2D arrow drag update: self._positions is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:/Users/Home/Desktop/HumanIgG1_1HZH_AF488_v1_labeled_arrows.cxs

Log from Tue Jun 8 11:40:41 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:/Users/Home/Desktop/HumanIgG1_1HZH_AF488_v1_labeled_arrows.cxs

Log from Tue Jun 8 11:31:26 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:/Users/Home/Desktop/HumanIgG1_1HZH_AF488_v1_labeled.cxs

Log from Mon Jun 7 10:23:57 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\Users\Home\Downloads\HumanIgG1_1HZH_AF488_v1_working.cxs format
> session

Log from Mon Apr 26 14:42:47 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\Users\robot\Desktop\Modeling\1IGT_Tail2_AF488_v1.cxs format session

Log from Fri Apr 23 13:09:06 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\Users\robot\Desktop\Modeling\Herceptin_FC_Lys_v1.cxs format session

Log from Mon Apr 19 13:13:53 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6IQG

Summary of feedback from opening 6IQG fetched from pdb  
---  
notes | Fetching compressed mmCIF 6iqg from
http://files.rcsb.org/download/6iqg.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
Fetching CCD HCS from http://ligand-expo.rcsb.org/reports/H/HCS/HCS.cif  
  
6iqg title:  
X-ray crystal structure of Fc and peptide complex [more info...]  
  
Chain information for 6iqg #1  
---  
Chain | Description  
A B | Immunoglobulin gamma-1 heavy chain  
C D | 18-mer peptide G(HCS)DCAYHRGELVWCT(HCS)H(NH2)  
  
Non-standard residues in 6iqg #1  
---  
BMA — beta-D-mannopyranose  
CL — chloride ion  
FUC — alpha-L-fucopyranose  
HCS — 2-amino-4-mercapto-butyric acid  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> select /C/D

228 atoms, 236 bonds, 28 residues, 1 model selected  

> remove

Unknown command: remove  

> remove selected

Unknown command: remove selected  

> remove /c

Unknown command: remove /c  

> hide /c

> select clear

> hide /c

> select /C:613

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

> select /C/D

228 atoms, 236 bonds, 28 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B

Alignment identifier is 1  

> select ::name="LYS"

324 atoms, 288 bonds, 36 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 324 atom styles  

> surface sel

> transparency (#!1 & sel) 50

> surface style mesh

> select clear

> select /B:246@CE

1 atom, 1 residue, 1 model selected  

> select /B:246@NZ

1 atom, 1 residue, 1 model selected  

> select /B:248@NZ

1 atom, 1 residue, 1 model selected  

> ui tool show Distances

> distance /B:246@NZ /B:248@NZ

Distance between /B LYS 246 NZ and LYS 248 NZ: 11.620Å  
Drag select of 2 residues  

> select /B:246@CE

1 atom, 1 residue, 1 model selected  

> distance /B:246@CE /B:290@CE

Distance between /B LYS 246 CE and LYS 290 CE: 13.306Å  

> select clear

> select ::name="LYS"

324 atoms, 288 bonds, 2 pseudobonds, 36 residues, 2 models selected  

> surface style dot

> surface style solid

> transparency (#!1 & sel) 80

> select clear

> select /B:290@CE

1 atom, 1 residue, 1 model selected  

> select /B:246@CG

1 atom, 1 residue, 1 model selected  

> select clear

> hide #2.1 models

> show #2.1 models

> hide #!2 models

> select /B:274@CE

1 atom, 1 residue, 1 model selected  

> distance /B:274@CE /B:322@CE

Distance between /B LYS 274 CE and LYS 322 CE: 7.003Å  

> show #!2 models

> select /B:274@CE

1 atom, 1 residue, 1 model selected  

> distance /B:274@CE /B:326@NZ

Distance between /B LYS 274 CE and LYS 326 NZ: 11.172Å  

> select /B:322@CE

1 atom, 1 residue, 1 model selected  

> select /B:274@CD

1 atom, 1 residue, 1 model selected  

> select /B:288@CE

1 atom, 1 residue, 1 model selected  

> distance /B:288@CE /B:290@CE

Distance between /B LYS 288 CE and LYS 290 CE: 9.280Å  

> select /B:322@CE

1 atom, 1 residue, 1 model selected  

> distance /B:320@NZ /B:322@CE

Distance between /B LYS 320 NZ and LYS 322 CE: 9.849Å  

> select /B:320@NZ

1 atom, 1 residue, 1 model selected  

> select /B:320@NZ

1 atom, 1 residue, 1 model selected  

> distance /B:317@CE /B:320@NZ

Distance between /B LYS 317 CE and LYS 320 NZ: 12.281Å  

> select clear

> select /B:317@CE

1 atom, 1 residue, 1 model selected  

> distance /B:317@CE /B:340@NZ

Distance between /B LYS 317 CE and LYS 340 NZ: 14.146Å  

> select /B:340@NZ

1 atom, 1 residue, 1 model selected  

> distance /B:338@NZ /B:340@NZ

Distance between /B LYS 338 NZ and LYS 340 NZ: 9.588Å  
Drag select of 6iqg_A SES surface, 15 of 202702 triangles, 6iqg_B SES surface,
414 of 203562 triangles, 5 atoms, 2 residues, 3 bonds  

> select /B:439@CE

1 atom, 1 residue, 1 model selected  

> distance /A:360@CE /B:439@CE

Distance between /A LYS 360 CE and /B LYS 439 CE: 9.669Å  

> select /B:370@NZ

1 atom, 1 residue, 1 model selected  

> distance /A:409@NZ /B:370@NZ

Distance between /A LYS 409 NZ and /B LYS 370 NZ: 5.420Å  

> select /A:414@CE

1 atom, 1 residue, 1 model selected  

> select clear

> select /B:414@CE

1 atom, 1 residue, 1 model selected  

> distance /B:360@CG /B:414@CE

Distance between /B LYS 360 CG and LYS 414 CE: 8.721Å  

> select /B:392@NZ

1 atom, 1 residue, 1 model selected  

> distance /B:392@NZ /B:409@NZ

Distance between /B LYS 392 NZ and LYS 409 NZ: 9.394Å  

> select /B:409@NZ

1 atom, 1 residue, 1 model selected  

> distance /A:370@CE /B:409@NZ

Distance between /A LYS 370 CE and /B LYS 409 NZ: 4.309Å  

> view sel

> select clear

> rotate

Unknown command: rotate  

> wobble

> stop

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\robot\Desktop\movie3.mp4

Movie saved to \C:Users\\...\Desktop\movie3.mp4  
  

> save C:/Users/robot/Desktop/Modeling/Herceptin_FC_Lys_v1.cxs

> set bgColor white

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> distance style color black

> distance style color #005500

> distance style color #aaaa00

> distance style color black

> distance style color #00007f

> distance style color #550000

> distance style color #55007f

> distance style color #005500

> distance style color #d7eaf8

> distance style color #cccccc

> distance style color #f0f0f0

> distance style color #fafafa

> distance style color white

> distance style color black

> distance style color white

> distance style color #ffefc3

> distance style color white

> distance style color #ff1a1a

> distance style color black

> distance style color white

> distance style color #c52a2a

> distance style color white

> distance style color #c72e2e

> distance style color white

> distance style color #7a5656

> distance style color #eddcdc

> distance style color #f2e1e1

> distance style color #2d1b1b

> distance style color #6769d2

> distance style color #6b72de

> distance style color #6565c3

> distance style color #554a6d

> distance style color #eddede

> distance style color white

> distance style color black

> distance style color #62594e

> distance style color white

> distance style color black

> distance style color #ff3939

> distance style color #ff3535

> distance style color black

> distance style color #f13131

> distance style color #ff3535

> distance style color #ff3636

> distance style color #b02d2d

> distance style color #9e2c2c

> distance style color black

> distance style color white

> distance style color black

> distance style color #6c2b2b

> distance style color #b22d2d

> distance style color #ff3232

> distance style color #ff3d3d

> distance style color #ff3535

> distance style color black

> distance style color white

> distance style color #e4d7d7

> distance style color #d7d4e9

> distance style color #d2cfe2

> distance style color #d7d4e9

> distance style color #dbd7ef

> distance style color #c0bcd8

> distance style color #bfbbd7

> distance style color #5e515a

> distance style color #f0f0f0

> distance style color black

> distance style color #828790

> distance style color #f0f0f0

> distance style color #aa0000

> distance style color #f0f0f0

> distance style color #005500

> lighting full

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\robot\Desktop\movie4.mp4

Movie saved to \C:Users\\...\Desktop\movie4.mp4  
  

> select /B:320@CD

1 atom, 1 residue, 1 model selected  

> select /B:317@CG

1 atom, 1 residue, 1 model selected  

> select /B:274@CD

1 atom, 1 residue, 1 model selected  

> select /B:290@CG

1 atom, 1 residue, 1 model selected  

> select /B:288@CG

1 atom, 1 residue, 1 model selected  

> select /B:334@CD

1 atom, 1 residue, 1 model selected  

> distance /B:334@CD /B:340@NZ

Distance between /B LYS 334 CD and LYS 340 NZ: 14.834Å  

> select /B:360@O

1 atom, 1 residue, 1 model selected  

> select /B:360@O

1 atom, 1 residue, 1 model selected  

> select /B:360@CG

1 atom, 1 residue, 1 model selected  

> ~distance /B:360@CG /B:414@CE

> select /B:414@NZ

1 atom, 1 residue, 1 model selected  

> distance /B:360@CE /B:414@NZ

Distance between /B LYS 360 CE and LYS 414 NZ: 9.752Å  

> distance style color #aa0000

> distance style color #005500

> select /B:414@NZ

1 atom, 1 residue, 1 model selected  

> select /A:439@CE

1 atom, 1 residue, 1 model selected  

> select /B:360@CE

1 atom, 1 residue, 1 model selected  

> distance /A:439@CE /B:360@CE

Distance between /A LYS 439 CE and /B LYS 360 CE: 10.094Å  

> distance style color #aa0000

> distance style color #005500

> select /B:414@CE

1 atom, 1 residue, 1 model selected  

> select clear

> select /B:414@CB

1 atom, 1 residue, 1 model selected  

> select /A:409@NZ

1 atom, 1 residue, 1 model selected  

> select /B:409@CG

1 atom, 1 residue, 1 model selected  

> select /A:370@NZ

1 atom, 1 residue, 1 model selected  

> select /B:392@CG

1 atom, 1 residue, 1 model selected  

> select /B:409@CG

1 atom, 1 residue, 1 model selected  

> select /B:409@CD

1 atom, 1 residue, 1 model selected  

> select /B:409@CA

1 atom, 1 residue, 1 model selected  

> select /A:370@CE

1 atom, 1 residue, 1 model selected  

> select /B:409@NZ

1 atom, 1 residue, 1 model selected  

> select /B:360@CD

1 atom, 1 residue, 1 model selected  

> select /A:360@CG

1 atom, 1 residue, 1 model selected  

> save C:/Users/robot/Desktop/Modeling/Herceptin_FC_Lys_v1.cxs

opened ChimeraX session  

> open 1HZH

Summary of feedback from opening 1HZH fetched from pdb  
---  
notes | Fetching compressed mmCIF 1hzh from
http://files.rcsb.org/download/1hzh.cif  
Fetching CCD GAL from http://ligand-expo.rcsb.org/reports/G/GAL/GAL.cif  
  
1hzh title:  
Crystal structure of the intact human igg B12 with broad and potent activity
against primary hiv-1 isolates: A template for hiv vaccine design [more
info...]  
  
Chain information for 1hzh #3  
---  
Chain | Description  
H K | immunoglobulin heavy chain  
L M | IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein  
  
Non-standard residues in 1hzh #3  
---  
BMA — beta-D-mannopyranose  
FUC — alpha-L-fucopyranose  
GAL — beta-D-galactopyranose  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> hide #2.1 models

> hide #!2 models

> hide #!1 models

> view orient

> select ::name="LYS"

1117 atoms, 997 bonds, 16 pseudobonds, 124 residues, 3 models selected  

> show sel & #!3 atoms

> color sel & #!3 bychain

> select clear

> select clear

> color #!3 bychain

> show #!3 atoms

> hide #!3 models

> show #!1 models

> show #!3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/H #3/K

Alignment identifier is 2  

> sequence chain #3/L #3/M

Alignment identifier is 3  

> select clear

> hide atoms

> close session

> open C:/Users/robot/Desktop/Modeling/1igt_eaaak_tails_2_AF488.pdb

Summary of feedback from opening
C:/Users/robot/Desktop/Modeling/1igt_eaaak_tails_2_AF488.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2021-04-23T12:35:55Z  
  
Chain information for 1igt_eaaak_tails_2_AF488.pdb #1  
---  
Chain | Description  
A C | No description available  
B | No description available  
D | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A /C

Alignment identifier is 1  

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /D

Alignment identifier is 1/D  

> show sel atoms

> show sel atoms

> show sel surfaces

> select clear

> color bychain

> select ::name="KAF"

6540 atoms, 6852 bonds, 102 residues, 1 model selected  

> show sel surfaces

> close session

> open C:\Users\robot\Desktop\Modeling\1igt_eaaak_tails_2_AF488.pdb format pdb

Summary of feedback from opening
C:\Users\robot\Desktop\Modeling\1igt_eaaak_tails_2_AF488.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2021-04-23T12:45:44Z  
  
Chain information for 1igt_eaaak_tails_2_AF488.pdb #1  
---  
Chain | Description  
A C | No description available  
B | No description available  
D | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /D

Alignment identifier is 1/D  

> select ::name="KAF"

6538 atoms, 6850 bonds, 102 residues, 1 model selected  

> show sel atoms

> show sel surfaces

> hide sel surfaces

> color (#!1 & sel) lime

> show sel surfaces

> show sel atoms

> color sel lime

> show sel surfaces

> color (#!1 & sel) lime

> hide sel atoms

> show sel atoms

> ui tool show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 531, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1253, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\\__init__.py", line 139, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\tool.py", line 186, in __init__  
self.isolde = isolde.Isolde(self)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 559, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 1027, in _update_model_list  
self._change_selected_model(model=current_model)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 2486, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 573, in __init__  
spotlight_mode=spotlight_mode)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 601, in add_model  
self.cell, self.spacegroup, self.grid, self.resolution, self._has_symmetry =
f(*args)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 202, in
symmetry_from_model_metadata  
return symmetry_from_model_metadata_pdb(model)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 447, in
symmetry_from_model_metadata_pdb  
spgr_descr = Spgr_descr(symstr, symstr_type)  
RuntimeError: Spgr_descr: No such HM symbol  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1501, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\cmd.py",
line 187, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Spgr_descr: No such HM symbol  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Spgr_descr: No such HM symbol  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  
'ISOLDE_ToolUI' object has no attribute 'isolde'  
File "C:\Program Files\ChimeraX 1.1\bin\lib\runpy.py", line 193, in
_run_module_as_main  
"__main__", mod_spec)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\runpy.py", line 85, in _run_code  
exec(code, run_globals)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\ChimeraX_main.py",
line 919, in <module>  
exit_code = init(sys.argv)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\ChimeraX_main.py",
line 772, in init  
sess.ui.event_loop()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 269, in event_loop  
self.exec_()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2069, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 607, in close_request  
tool_instance.delete()  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\tool.py", line 197, in delete  
traceback.print_stack(file=sys.__stderr__)  

> ui tool show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 531, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1253, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\\__init__.py", line 139, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\tool.py", line 186, in __init__  
self.isolde = isolde.Isolde(self)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 312, in __init__  
self._start_gui(gui)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 456, in _start_gui  
self._populate_menus_and_update_params()  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 559, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 1027, in _update_model_list  
self._change_selected_model(model=current_model)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 2486, in _change_selected_model  
sh = get_symmetry_handler(m, create=True, auto_add_to_session=True)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 159, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 170, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 573, in __init__  
spotlight_mode=spotlight_mode)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 601, in add_model  
self.cell, self.spacegroup, self.grid, self.resolution, self._has_symmetry =
f(*args)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 202, in
symmetry_from_model_metadata  
return symmetry_from_model_metadata_pdb(model)  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\clipper\symmetry.py", line 447, in
symmetry_from_model_metadata_pdb  
spgr_descr = Spgr_descr(symstr, symstr_type)  
RuntimeError: Spgr_descr: No such HM symbol  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1501, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\cmd.py",
line 187, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Spgr_descr: No such HM symbol  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Spgr_descr: No such HM symbol  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  
'ISOLDE_ToolUI' object has no attribute 'isolde'  
File "C:\Program Files\ChimeraX 1.1\bin\lib\runpy.py", line 193, in
_run_module_as_main  
"__main__", mod_spec)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\runpy.py", line 85, in _run_code  
exec(code, run_globals)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\ChimeraX_main.py",
line 919, in <module>  
exit_code = init(sys.argv)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\ChimeraX_main.py",
line 772, in init  
sess.ui.event_loop()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 269, in event_loop  
self.exec_()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 2069, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 607, in close_request  
tool_instance.delete()  
File "C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\tool.py", line 197, in delete  
traceback.print_stack(file=sys.__stderr__)  

> select clear

> color bychain

> color (#!1 & sel) lime

> color (#!1 & sel) lime

> ui mousemode right "bond rotation"

> ui mousemode right "bond rotation"

> ui mousemode right rotate

> ui mousemode right rotate

> ui mousemode right "bond rotation"

> show sel atoms

> show sel atoms

> hide sel cartoons

> ui mousemode right "bond rotation"

> ui mousemode right "bond rotation"

> torsion /D:476@C,CA,N,HN 60.06

> torsion /D:476@C,CA,N,HN 60.06

> torsion /D:476@C,CA,N,HN 72.06

> torsion /D:476@C,CA,N,HN 75.06

> torsion /D:476@C,CA,N,HN 169.06

> torsion /D:476@O,C,CA,N -131.01

> torsion /D:476@O,C,CA,N -154.01

> ui mousemode right "bond rotation"

> ui mousemode right rotate

> select clear

> hide sel atoms

> show sel cartoons

> select clear

> ui mousemode right select

Drag select of 1 residues  
Drag select of 5 residues  

> select clear

> hide #!1 models

> show #!1 models

> select clear

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> save C:/Users/robot/Desktop/Modeling/1IGT_Tail2_AF488_v1.cxs

opened ChimeraX session  
Drag select of 20 residues  

> select clear

Drag select of 5 atoms, 7 residues, 4 bonds  

> select clear

> save C:/Users/robot/Desktop/Modeling/1IGT_Tail2_AF488_v1.cxs

> open C:/Users/robot/Desktop/Modeling/1hzh_closed_loop.dsv

Unrecognized file suffix '.dsv'  

> open C:/Users/robot/Desktop/Modeling/1hzh_closed_loop.pdb

Summary of feedback from opening
C:/Users/robot/Desktop/Modeling/1hzh_closed_loop.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2021-04-23T15:13:23Z  
  
Chain information for 1hzh_closed_loop.pdb #2  
---  
Chain | Description  
H | No description available  
K | No description available  
L M | No description available  
  

> close #2

> close session

> open C:/Users/robot/Desktop/Modeling/1hzh_closed_loop.pdb

Summary of feedback from opening
C:/Users/robot/Desktop/Modeling/1hzh_closed_loop.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2021-04-23T15:13:23Z  
  
Chain information for 1hzh_closed_loop.pdb #1  
---  
Chain | Description  
H | No description available  
K | No description available  
L M | No description available  
  
Drag select of 61 residues  

> select clear

> close session

> open C:/Users/robot/Desktop/Modeling/1hzh_V1.pdb

Summary of feedback from opening C:/Users/robot/Desktop/Modeling/1hzh_V1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2021-04-23T14:52:16Z  
  
Chain information for 1hzh_V1.pdb #1  
---  
Chain | Description  
H | No description available  
K | No description available  
L M | No description available  
  
Drag select of 13 residues  

> close session

> open C:/Users/robot/Desktop/Modeling/1hzh_V1_AF488.pdb

Summary of feedback from opening
C:/Users/robot/Desktop/Modeling/1hzh_V1_AF488.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2021-04-23T14:53:18Z  
  
Chain information for 1hzh_V1_AF488.pdb #1  
---  
Chain | Description  
H | No description available  
K | No description available  
L M | No description available  
  

> close session

> open C:/Users/robot/Desktop/Modeling/1hzh_V1_AF488_PDB_20210423.pdb

Summary of feedback from opening
C:/Users/robot/Desktop/Modeling/1hzh_V1_AF488_PDB_20210423.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2021-04-23T16:26:00Z  
  
Chain information for 1hzh_V1_AF488_PDB_20210423.pdb #1  
---  
Chain | Description  
H | No description available  
K | No description available  
L M | No description available  
  
Drag select of 5 residues  

> undo

Alignment identifier is 1/H  
Alignment identifier is 1/K  
Alignment identifier is 1  

> select /H

4533 atoms, 4749 bonds, 457 residues, 1 model selected  

> style sel ball

Changed 4533 atom styles  

> rainbow sel

> select clear

> color bychain

> color bychain

> color bychain

> color bychain

> color bychain

> select clear

> ui tool show "Basic Actions"

> select clear

> color /H #ffaa00 target c

> select /K

4400 atoms, 4607 bonds, 2 pseudobonds, 447 residues, 2 models selected  

> color /K #ffaa7f target abp

> select clear

> color /K #ffaa7f target c

> select /L

2018 atoms, 2096 bonds, 215 residues, 1 model selected  

> color /L #55aaff target c

> color /M #5555ff target c

> select clear

> select clear

> select ::name="KAF"

3257 atoms, 3481 bonds, 74 residues, 1 model selected  

> show sel atoms

> show sel surfaces

> transparency (#!1 & sel) 70

> select clear

> select #1

13190 atoms, 13787 bonds, 2 pseudobonds, 1352 residues, 2 models selected  

> show sel surfaces

> select ::name="KAF"

3257 atoms, 3481 bonds, 74 residues, 1 model selected  

> color (#!1 & sel) lime

> select clear

> select clear

> select ::name="KAF"

3257 atoms, 3481 bonds, 74 residues, 1 model selected  

> surface style mesh

> surface style solid

> color (#!1 & sel) purple

> select clear

> color /H #ffaa00 target s

> color /K #ffaa7f target s

> color /L #55aaff target s

> color /M #55ffff target s

> select ::name="KAF"

3257 atoms, 3481 bonds, 74 residues, 1 model selected  

> color (#!1 & sel) hot pink

> color (#!1 & sel) magenta

> transparency (#!1 & sel) 70

> select clear

> view orient

> view

Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 408 of 594364
triangles, 1hzh_V1_AF488_PDB_20210423.pdb_K SES surface, 868 of 581162
triangles, 1hzh_V1_AF488_PDB_20210423.pdb_L SES surface, 496 of 261774
triangles, 1 atoms, 9 residues  

> view

> select clear

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> lighting simple

> lighting simple

> lighting soft

> open http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup

Opened http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup  

> movie record

> turn y 2 180

> wait 180

> turn x 2 180

> wait 180

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488.mp4  
  

> select clear

> save C:/Users/robot/Desktop/Modeling/HumanIgG1_1HZH_AF488_v1.cxs

> select
> ::name="BMA"::name="FUC"::name="GAL"::name="KAF"::name="MAN"::name="NAG"

3478 atoms, 3718 bonds, 92 residues, 1 model selected  

> select ~sel

9712 atoms, 10069 bonds, 2 pseudobonds, 1260 residues, 2 models selected  

> transparency (#!1 & sel) 50

> hide sel cartoons

> select clear

> select clear

> select clear

> select clear

Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 210 of 594364
triangles  

> select clear

> select up

45 atoms, 48 bonds, 1 residue, 1 model selected  

> select up

4533 atoms, 4749 bonds, 457 residues, 1 model selected  

> select down

45 atoms, 48 bonds, 1 residue, 2 models selected  

> wobble

> stop

> wobble 180; wait 180

Expected an axis vector or a keyword  

> wobble x 180

> wait 180

> stop

> wobble sel 180; wait 180

Expected an axis vector or a keyword  

> wobble selection 180; wait 180

Expected an axis vector or a keyword  

> wobble camera 180; wait 180

Expected an axis vector or a keyword  

> wobble sel 180; wait 180

Expected an axis vector or a keyword  

> wobble sel 180; wait 180

Expected an axis vector or a keyword  

> wobble zonesel 180; wait 180

Expected an axis vector or a keyword  

> turn esel 180; wait 180

Expected an axis vector or a keyword  

> turn sel 180; wait 180

Expected an axis vector or a keyword  

> turn z 2 360 precess 20; wait 180

Expected a keyword  

> turn z 2 360 precess 20

Expected a keyword  

> wobble

> wobble: wait 180

Unknown command: wobble: wait 180  

> wobble: wait 180

Unknown command: wobble: wait 180  

> wobble

> wait 180

> select clear

> stop

> select up

45 atoms, 48 bonds, 1 residue, 1 model selected  

> select up

4533 atoms, 4749 bonds, 457 residues, 1 model selected  

> select up

13190 atoms, 13787 bonds, 1352 residues, 2 models selected  

> select down

4533 atoms, 4749 bonds, 457 residues, 5 models selected  

> select down

45 atoms, 48 bonds, 1 residue, 2 models selected  

> movie record

> wobble

> wait 180

> stop

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4  
  
Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_K SES surface, 2380 of 581162
triangles  

> select up

45 atoms, 48 bonds, 1 residue, 1 model selected  

> turn sel 180; wait 180

Expected an axis vector or a keyword  

> turn y sel 180; wait 180

Expected a number or a keyword  

> turn y 180

> wait 180

> turn y 180

> wait 180

> turn y 2 180

> wait 180

> rock

> wait 180

> stop

> wobble 60; wait 60

Expected an axis vector or a keyword  

> rock 60; wait 60

Expected an axis vector or a keyword  

> rock 60; wait 60

Expected an axis vector or a keyword  

> rock y 3 60

> wait 60

> movie record

> rock y 3 60

> wait 60

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4  
  

> movie record

> rock y 3 180

> wait 180

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4  
  

> rock y 3 136 136; wait 136

Expected a keyword  

> rock y 3 136 cycle 136

> wait 136

> rock y 3 136 cycle 68

> wait 136

> movie record

> rock y 3 136 cycle 68

> wait 136

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4  
  

> rock y 3 68 cycle 68

> wait 68

> select up

4533 atoms, 4749 bonds, 457 residues, 1 model selected  

> select down

45 atoms, 48 bonds, 1 residue, 2 models selected  

> movie record

> rock y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4  
  

> wobble y 3 68 cycle 68

> wait 68

> wobble y 3 68 cycle 68

> wait 68

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K450.mp4  
  
Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 664 of 594364
triangles  

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K442.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K442.mp4  
  

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K417HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K417HC.mp4  
  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> hide /K target abp

> show /K target abp

> undo

> undo

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K412HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K412HC.mp4  
  

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K395HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K395HC.mp4  
  

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K373HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K373HC.mp4  
  

> hide sel surfaces

> show sel surfaces

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K363HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K363HC.mp4  
  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K343HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K343HC.mp4  
  

> select ::name="TRP"

336 atoms, 360 bonds, 24 residues, 1 model selected  

> color (#!1 & sel) black

> undo

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K341HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K341HC.mp4  
  
Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 503 of 594364
triangles, 2 atoms, 2 bonds  

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K337HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K337HC.mp4  
  

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K329HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K329HC.mp4  
  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> movie record

> movie record

Already recording a movie  

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K325HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K325HC.mp4  
  

> movie record

> wobble y 3 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K323HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K323HC.mp4  
  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> wobble y 10 68 cycle 68

> wait 68

> wobble y 10 90 cycle 90

> wait 90

> wobble y 10 90 cycle 90

> wait 90

> wobble y 30 68 cycle 68

> wait 68

> wobble y 30 68 cycle 68

> wait 68

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K320HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K320HC.mp4  
  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K320HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K320HC.mp4  
  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> select up

95 atoms, 102 bonds, 3 residues, 2 models selected  

> select up

4533 atoms, 4749 bonds, 457 residues, 2 models selected  

> select down

95 atoms, 102 bonds, 3 residues, 2 models selected  

> select down

44 atoms, 47 bonds, 1 residue, 2 models selected  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K293HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K293HC.mp4  
  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K291HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K291HC.mp4  
  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K277HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K277HC.mp4  
  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K251HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K251HC.mp4  
  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K249HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K249HC.mp4  
  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K225HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K225HC.mp4  
  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> wobble x 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K225HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K225HC.mp4  
  

> select up

44 atoms, 47 bonds, 1 residue, 2 models selected  

> view orient

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K221HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K221HC.mp4  
  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K217HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K217HC.mp4  
  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> select up

154 atoms, 165 bonds, 6 residues, 2 models selected  

> select down

44 atoms, 47 bonds, 1 residue, 2 models selected  

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K216HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K216HC.mp4  
  

> hide sel surfaces

> show sel surfaces

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K213HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K213HC.mp4  
  

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K208HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K208HC.mp4  
  
Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_L SES surface, 934 of 261774
triangles  

> hide sel surfaces

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K150HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K150HC.mp4  
  

> show sel surfaces

> view #!1 clip false

> hide sel surfaces

> movie record

> wobble y 30 68 cycle 68

> wait 68

> movie encode output C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K136HC.mp4

Movie saved to C:\Users\robot/Desktop/HumanIgG1_1HZH_af488_K136HC.mp4  
  

> show sel surfaces

> hide sel surfaces

Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 204699 of 594364
triangles, 1hzh_V1_AF488_PDB_20210423.pdb_L SES surface, 218250 of 261774
triangles, 739 atoms, 18 residues, 795 bonds  
Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 255997 of 594364
triangles, 1hzh_V1_AF488_PDB_20210423.pdb_L SES surface, 256082 of 261774
triangles, 748 atoms, 18 residues, 806 bonds  
Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 259857 of 594364
triangles, 1hzh_V1_AF488_PDB_20210423.pdb_L SES surface, 256995 of 261774
triangles, 756 atoms, 18 residues, 813 bonds  

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> select clear

> save C:/Users/robot/Desktop/Modeling/HumanIgG1_1HZH_AF488_v1_working.cxs

——— End of log from Mon Apr 26 14:42:47 2021 ———

opened ChimeraX session  

> select clear

> 2dlabels text Fluorophore color magenta size 26 xpos .5 ypos .5

> wait 60

> ui mousemode right "move label"

> 2dlabels #2.1 xpos 0.394 ypos 0.137

> 2dlabels text "Heavy Chain" color gold size 26 xpos .5 ypos .5

> wait 60

> 2dlabels #2.2 xpos 0.504 ypos 0.455

> 2dlabels #2.2 xpos 0.504 ypos 0.455

> 2dlabels #2.2 xpos 0.075 ypos 0.220

> 2dlabels text "Heavy Chain" color cyan size 26 xpos .5 ypos .5

> wait 60

> 2dlabels delete

> 2dlabels text " Fluorophore" color magenta size 26 xpos .5 ypos .5

> wait 60

> 2dlabels #3.1 xpos 0.496 ypos 0.380

> 2dlabels #3.1 xpos 0.372 ypos 0.154

> 2dlabels text " Heavy Chain" color gold size 26 xpos .5 ypos .5

> wait 60

> 2dlabels #3.2 xpos 0.049 ypos 0.226

> 2dlabels text " Heavy Chain" color light salmon size 26 xpos .5 ypos .5

> wait 60

> 2dlabels #3.3 xpos 0.713 ypos 0.318

> 2dlabels text " Light Chain" color cyan size 26 xpos .5 ypos .5

> wait 60

> 2dlabels #3.4 xpos 0.690 ypos 0.505

> 2dlabels text " Light Chain" color blue size 26 xpos .5 ypos .5

> wait 60

> 2dlabels #3.5 xpos 0.080 ypos 0.491

> 2dlabels arrow start .5,.5 end .5,.5 color magenta

> wait 60

Can't find font for arrow  

> 2dlabels arrow start .5,.5 end .5,.5 color magenta

> wait 45

Can't find font for arrow  

> 2dlabels arrow start .1,.5 end .1,.8 color magenta

> wait 45

> 2dlabels #3.5 xpos 0.057 ypos 0.511

> 2dlabels arrow #4.3 end 0.455,0.335

> 2dlabels arrow #4.3 start 0.457,0.231

> 2dlabels #3.1 xpos 0.393 ypos 0.048

> 2dlabels arrow #4.3 end 0.463,0.341

> 2dlabels arrow #4.3 start 0.463,0.139

> 2dlabels #3.2 xpos 0.035 ypos 0.174

> 2dlabels arrow start .1,.5 end .1,.8 color gold

> wait 45

> 2dlabels #3.5 xpos 0.152 ypos 0.683

> 2dlabels arrow #4.4 start 0.143,0.236

> 2dlabels arrow #4.4 end 0.162,0.564

> 2dlabels arrow #4.4 end 0.246,0.332

> 2dlabels #3.2 xpos 0.054 ypos 0.064

> 2dlabels arrow #4.4 start 0.225,0.127

> 2dlabels arrow #4.4 end 0.284,0.273

> 2dlabels #3.5 xpos 0.060 ypos 0.658

> 2dlabels arrow start .1,.5 end .1,.8 color blue

> wait 45

> 2dlabels arrow #4.5 start 0.139,0.528

> 2dlabels arrow #4.5 end 0.240,0.408

> 2dlabels arrow #4.5 start 0.169,0.635

> 2dlabels arrow #4.5 end 0.257,0.482

> hide #4.1 models

> show #4.1 models

> hide #4.2 models

> show #4.2 models

> hide #4.3 models

> show #4.3 models

> hide #4.2 models

> hide #4.1 models

> 2dlabels arrow #4.5 end 0.272,0.490

> 2dlabels #3.5 xpos 0.041 ypos 0.666

> 2dlabels arrow #4.5 start 0.209,0.643

> 2dlabels arrow #4.5 end 0.290,0.518

> 2dlabels #3.4 xpos 0.711 ypos 0.648

> 2dlabels arrow start .1,.1 end .1,.4 color cyan

> wait 45

> 2dlabels arrow #4.6 start 0.746,0.606

> 2dlabels arrow #4.6 end 0.684,0.493

> 2dlabels #3.4 xpos 0.707 ypos 0.691

> 2dlabels arrow #4.6 start 0.742,0.663

> 2dlabels arrow #4.6 end 0.681,0.515

> 2dlabels #3.4 xpos 0.716 ypos 0.673

> 2dlabels arrow #4.6 start 0.747,0.646

> 2dlabels arrow #4.6 end 0.678,0.517

> 2dlabels arrow #4.6 end 0.675,0.517

> 2dlabels arrow start .1,.1 end .1,.4 color light salmon

> wait 45

> 2dlabels #3.3 xpos 0.722 ypos 0.119

> 2dlabels #3.2 xpos 0.054 ypos 0.040

> 2dlabels arrow #4.7 end 0.610,0.292

> 2dlabels arrow #4.7 start 0.679,0.139

> 2dlabels #3.3 xpos 0.715 ypos 0.086

> 2dlabels arrow #4.7 end 0.660,0.310

> 2dlabels arrow #4.7 start 0.739,0.161

> 2dlabels arrow #4.7 end 0.678,0.303

> 2dlabels #3.3 xpos 0.711 ypos 0.076

> 2dlabels arrow #4.7 start 0.743,0.152

> 2dlabels arrow #4.3 end 0.463,0.326

> 2dlabels arrow #4.3 start 0.480,0.120

> 2dlabels arrow #4.3 end 0.478,0.311

> 2dlabels #3.5 xpos 0.051 ypos 0.691

> 2dlabels arrow #4.5 start 0.219,0.661

> 2dlabels arrow #4.5 end 0.288,0.530

> 2dlabels arrow #4.4 start 0.228,0.133

> 2dlabels arrow #4.7 end 0.681,0.284

> 2dlabels arrow #4.3 end 0.480,0.294

> 2dlabels arrow #4.7 start 0.752,0.162

> 2dlabels arrow #4.7 end 0.693,0.302

> select #4.1

1 model selected  

> select #4.2

1 model selected  

> select #4.1

1 model selected  

> 2dlabels delete 4.1

Expected 'all' or a label/arrow models specifier or a keyword  

> ui tool show Log

> 2dlabels delete #4.1

> 2dlabels delete #4.2

> 2dlabels arrow #4.5 end 0.282,0.541

> 2dlabels arrow #4.4 end 0.277,0.262

> 2dlabels arrow #4.3 end 0.480,0.282

> 2dlabels arrow #4.7 end 0.696,0.293

> 2dlabels arrow #4.4 end 0.272,0.248

> 2dlabels arrow #4.5 end 0.280,0.546

> 2dlabels arrow #4.3 end 0.478,0.280

> 2dlabels arrow #4.6 end 0.687,0.531

> save C:/Users/Home/Desktop/HumanIgG1_1HZH_AF488_v1_labeled.cxs

——— End of log from Mon Jun 7 10:23:57 2021 ———

opened ChimeraX session  
Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 297 of 594364
triangles, 40 atoms, 43 bonds  

> show sel cartoons

> hide sel atoms

> show sel atoms

Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 6084 of 594364
triangles, 26 atoms, 1 residues, 28 bonds  

> hide #1.5 models

> hide #1.4 models

> hide #!1 models

> show #!1 models

> hide #1.2 models

> show #1.2 models

> hide #1.1 models

> hide #1.3 models

> show #1.3 models

> show #1.4 models

> show #1.5 models

> select /H:1

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /H:1-2

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /H:358

44 atoms, 47 bonds, 1 residue, 1 model selected  

> select /H:358-359

49 atoms, 52 bonds, 2 residues, 1 model selected  

> select /H:360

44 atoms, 47 bonds, 1 residue, 1 model selected  

> select /H:360

44 atoms, 47 bonds, 1 residue, 1 model selected  
Drag select of 36 atoms, 39 bonds  

> select /H:358-359

49 atoms, 52 bonds, 2 residues, 1 model selected  

> select /H:359-360

49 atoms, 52 bonds, 2 residues, 1 model selected  

> select
> /H:3-6,10-12,18-20,22-25,34-39,46-52,56-59,67-72,77-82,88-94,107-111,120-124,138-145,153-157,171-174,188-193,207-212,217-222,252-256,272-277,287-292,299-301,305-307,321-325,338-343,351-355,368-372,385-395,401-408,419-421,435-444,454-459,468-472

1933 atoms, 1995 bonds, 179 residues, 1 model selected  

> select /H:360

44 atoms, 47 bonds, 1 residue, 1 model selected  

> select /H:360

44 atoms, 47 bonds, 1 residue, 1 model selected  

> select /H:118

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /H:117-118

48 atoms, 51 bonds, 2 residues, 1 model selected  

> select /H:82A

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

> select /H:82A

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

> select /H:57

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /H:57

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /H:12

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /H:12

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /H:477

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /H:477

4 atoms, 3 bonds, 1 residue, 1 model selected  

> hide #1.5 models

> hide #1.4 models

> hide #1.3 models

> select clear

> select /H:477

4 atoms, 3 bonds, 1 residue, 1 model selected  
Drag select of 33 atoms, 37 bonds  
Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 448 of 594364
triangles, 36 atoms, 40 bonds  

> select /H:477

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /H:476-477

11 atoms, 11 bonds, 2 residues, 1 model selected  

> select clear

> select /h kaf 478

Expected a keyword  

> select ::name="KAF"

3257 atoms, 3481 bonds, 74 residues, 1 model selected  

> select :h

Nothing selected  

> ui tool show Log

> select /H:477

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /H:477

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /H:474

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /H:474

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select/H:478

Unknown command: select/H:478  

> select/h:478

Unknown command: select/h:478  

> select/h:kaf478

Unknown command: select/h:kaf478  

> select/H: 478

Unknown command: select/H: 478  
Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 2598 of 594364
triangles, 35 atoms, 1 residues, 35 bonds  
Drag select of 30 atoms, 33 bonds  

> select clear

Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 3037 of 594364
triangles, 37 atoms, 1 residues, 36 bonds  

> select clear

> select h:478

Expected an objects specifier or a keyword  

> select/ h:478

Unknown command: select/ h:478  

> select/h:478

Unknown command: select/h:478  
Drag select of 25 atoms, 27 bonds  
Drag select of 30 atoms, 33 bonds  

> select clear

Drag select of 31 atoms, 33 bonds  

> hide sel atoms

> select /H:478@C8

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of 4 atoms, 4 bonds  

> hide sel atoms

> hide #1.2 models

Drag select of 4 atoms, 4 bonds  

> hide sel atoms

Drag select of 1 atoms  

> hide sel atoms

Drag select of 3 atoms, 4 bonds  

> hide sel atoms

Drag select of 1 atoms  

> hide sel atoms

Drag select of 1 atoms  

> hide sel atoms

> show #1.1 models

> show #1.2 models

> show #1.3 models

> show #1.4 models

> show #1.5 models

Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 339 of 594364
triangles  

> select clear

> ui mousemode right label

> ui mousemode right "move label"

> 2dlabels arrow #4.1 end 0.483,0.303

> 2dlabels arrow #4.1 start 0.483,0.118

> select clear

> 2dlabels arrow #4.2 end 0.278,0.264

> 2dlabels #3.5 xpos 0.071 ypos 0.701

> 2dlabels arrow #4.3 start 0.219,0.673

Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 371 of 594364
triangles  

> 2dlabels arrow #4.5 start 0.757,0.151

> 2dlabels arrow #4.5 end 0.700,0.282

> 2dlabels arrow #4.5 end 0.702,0.285

> 2dlabels arrow #4.5 start 0.760,0.142

> 2dlabels arrow #4.5 end 0.708,0.283

Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 1374 of 594364
triangles  

> 2dlabels arrow #4.5 end 0.710,0.279

Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 3502 of 594364
triangles, 1hzh_V1_AF488_PDB_20210423.pdb_K SES surface, 4723 of 581162
triangles, 1hzh_V1_AF488_PDB_20210423.pdb_L SES surface, 1018 of 261774
triangles, 1hzh_V1_AF488_PDB_20210423.pdb_M SES surface, 6460 of 256910
triangles, 50 atoms, 55 bonds  

> 2dlabels arrow #4.4 end 0.686,0.548

> select clear

> 2dlabels #3.4 xpos 0.715 ypos 0.709

> 2dlabels #3.4 xpos 0.712 ypos 0.704

> 2dlabels #3.4 xpos 0.711 ypos 0.704

Drag select of 1hzh_V1_AF488_PDB_20210423.pdb_H SES surface, 8143 of 594364
triangles, 1hzh_V1_AF488_PDB_20210423.pdb_K SES surface, 6869 of 581162
triangles, 31 atoms, 2 residues, 36 bonds  

> 2dlabels arrow #4.4 start 0.745,0.677

> select clear

> select ::name="FUC"

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

> select clear

> 2dlabels arrow #4.3 end 0.289,0.544

> 2dlabels arrow #4.3 start 0.230,0.675

> 2dlabels arrow #4.3 end 0.287,0.557

> 2dlabels #3.5 xpos 0.113 ypos 0.704

> 2dlabels #3.2 xpos 0.086 ypos 0.040

> 2dlabels #3.3 xpos 0.686 ypos 0.045

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Home\Desktop\movie2.mp4

Movie saved to \C:Users\\...\Desktop\movie2.mp4  
  

> hide #4.3 models

> hide #4.4 models

> hide #4.5 models

> hide #4.1 models

> hide #4.2 models

> show #4.1 models

> show #4.2 models

> show #4.3 models

> show #4.4 models

> show #4.5 models

> save C:/Users/Home/Desktop/HumanIgG1_1HZH_AF488_v1_labeled_arrows.cxs

——— End of log from Tue Jun 8 11:31:26 2021 ———

opened ChimeraX session  
Can't find font for arrow  
Can't find font for arrow  
Can't find font for arrow  
Can't find font for arrow  
Can't find font for arrow  

> select ::name="BMA"

22 atoms, 22 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select ::name="BMA"

22 atoms, 22 bonds, 2 residues, 1 model selected  

> select ::name="FUC"

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

> hide sel atoms

> select ::name="GAL"

33 atoms, 33 bonds, 3 residues, 1 model selected  

> hide sel atoms

> select ::name="MAN"

44 atoms, 44 bonds, 4 residues, 1 model selected  

> hide sel atoms

> select ::name="NAG"

112 atoms, 114 bonds, 8 residues, 1 model selected  

> hide sel atoms

> save C:/Users/Home/Desktop/HumanIgG1_1HZH_AF488_v1_labeled_arrows.cxs

——— End of log from Tue Jun 8 11:40:41 2021 ———

opened ChimeraX session  

> ui mousemode right "move label"

> 2dlabels #3.2 xpos 0.016 ypos 0.001

> 2dlabels arrow #4.2 start 0.125,0.075

> 2dlabels arrow #4.2 end 0.166,0.177

> 2dlabels arrow #4.2 start 0.104,0.078

> 2dlabels arrow #4.2 end 0.157,0.172

> close #4.2

> 2dlabels arrow color gold .5,.5; .5,.7; wait 25

Expected a keyword  

> 2dlabels arrow color gold .5,.5; .5,.7; wait 25

Expected a keyword  

> 2dlabels arrow start .5,.5 end .5,.7 color gold

> wait 25

> 2dlabels arrow #4.2 start 0.366,0.528

> 2dlabels arrow #4.2 end 0.420,0.621

> 2dlabels arrow #4.2 end 0.316,0.680

> close #4.2

> 2dlabels arrow start .5,.5 end .5,.7 color gold

> wait 20

> 2dlabels arrow #4.2 start 0.243,0.625

> 2dlabels arrow #4.2 end 0.341,0.452

> 2dlabels arrow #4.2 start 0.143,0.090

> 2dlabels arrow #4.2 end 0.189,0.138

> 2dlabels arrow #4.2 start 0.131,0.058

> 2dlabels arrow #4.2 end 0.187,0.136

> 2dlabels arrow #4.2 start 0.131,0.058

> 2dlabels arrow #4.2 end 0.187,0.156

> 2dlabels #3.2 xpos 0.010 ypos 0.001

> 2dlabels arrow #4.2 start 0.100,0.067

> 2dlabels arrow #4.2 end 0.163,0.192

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  

> 2dlabels arrow # start 0.096,0.073

Expected an arrow models specifier or a keyword  

> 2dlabels arrow #4.2 end 0.154,0.187

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\movelabel.py", line 62, in mouse_drag  
arrow(ses, [lbl], **{self._arr_part: (xpos, ypos)})  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 43, in arrow  
_update_arrow(session, a, **cmd_kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 119, in _update_arrow  
a.update_drawing()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\label\arrows.py", line 402, in update_drawing  
d.display = self.visibility  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\models.py", line 308, in _set_display  
Drawing.set_display(self, display)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 368, in set_display  
dp = self.display_positions  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 382, in get_display_positions  
dp = ones((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  

> 2dlabels arrow # start 0.089,0.075

Expected an arrow models specifier or a keyword  




OpenGL version: 3.3.0 - Build 26.20.100.8142
OpenGL renderer: Intel(R) HD Graphics 530
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude E5570
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 8,476,172,288
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6440HQ CPU @ 2.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
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    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
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    line-profiler: 2.1.2
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    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
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    Pillow: 7.2.0
    pip: 21.0.1
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    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
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