VR error on button press: NoneType' object has no attribute 'inverse'

[goddard@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.1.dev202006302005 (2020-06-30 20:05:09 UTC)
Description
Tried using VR mode "move picked models" moving two different structures at the same time each with one hand.

Log:
UCSF ChimeraX version: 1.1.dev202006302005 (2020-06-30)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\cygwin64\home\goddard\ucsf\presentations\remdesivir-ar-
> may2020\data\remdesivir6.cxs format session

Log from Tue Jun 30 11:14:43 2020UCSF ChimeraX version: 1.1.dev202006300344
(2020-06-30)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir5.cxs format session

Log from Mon Jun 29 17:54:58 2020UCSF ChimeraX version: 1.1.dev202006250254
(2020-06-25)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir4.cxs format session

Log from Mon Jun 29 17:08:38 2020UCSF ChimeraX version: 1.1.dev202006250254
(2020-06-25)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir3.cxs format session

Log from Mon Jun 29 15:43:02 2020UCSF ChimeraX version: 1.1.dev202006250254
(2020-06-25)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir2.cxs format session

Log from Mon Jun 29 14:05:28 2020UCSF ChimeraX version: 1.1.dev202006250254
(2020-06-25)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/cov2_rna_twist.cxs format session

Log from Sat Jun 6 17:27:41 2020UCSF ChimeraX version: 1.1.dev202006052335
(2020-06-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/goddard/Desktop/cov2_rna_twist.cxs format session

Log from Sat Jun 6 17:17:30 2020UCSF ChimeraX version: 1.1.dev202006052335
(2020-06-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> rna path ~/ucsf/presentations/sars-rna-may2020/stems pattern sphere length
> 500 randomLoopTwist 180

RNA sphere radius 47.8  

> rna model ~/ucsf/presentations/sars-rna-may2020/sequence.fasta #1

Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  

Chain information for RNA #2  
---  
Chain | Description  
I | No description available  
  

> style stick

Changed 11096 atom styles  

> hide #1 models

> close

> rna path ~/ucsf/presentations/sars-rna-may2020/stems pattern sphere
> randomLoopTwist 180

RNA sphere radius 340.4  

> rna model ~/ucsf/presentations/sars-rna-may2020/sequence.fasta #1

Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  

Chain information for RNA #2  
---  
Chain | Description  
I | No description available  
  

> hide #1 models

> lighting soft

> lighting simple

> lighting soft

> set bgColor white

> set bgColor black

> save /Users/goddard/Desktop/image1.png supersample 3

> save /Users/goddard/Desktop/cov2_rna_twist.cxs

opened ChimeraX session  

> shape sphere color black

> hide #2 models

> set bgColor white

> close #3

> show #2 models

> shape sphere color black radius 400

> close #3

> shape sphere color black radius 350

> close #3

> shape sphere color black radius 300

> close #3

> shape sphere color black radius 340

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting full

> lighting soft

> save /Users/goddard/Desktop/cov2_rna_twist.cxs

opened ChimeraX session  

> close #1

> rename #2 id #4

> rename #3 id #4.1

> open /Users/goddard/ucsf/presentations/remdesivir-ar-may2020/data/rdv.pdb

> hide #4 models

> rename #2 id #1

> set bgColor black

> show #4 models

> hide #4 models

> lighting simple

> show #4 models

> hide #4 models

> view

> open /Users/goddard/ucsf/presentations/remdesivir-ar-may2020/data/atp.pdb

> ui mousemode right "translate selected models"

> select #2:1@O6

1 atom, 1 model selected  

> select clear

> color #1 & C tan

> open /Users/goddard/ucsf/presentations/remdesivir-ar-may2020/data/rtp.pdb

> select #3:1@O12

1 atom, 1 model selected  

> select clear

> rename #1 Remdesivir

> rename #2 ATP

> rename #3 RTP

> rename #4 "SARS-CoV-2 RNA"

> rename #4.1 sphere

> show #4 models

> select #1-3

165 atoms, 172 bonds, 3 models selected  

> hide #4 models

> show #4 models

> select clear

> save data/remdesivir1.cxs

> select #1-3

165 atoms, 172 bonds, 3 models selected  

> select clear

> open 7bv2

7bv2 title:  
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate
form of Remdesivir(RTP) [more info...]  
  
Chain information for 7bv2 #5  
---  
Chain | Description  
A | SARS-CoV-2 Nsp12  
B | SARS-CoV-2 nsp8  
C | SARS-CoV-2 nsp7  
P | Primer  
T | Templete  
  
Non-standard residues in 7bv2 #5  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> hide #4 models

> select #5/A:133@ND1

1 atom, 1 model selected  

> show #4 models

> lighting simple

> set bgColor white

> select clear

> save /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir1.cxs

> hide #2 models

> hide #3 models

> set bgColor black

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/7bv2_particles.tif

Opened 7bv2_particles.tif, grid size 1600,1654,1, pixel 1, shown at step 1,
values uint8  

> hide #1 models

> hide #4 models

> hide #!5 models

> volume #6 level 105,0 level 223,0.8 level 255,1

> volume #6 level 105,0 level 179.6,0.9853 level 255,1

> volume #6 level 18.43,0.9853 level 179.6,0.9853 level 255,1

> volume #6 level 18.43,0.9853 level 179.6,0.9853 level 249.5,0

> volume #6 level 18.43,0.9853 level 144.7,0.4118 level 249.5,0

> volume #6 level 18.43,0.9853 level 144.7,0.4118 level 255,1

> volume #6 level 18,0.02941 level 144.7,0.4118 level 255,1

> volume #6 level 18,0.02941 level 255,1 color white color white

> volume #6 level 18,0 level 255,1

> show #!5 models

> ui mousemode right "tape measure"

> marker segment #7 position 1438,1513,0 toPosition 1560,1524,1.137e-13 color
> yellow radius 0.25 label 122.7 labelHeight 12.27 labelColor yellow

> marker delete #7

> marker segment #7 position 1434,1615,0 toPosition 1562,1612,-1.137e-13 color
> yellow radius 0.25 label 128.2 labelHeight 12.82 labelColor yellow

> volume #6 voxelSize 2.34

> select clear

> marker segment #7 position 3357,3776,0 toPosition 3654,3774,0 color yellow
> radius 0.585 label 296.7 labelHeight 29.67 labelColor yellow

> select clear

> marker delete #7

> ui mousemode right "translate selected models"

> save /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir1.cxs

> select #6

2 models selected  

> show #4 models

> hide #4 models

> set bgColor white

> set bgColor black

> volume #6 level 18,0 level 255,1 level 135.9,0.6471 color white color white
> color white

> volume #6 level 18,0 level 255,1 level 137.6,0.6912

> volume #6 level 101.8,0 level 255,1 level 137.6,0.6912

> volume #6 level 101.8,0 level 255,1 level 137.1,0.6324

> volume #6 level 19.28,0 level 255,1 level 137.1,0.6324

> volume #6 level 19.28,0 level 255,1 level 201,1

> volume #6 level 18,1 level 255,1 level 201,1

> volume #6 level 18,1 level 255,0 level 201,1

> volume #6 level 18,1 level 255,0 level 117.1,0.7059

> volume #6 level 18,0 level 255,0 level 117.1,0.7059

> volume #6 level 18,0 level 255,1 level 117.1,0.7059

> volume #6 level 18,0 level 255,1 level 183.9,0.6618

> volume #6 level 18,0 level 255,1 level 179.3,0.6912

> volume #6 level 18,0 level 255,1 color white color white

> set bgColor white

> volume #6 backingColor black

> ui tool show Shell

> save data/remdesivir2.cxs

opened ChimeraX session  

> show #!4 models

> show #4.1 models

> hide #!4 models

> hide #!5 models

> show #!5 models

> open 30210 fromDatabase emdb

Opened emd_30210.map, grid size 192,192,192, pixel 1.01, shown at level
0.0278, step 1, values float32  

> hide #!6 models

> usage view pos

view position models sameAsModels a models specifier  
— move models to have same scene position as another model  

> view position #7 sameAsModels #5

> hide #!5 models

> volume #7 level 0.07363

> lighting soft

> show #!5 models

> style #!5 ball

Changed 8555 atom styles  

> volume #7 level 0.05142

> hide #!7 models

> color #5/A gold

> show #!6 models

> color #5/A byelement

> color #5/A gold

> color #5/A byhetero

> hide #!6 models

> show #!7 models

> hide #!7 models

> lighting simple

> color #5/P orange

> rename #!5 Polymerase

> rename #!6 "EM micrograph"

> rename #!7 "EM map polymerase"

> show #!6 models

> hide #!6 models

> open 7bv2

7bv2 title:  
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate
form of Remdesivir(RTP) [more info...]  
  
Chain information for 7bv2 #8  
---  
Chain | Description  
A | SARS-CoV-2 Nsp12  
B | SARS-CoV-2 nsp8  
C | SARS-CoV-2 nsp7  
P | Primer  
T | Templete  
  
Non-standard residues in 7bv2 #8  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> hide #!5 models

> view position #8 sameAsModels #5

> surface #8/A-C

> hide #8/A-C

> style #8/P,T stick

Changed 548 atom styles  

> nucleotides #!8 tube/slab shape box

> color #8/P orange

> rename #!8 "Polymerase surfaces"

> save data/remdesivir3.cxs

[Errno 20] Not a directory: 'data'  

> save /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir3.cxs

> rename #!8 "Protein surfaces"

incomplete quoted text  

> rename #!5 "RNA polymerase"

> save /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir3.cxs

opened ChimeraX session  

> open /Users/goddard/ucsf/presentations/remdesivir-may2020/data/poly0.pdb
> /Users/goddard/ucsf/presentations/remdesivir-may2020/data/poly1.pdb
> /Users/goddard/ucsf/presentations/remdesivir-may2020/data/poly2.pdb
> /Users/goddard/ucsf/presentations/remdesivir-may2020/data/poly3.pdb
> /Users/goddard/ucsf/presentations/remdesivir-may2020/data/poly4.pdb
> /Users/goddard/ucsf/presentations/remdesivir-may2020/data/poly5.pdb
> /Users/goddard/ucsf/presentations/remdesivir-may2020/data/poly6.pdb

Chain information for poly0.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  
Chain information for poly1.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  
Chain information for poly2.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  
Chain information for poly3.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  
Chain information for poly4.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  
Chain information for poly5.pdb #14  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  
Chain information for poly6.pdb #15  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  

> morph #9-15 same true

Computed 121 frame morph #16  

> coordset #16 1,121

> view position #16 sameAsModels #8

> hide #!8 models

> close #9-15

> rename #!16 id #9

> rename #9 "RNA elongate"

> nucleotides #!9 slab

> style nucleic & #!9 stick

Changed 803 atom styles  

> hide #9/A-C

> show #!8 models

> hide #!8 models

> save /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir4.cxs

opened ChimeraX session  

> delete #9/A-C

> ui mousemode right "play coordinates"

> show #!8 models

> view

> hide #!9 models

> view

> hide #!8 models

> show #!8 models

> surface #8/A-C

> hide #8.4 models

> show #8.4 models

> hide #8.5 models

> show #8.5 models

> hide #8.6 models

> show #8.6 models

> close #8.4-6

> surface #8/A-C

> hide #8/P,T

> show #!9 models

> hide #!8 models

> select #9:RTP

Nothing selected  

> select #9:RDV

Nothing selected  

> select #9:F86

24 atoms, 26 bonds, 1 model selected  

> ~nucleotides #9:F86

> color #9:F86 majenta

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #9:F86 magenta

> color #9:F86 byhetero

> style #9:F86 ball

Changed 24 atom styles  

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/scripts/elongate.py

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 95, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 146, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 359, in collated_open  
return func(*func_args, **func_kw)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 48, in open  
return open_python_script(session, data, file_name)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 82, in open_python_script  
_exec_python(session, code, argv)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 59, in _exec_python  
exec(code, sandbox.__dict__)  
File "elongate.py", line 22, in <module>  
File "elongate.py", line 16, in added_residues  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "elongate.py", line 16, in added_residues  
  
See log for complete Python traceback.  
  

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/scripts/elongate.py

executed elongate.py  

> select clear

> cartoon #9

> save /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir5.cxs

opened ChimeraX session  

> delete #9:/A-C

Missing or invalid "atoms" argument: only initial part "#9" of atom specifier
valid  

> delete #9/A-C

> show #!8 models

> delete #8/P,T

> ui mousemode right "play coordinates"

> open /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/scripts/elongate.py format python

executed elongate.py  

> select #8/A:861@OG

1 atom, 1 model selected  

> select up

6 atoms, 5 bonds, 2 models selected  

> color sel orange

> select clear

> hide #!8 models

> show #!8 models

> save /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir6.cxs

> show #1 models

> hide #!9 models

> hide #!8 models

> show #2 models

> show #3 models

> hide #1 models

> show #1 models

> style #1-3 ball

Changed 165 atom styles  

> view

> cofr

Center of rotation: -1.8372 25.417 520.1 front center  

> hide #3 models

> hide #2 models

> set bgColor black

> save /Users/goddard/ucsf/presentations/remdesivir-ar-
> may2020/data/remdesivir6.cxs

opened ChimeraX session  

> vr true

started SteamVR rendering  

> vr button grip "move picked models"

> show #2 models

Traceback (most recent call last):  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\vive\vr.py", line 769, in next_frame  
self.process_controller_events()  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\vive\vr.py", line 798, in process_controller_events  
self.process_controller_motion()  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\vive\vr.py", line 842, in process_controller_motion  
hc.process_motion()  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\vive\vr.py", line 2725, in process_motion  
m.drag(HandMotionEvent(self, m._button_down, previous_pose, pose))  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\vive\vr.py", line 3488, in drag  
if m.vr_motion(e) != 'accumulate drag':  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 478, in vr_motion  
self.view.move(event.motion, self.models())  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\vive\vr.py", line 3120, in motion  
room_move = rp * ldp.inverse()  
AttributeError: 'NoneType' object has no attribute 'inverse'  
  
Error processing trigger "new frame":  
AttributeError: 'NoneType' object has no attribute 'inverse'  
  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\vive\vr.py", line 3120, in motion  
room_move = rp * ldp.inverse()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 442.19
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z270X-Gaming K7
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 17,129,693,184
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tom Goddard]

Fixed.

When a mouse mode gets a VR hand event and called event.motion before a preceeding hand position was recorded it caused this error. Put in code to report no motion in that case.