.98025,-67.517,#6,0.5255,0.82936,-0.18979,-82.134,-0.84856,0.52707,-0.046288,379.02,0.061645,0.18537,0.98073,-99.736
> ui tool show "Fit in Map"
> fitmap #5 inMap #1
Fit molecule TSA_MT_GMPCP_FINAL.pdb (#5) to map TSA_GMPCPP_PF1-3.mrc (#1)
using 13723 atoms
average map value = 0.0101, steps = 152
shifted from previous position = 12.2
rotated from previous position = 22.2 degrees
atoms outside contour = 1844, contour level = 0.0048592
Position of TSA_MT_GMPCP_FINAL.pdb (#5) relative to TSA_GMPCPP_PF1-3.mrc (#1)
coordinates:
Matrix rotation and translation
-0.21893478 0.97573932 -0.00058658 72.97041403
-0.97573864 -0.21893535 -0.00118783 661.89450615
-0.00128744 0.00031229 0.99999912 -4.52016560
Axis 0.00076871 0.00035914 -0.99999964
Axis point 301.40111596 301.74205866 0.00000000
Rotation angle (degrees) 102.64651770
Shift along axis 4.81397198
> fitmap #6 inMap #1
Fit molecule TSA_MT_GMPCP_FINAL.pdb (#6) to map TSA_GMPCPP_PF1-3.mrc (#1)
using 13723 atoms
average map value = 0.01034, steps = 164
shifted from previous position = 8.07
rotated from previous position = 21.9 degrees
atoms outside contour = 1787, contour level = 0.0048592
Position of TSA_MT_GMPCP_FINAL.pdb (#6) relative to TSA_GMPCPP_PF1-3.mrc (#1)
coordinates:
Matrix rotation and translation
0.23128538 0.97288536 0.00107115 -61.94788636
-0.97288555 0.23128614 -0.00064977 524.27933931
-0.00087989 -0.00089182 0.99999922 -13.57961162
Axis -0.00012440 0.00100271 -0.99999949
Axis point 300.78232486 301.33242169 0.00000000
Rotation angle (degrees) 76.62724161
Shift along axis 14.11300937
> select add #1
27446 atoms, 28062 bonds, 4 pseudobonds, 3494 residues, 7 models selected
> view matrix models
> #5,-0.21893,0.97574,-0.00058658,98.465,-0.97574,-0.21894,-0.0011878,704.66,-0.0012874,0.00031229,1,8.6816,#6,0.23129,0.97289,0.0010711,-36.453,-0.97289,0.23129,-0.00064977,567.04,-0.00087989,-0.00089182,1,-0.37785,#1,1,0,0,25.495,0,1,0,42.761,0,0,1,13.202
> ui mousemode right zoom
> volume #1 level 0.007522
> volume #1 level 0.008026
> volume #1 level 0.008602
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/MAPS/TSA_GMPCPP/PF_ref/job021/deepEMHancer2/TSA_GMPCPP_deepemhancer.mrc
Opened TSA_GMPCPP_deepemhancer.mrc as #2, grid size 568,568,568, pixel 1.06,
shown at level 0.0351, step 4, values float32
> volume #2 step 1
> hide #!1 models
> show #!1 models
> hide #!1 models
> close #2
> close #1
> select clear
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/PF1.mrc
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/PF2.mrc
Opened PF1.mrc as #1.1, grid size 568,568,568, pixel 1.06, shown at level
7.09e-05, step 4, values float32
Opened PF2.mrc as #1.2, grid size 568,568,568, pixel 1.06, shown at level
2.23e-05, step 4, values float32
> volume #1.2 level 0.08034
> volume #1.1 level 0.06136
> volume #1.1 step 1
> volume #1.2 step 1
> hide #!1 models
> show #!1 models
> select add #5
13723 atoms, 14031 bonds, 2 pseudobonds, 1747 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.21893,0.97574,-0.00058658,-11.511,-0.97574,-0.21894,-0.0011878,810.28,-0.0012874,0.00031229,1,-4.7575
> select add #1.2
13723 atoms, 14031 bonds, 2 pseudobonds, 1747 residues, 4 models selected
> select add #6
27446 atoms, 28062 bonds, 4 pseudobonds, 3494 residues, 6 models selected
> select add #1.1
27446 atoms, 28062 bonds, 4 pseudobonds, 3494 residues, 8 models selected
> select subtract #1.1
27446 atoms, 28062 bonds, 4 pseudobonds, 3494 residues, 6 models selected
> select subtract #1.2
27446 atoms, 28062 bonds, 4 pseudobonds, 3494 residues, 4 models selected
> select subtract #6
13723 atoms, 14031 bonds, 2 pseudobonds, 1747 residues, 2 models selected
> view matrix models
> #5,-0.21893,0.97574,-0.00058658,-11.297,-0.97574,-0.21894,-0.0011878,867.69,-0.0012874,0.00031229,1,-2.2623
> view matrix models
> #5,-0.21893,0.97574,-0.00058658,43.04,-0.97574,-0.21894,-0.0011878,860.59,-0.0012874,0.00031229,1,5.0104
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.095106,0.92879,-0.35821,104.45,-0.98747,-0.13355,-0.084104,854.88,-0.12595,0.34572,0.92985,-56.42
> view matrix models
> #5,-0.33873,0.87705,0.34066,38.441,-0.71677,-0.47509,0.51043,722.05,0.60951,-0.071271,0.78957,-153.32
> view matrix models
> #5,0.1547,0.86843,0.47106,-185.44,-0.83819,0.36776,-0.40272,692.39,-0.52297,-0.33254,0.7848,388.85
> view matrix models
> #5,0.67164,0.49083,-0.55496,17.689,-0.72232,0.60041,-0.34316,545.08,0.16477,0.63134,0.7578,-232.05
> view matrix models
> #5,0.61512,0.65566,-0.43788,-51.72,-0.74375,0.66686,-0.046269,452,0.26166,0.35413,0.89784,-203.17
> view matrix models
> #5,0.63534,0.73307,-0.24281,-138.86,-0.7722,0.60621,-0.19032,522.95,0.0076776,0.30842,0.95122,-100.44
> view matrix models
> #5,0.6581,0.44703,-0.60586,52.443,-0.70744,0.64259,-0.2943,510.93,0.25776,0.62229,0.73913,-260.3
> view matrix models
> #5,0.51378,0.85759,0.023798,-206.47,-0.85389,0.51386,-0.082593,561.44,-0.08306,0.022114,0.9963,29.905
> view matrix models
> #5,0.50832,0.86058,0.032027,-207.56,-0.8577,0.50925,-0.070758,561.59,-0.077203,0.0084977,0.99698,32.497
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.50832,0.86058,0.032027,-183.52,-0.8577,0.50925,-0.070758,579.86,-0.077203,0.0084977,0.99698,35.402
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.5449,0.83666,-0.055511,-166.33,-0.83401,0.53394,-0.13908,579.06,-0.086724,0.12208,0.98872,-0.96306
> view matrix models
> #5,0.82855,0.55351,0.084486,-208.41,-0.55203,0.83276,-0.042055,332.37,-0.093634,-0.011795,0.99554,49.758
> view matrix models
> #5,0.83173,0.54845,0.086192,-208.22,-0.54714,0.83607,-0.040236,328.75,-0.09413,-0.013694,0.99547,50.677
> view matrix models
> #5,0.95773,0.23784,0.1618,-161.66,-0.25219,0.9648,0.074606,135.62,-0.13836,-0.11226,0.984,107.62
> view matrix models
> #5,0.97836,0.2068,0.0064353,-118.03,-0.20688,0.97724,0.046996,120.37,0.0034302,-0.047311,0.99887,24.064
> ui tool show "Fit in Map"
> fitmap #5 inMap #1.2
Fit molecule TSA_MT_GMPCP_FINAL.pdb (#5) to map PF2.mrc (#1.2) using 13723
atoms
average map value = 0.09591, steps = 112
shifted from previous position = 5.74
rotated from previous position = 2.53 degrees
atoms outside contour = 9741, contour level = 0.080338
Position of TSA_MT_GMPCP_FINAL.pdb (#5) relative to PF2.mrc (#1.2)
coordinates:
Matrix rotation and translation
0.97587569 0.21811344 0.00965119 -119.59359760
-0.21816304 0.97590235 0.00441209 132.19809920
-0.00845628 -0.00641119 0.99994369 10.06559759
Axis -0.02477935 0.04145614 -0.99883301
Axis point 539.09511298 608.11833503 0.00000000
Rotation angle (degrees) 12.61466983
Shift along axis -1.60997729
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.97588,0.21811,0.0096512,-118.97,-0.21816,0.9759,0.0044121,131.6,-0.0084563,-0.0064112,0.99994,10.028
> select subtract #5
Nothing selected
> select add #6
13723 atoms, 14031 bonds, 2 pseudobonds, 1747 residues, 2 models selected
> view matrix models
> #6,0.23129,0.97289,0.0010711,-47.533,-0.97289,0.23129,-0.00064977,661.35,-0.00087989,-0.00089182,1,2.5647
> view matrix models
> #6,0.23129,0.97289,0.0010711,-52.761,-0.97289,0.23129,-0.00064977,661.64,-0.00087989,-0.00089182,1,2.7511
> view matrix models
> #6,0.23129,0.97289,0.0010711,-54.663,-0.97289,0.23129,-0.00064977,667.49,-0.00087989,-0.00089182,1,3.0012
> fitmap #6 inMap #1.1
Fit molecule TSA_MT_GMPCP_FINAL.pdb (#6) to map PF1.mrc (#1.1) using 13723
atoms
average map value = 0.1042, steps = 80
shifted from previous position = 4.15
rotated from previous position = 0.603 degrees
atoms outside contour = 8844, contour level = 0.061359
Position of TSA_MT_GMPCP_FINAL.pdb (#6) relative to PF1.mrc (#1.1)
coordinates:
Matrix rotation and translation
0.23001747 0.97312869 0.01060757 -59.47140278
-0.97318593 0.22999191 0.00358564 667.79752852
0.00104964 -0.01114789 0.99993731 3.09817527
Axis -0.00756966 0.00491058 -0.99995929
Axis point 392.26519883 371.48629855 0.00000000
Rotation angle (degrees) 76.70449753
Shift along axis 0.63140498
> select add #1
13723 atoms, 14031 bonds, 2 pseudobonds, 1747 residues, 7 models selected
> view matrix models
> #6,0.23002,0.97313,0.010608,-59.018,-0.97319,0.22999,0.0035856,667.56,0.0010496,-0.011148,0.99994,-3.2287,#1,1,0,0,0.45368,0,1,0,-0.235,0,0,1,-6.3268
> view matrix models
> #6,0.23002,0.97313,0.010608,-60.171,-0.97319,0.22999,0.0035856,668.32,0.0010496,-0.011148,0.99994,1.7995,#1,1,0,0,-0.69951,0,1,0,0.52454,0,0,1,-1.2987
> select add #5
27446 atoms, 28062 bonds, 4 pseudobonds, 3494 residues, 9 models selected
> view matrix models
> #5,0.97588,0.21811,0.0096512,-117.79,-0.21816,0.9759,0.0044121,131.16,-0.0084563,-0.0064112,0.99994,-18.005,#6,0.23002,0.97313,0.010608,-58.997,-0.97319,0.22999,0.0035856,667.89,0.0010496,-0.011148,0.99994,-26.233,#1,1,0,0,0.47399,0,1,0,0.0879,0,0,1,-29.331
> view matrix models
> #5,0.97588,0.21811,0.0096512,-106.62,-0.21816,0.9759,0.0044121,122.9,-0.0084563,-0.0064112,0.99994,-5.937,#6,0.23002,0.97313,0.010608,-47.819,-0.97319,0.22999,0.0035856,659.63,0.0010496,-0.011148,0.99994,-14.165,#1,1,0,0,11.652,0,1,0,-8.1669,0,0,1,-17.264
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> select subtract #1
27446 atoms, 28062 bonds, 4 pseudobonds, 3494 residues, 4 models selected
> select subtract #5
13723 atoms, 14031 bonds, 2 pseudobonds, 1747 residues, 2 models selected
> view matrix models
> #6,0.98607,-0.15645,-0.056457,93.227,0.14465,0.97421,-0.17319,-9.4094,0.082097,0.16261,0.98327,-106.22
> fitmap #6 inMap #1.1
Fit molecule TSA_MT_GMPCP_FINAL.pdb (#6) to map PF1.mrc (#1.1) using 13723
atoms
average map value = 0.3651, steps = 136
shifted from previous position = 3.57
rotated from previous position = 13.3 degrees
atoms outside contour = 1283, contour level = 0.061359
Position of TSA_MT_GMPCP_FINAL.pdb (#6) relative to PF1.mrc (#1.1)
coordinates:
Matrix rotation and translation
0.99995626 -0.00919020 0.00173670 14.29597181
0.00919104 0.99995765 -0.00048149 -11.01888220
-0.00173220 0.00049743 0.99999838 -15.92777265
Axis 0.05226099 0.18519250 0.98131164
Axis point 865.46693215 1647.68652929 0.00000000
Rotation angle (degrees) 0.53661999
Shift along axis -16.92360129
> fitmap #5 inMap #1.2
Fit molecule TSA_MT_GMPCP_FINAL.pdb (#5) to map PF2.mrc (#1.2) using 13723
atoms
average map value = 0.1137, steps = 228
shifted from previous position = 5.71
rotated from previous position = 21.5 degrees
atoms outside contour = 9084, contour level = 0.080338
Position of TSA_MT_GMPCP_FINAL.pdb (#5) relative to PF2.mrc (#1.2)
coordinates:
Matrix rotation and translation
0.98792343 -0.15473677 0.00798852 29.12262980
0.15467603 0.98793496 0.00773465 -33.83553109
-0.00908898 -0.00640561 0.99993817 -9.68605842
Axis -0.04558344 0.05505209 0.99744244
Axis point 227.17911675 166.69128331 0.00000000
Rotation angle (degrees) 8.92277493
Shift along axis -12.85151225
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/Lateral_panelA_wMap.cxs
> volume #1.1 color #b2b2b266
> volume #1.2 color #b2b2b266
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.99996,-0.0091902,0.0017367,14.632,0.009191,0.99996,-0.00048149,-11.268,-0.0017322,0.00049743,1,-15.531
> select subtract #6
Nothing selected
> select add #5
13723 atoms, 14031 bonds, 2 pseudobonds, 1747 residues, 2 models selected
> view matrix models
> #5,0.98792,-0.15474,0.0079885,30.328,0.15468,0.98793,0.0077347,-34.552,-0.009089,-0.0064056,0.99994,-20.221
> fitmap #5 inMap #1.2
Fit molecule TSA_MT_GMPCP_FINAL.pdb (#5) to map PF2.mrc (#1.2) using 13723
atoms
average map value = 0.3821, steps = 116
shifted from previous position = 1.97
rotated from previous position = 17.3 degrees
atoms outside contour = 1636, contour level = 0.080338
Position of TSA_MT_GMPCP_FINAL.pdb (#5) relative to PF2.mrc (#1.2)
coordinates:
Matrix rotation and translation
0.89697466 -0.44207886 0.00165076 175.63302639
0.44207892 0.89697608 0.00035028 -110.38361865
-0.00163555 0.00041557 0.99999857 -24.99441915
Axis 0.00007385 0.00371685 0.99999309
Axis point 324.44476895 321.68213199 0.00000000
Rotation angle (degrees) 26.23679313
Shift along axis -25.39155632
> select add #1
13723 atoms, 14031 bonds, 2 pseudobonds, 1747 residues, 7 models selected
> select add #6
27446 atoms, 28062 bonds, 4 pseudobonds, 3494 residues, 9 models selected
> view matrix models
> #5,0.89697,-0.44208,0.0016508,177.73,0.44208,0.89698,0.00035028,-112.11,-0.0016355,0.00041557,1,-10.826,#6,0.99996,-0.0091902,0.0017367,16.727,0.009191,0.99996,-0.00048149,-12.989,-0.0017322,0.00049743,1,-1.3625,#1,1,0,0,13.747,0,1,0,-9.8883,0,0,1,-3.0949
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/Lateral_panelA_wMap.cxs
> includeMaps true
> view matrix models
> #5,0.89697,-0.44208,0.0016508,178.24,0.44208,0.89698,0.00035028,-112.41,-0.0016355,0.00041557,1,-8.6571,#6,0.99996,-0.0091902,0.0017367,17.234,0.009191,0.99996,-0.00048149,-13.293,-0.0017322,0.00049743,1,0.80623,#1,1,0,0,14.254,0,1,0,-10.192,0,0,1,-0.92617
> view matrix models
> #5,0.89697,-0.44208,0.0016508,178.57,0.44208,0.89698,0.00035028,-113.81,-0.0016355,0.00041557,1,-15.921,#6,0.99996,-0.0091902,0.0017367,17.569,0.009191,0.99996,-0.00048149,-14.694,-0.0017322,0.00049743,1,-6.4577,#1,1,0,0,14.589,0,1,0,-11.593,0,0,1,-8.1901
> view matrix models
> #5,0.89697,-0.44208,0.0016508,179.71,0.44208,0.89698,0.00035028,-114.38,-0.0016355,0.00041557,1,-10.232,#6,0.99996,-0.0091902,0.0017367,18.707,0.009191,0.99996,-0.00048149,-15.26,-0.0017322,0.00049743,1,-0.76868,#1,1,0,0,15.727,0,1,0,-12.159,0,0,1,-2.5011
> ui mousemode right zoom
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/Lateral_panelA_wMap.cxs
> includeMaps true
> surface dust #1.1 size 10.6
> surface dust #1.2 size 10.6
> save PanelA.tif supersample 4 transparentBackground true
> save PanelA.tif supersample 4
> volume #1.1 color #b2b2b24d
> volume #1.2 color #b2b2b24d
> save PanelA.tif supersample 4
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/Lateral_panelA_wMap.cxs
> volume #1.1 level 0.06963
> volume #1.1 level 0.1275
> volume #1.2 level 0.1349
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/PF2.pdb
> models #5
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/PF1.pdb
> models #6
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/lateral_interface_obBeta.cxs
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/lateral_interface_obBeta.cxs
> includeMaps true
> volume #1.2 level 0.04395
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/lateral_interface_obBeta.cxs
> cd
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New
Current working directory is:
/Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New
> save lateral_interface_beta.tif supersample 4
> volume #1.1 color #b2b2b233
> volume #1.2 color #b2b2b21a
> volume #1.1 color #b2b2b21a
> save lateral_interface_beta.tif supersample 4
[Repeated 1 time(s)]
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/lateral_interface_obBeta.cxs
> includeMaps true
——— End of log from Mon Oct 2 13:45:49 2023 ———
opened ChimeraX session
> save lateral_interface_beta.tif supersample 4
[Repeated 1 time(s)]
> select /Q :216,88
34 atoms, 30 bonds, 4 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select #6/Q:281
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/Q:87
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #6/Q:281
19 atoms, 19 bonds, 2 residues, 2 models selected
> color sel byhetero
> select /Q :278
12 atoms, 10 bonds, 2 residues, 2 models selected
> show sel atoms
> color sel byhetero
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/lateral_interface_obBeta_esid.cxs
> select /Q :190,85
42 atoms, 42 bonds, 4 residues, 2 models selected
> show sel atoms
> select /Q :85
22 atoms, 22 bonds, 2 residues, 2 models selected
> select /Q :190
20 atoms, 20 bonds, 2 residues, 2 models selected
> select /Q :90,85
44 atoms, 44 bonds, 4 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select /Q :58
18 atoms, 16 bonds, 2 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select /Q :5
14 atoms, 12 bonds, 2 residues, 2 models selected
> select /Q :55
14 atoms, 12 bonds, 2 residues, 2 models selected
> show sel atoms
> color sel byhetero
> select /Q :280
18 atoms, 16 bonds, 2 residues, 2 models selected
> show sel atoms
> show #!1.1 models
> color sel byhetero
> ui tool show Rotamers
> swapaa interactive sel GLN rotLib Dunbrack
TSA_MT_GMPCP_FINAL.pdb #5/Q GLN 280: phi -70.0, psi -41.0 trans
Changed 648 bond radii
TSA_MT_GMPCP_FINAL.pdb #6/Q GLN 280: phi -70.0, psi -41.0 trans
Changed 648 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa interactive sel GLN rotLib Dunbrack
TSA_MT_GMPCP_FINAL.pdb #!5/Q GLN 280: phi -70.0, psi -41.0 trans
Changed 648 bond radii
TSA_MT_GMPCP_FINAL.pdb #!6/Q GLN 280: phi -70.0, psi -41.0 trans
Changed 648 bond radii
> swapaa interactive sel GLN rotLib Dunbrack
TSA_MT_GMPCP_FINAL.pdb #!5/Q GLN 280: phi -70.0, psi -41.0 trans
Changed 648 bond radii
TSA_MT_GMPCP_FINAL.pdb #!6/Q GLN 280: phi -70.0, psi -41.0 trans
Changed 648 bond radii
> undo
Undo failed, probably because structures have been modified.
> hide sel atoms
> select #1.1
4 models selected
> ui tool show Rotamers
> select #1.1
4 models selected
> select #!6/Q:280
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel GLN rotLib Dunbrack
TSA_MT_GMPCP_FINAL.pdb #6/Q GLN 280: phi -70.0, psi -41.0 trans
Changed 648 bond radii
> swapaa #!6/Q:280 GLN criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
TSA_MT_GMPCP_FINAL.pdb #!6/Q GLN 280: phi -70.0, psi -41.0 trans
Applying GLN rotamer (chi angles: -69.0 176.9 -24.5) to TSA_MT_GMPCP_FINAL.pdb
#!6/Q GLN 280
> show sel atoms
[Repeated 1 time(s)]
> select #6/Q:280
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel GLN rotLib Dunbrack
TSA_MT_GMPCP_FINAL.pdb #6/Q GLN 280: phi -70.0, psi -41.0 trans
Changed 648 bond radii
> swapaa #!6/Q:280 GLN criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
TSA_MT_GMPCP_FINAL.pdb #!6/Q GLN 280: phi -70.0, psi -41.0 trans
Applying GLN rotamer (chi angles: -69.0 176.9 -24.5) to TSA_MT_GMPCP_FINAL.pdb
#!6/Q GLN 280
> select clear
> select #!5/Q:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #!5/Q:34
11 atoms, 9 bonds, 2 residues, 1 model selected
> select add #!5/Q:35
18 atoms, 15 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #!5/Q:35
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #!5/Q:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel THR rotLib Dunbrack
TSA_MT_GMPCP_FINAL.pdb #!5/Q THR 33: phi -62.9, psi -27.2 trans
Changed 12 bond radii
> swapaa #!5/Q:33 THR criteria 3 rotLib Dunbrack retain false
Using Dunbrack library
TSA_MT_GMPCP_FINAL.pdb #!5/Q THR 33: phi -62.9, psi -27.2 trans
Applying THR rotamer (chi angles: -169.7) to TSA_MT_GMPCP_FINAL.pdb #!5/Q THR
33
> select clear
> select #6/Q:285
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/lateral_interface_obBeta_esid.cxs
> select /Q :90
22 atoms, 22 bonds, 2 residues, 2 models selected
> select /Q :92,70
36 atoms, 36 bonds, 4 residues, 2 models selected
> show sel atoms
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> show #!1.2 models
> volume #1.2 level 0.1941
> select :Phe
1848 atoms, 1856 bonds, 168 residues, 2 models selected
> show sel atoms
> select :Pro
1120 atoms, 1128 bonds, 160 residues, 2 models selected
> show sel atoms
> select :Tyr
1632 atoms, 1636 bonds, 136 residues, 2 models selected
> show sel atoms
Drag select of 204 atoms, 179 residues, 188 bonds
> color sel byhetero
> select clear
> select :Tyr
1632 atoms, 1636 bonds, 136 residues, 2 models selected
> color sel byhetero
> select :Pro
1120 atoms, 1128 bonds, 160 residues, 2 models selected
> color sel byhetero
> select :Phe
1848 atoms, 1856 bonds, 168 residues, 2 models selected
> color sel byhetero
> select :His
920 atoms, 920 bonds, 92 residues, 2 models selected
> show sel atoms
> select clear
> select add #!5/Q:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #!5/Q:15
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select add #!5/Q:88
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #6/Q:278
14 atoms, 12 bonds, 2 residues, 2 models selected
> hide sel atoms
> select #6/Q:280
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add #6/Q:216
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #!5/Q:85
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #!5/Q:69
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #!5/Q:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #!5/Q:59
21 atoms, 20 bonds, 2 residues, 1 model selected
> hide sel atoms
> select add #!5/Q:60
28 atoms, 26 bonds, 3 residues, 1 model selected
> select subtract #!5/Q:60
21 atoms, 20 bonds, 2 residues, 1 model selected
> select add #!5/Q:60
28 atoms, 26 bonds, 3 residues, 1 model selected
> select clear
Drag select of 21 atoms, 14 residues, 19 bonds
> hide sel atoms
> select clear
Drag select of 5 atoms, 3 residues, 5 bonds
> hide sel atoms
> select clear
Drag select of 5 atoms, 3 residues, 5 bonds
> hide sel atoms
> select clear
Drag select of 8 atoms, 3 residues, 8 bonds
> hide sel atoms
> select clear
Drag select of 6 atoms, 10 residues, 7 bonds
> hide sel atoms
Drag select of 2 atoms, 3 residues, 1 bonds
> select #!5/Q:143
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/Mloop_Nucleotide_sensing.cxs
Drag select of 3 atoms, 1 residues, 3 bonds
> hide sel atoms
Drag select of 2 atoms
> hide sel atoms
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Lateral_inter_TSA_bIII_New/Mloop_Nucleotide_sensing.cxs
——— End of log from Mon Oct 2 14:31:26 2023 ———
opened ChimeraX session
> select #5/Q:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Nucleotide_sensing/Mloop_Nucleotide_sensing.cxs
——— End of log from Tue Oct 3 17:01:46 2023 ———
opened ChimeraX session
> ui tool show "Side View"
> save M-loop_nucleotide_sensing.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/Nucleotide_sensing/Mloop_Nucleotide_sensing.cxs
——— End of log from Tue Oct 3 17:12:51 2023 ———
opened ChimeraX session
> show #!1.1 models
> hide #!1.1 models
> show #!1.2 models
> hide #!1.2 models
> select :204
60 atoms, 52 bonds, 8 residues, 2 models selected
> show sel atoms
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/check_structures/2PF_G2P.pdb
Chain information for 2PF_G2P.pdb #2
---
Chain | Description
A C | No description available
B D F Q | No description available
E I | No description available
> select add #2
27506 atoms, 28114 bonds, 4 pseudobonds, 3502 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> select #2 /C,A
6902 atoms, 7058 bonds, 2 pseudobonds, 880 residues, 2 models selected
> select #2 /C,A, sel #5 /Q, sel #6 /Q
13730 atoms, 14038 bonds, 2 pseudobonds, 1748 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #!2 & sel to #5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TSA_MT_GMPCP_FINAL.pdb, chain Q (#5) with 2PF_G2P.pdb, chain A
(#2), sequence alignment score = 1261.4
RMSD between 404 pruned atom pairs is 0.622 angstroms; (across all 430 pairs:
1.239)
> select clear
[Repeated 1 time(s)]
> select #2/C:283
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select #2/A:89
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #2/A:92
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #2/A:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #2/A:94
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #2/A:72
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #2/A:71
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select :G2P,Mg
272 atoms, 272 bonds, 24 residues, 3 models selected
> select :G2P,Mg,69-100
4224 atoms, 4304 bonds, 536 residues, 3 models selected
> select :G2P,Mg,69-100,273-284
5728 atoms, 5824 bonds, 728 residues, 3 models selected
> ~sel
Unknown command: segmentation ~sel
> select ~sel
49164 atoms, 50236 bonds, 8 pseudobonds, 6260 residues, 11 models selected
> hide sel cartoons
> hide sel atoms
> select :274
112 atoms, 104 bonds, 16 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> undo
> select :273-274
216 atoms, 208 bonds, 32 residues, 3 models selected
> hide sel cartoons
Drag select of 5 atoms, 4 residues, 4 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 2 atoms, 2 residues, 1 bonds
> hide sel atoms
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/a-b-
> E-site_lateral.cxs
> select /Q
10242 atoms, 10470 bonds, 1302 residues, 3 models selected
> ui tool show "Color Actions"
> color sel green
> undo
> select #6 '/Q
incomplete quoted text
> select #6 /Q
3414 atoms, 3490 bonds, 434 residues, 1 model selected
> color sel blue
> color sel byhetero
> select #2 /C
3451 atoms, 3529 bonds, 1 pseudobond, 440 residues, 2 models selected
> color sel green
> color (#!2 & sel) byhetero
> select #2 /A
3451 atoms, 3529 bonds, 1 pseudobond, 440 residues, 2 models selected
> color sel dark sea green
> select #5 /Q
3414 atoms, 3490 bonds, 434 residues, 1 model selected
> color sel sky blue
> color sel byhetero
> select #2 /A
3451 atoms, 3529 bonds, 1 pseudobond, 440 residues, 2 models selected
> color (#!2 & sel) byhetero
> lighting simple
> lighting soft
> select clear
> select #2/A:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 5 residues
> show sel atoms
> style sel stick
Changed 51 atom styles
> undo
[Repeated 1 time(s)]
> select #2/A:78
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/a-b-
> E-site_lateral.cxs
——— End of log from Tue Oct 17 11:36:42 2023 ———
opened ChimeraX session
Drag select of 118 atoms, 76 residues, 112 bonds
> show #!1.1 models
> show #!1.2 models
> ui tool show "Surface Zone"
> surface zone #1.1 nearAtoms sel distance 6.36
> surface zone #1.2 nearAtoms sel distance 6.36
> surface zone #1.2 nearAtoms sel distance 6.9
> surface zone #1.2 nearAtoms sel distance 1.94
> surface zone #1.1 nearAtoms sel distance 5.96
> surface zone #1.1 nearAtoms sel distance 2.43
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/a-b-
> E-site_lateral.cxs includeMaps true
> select clear
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/a-b-
> E-site_lateral.cxs
——— End of log from Tue Oct 17 11:39:56 2023 ———
opened ChimeraX session
Drag select of 6 residues
> hide sel cartoons
Drag select of 2 atoms, 4 residues, 1 bonds
> select clear
Drag select of 2 atoms, 4 residues, 1 bonds
> hide sel cartoons
Drag select of 9 atoms, 8 bonds
> hide sel cartoons
> hide sel atoms
> select clear
> save E-site_network.tif supersample 4 transparentBackground true
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/a-b-
> E-site_lateral.cxs
> save E-site_network.tif supersample 4 transparentBackground true
[Repeated 1 time(s)]
> vwd
Unknown command: vwd
> vdw
Unknown command: vdw
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/test_G2P.pdb
> models #5
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/test_GDP.pdb
> models #2 relModel #5
> select #5 /Q, sel #2 /A
6865 atoms, 7019 bonds, 1 pseudobond, 874 residues, 3 models selected
> select #5 /Q, sel #2 /A,C, sel #6 /Q
13730 atoms, 14038 bonds, 2 pseudobonds, 1748 residues, 4 models selected
> select ~sel
41162 atoms, 42086 bonds, 6 pseudobonds, 5240 residues, 11 models selected
> delete sel
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/testG2P.pdb
> models #2
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/testG2P1.pdb
> models #5 relModel #2
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/E-side_linkage/testG2P2.pdb
> models #6 relModel #2
> select #5/Q:90
11 atoms, 11 bonds, 1 residue, 1 model selected
> rmsd
Missing or invalid "atoms" argument: empty atom specifier
> close session
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/check_structures/for_Antonina/Aligned_on221-227_10-20/bAli_GDP.pdb
Chain information for bAli_GDP.pdb #1
---
Chain | Description
A | No description available
E | No description available
> open
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/check_structures/for_Antonina/Aligned_on221-227_10-20/bAli_GMPCPP.pdb
Chain information for bAli_GMPCPP.pdb #2
---
Chain | Description
A | No description available
Q | No description available
> set bgColor white
> select /E :221-227,:10-20, sel /Q :221-227, sel :10-20
Expected a keyword
> select /E :221-227,:10-20, sel /Q :221-227,sel :10-20
Expected a keyword
> select /E :221-227,:10-20, sel /Q :221-227,:10-20
Expected a keyword
> select /E :221-227, sel /E :10-20, sel /Q :221-227, sel /Q :10-20
268 atoms, 270 bonds, 36 residues, 2 models selected
> matchmaker sel showAlignment true
Missing required "to" argument
> matchmaker sel to sel showAlignment true
Specify a single 'to' model only
> matchmaker sel to #1 showAlignment true
Must use different reference and match structures
> matchmaker sel to #0 showAlignment true
No 'to' model specified
> select /E :221-227, sel /E :10-20, sel /Q :221-227, sel /Q :10-20
268 atoms, 270 bonds, 36 residues, 2 models selected
> matchmaker sel showAlignment true
Missing required "to" argument
> matchmaker sel showAlignment true
Missing required "to" argument
> matchmaker sel to sel showAlignment true
Specify a single 'to' model only
> select /E :221-227, sel /E :10-20
134 atoms, 135 bonds, 18 residues, 1 model selected
> matchmaker sel to #1 sel showAlignment true
Expected a keyword
> matchmaker sel to #1 showAlignment true
Must use different reference and match structures
> matchmaker sel to #2 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bAli_GMPCPP.pdb, chain Q (#2) with bAli_GDP.pdb, chain E (#1),
sequence alignment score = 104.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: bAli_GDP.pdb #1/E,
bAli_GMPCPP.pdb #2/Q
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 18 pruned atom pairs is 0.232 angstroms; (across all 18 pairs:
0.232)
> select /E :221-227, sel /E :10-20, sel /Q :221-227, sel /Q :10-20
268 atoms, 270 bonds, 36 residues, 2 models selected
> matchmaker sel to sel showAlignment true
Specify a single 'to' model only
> matchmaker sel to #2 sel showAlignment true
Expected a keyword
> matchmaker sel to #2 showAlignment true
Must use different reference and match structures
> matchmaker sel to #1 showAlignment true
Must use different reference and match structures
> matchmaker sel to #1 showAlignment true
Must use different reference and match structures
> select /E :221-227, sel /E :10-20
134 atoms, 135 bonds, 18 residues, 1 model selected
> matchmaker sel to #2 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bAli_GMPCPP.pdb, chain Q (#2) with bAli_GDP.pdb, chain E (#1),
sequence alignment score = 104.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: bAli_GDP.pdb #1/E,
bAli_GMPCPP.pdb #2/Q
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 18 pruned atom pairs is 0.232 angstroms; (across all 18 pairs:
0.232)
> lighting soft
> ui tool show "Render By Attribute"
> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 0.0540825,#0fc7cf:1,white:2,#9e205e
13705 atoms, 1746 residues, atom seq_rmsd range 0.0541 to 3.45
> key cyan-white-maroon :0.05 :1.00 :2.00 showTool true
> ui mousemode right "color key"
> ui mousemode right zoom
> save
> /Users/zehrea/Documents/Lab_work/Papers/2023/JBM_acceletated_forTTLL6_submission/Figure3/NEW/Longitudinal_interface/E-site_aliON221-227_10-20.cxs
> select /A
6894 atoms, 7050 bonds, 2 pseudobonds, 879 residues, 4 models selected
> delete atoms (#!1-2 & sel)
> delete bonds (#!1-2 & sel)
> hide (protein|nucleic) target a
> cartoon hide
> show ((protein&@ca)|(nucleic&@p)) target ab
> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 0.0540825,#0fc7cf:1,#b2b2b2:2,#9e205e
6811 atoms, 867 residues, atom seq_rmsd range 0.0541 to 3.45
> color byattribute r:seq_rmsd #!1-2 target sabc palette
> 0.0540825,#0fc7cf:1,#b2b2b2:2,#9e205e
6811 atoms, 867 residues, atom seq_rmsd range 0.0541 to 3.45
> key cyan-gray-maroon :0.05 :1.00 :2.00 showTool true
> ui mousemode right "color key"
> ui mousemode right zoom
> key cyan-gray-maroon :0.05 :1.00 :2.00 showTool true
> ui mousemode right "color key"
> key fontSize 8
> key size 0.24000,0.05000
> key size 0.23000,0.05000
> key size 0.22000,0.05000
> key size 0.21000,0.05000
[Repeated 1 time(s)]
> key size 0.2,0.05000
> key size 0.0000,0.05000
> key size 0.01000,0.05000
> key size 0.02000,0.05000
> key size 0.03000,0.05000
> key size 0.04000,0.05000
> key size 0.05000,0.05000
> key size 0.06000,0.05000
> key size 0.07000,0.05000
> key size 0.08000,0.05000
> key size 0.09000,0.05000
> key size 0.10000,0.05000
> key size 0.11000,0.05000
> key size 0.12000,0.05000
> key size 0.13000,0.05000
> key size 0.14000,0.05000
> key size 0.15000,0.05000
> key size 0.16000,0.05000
> key size 0.17000,0.05000
> key size 0.18000,0.05000
> key size 0.19000,0.05000
> key size 0.20000,0.05000
> key size 0.21000,0.05000
> key size 0.22000,0.05000
> key size 0.23000,0.05000
> key size 0.23000,0.04000
> key size 0.23000,0.03000
> key fontSize 9
> key fontSize 10
> key fontSize 11
> key fontSize 12
> key fontSize 13
> key fontSize 14
> key fontSize 15
> key fontSize 16
> key fontSize 17
> key fontSize 18
> key fontSize 19
> key fontSize 20
> ui tool show "Side View"
> key pos 0.779489,0.631352 size 0.0215485,0.0790633
> key pos 0.838187,0.0773591 size 0.0424795,0.32497
> ui mousemode right zoom
> ui tool show "Render By Attribute"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 756, in _set_value_cb
self._redraw_cb()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb
self._bins = left + filled_bins + right
ValueError: operands could not be broadcast together with shapes (4,) (297,)
ValueError: operands could not be broadcast together with shapes (4,) (297,)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb
self._bins = left + filled_bins + right
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 179, in <lambda>
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 714, in _select_marker_cb
self._set_sel_marker(marker, drag_start=event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 743, in _set_sel_marker
self._last_mouse_xy = self._abs_xy((drag_start.scenePos().x(),
drag_start.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 179, in <lambda>
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 714, in _select_marker_cb
self._set_sel_marker(marker, drag_start=event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 743, in _set_sel_marker
self._last_mouse_xy = self._abs_xy((drag_start.scenePos().x(),
drag_start.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 179, in <lambda>
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 714, in _select_marker_cb
self._set_sel_marker(marker, drag_start=event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 743, in _set_sel_marker
self._last_mouse_xy = self._abs_xy((drag_start.scenePos().x(),
drag_start.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 760, in _set_value_cb
self._move_cur_marker(v)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 570, in _move_cur_marker
self._active_markers._update_plot()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 1222, in _update_plot
self._update_marker_coordinates()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 1207, in
_update_marker_coordinates
x, y = self._scene_xy(m.xy)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 1090, in _scene_xy
return self.histogram._scene_xy(abs_xy)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 179, in <lambda>
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 714, in _select_marker_cb
self._set_sel_marker(marker, drag_start=event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 743, in _set_sel_marker
self._last_mouse_xy = self._abs_xy((drag_start.scenePos().x(),
drag_start.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,10
Model Number: Z175000ZKLL/A
Chip: Apple M2 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 3 days, 14 hours, 48 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 19
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
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: 2021.10.8
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-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-PICKLUSTER: 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
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: 2022.2.22
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: 21.3
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
setuptools-scm: 7.0.5
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 , 2 years ago
| Component: | Unassigned → Depiction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Render by attribute: TypeError: object of type 'function' has no len() |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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This ChimeraX Render by Attribute bug was fixed 3 months ago (after the ChimeraX 1.6.1 release), ticket #9328. It is fixed in the current ChimeraX daily build.