hbonds: More than 2 coplanar positions specified

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.1-arm64-arm-64bit
ChimeraX Version: 1.7rc202312062342 (2023-12-06 23:42:44 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7rc202312062342 (2023-12-06)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/katrinawarner/Downloads/Figure_Mapping/Fig1.cxs format session

Opened cryosparc_P78_J250_006_volume_map_sharp.mrc z flip as #3, grid size
240,240,240, pixel 1.33, shown at level 0.147, step 1, values float32  
Opened cryosparc_P77_cryosparc_P77_J229_007_volume_map.mrc as #5, grid size
260,260,260, pixel 1.15, shown at level 0.156, step 1, values float32  
Log from Thu Mar 21 16:01:32 2024UCSF ChimeraX version: 1.7rc202312062342
(2023-12-06)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/katrinawarner/Downloads/Figure_Mapping/Figure1_try2.cxs format
> session

Opened cryosparc_P78_J250_006_volume_map_sharp.mrc z flip as #3, grid size
240,240,240, pixel 1.33, shown at level 0.147, step 1, values float32  
Opened cryosparc_P77_cryosparc_P77_J229_007_volume_map.mrc as #5, grid size
260,260,260, pixel 1.15, shown at level 0.156, step 1, values float32  
Log from Tue Mar 19 23:45:33 2024UCSF ChimeraX version: 1.7rc202312062342
(2023-12-06)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/katrinawarner/Downloads/Figure_Mapping/P229_figure1_Tom1.cxs
> format session

Opened cryosparc_P78_J250_006_volume_map_sharp.mrc z flip as #3, grid size
240,240,240, pixel 1.33, shown at level 0.158, step 1, values float32  
Opened cryosparc_P77_cryosparc_P77_J229_007_volume_map.mrc as #5, grid size
260,260,260, pixel 1.15, shown at level 0.201, step 2, values float32  
Log from Tue Mar 19 13:44:07 2024UCSF ChimeraX version: 1.7rc202312062342
(2023-12-06)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/katrinawarner/Downloads/Figure_Mapping/apo-structure.cxs

Opened cryosparc_P78_J250_006_volume_map_sharp.mrc z flip as #3, grid size
240,240,240, pixel 1.33, shown at level 0.158, step 1, values float32  
Log from Wed Mar 6 14:46:03 2024UCSF ChimeraX version: 1.7rc202312062342
(2023-12-06)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/katrinawarner/Downloads/apo figures.cxs" format session

Opened cryosparc_P78_J250_006_volume_map_sharp.mrc z flip as #3, grid size
240,240,240, pixel 1.33, shown at level 0.158, step 1, values float32  
Log from Mon Jan 15 18:05:46 2024UCSF ChimeraX version: 1.7rc202312062342
(2023-12-06)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/katrinawarner/Downloads/apo-Tom1.pdb format pdb

Chain information for apo-Tom1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> volume style surface

No volumes specified  

> open
> /Users/katrinawarner/Downloads/cryosparc_P78_J250_006_volume_map_sharp.mrc

Opened cryosparc_P78_J250_006_volume_map_sharp.mrc as #2, grid size
240,240,240, pixel 1.33, shown at level 0.101, step 1, values float32  

> select add #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.096496,-0.57323,-0.81369,364.69,0.99533,0.058428,0.076874,-21.514,0.0034761,-0.81731,0.57619,196.69

> view matrix models
> #2,-0.28352,-0.4576,-0.84275,411.72,0.95889,-0.14678,-0.24289,67.574,-0.012557,-0.87696,0.4804,223.91

> view matrix models
> #2,-0.6869,0.33333,-0.6458,319.15,0.42815,-0.53243,-0.73021,291.07,-0.58725,-0.77808,0.22301,340.88

> view matrix models
> #2,-0.79487,-0.04113,-0.60538,389.73,0.1645,-0.97494,-0.14975,312.06,-0.58406,-0.21861,0.78172,162.89

> view matrix models
> #2,-0.52674,-0.4554,-0.71774,430.56,0.83369,-0.44151,-0.3317,148.63,-0.16583,-0.7731,0.61223,211.06

> select subtract #2

Nothing selected  

> volume #2 level 0.2187

> fitmap #1 inMap #2

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc (#2) using 41332 atoms  
average map value = 0.07291, steps = 136  
shifted from previous position = 12.8  
rotated from previous position = 13.3 degrees  
atoms outside contour = 35907, contour level = 0.21871  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.63442326 0.76658378 -0.09927963 143.68641379  
-0.54716840 -0.53608663 -0.64282025 435.34304534  
-0.54599806 -0.35349744 0.75955624 187.33184654  
Axis 0.20411270 0.31515284 -0.92683154  
Axis point 190.56961021 216.98391751 0.00000000  
Rotation angle (degrees) 134.86807858  
Shift along axis -7.09724489  
  

> hide #!1 models

> volume #2 level 0.404

> flip #2

Unknown command: flip #2  

> vop flip #2

Opened cryosparc_P78_J250_006_volume_map_sharp.mrc z flip as #3, grid size
240,240,240, pixel 1.33, shown at step 1, values float32  

> show #!1 models

> select add #3

2 models selected  

> view matrix models
> #3,-0.41383,0.21624,0.8843,55.494,0.013108,0.97269,-0.23172,35.945,-0.91026,-0.084303,-0.40537,376.73

> volume #3 level 0.2019

> ui mousemode right "contour level"

[Repeated 1 time(s)]

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.06897, steps = 84  
shifted from previous position = 6.22  
rotated from previous position = 5.35 degrees  
atoms outside contour = 35063, contour level = 0.20186  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.62474075 -0.01457425 -0.78069622 379.15290706  
0.11680008 0.98683249 -0.11189002 -4.88002225  
0.77204711 -0.16108763 -0.61481220 149.77289651  
Axis -0.03155579 -0.99594362 0.08426468  
Axis point 153.72546159 0.00000000 165.95822290  
Rotation angle (degrees) 128.78209460  
Shift along axis 5.51632157  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.49453,0.39101,0.77624,56.652,0.34429,0.90816,-0.23812,-2.6956,-0.79806,0.1495,-0.58374,350.37

> view matrix models
> #3,-0.51566,0.29715,0.80362,70.517,0.29273,0.94259,-0.16071,-12.459,-0.80524,0.15238,-0.57304,349.32

> view matrix models
> #3,-0.52214,0.31679,0.79184,70.201,0.315,0.93444,-0.16613,-13.672,-0.79256,0.16269,-0.58769,348.05

> view matrix models
> #3,-0.92603,-0.0027982,0.37743,246.47,0.0095081,0.99948,0.030739,-8.6383,-0.37732,0.032054,-0.92553,358.87

> view matrix models
> #3,-0.7409,-0.10947,0.66263,191.16,-0.20728,0.97573,-0.070564,43.584,-0.63883,-0.18963,-0.74561,405.57

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.3102, steps = 132  
shifted from previous position = 3.21  
rotated from previous position = 16.6 degrees  
atoms outside contour = 20405, contour level = 0.20186  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.95218062 -0.11697041 -0.28225871 369.34797906  
-0.04692639 0.96884203 -0.24319341 47.48780730  
0.30191054 -0.21831867 -0.92800161 287.46310685  
Axis 0.04224082 -0.99200196 0.11894466  
Axis point 163.89503640 0.00000000 174.59803247  
Rotation angle (degrees) 162.87606579  
Shift along axis 2.68576565  
  

> select subtract #3

Nothing selected  

> volume #3 level 0.1682

> close #2

> surface dust #3 size 13.3

> volume #3 level 0.08392

> volume #3 level 0.244

> volume #3 level 0.1092

> hide #!3 models

> select #1:2890-

Expected an objects specifier or a keyword  

> select #1:2890-3268

6072 atoms, 6143 bonds, 379 residues, 1 model selected  

> coulombic sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1376, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run  
f(s)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 582, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 525, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 99, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 95, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 259, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 585, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 84, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 140, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
ValueError: More than 2 coplanar positions specified!  
  
ValueError: More than 2 coplanar positions specified!  
  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
See log for complete Python traceback.  
  

> lighting full

[Repeated 1 time(s)]

> lighting soft

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting soft

> set bgColor gray

> set bgColor white

> ui tool show "Color Actions"

> color sel brown

> color sel crimson

> color sel orange red

> color sel coral

> color sel sienna

> color sel coral

> color sel chocolate

> color sel salmon

> select #1:3136-3268

2072 atoms, 2097 bonds, 133 residues, 1 model selected  

> color sel dark salmon

> color sel light salmon

> select #2

Nothing selected  

> select #1:1-766

11587 atoms, 11711 bonds, 747 residues, 1 model selected  

> color sel slate gray

> color sel light slate gray

> select #1:767-1194+1267-1405

Expected an objects specifier or a keyword  

> select #1:767-1194,1267-1405

7864 atoms, 7962 bonds, 564 residues, 1 model selected  

> color sel light gray

> color sel gray

> color sel light gray

> color sel dim gray

> color sel dark gray

> select #1:1-766

11587 atoms, 11711 bonds, 747 residues, 1 model selected  

> color sel dark gray

> color sel light slate gray

> select #1:1-750

11458 atoms, 11579 bonds, 731 residues, 1 model selected  

> select #1:1432-1515,1600-1875

6035 atoms, 6549 bonds, 336 residues, 1 model selected  

> select #1:1432-1515,1599-1875

6035 atoms, 6549 bonds, 336 residues, 1 model selected  

> select #1:1432-1515,1590-1875

6064 atoms, 6582 bonds, 338 residues, 1 model selected  

> select #1:1432-1515,1600-1875

6035 atoms, 6549 bonds, 336 residues, 1 model selected  

> select #1:1432-1514,1600-1875

6021 atoms, 6535 bonds, 335 residues, 1 model selected  

> select #1:1432-1512,1600-1875

5992 atoms, 6506 bonds, 333 residues, 1 model selected  

> color sel light gray

> color sel dark gray

> select #1:2456-2889

6006 atoms, 6056 bonds, 403 residues, 1 model selected  

> color sel light gray

> select #2

Nothing selected  

> select #1:2456-2889

6006 atoms, 6056 bonds, 403 residues, 1 model selected  

> color sel light gray

> select #2

Nothing selected  

> select #1:1195-1266

1139 atoms, 1157 bonds, 72 residues, 1 model selected  

> color sel steel blue

> select #1:1403-1431

494 atoms, 499 bonds, 29 residues, 1 model selected  

> color sel orange

> select #1:1516-1599

1146 atoms, 1175 bonds, 71 residues, 1 model selected  

> color sel yellow

> color sel gold

> color sel burly wood

> color sel peru

> color sel goldenrod

> select #1:2222-2281

1037 atoms, 1044 bonds, 60 residues, 1 model selected  

> color sel olive drab

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> show #!3 models

> color zone #3 near sel & #1 distance 7.97

> select #1

41332 atoms, 42254 bonds, 2658 residues, 1 model selected  

> color zone #3 near sel & #1 distance 7.97

> volume #3 level 0.2253

> volume #3 level 0.1092

> save /Users/katrinawarner/Desktop/apo-Tom1_figure.cxs

> volume #3 level 0.1905

> volume #3 level 0.1731

> volume #3 level -1.863

> volume #3 level 0.2103

> select subtract #1

Nothing selected  

> volume #3 level 0.2045

> volume #3 level 0.158

> lighting soft

> lighting full

> lighting flat

> graphics silhouettes false

> lighting soft

> ui tool show "Model Panel"

> volume #3 level 0.07623

> volume #3 level 0.1273

> volume #3 level 0.1989

> volume #3 level 0.1785

> volume #3 level 0.158

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/katrinawarner/Desktop/movie5.mp4

Movie saved to /Users/katrinawarner/Desktop/movie5.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/katrinawarner/Desktop/movie6.mp4

Movie saved to /Users/katrinawarner/Desktop/movie6.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/katrinawarner/Desktop/movie7.mp4

Movie saved to /Users/katrinawarner/Desktop/movie7.mp4  
  

> lighting full

> lighting simple

> lighting full

> lighting shadows false

> lighting soft

> lighting full

> lighting simple

> lighting shadows true

> lighting soft

> save /Users/katrinawarner/Desktop/apo-Tom1.jpg width 1019 height 820
> supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/katrinawarner/Desktop/movie8.mp4

Movie saved to /Users/katrinawarner/Desktop/movie8.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/katrinawarner/Desktop/movie9.mp4

Movie saved to /Users/katrinawarner/Desktop/movie9.mp4  
  

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> graphics silhouettes false

> lighting flat

> save /Users/katrinawarner/Desktop/Downloads/apo-Tom1.jpg width 1019 height
> 820 supersample 3

> open /Users/katrinawarner/Downloads/4v3l.pdb

4v3l.pdb title:  
RNF38-ub-UBCH5B-ub complex [more info...]  
  
Chain information for 4v3l.pdb #2  
---  
Chain | Description | UniProt  
A | ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 2-147  
B D | ubiquitin | UBC_HUMAN 1-76  
C | E3 ubiquitin-protein ligase RNF38 | RNF38_HUMAN 389-465  
  
Non-standard residues in 4v3l.pdb #2  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
ZN — zinc ion  
  

> open /Users/katrinawarner/Downloads/3cmm.pdb

3cmm.pdb title:  
Crystal structure of the UBA1-ubiquitin complex [more info...]  
  
Chain information for 3cmm.pdb #4  
---  
Chain | Description | UniProt  
A C | ubiquitin-activating enzyme E1 1 | UBA1_YEAST 10-1024  
B D | ubiquitin | UBIQ_YEAST 1-76  
  
Non-standard residues in 3cmm.pdb #4  
---  
PRO — proline  
  

> hide #!1 models

> hide #!2 models

> show #!4 surfaces

> color #!4 bychain

> select #4/A

7997 atoms, 8082 bonds, 1081 residues, 1 model selected  

> select ~sel & ##selected

9244 atoms, 9321 bonds, 1256 residues, 1 model selected  

> select #4/B

605 atoms, 606 bonds, 80 residues, 1 model selected  

> select #4/C

8032 atoms, 8109 bonds, 1094 residues, 1 model selected  

> select #4/D

607 atoms, 606 bonds, 82 residues, 1 model selected  

> select #4/A,B

8602 atoms, 8688 bonds, 1161 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> save /Users/katrinawarner/Downloads/uba1-ub_cartoon.jpg width 1019 height
> 820 supersample 3

> hide #!4 models

> show #!2 models

> hide #!2 atoms

> color #!2 bychain

> select #2/D

603 atoms, 555 bonds, 126 residues, 1 model selected  

> hide sel cartoons

> select #2/C

622 atoms, 565 bonds, 8 pseudobonds, 139 residues, 2 models selected  

> hide sel cartoons

> show sel surfaces

> hide sel cartoons

> hide sel surfaces

> select #2/A,B

2028 atoms, 1803 bonds, 490 residues, 1 model selected  

> show sel surfaces

> select #2/A

1367 atoms, 1205 bonds, 344 residues, 1 model selected  

> select #2/B

661 atoms, 598 bonds, 146 residues, 1 model selected  

> color (#!2 & sel) yellow

> select #2/C

622 atoms, 565 bonds, 8 pseudobonds, 139 residues, 2 models selected  

> select #2/A

1367 atoms, 1205 bonds, 344 residues, 1 model selected  

> color (#!2 & sel) forest green

> save /Users/katrinawarner/Downloads/Ube2d2_ub.jpg width 1019 height 820
> supersample 3

> save /Users/katrinawarner/Downloads/d2.png width 1019 height 820 supersample
> 3

> hide #!2 models

> show #!4 models

> save /Users/katrinawarner/Downloads/uba1.png width 1019 height 820
> supersample 3

> save "/Users/katrinawarner/Downloads/apo figures.cxs"

——— End of log from Mon Jan 15 18:05:46 2024 ———

opened ChimeraX session  

> show #!1 models

> hide #!4 models

> show #!3 models

> volume #3 level -0.1031

> volume #3 level 0.1412

> volume #3 level 0.158

> lighting full

> volume #3 level 0.2254

> volume #3 level 0.1833

> lighting shadows false

> graphics silhouettes false

> volume #3 level 0.2591

> volume #3 level 0.217

> save /Users/katrinawarner/Downloads/Figure_Mapping/apo_1.png width 685
> height 753 supersample 3

> volume #3 level 0.1243

> volume #3 level 0.158

> save /Users/katrinawarner/Downloads/Figure_Mapping/apo-structure.cxs
> includeMaps true

——— End of log from Wed Mar 6 14:46:03 2024 ———

opened ChimeraX session  

> select #3

2 models selected  

> open "/Users/katrinawarner/Downloads/Unconfirmed 178093.crdownload"

Unrecognized file suffix '.crdownload'  

> open
> /Users/katrinawarner/Downloads/cryosparc_P77_cryosparc_P77_J229_007_volume_map.mrc

Opened cryosparc_P77_cryosparc_P77_J229_007_volume_map.mrc as #5, grid size
260,260,260, pixel 1.15, shown at level 0.118, step 2, values float32  
Drag select of 74 residues, 3 cryosparc_P78_J250_006_volume_map_sharp.mrc z
flip , 5 cryosparc_P77_cryosparc_P77_J229_007_volume_map.mrc  

> select subtract #3

1106 atoms, 74 residues, 3 models selected  

> ui mousemode right translate

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.89827,-0.42781,-0.10041,102.77,0.41559,0.9013,-0.12223,-37.729,0.14279,0.068068,0.98741,-27.479,#5,0.92629,-0.29299,0.23697,18.256,0.27694,0.95576,0.099164,-54.252,-0.25554,-0.026229,0.96644,50.527

> undo

> select add #1

41332 atoms, 42254 bonds, 2658 residues, 3 models selected  

> select subtract #1

2 models selected  

> hide #!3 models

> view matrix models
> #5,0.19572,0.95566,0.22003,-52.084,0.76913,-0.28878,0.57013,-8.0034,0.60838,0.057646,-0.79155,159.76

> view matrix models
> #5,0.8092,0.53042,0.25268,-87.645,0.42387,-0.82486,0.3741,155.22,0.40685,-0.19562,-0.8923,244.02

> fitmap #1 inMap #5

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P77_cryosparc_P77_J229_007_volume_map.mrc (#5) using 41332 atoms  
average map value = 0.2574, steps = 260  
shifted from previous position = 21.1  
rotated from previous position = 36.4 degrees  
atoms outside contour = 9585, contour level = 0.11764  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P77_cryosparc_P77_J229_007_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.97454500 0.11628204 0.19167818 -52.35752321  
0.06362345 -0.96326952 0.26089055 256.36887530  
0.21497463 -0.24205436 -0.94614777 303.31813473  
Axis -0.99350986 -0.04601947 -0.10402098  
Axis point 0.00000000 149.09416902 137.77521508  
Rotation angle (degrees) 165.33806893  
Shift along axis 8.66830584  
  

> color zone #5 near #1 distance 6.93

> volume #5 level 0.1742

> volume #5 level 0.0475

> volume #5 level 0.07466

> volume #5 level 0.1109

> volume #5 level 0.1176

> volume #5 level 0.1448

> volume #5 level 0.1538

> volume #5 level 0.1697

> volume #5 level 0.1742

> select subtract #5

Nothing selected  

> volume #5 level 0.1991

> volume #5 level 0.1652

> volume #5 level 0.2014

> volume #!5 style surface

[Repeated 1 time(s)]

> lighting flat

> lighting full

> lighting soft

> lighting simple

> graphics silhouettes false

> save /Users/katrinawarner/Downloads/Figure_Mapping/P229_figure1_Tom1.cxs

——— End of log from Tue Mar 19 13:44:07 2024 ———

opened ChimeraX session  

> volume #5 level 0.1584

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!3 models

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.1363, steps = 400  
shifted from previous position = 17.2  
rotated from previous position = 35.4 degrees  
atoms outside contour = 27469, contour level = 0.15802  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.95113948 -0.12322080 -0.28310833 375.48624626  
-0.04663256 0.96372642 -0.26278659 51.17207922  
0.30521975 -0.23674464 -0.92238434 288.24692027  
Axis 0.04385175 -0.99067895 0.12896607  
Axis point 166.80774346 0.00000000 176.22915665  
Rotation angle (degrees) 162.72658978  
Shift along axis 2.94469868  
  

> volume #3 level 0.1434

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.1362, steps = 48  
shifted from previous position = 0.0226  
rotated from previous position = 0.0226 degrees  
atoms outside contour = 26497, contour level = 0.14335  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.95114763 -0.12306960 -0.28314671 375.47429469  
-0.04659432 0.96383116 -0.26240895 51.10097063  
0.30520018 -0.23639662 -0.92248007 288.22668055  
Axis 0.04380166 -0.99070599 0.12877523  
Axis point 166.80079610 0.00000000 176.20787302  
Rotation angle (degrees) 162.72650652  
Shift along axis 2.93681717  
  

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.1362, steps = 40  
shifted from previous position = 0.018  
rotated from previous position = 0.0106 degrees  
atoms outside contour = 26513, contour level = 0.14335  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.95110484 -0.12306514 -0.28329233 375.47468329  
-0.04658833 0.96386134 -0.26229916 51.08415090  
0.30533441 -0.23627589 -0.92246659 288.19004543  
Axis 0.04379959 -0.99071357 0.12871758  
Axis point 166.79264997 0.00000000 176.20088252  
Rotation angle (degrees) 162.71816812  
Shift along axis 2.93100253  
  

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.136, steps = 28  
shifted from previous position = 0.0807  
rotated from previous position = 0.0893 degrees  
atoms outside contour = 26527, contour level = 0.14335  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.95121243 -0.12248933 -0.28318064 375.42258864  
-0.04652287 0.96426584 -0.26081989 50.81408908  
0.30500907 -0.23492075 -0.92292021 288.14642901  
Axis 0.04362767 -0.99081837 0.12796715  
Axis point 166.78095814 0.00000000 176.10946345  
Rotation angle (degrees) 162.73328630  
Shift along axis 2.90455929  
  

> select add #3

2 models selected  

> view matrix models
> #3,-0.64991,-0.24466,0.71955,190.08,-0.40269,0.9138,-0.053002,80.138,-0.64456,-0.3242,-0.69241,419.55

> view matrix models
> #3,-0.92192,-0.12718,0.3659,267.33,-0.12431,0.99174,0.031504,12.688,-0.36688,-0.01644,-0.93012,365.74

> view matrix models
> #3,-0.63337,-0.2825,0.72044,193.46,-0.48495,0.8704,-0.085035,104.4,-0.60305,-0.40324,-0.68828,425.2

> view matrix models
> #3,0.242,-0.85117,0.46578,191.45,-0.88222,0.0067923,0.47078,215.12,-0.40388,-0.52485,-0.74928,423.98

> view matrix models
> #3,-0.64128,-0.60608,-0.47057,431.03,-0.75651,0.39687,0.5198,126.6,-0.12828,0.68932,-0.71301,183.96

> view matrix models
> #3,-0.95645,-0.12938,0.26167,289.07,0.0040351,0.89047,0.45503,-56.343,-0.29188,0.43627,-0.85116,270.26

> view matrix models
> #3,-0.68001,-0.49228,0.54336,261.31,-0.30696,0.86416,0.39875,3.4362,-0.66585,0.10437,-0.73875,361.87

> view matrix models
> #3,-0.55434,-0.365,0.74799,190.38,-0.31385,0.92403,0.21831,22.987,-0.77085,-0.11373,-0.62678,394.95

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.3102, steps = 184  
shifted from previous position = 4.93  
rotated from previous position = 19.6 degrees  
atoms outside contour = 16100, contour level = 0.14335  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.95221691 -0.11692667 -0.28215442 369.33542711  
-0.04692692 0.96885750 -0.24313167 47.47215013  
0.30179600 -0.21827345 -0.92804950 287.48625008  
Axis 0.04222877 -0.99200608 0.11891451  
Axis point 163.89513927 0.00000000 174.59574709  
Rotation angle (degrees) 162.88275178  
Shift along axis 2.69020521  
  

> select subtract #3

Nothing selected  

> volume #5 level 0.1561

> volume #5 step 1

> volume #3 level 0.158

> hide #!3 models

> lighting simple

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> graphics silhouettes false

> set bgColor black

> set bgColor white

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> help help:user

> lighting soft

> graphics silhouettes true

> lighting flat

> lighting full

> lighting soft

> show #!1 atoms

> hide #!1 atoms

> show #!1 surfaces

> hide #!1 surfaces

> show #!1 surfaces

> hide #!1 surfaces

> open /Users/katrinawarner/Downloads/Figure_Mapping/ARLD.pdb

Chain information for ARLD.pdb #6  
---  
Chain | Description  
A | No description available  
  

> open /Users/katrinawarner/Downloads/Figure_Mapping/HBD.pdb

Chain information for HBD.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open /Users/katrinawarner/Downloads/Figure_Mapping/HECT.pdb

Chain information for HECT.pdb #8  
---  
Chain | Description  
A | No description available  
  

> open /Users/katrinawarner/Downloads/Figure_Mapping/Tower.pdb

Chain information for Tower.pdb #9  
---  
Chain | Description  
A | No description available  
  

> hide #!6 models

> hide #7 models

> hide #8 models

> hide #!9 models

> hide #!1 models

> show #!6 models

> show #!3 models

> fitmap #6 inMap #3

Fit molecule ARLD.pdb (#6) to map cryosparc_P78_J250_006_volume_map_sharp.mrc
z flip (#3) using 31387 atoms  
average map value = 0.09917, steps = 240  
shifted from previous position = 2.92  
rotated from previous position = 24.5 degrees  
atoms outside contour = 23221, contour level = 0.15802  
  
Position of ARLD.pdb (#6) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.83943515 -0.24352521 -0.48584369 403.01484454  
-0.31762458 0.94524652 0.07499095 51.11863945  
0.44097987 0.21726594 -0.87082275 182.99251477  
Axis 0.15125927 -0.98534998 -0.07877855  
Axis point 182.27105970 0.00000000 140.61673354  
Rotation angle (degrees) 151.94611678  
Shift along axis -3.82590219  
  

> select add #3

2 models selected  

> view matrix models
> #3,-0.51997,-0.488,0.70106,212.01,-0.33823,0.87128,0.35563,13.527,-0.78437,-0.052204,-0.61809,385.89

> view matrix models
> #3,-0.35484,-0.5896,0.72558,199.35,-0.6422,0.71773,0.26915,97.237,-0.67946,-0.37047,-0.63331,422.83

> view matrix models
> #3,-0.43222,-0.10221,0.89596,107.18,-0.56422,0.8057,-0.18027,141.88,-0.70345,-0.58343,-0.40591,424.58

> view matrix models
> #3,-0.61413,0.015271,0.78905,132.76,-0.1657,0.97503,-0.14784,49.87,-0.77161,-0.22154,-0.59627,407.36

> view matrix models
> #3,-0.82055,-0.07604,0.56649,213.2,-0.29474,0.90547,-0.30538,105.01,-0.48971,-0.41755,-0.7654,422.33

> view matrix models
> #3,-0.832,0.059542,0.55158,195.79,-0.21201,0.88464,-0.41528,113.03,-0.51267,-0.46245,-0.7234,426.33

> view matrix models
> #3,-0.89316,0.15197,0.42328,210.46,0.039584,0.96409,-0.26261,38.593,-0.44799,-0.2178,-0.86711,400.33

> view matrix models
> #3,-0.71545,0.14174,0.68414,144.44,0.085924,0.98962,-0.11517,4.482,-0.69336,-0.023613,-0.7202,383.61

> fitmap #6 inMap #3

Fit molecule ARLD.pdb (#6) to map cryosparc_P78_J250_006_volume_map_sharp.mrc
z flip (#3) using 31387 atoms  
average map value = 0.3558, steps = 100  
shifted from previous position = 5.22  
rotated from previous position = 11.9 degrees  
atoms outside contour = 11089, contour level = 0.15802  
  
Position of ARLD.pdb (#6) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.96411656 -0.00843090 -0.26534539 349.75760110  
0.04339692 0.98104634 -0.18885120 26.57354056  
0.26190831 -0.19358974 -0.94547715 290.75873934  
Axis -0.00894375 -0.99516371 0.09782229  
Axis point 155.05030226 0.00000000 170.38405598  
Rotation angle (degrees) 164.63851241  
Shift along axis -1.13048111  
  

> select subtract #3

Nothing selected  

> save /Users/katrinawarner/Downloads/Figure_Mapping/Figure1_sectioining.cxs

> color zone #3 near #6 distance 7.97

> color #3 white models

> hide #!3 models

> select #6:-765

Nothing selected  

> select #6:1-765

11579 atoms, 11703 bonds, 746 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel slate gray

> select #6:766-1195

5556 atoms, 5622 bonds, 426 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark gray

> select #6:1196-1875

8246 atoms, 8790 bonds, 468 residues, 1 model selected  

> color sel gray

> color sel light gray

> color sel silver

> select #6:1876-

Expected an objects specifier or a keyword  

> select #6:1876-3236

6006 atoms, 6056 bonds, 403 residues, 1 model selected  

> color sel light gray

[Repeated 1 time(s)]

> show #!3 models

> select #5

2 models selected  

> color zone #3 near #6 distance 7.97

> view matrix models
> #5,0.8092,0.53042,0.25268,-87.645,0.42387,-0.82486,0.3741,155.22,0.40685,-0.19562,-0.8923,244.02

> save /Users/katrinawarner/Downloads/Figure_Mapping/ARLD.cxs includeMaps true

> save /Users/katrinawarner/Downloads/Figure_Mapping/ARLD.png width 895 height
> 753 supersample 3

> color #3 white models

> show #7 models

> select subtract #5

Nothing selected  

> select add #7

1139 atoms, 1157 bonds, 72 residues, 1 model selected  

> view matrix models
> #7,0.92956,-0.3589,-0.084323,60.775,0.34021,0.92318,-0.17889,-32.704,0.14205,0.1376,0.98025,-38.103

> view matrix models
> #7,0.99661,0.009194,-0.081764,8.9338,-0.035299,0.94542,-0.32395,49.095,0.074323,0.32574,0.94253,-41.777

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.99661,0.009194,-0.081764,25.426,-0.035299,0.94542,-0.32395,42.363,0.074323,0.32574,0.94253,-27.314

> fitmap #7 inMap #3

Fit molecule HBD.pdb (#7) to map cryosparc_P78_J250_006_volume_map_sharp.mrc z
flip (#3) using 1139 atoms  
average map value = 0.1551, steps = 184  
shifted from previous position = 10.3  
rotated from previous position = 12.4 degrees  
atoms outside contour = 677, contour level = 0.15802  
  
Position of HBD.pdb (#7) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.67611130 -0.05565246 -0.73469471 355.73807142  
0.29433385 0.89372408 -0.33856291 7.01951554  
0.67545621 -0.44515173 -0.58787655 199.18453020  
Axis -0.07316449 -0.96795309 0.24023693  
Axis point 133.93467355 0.00000000 180.14050947  
Rotation angle (degrees) 133.24598004  
Shift along axis 15.02952222  
  

> hide #!3 models

> color sel royal blue

> hide #!6 models

> show #!3 models

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.99307,-0.089583,0.076033,20.937,0.10728,0.95525,-0.27566,18.879,-0.047936,0.28191,0.95824,1.5723

> view matrix models
> #7,0.99534,-0.056654,0.078012,16.772,0.073777,0.96846,-0.238,19.212,-0.062068,0.24264,0.96813,7.2035

> view matrix models
> #7,0.99327,-0.10924,-0.03841,36.038,0.099993,0.97644,-0.19122,8.3061,0.058393,0.18609,0.9808,-9.8826

> fitmap #7 inMap #3

Fit molecule HBD.pdb (#7) to map cryosparc_P78_J250_006_volume_map_sharp.mrc z
flip (#3) using 1139 atoms  
average map value = 0.2721, steps = 104  
shifted from previous position = 2.12  
rotated from previous position = 28.1 degrees  
atoms outside contour = 388, contour level = 0.15802  
  
Position of HBD.pdb (#7) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.96740860 -0.00498173 -0.25317144 348.45983416  
0.04796064 0.97810468 -0.20251175 27.67242389  
0.24863703 -0.20805388 -0.94598795 294.82025654  
Axis -0.01098268 -0.99442060 0.10491450  
Axis point 155.06579138 0.00000000 171.33651961  
Rotation angle (degrees) 165.38563393  
Shift along axis -0.41413042  
  

> hide #!3 models

> show #!3 models

> select subtract #7

Nothing selected  

> color zone #3 near #7 distance 7.97

> save /Users/katrinawarner/Downloads/Figure_Mapping/HBD.png width 895 height
> 753 supersample 3

> color #3 white models

> hide #7 models

> hide #!3 models

> show #!6 models

> show #7 models

> show #!9 models

> show #!3 models

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 1 maps.  

> ui mousemode right "move picked models"

> view matrix models #9,1,0,0,0.088221,0,1,0,0.10251,0,0,1,-0.12094

> view matrix models
> #3,-0.71545,0.14174,0.68414,123.89,0.085924,0.98962,-0.11517,-30.049,-0.69336,-0.023613,-0.7202,344.57

> select add #9

2734 atoms, 2776 bonds, 164 residues, 1 model selected  

> view matrix models
> #6,0.87511,0.012639,-0.48376,97.234,-0.070058,0.99244,-0.1008,27.606,0.47883,0.1221,0.86938,-68.975

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.99709,-0.075505,-0.010508,15.647,0.073195,0.98674,-0.14489,5.8804,0.021308,0.14369,0.98939,-29.08

> ui mousemode right "move picked models"

> view matrix models
> #6,0.87511,0.012639,-0.48376,101.46,-0.070058,0.99244,-0.1008,29.094,0.47883,0.1221,0.86938,-65.575

> undo

[Repeated 4 time(s)]

> hide #!3 models

> select add #9

2734 atoms, 2776 bonds, 164 residues, 1 model selected  

> ui mousemode right translate

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> view matrix models #9,1,0,0,11.253,0,1,0,6.672,0,0,1,15.654

> view matrix models #9,1,0,0,14.391,0,1,0,11.317,0,0,1,18.403

> view matrix models #9,1,0,0,19.591,0,1,0,10.523,0,0,1,18.197

> view matrix models #9,1,0,0,21.43,0,1,0,11.742,0,0,1,17.722

> view matrix models #9,1,0,0,26.265,0,1,0,12.806,0,0,1,19.697

> show #!3 models

> view matrix models #9,1,0,0,15.097,0,1,0,9.584,0,0,1,24.203

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.94318,-0.31813,-0.095978,95.392,0.19223,0.75796,-0.62333,91.601,0.27105,0.56946,0.77605,-104.48

> view matrix models
> #9,0.83442,0.38757,-0.39184,23.298,-0.31603,0.91894,0.23595,56.559,0.45152,-0.073047,0.88927,-35.704

> fitmap #9 inMap #3

Fit molecule Tower.pdb (#9) to map cryosparc_P78_J250_006_volume_map_sharp.mrc
z flip (#3) using 2734 atoms  
average map value = 0.1346, steps = 68  
shifted from previous position = 5.38  
rotated from previous position = 2.97 degrees  
atoms outside contour = 1739, contour level = 0.15802  
  
Position of Tower.pdb (#9) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.93165235 -0.13787687 -0.33617535 381.58181498  
-0.21419067 0.95576075 0.20160294 37.15363620  
0.29350683 0.25982948 -0.91996869 199.50805578  
Axis 0.09141366 -0.98857933 -0.11981004  
Axis point 176.26604467 0.00000000 129.25115151  
Rotation angle (degrees) 161.42907455  
Shift along axis -25.75059572  
  

> ui mousemode right "move picked models"

> view matrix models
> #3,-0.71545,0.14174,0.68414,143.49,0.085924,0.98962,-0.11517,5.9913,-0.69336,-0.023613,-0.7202,381.28

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.83699,0.41187,-0.36029,19.49,-0.32582,0.90407,0.27658,49.538,0.43964,-0.1141,0.8909,-22.401

> view matrix models
> #9,0.83699,0.41187,-0.36029,19.243,-0.32582,0.90407,0.27658,50.502,0.43964,-0.1141,0.8909,-21.792

> fitmap #9 inMap #3

Fit molecule Tower.pdb (#9) to map cryosparc_P78_J250_006_volume_map_sharp.mrc
z flip (#3) using 2734 atoms  
average map value = 0.2273, steps = 116  
shifted from previous position = 3.24  
rotated from previous position = 27.6 degrees  
atoms outside contour = 1340, contour level = 0.15802  
  
Position of Tower.pdb (#9) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.96143270 0.01219618 -0.27476975 346.57168100  
0.06397038 0.98153511 -0.18026816 22.64228305  
0.26749758 -0.19089283 -0.94446015 289.67827022  
Axis -0.01950064 -0.99528368 0.09502696  
Axis point 152.84833225 0.00000000 170.08973192  
Rotation angle (degrees) 164.19176868  
Shift along axis -1.76661904  
  

> select subtract #9

Nothing selected  

> hide #7 models

> hide #!6 models

> hide #!3 models

> show #!6 models

> hide #!6 models

> show #!3 models

> hide #!3 models

> select #9:1513-1599

1189 atoms, 1218 bonds, 74 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel gold

> select #9:1403-1432

508 atoms, 514 bonds, 30 residues, 1 model selected  

> color sel dark orange

> select #9:2222-2289

1037 atoms, 1044 bonds, 60 residues, 1 model selected  

> color sel olive drab

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> show #!3 models

> color zone #3 near sel & #9 distance 7.97

> hide #!3 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

[Repeated 1 time(s)]

> select #9

2734 atoms, 2776 bonds, 164 residues, 1 model selected  

> show #!3 models

> color zone #3 near sel & #9 distance 7.97

> select subtract #9

Nothing selected  

> volume #3 level 0.1505

> save /Users/katrinawarner/Downloads/Figure_Mapping/Tower_module.png width
> 895 height 753 supersample 3

> hide #!9 models

> color #3 white models

> show #8 models

> select add #8

6072 atoms, 6143 bonds, 379 residues, 1 model selected  

> view matrix models #8,1,0,0,-25.865,0,1,0,-8.5915,0,0,1,10.534

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.85182,-0.51766,0.080183,56.712,0.51143,0.85497,0.086436,-101.21,-0.1133,-0.03262,0.99303,37.5

> view matrix models
> #8,0.15482,-0.51972,-0.84019,380.16,0.42134,0.80396,-0.41966,29.388,0.89359,-0.28904,0.34345,24.146

> view matrix models
> #8,0.18844,-0.18839,-0.96385,353.9,0.37281,0.92169,-0.10726,-43.98,0.90857,-0.33912,0.24391,49.363

> view matrix models
> #8,0.44151,0.11633,-0.88968,249,-0.54855,0.81967,-0.16504,152.8,0.71004,0.56091,0.42571,-77.662

> view matrix models
> #8,0.72206,0.18568,-0.66645,140.34,-0.67642,0.39165,-0.62375,332.89,0.1452,0.90118,0.4084,-16.957

> view matrix models
> #8,0.54958,0.28364,-0.78581,183.79,-0.83496,0.15454,-0.52817,375.05,-0.028374,0.9464,0.32176,27.129

> view matrix models
> #8,0.83342,0.04356,-0.55092,115.16,-0.02437,0.99882,0.042107,-12.808,0.55211,-0.021666,0.83349,-53.392

> fitmap #8 inMap #3

Fit molecule HECT.pdb (#8) to map cryosparc_P78_J250_006_volume_map_sharp.mrc
z flip (#3) using 6072 atoms  
average map value = 0.1296, steps = 92  
shifted from previous position = 1.15  
rotated from previous position = 10.2 degrees  
atoms outside contour = 4180, contour level = 0.1505  
  
Position of HECT.pdb (#8) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.96364146 -0.00692665 -0.26710885 349.47734575  
0.04798587 0.97892492 -0.19850275 27.76385164  
0.26285447 -0.20410294 -0.94300027 291.76439010  
Axis -0.01051026 -0.99461980 0.10305822  
Axis point 154.68613306 0.00000000 171.15280427  
Rotation angle (degrees) 164.54894877  
Shift along axis -1.21885571  
  

> view matrix models
> #8,0.88391,-0.052336,-0.46472,100.68,0.019677,0.997,-0.074854,4.2914,0.46725,0.05702,0.88229,-60.37

> fitmap #8 inMap #3

Fit molecule HECT.pdb (#8) to map cryosparc_P78_J250_006_volume_map_sharp.mrc
z flip (#3) using 6072 atoms  
average map value = 0.1296, steps = 76  
shifted from previous position = 0.0927  
rotated from previous position = 5.38 degrees  
atoms outside contour = 4171, contour level = 0.1505  
  
Position of HECT.pdb (#8) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.96369371 -0.00713422 -0.26691484 349.48252811  
0.04774834 0.97892491 -0.19856008 27.81572406  
0.26270616 -0.20409584 -0.94304314 291.79567537  
Axis -0.01039607 -0.99461992 0.10306857  
Axis point 154.70122019 0.00000000 171.15566042  
Rotation angle (degrees) 164.55918022  
Shift along axis -1.22435668  
  

> view matrix models
> #8,0.86879,0.019815,-0.49479,99.76,-0.1019,0.98497,-0.13947,42.084,0.48459,0.17159,0.85775,-74.356

> ui mousemode right "move picked models"

> view matrix models
> #3,-0.71545,0.14174,0.68414,144.35,0.085924,0.98962,-0.11517,3.8212,-0.69336,-0.023613,-0.7202,383.59

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.86879,0.019815,-0.49479,100.77,-0.1019,0.98497,-0.13947,43.691,0.48459,0.17159,0.85775,-74.427

> fitmap #8 inMap #3

Fit molecule HECT.pdb (#8) to map cryosparc_P78_J250_006_volume_map_sharp.mrc
z flip (#3) using 6072 atoms  
average map value = 0.1296, steps = 72  
shifted from previous position = 1.91  
rotated from previous position = 2.75 degrees  
atoms outside contour = 4170, contour level = 0.1505  
  
Position of HECT.pdb (#8) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.96368031 -0.00723151 -0.26696059 349.50201870  
0.04770438 0.97889442 -0.19872092 27.86084543  
0.26276329 -0.20423863 -0.94299631 291.79755058  
Axis -0.01036008 -0.99461208 0.10314788  
Axis point 154.70670638 0.00000000 171.16656583  
Rotation angle (degrees) 164.55598129  
Shift along axis -1.23330070  
  

> view matrix models
> #8,0.87599,0.0041907,-0.48231,97.888,-0.065856,0.99164,-0.11099,28.561,0.47781,0.12899,0.86894,-69.467

> fitmap #8 inMap #3

Fit molecule HECT.pdb (#8) to map cryosparc_P78_J250_006_volume_map_sharp.mrc
z flip (#3) using 6072 atoms  
average map value = 0.1296, steps = 48  
shifted from previous position = 0.117  
rotated from previous position = 0.0602 degrees  
atoms outside contour = 4163, contour level = 0.1505  
  
Position of HECT.pdb (#8) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.96370889 -0.00644562 -0.26687753 349.38665483  
0.04824689 0.97904063 -0.19786782 27.58999489  
0.26255932 -0.20356299 -0.94319919 291.77935713  
Axis -0.01069948 -0.99464962 0.10275046  
Axis point 154.65995320 0.00000000 171.11477279  
Rotation angle (degrees) 164.56515528  
Shift along axis -1.20017107  
  

> select #9:2890-3100

Nothing selected  

> select #8:2890-3100

3409 atoms, 3450 bonds, 211 residues, 1 model selected  

> hide #!3 models

> select #8:2890-3050

2622 atoms, 2657 bonds, 161 residues, 1 model selected  

> select #8:2890-3100

3409 atoms, 3450 bonds, 211 residues, 1 model selected  

> select #8:2890-3199

5028 atoms, 5085 bonds, 310 residues, 1 model selected  

> select #8:2890-3150

4233 atoms, 4280 bonds, 261 residues, 1 model selected  

> color sel salmon

> select #8:3151-4000

1839 atoms, 1862 bonds, 118 residues, 1 model selected  

> color sel light salmon

> show #!3 models

> select add #8

6072 atoms, 6143 bonds, 379 residues, 1 model selected  

> color zone #3 near sel & #8 distance 7.97

> select subtract #8

Nothing selected  

> volume #3 level 0.2031

> volume #3 level 0.1355

> show #!6 models

> hide #!6 models

> open /Users/katrinawarner/Downloads/Figure_Mapping/ARLD.pdb

Chain information for ARLD.pdb #10  
---  
Chain | Description  
A | No description available  
  

> hide #!10 models

> save /Users/katrinawarner/Downloads/Figure_Mapping/HECT.png width 895 height
> 753 supersample 3

> hide #!3 models

> show #!6 models

> show #7 models

> show #!9 models

> hide #!6 models

> show #!6 models

> select #9

2734 atoms, 2776 bonds, 164 residues, 1 model selected  

> show #!3 models

> color #3 #ffffff51 models

> color #3 #ffffff4b models

> color zone #3 near sel & #9 distance 7.97

> color #3 #ffffff4d models

> hide #!6 models

> hide #7 models

> hide #8 models

> hide #!9 models

> show #!9 models

> select subtract #9

Nothing selected  

> volume #3 level 0.02266

> volume #3 level 0.09034

> volume #3 level 0.06778

> color #3 white models

> color #3 #ffffffdb models

> color zone #3 near #9 distance 7.97

> color #3 #cfcfcfdb models

> color zone #3 near #9 distance 7.97

> volume #3 level 0.0809

> volume #3 level 0.1137

> volume #3 level 0.1465

> volume #3 level 0.1728

> volume #3 level 0.1531

> volume #!3 style image

[Repeated 1 time(s)]

> volume #!3 style surface

> volume #!3 style mesh

> volume #!3 style surface

> transparency #3.1 0

> volume #!3 style surface

[Repeated 1 time(s)]

> color #3 #ecececff models

> color #3 #e9e9e9ff models

> color #3 #e9e9e9fa models

> color #3 #e9e9e9ff models

> color #3 #e9e9e9f4 models

> color zone #3 near #9 distance 7.97

> color #3 #e9e9e9f5 models

> color #3 #c7c7c7f5 models

> color #3 #c7c7c7ff models

> color #3 #c7c7c7fc models

> color zone #3 near #9 distance 7.97

> save /Users/katrinawarner/Downloads/Figure_Mapping/Fig1_tower.png width 1008
> height 753 supersample 3

> color #3 #d1d1d1fc models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!6 models

> color zone #3 near #6 distance 7.97

> volume #3 change image level -0.03228,0 level 0.1005,0.8 level 2.829,1

> volume #3 level 0.1728

> save /Users/katrinawarner/Downloads/Figure_Mapping/Fig1_ARLD_N-C.png width
> 1008 height 753 supersample 3

> hide #!6 models

> hide #!3 models

> show #!3 models

> color #3 #d1d1d1ff models

> color #3 #d1d1d1f9 models

> color #3 #d1d1d1fb models

> show #8 models

> color zone #3 near #8 distance 7.97

> hide #8 models

> show #!6 models

> show #8 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.  

[Repeated 1 time(s)]

> hide #!6 models

> color zone #3 near #8 distance 7.97

> color #3 #d1d1d1fa models

> color zone #3 near #8 distance 7.97

> volume #3 level 0.1662

> volume #3 level 0.1465

> show #7 models

> show #!6 models

> hide #7 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.  

> hide #8 models

> color zone #3 near #6 distance 7.97

> show #8 models

> hide #!6 models

> color zone #3 near #8 distance 7.97

[Repeated 1 time(s)]

> help help:user/tools/toolbar.html

> select #8:3236

20 atoms, 20 bonds, 1 residue, 1 model selected  

> color sel red

> style sel stick

Changed 20 atom styles  

> select add #8

6072 atoms, 6143 bonds, 379 residues, 1 model selected  

> select subtract #8

Nothing selected  

> hide #!3 models

> select #8:3236

20 atoms, 20 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 20 atom styles  

> style sel stick

Changed 20 atom styles  

> show sel atoms

> select #8:3235

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> show sel atoms

> select #8:3237

14 atoms, 13 bonds, 1 residue, 1 model selected  

> show sel atoms

> view matrix models
> #8,0.87595,0.0041114,-0.48238,98.003,-0.065298,0.99177,-0.11012,28.203,0.47796,0.12796,0.86901,-69.434

> hide sel atoms

> select #8:3236

20 atoms, 20 bonds, 1 residue, 1 model selected  

> hide sel atoms

> undo

[Repeated 9 time(s)]

> color sel light salmon

> select #8:3235

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> show sel atoms

> style sel ball

Changed 11 atom styles  

> color sel byelement

> style sel ball

Changed 11 atom styles  

> style sel sphere

Changed 11 atom styles  

> view matrix models
> #8,0.87595,0.0041114,-0.48238,103.75,-0.065298,0.99177,-0.11012,34.077,0.47796,0.12796,0.86901,-57.384

> show #!3 models

> fitmap #8 inMap #3

Fit molecule HECT.pdb (#8) to map cryosparc_P78_J250_006_volume_map_sharp.mrc
z flip (#3) using 6072 atoms  
average map value = 0.1296, steps = 116  
shifted from previous position = 14.6  
rotated from previous position = 0.0488 degrees  
atoms outside contour = 4072, contour level = 0.14653  
  
Position of HECT.pdb (#8) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.96369032 -0.00710653 -0.26692780 349.47978044  
0.04777440 0.97892721 -0.19854249 27.80719521  
0.26271383 -0.20408580 -0.94304317 291.79279061  
Axis -0.01040984 -0.99462050 0.10306158  
Axis point 154.69912511 0.00000000 171.15442412  
Rotation angle (degrees) 164.55857317  
Shift along axis -1.22300776  
  

> hide #!3 models

> color sel orange red

> view matrix models
> #8,0.87598,0.0042105,-0.48234,103.54,-0.065782,0.99166,-0.11081,26.444,0.47785,0.1288,0.86895,-85.404

> select add #8

6072 atoms, 6143 bonds, 379 residues, 1 model selected  

> undo

[Repeated 1 time(s)]

> select add #8

6072 atoms, 6143 bonds, 379 residues, 1 model selected  

> select subtract #8

Nothing selected  

> show #!5 models

> select add #8

6072 atoms, 6143 bonds, 379 residues, 1 model selected  

> view matrix models
> #8,0.87598,0.0042105,-0.48234,124.88,-0.065782,0.99166,-0.11081,8.241,0.47785,0.1288,0.86895,-81.171

> view matrix models
> #8,0.87598,0.0042105,-0.48234,132.42,-0.065782,0.99166,-0.11081,12.89,0.47785,0.1288,0.86895,-85.493

> fitmap #8 inMap #5

Fit molecule HECT.pdb (#8) to map
cryosparc_P77_cryosparc_P77_J229_007_volume_map.mrc (#5) using 6072 atoms  
average map value = 0.1745, steps = 208  
shifted from previous position = 15.8  
rotated from previous position = 46.4 degrees  
atoms outside contour = 2658, contour level = 0.15611  
  
Position of HECT.pdb (#8) relative to
cryosparc_P77_cryosparc_P77_J229_007_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99034227 -0.01559576 0.13776413 -22.50490850  
-0.04765689 -0.97139897 0.23262170 275.19437285  
0.13019602 -0.23694051 -0.96276071 316.73805672  
Axis -0.99754817 0.01607785 -0.06811136  
Axis point 0.00000000 156.38610029 142.67908344  
Rotation angle (degrees) 166.38726388  
Shift along axis 5.30080505  
  

> select subtract #8

Nothing selected  

> hide #!5 models

> show #!3 models

> select add #8

6072 atoms, 6143 bonds, 379 residues, 1 model selected  

> view matrix models
> #8,0.80901,-0.58774,-0.0084008,92.223,0.50779,0.70601,-0.49366,48.784,0.29607,0.3951,0.86962,-74.336

> fitmap #8 inMap #3

Fit molecule HECT.pdb (#8) to map cryosparc_P78_J250_006_volume_map_sharp.mrc
z flip (#3) using 6072 atoms  
average map value = 0.1296, steps = 160  
shifted from previous position = 4.04  
rotated from previous position = 46.4 degrees  
atoms outside contour = 4073, contour level = 0.14653  
  
Position of HECT.pdb (#8) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.96368994 -0.00679030 -0.26693741 349.43459253  
0.04801795 0.97897336 -0.19825597 27.71123566  
0.26267083 -0.20387507 -0.94310073 291.78459708  
Axis -0.01055297 -0.99463233 0.10293279  
Axis point 154.67744325 0.00000000 171.13832392  
Rotation angle (degrees) 164.55975884  
Shift along axis -1.21586220  
  

> select subtract #8

Nothing selected  

> color zone #3 near #8 distance 7.97

[Repeated 1 time(s)]

> hide #8 models

> show #!1 models

> select add #1

41332 atoms, 42254 bonds, 2658 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.45361,0.015434,-0.89106,234.89,-0.73195,0.57685,-0.36262,233.48,0.50842,0.8167,0.27297,-85.228

> view matrix models
> #1,0.97478,0.12556,-0.1845,17.128,-0.22317,0.55029,-0.8046,229.92,0.00050383,0.82548,0.56443,-54.016

> view matrix models
> #1,0.86178,0.090132,-0.4992,92.993,-0.17021,0.97842,-0.11718,40.691,0.47787,0.18596,0.85852,-79.817

> view matrix models
> #1,0.83731,0.14857,-0.52615,92.308,-0.26659,0.95116,-0.15567,66.701,0.47732,0.27061,0.83602,-89.129

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.3102, steps = 172  
shifted from previous position = 5.83  
rotated from previous position = 6.76 degrees  
atoms outside contour = 16391, contour level = 0.14653  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.95226463 -0.11686569 -0.28201859 369.32914364  
-0.04689592 0.96885786 -0.24313618 47.46864052  
0.30165021 -0.21830447 -0.92808960 287.52127676  
Axis 0.04220411 -0.99200636 0.11892098  
Axis point 163.89968313 0.00000000 174.59858415  
Rotation angle (degrees) 162.89126608  
Shift along axis 2.69032428  
  

> select subtract #1

1 model selected  

> select add #1

41332 atoms, 42254 bonds, 2658 residues, 1 model selected  

> select subtract #1

1 model selected  

> select add #1

41332 atoms, 42254 bonds, 2658 residues, 1 model selected  

> select subtract #1

1 model selected  

> select add #1

41332 atoms, 42254 bonds, 2658 residues, 1 model selected  

> select #1:745-2100

16800 atoms, 17472 bonds, 1091 residues, 1 model selected  

> hide sel cartoons

> select #1:745-2500

18582 atoms, 19268 bonds, 1195 residues, 1 model selected  

> hide sel cartoons

> color zone #3 near sel & #1 distance 7.97

> select #1:1-745,2500-4000

22778 atoms, 23013 bonds, 1465 residues, 1 model selected  

> color zone #3 near sel & #1 distance 7.97

> select #1:625

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1:615

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1:2890-

Expected an objects specifier or a keyword  

> select #1:2890-4000

6072 atoms, 6143 bonds, 379 residues, 1 model selected  

> color zone #3 near sel & #1 distance 7.97

> hide #!1 models

> select #1:1-700,2500-2889

16323 atoms, 16475 bonds, 1041 residues, 1 model selected  

> show #!1 models

> color sel white

> select #1:1-700,2500-4000

22395 atoms, 22619 bonds, 1420 residues, 1 model selected  

> color zone #3 near sel & #1 distance 7.97

> hide #!1 models

> volume #!3 style surface

> lighting soft

> view matrix models
> #1,0.88102,0.071583,-0.46763,83.639,-0.16297,0.9739,-0.15796,50.079,0.44412,0.21538,0.8697,-80.664

[Repeated 1 time(s)]

> select #1:3235

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color #3.1#!3 orange red

> undo

> show #!1 models

> hide #!3 models

> color (#!1 & sel) orange red

> style sel sphere

Changed 11 atom styles  

> style sel sphere

Changed 11 atom styles  

> show sel atoms

> select add #1

41332 atoms, 42254 bonds, 2658 residues, 2 models selected  

> select subtract #1

1 model selected  

> show #!3 models

> color zone #3 near #1 distance 7.97

[Repeated 1 time(s)]

> select #1:1-745,2500-4000

22778 atoms, 23013 bonds, 1465 residues, 1 model selected  

> color zone #3 near sel & #1 distance 7.97

> select #1:1-700,2500-4000

22395 atoms, 22619 bonds, 1420 residues, 1 model selected  

> color zone #3 near sel & #1 distance 7.97

[Repeated 1 time(s)]

> select add #1

41332 atoms, 42254 bonds, 2658 residues, 2 models selected  

> select subtract #1

1 model selected  

> select #1:1-700

11042 atoms, 11151 bonds, 681 residues, 1 model selected  

> color sel light slate gray

[Repeated 1 time(s)]

> select #1:1-700,2500-4000

22395 atoms, 22619 bonds, 1420 residues, 1 model selected  

> color zone #3 near sel & #1 distance 7.97

> hide #!1 models

> hide #!3 models

> show #!3 models

> show #!1 models

> select add #1

41332 atoms, 42254 bonds, 2658 residues, 2 models selected  

> select subtract #1

1 model selected  

> hide #!3 models

> select #1:701-2499

18937 atoms, 19633 bonds, 1238 residues, 1 model selected  

> color sel white

> show sel cartoons

> select add #2

22190 atoms, 22556 bonds, 8 pseudobonds, 1993 residues, 4 models selected  

> select add #1

44585 atoms, 45177 bonds, 8 pseudobonds, 3413 residues, 7 models selected  

> select subtract #1

3253 atoms, 2923 bonds, 8 pseudobonds, 755 residues, 6 models selected  

> show #!3 models

> hide #!3 models

> show #!3 models

> view matrix models #2,1,0,0,0,0,1,0,0,0,0,1,0

> save /Users/katrinawarner/Downloads/Figure_Mapping/Cat_module.png width 1008
> height 753 supersample 3

> hide #!3 models

> show #7 models

> hide #!1 models

> show #!3 models

> select subtract #2

3 models selected  

> color zone #3 near #7 distance 7.97

> save /Users/katrinawarner/Downloads/Figure_Mapping/Tom1_domain.png width
> 1008 height 753 supersample 3

> hide #7 models

> show #8 models

> color zone #3 near #8 distance 7.97

> volume #3 level 0.1597

> volume #3 level 0.1465

> save /Users/katrinawarner/Downloads/Figure_Mapping/hect.png width 1008
> height 753 supersample 3

> save /Users/katrinawarner/Downloads/Figure_Mapping/Figure1_try2.cxs

——— End of log from Tue Mar 19 23:45:33 2024 ———

opened ChimeraX session  

> show #!1 models

> hide #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #8 models

> show #!1 models

> select #1:1831-1938

694 atoms, 701 bonds, 45 residues, 1 model selected  

> select #1:1512-1599

1203 atoms, 1232 bonds, 75 residues, 1 model selected  

> color sel khaki

> select #1:1403-1432

508 atoms, 514 bonds, 30 residues, 1 model selected  

> color sel orange

> select #1:2222-2289

1037 atoms, 1044 bonds, 60 residues, 1 model selected  

> color sel olive drab

> select #1:1195-1266

1139 atoms, 1157 bonds, 72 residues, 1 model selected  

> view matrix models
> #1,0.92323,-0.12585,-0.36306,90.162,0.12177,0.99197,-0.034192,-18.744,0.36444,-0.012643,0.93114,-42.771

> color sel cornflower blue

> select #1:1513-1599

1189 atoms, 1218 bonds, 74 residues, 1 model selected  

> color sel gold

> save /Users/katrinawarner/Downloads/Figure_Mapping/Fig1.cxs

> select #0

Nothing selected  

> show #!3 models

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.3102, steps = 152  
shifted from previous position = 3.16  
rotated from previous position = 18.7 degrees  
atoms outside contour = 16390, contour level = 0.14653  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.95226302 -0.11684814 -0.28203129 369.33002108  
-0.04691683 0.96888912 -0.24300755 47.44810157  
0.30165203 -0.21817509 -0.92811943 287.51278609  
Axis 0.04220466 -0.99201441 0.11885361  
Axis point 163.90011369 0.00000000 174.59180409  
Rotation angle (degrees) 162.89097056  
Shift along axis 2.69018126  
  

> color zone #3 near #1 distance 7.97

> select #1:1195-1266

1139 atoms, 1157 bonds, 72 residues, 1 model selected  

> color sel light sky blue

> color zone #3 near sel & #1 distance 7.97

> color sel dodger blue

> color zone #3 near sel & #1 distance 7.97

> color sel royal blue

> color zone #3 near sel & #1 distance 7.97

> color sel blue

> color zone #3 near sel & #1 distance 7.97

> color sel steel blue

> color zone #3 near sel & #1 distance 7.97

> select #1

41332 atoms, 42254 bonds, 2658 residues, 1 model selected  

> color zone #3 near sel & #1 distance 7.97

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.3102, steps = 36  
shifted from previous position = 0.0198  
rotated from previous position = 0.0143 degrees  
atoms outside contour = 16363, contour level = 0.14653  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.95219417 -0.11695254 -0.28222039 369.34742339  
-0.04694143 0.96885986 -0.24311945 47.47401436  
0.30186545 -0.21824910 -0.92803264 287.47177494  
Axis 0.04223961 -0.99200661 0.11890630  
Axis point 163.89725707 0.00000000 174.59610192  
Rotation angle (degrees) 162.87866898  
Shift along axis 2.68875850  
  

> hide #!1 models

> save /Users/katrinawarner/Downloads/Figure_Mapping/Fig1.cxs

> show #!1 models

> select subtract #1

1 model selected  

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> fitmap #1 inMap #3

Fit molecule apo-Tom1.pdb (#1) to map
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) using 41332 atoms  
average map value = 0.3102, steps = 44  
shifted from previous position = 0.0242  
rotated from previous position = 0.0168 degrees  
atoms outside contour = 16396, contour level = 0.14653  
  
Position of apo-Tom1.pdb (#1) relative to
cryosparc_P78_J250_006_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.95227396 -0.11682058 -0.28200578 369.32762789  
-0.04690434 0.96889702 -0.24297847 47.44226208  
0.30161944 -0.21815478 -0.92813479 287.51671760  
Axis 0.04219406 -0.99201648 0.11884008  
Axis point 163.90058131 0.00000000 174.58988181  
Rotation angle (degrees) 162.89276284  
Shift along axis 2.68843306  
  

> save /Users/katrinawarner/Downloads/Figure_Mapping/Fig1.cxs

——— End of log from Thu Mar 21 16:01:32 2024 ———

opened ChimeraX session  

> coulombic #!1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1376, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run  
f(s)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 582, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 525, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 99, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 95, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 259, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 585, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 84, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 140, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
ValueError: More than 2 coplanar positions specified!  
  

Window position QRect(2487,361 600x300) outside any known screen, using
primary screen  

ValueError: More than 2 coplanar positions specified!  
  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
See log for complete Python traceback.  
  

> show #!6 models

> hide #!1 models

> coulombic #!6

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1376, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run  
f(s)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 582, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 525, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 99, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 95, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/cmd.py", line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/hbond.py", line 259, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hbond.py", line 585, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 84, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 140, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
ValueError: More than 2 coplanar positions specified!  
  
ValueError: More than 2 coplanar positions specified!  
  
File
"/Applications/ChimeraX-1.7-rc2023.12.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/bond_geom.py", line 242, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK193LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.60.44
      OS Loader Version: 8419.60.44

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 337 days, 20 hours, 34 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      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: 2.4.1
    Babel: 2.13.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7rc202312062342
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.46.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.3
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.0
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.41
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    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: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

Probable bad structure