Front center of rotation problem with Acer 3D display

[goddard@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.11.dev202507172023 (2025-07-17 20:23:32 UTC)
Description
Front center center of rotation mode does not work as expected when Acer 3D display is being used with OpenXR.  It seems to work when zoomed in very close but when zoomed out so that about 1/4 of the scene is in view it switches to rotating about the center of the scene.  The transition point between center of scene and front center seems to be way off.

Log:
UCSF ChimeraX version: 1.11.dev202507172023 (2025-07-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\cygwin64\home\goddard\ucsf\presentations\paxlovid.cxs format session

Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.48, step 1, values float32  
Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.478, step 1, values float32  
Log from Tue Mar 11 13:22:41 2025UCSF ChimeraX version: 1.10.dev202502220014
(2025-02-22)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\cygwin64\home\goddard\ucsf\presentations\paxlovid-vr-
> mar2023\data\paxlovid.cxs format session

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.48, step 1, values float32  
Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.478, step 1, values float32  
Log from Mon Mar 20 10:30:55 2023UCSF ChimeraX version: 1.6.dev202302100235
(2023-02-10)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7tgr format mmcif fromDatabase pdb

7tgr title:  
Structure of SARS-CoV-2 main protease in complex with GC376 [more info...]  
  
Chain information for 7tgr #1  
---  
Chain | Description | UniProt  
A | 3C-like proteinase | R1AB_SARS2 1-304  
  
Non-standard residues in 7tgr #1  
---  
B1S —
(1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic
acid  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
K — potassium ion  
K36 —
(1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic
acid (GC376)  
NA — sodium ion  
  
7tgr mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> ui tool show "Send to Quest"

> graphics quality atomTriangles 100

> graphics quality bondTriangles 20

> graphics quality ribbonDivisions 10

> open 7tgr fromDatabase eds

Summary of feedback from opening 7tgr fetched from eds  
---  
note | Fetching map 7tgr from http://www.ebi.ac.uk/pdbe/coordinates/files/7tgr.ccp4  
  
Opened eds 7tgr as #2, grid size 204,96,80, pixel 0.562,0.551,0.574, shown at
level 0.818, step 1, values float32  

> volume #2 level 0.7671

> select :166

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

> select clear

> select ligand

62 atoms, 63 bonds, 3 residues, 1 model selected  

> select sel :< 5

263 atoms, 248 bonds, 39 residues, 1 model selected  

> usage volume cover

volume cover volumes [atomBox an atoms specifier] [pad a number] [box box
bounds] [x 2 floats] [y 2 floats] [z 2 floats] [fBox box bounds] [fx 2 floats]
[fy 2 floats] [fz 2 floats] [iBox box bounds] [ix 2 floats] [iy 2 floats] [iz
2 floats] [useSymmetry true or false] [cellSize cellSize] [step map step]
[modelId modelId]  
— Use symmetry to extend a map to cover a region  
cellSize: some integers  
modelId: a model id  

> volume cover #2 atomBox sel

Extended map eds 7tgr to box of size (60, 77, 95),  
cell size (204, 96, 80) grid points, 4 symmetry operations,  
0 points not covered by any symmetry,  
maximum value difference where symmetric map copies overlap = 1.308e-06  
  
Opened eds 7tgr extended as #3, grid size 60,77,95, pixel 0.562,0.551,0.574,
shown at step 1, values float32  

> close #3

Drag select of 14 atoms, 32 residues, 9 bonds  

> select clear

> select :B1S

29 atoms, 30 bonds, 1 residue, 1 model selected  

> select sel :< 4

182 atoms, 179 bonds, 20 residues, 1 model selected  

> select :B1S :< 3

97 atoms, 98 bonds, 9 residues, 1 model selected  

> select :B1S :< 5

229 atoms, 223 bonds, 29 residues, 1 model selected  

> volume cover #2 atomBox sel

Extended map eds 7tgr to box of size (58, 50, 47),  
cell size (204, 96, 80) grid points, 4 symmetry operations,  
0 points not covered by any symmetry,  
maximum value difference where symmetric map copies overlap = 1.308e-06  
  
Opened eds 7tgr extended as #3, grid size 58,50,47, pixel 0.562,0.551,0.574,
shown at step 1, values float32  

> volume #3 level 0.6057

> volume #3 level 0.4812

> volume zone #3 nearAtoms sel & #1 range 3.44

> volume #3 level 0.3982

> volume #3 level 0.472

> select :166

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

> color :166 magenta

> color :166 orange

> color :166 byhetero

> color :B1S pink

> graphics quality bondTriangles 20

[Repeated 2 time(s)]

> save 7tgr.cxs

> close

> open 7rfw

7rfw title:  
Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor
[more info...]  
  
Chain information for 7rfw #1  
---  
Chain | Description | UniProt  
A | 3C-like proteinase | R1AB_SARS2 1-306  
  
Non-standard residues in 7rfw #1  
---  
4WI —
(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
(PF-07321332, bound form; nirmatrelvir, bound form; Paxlovid, bound form)  
  
7rfw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> graphics quality bondTriangles 20

> graphics quality

Quality 1, atom triangles 100, bond triangles 20, ribbon divisions 10  

> color :4WI pink

> color :4WI byhetero

> select ligand

68 atoms, 70 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

7 hydrogen bonds found  

> color :166 orange

> color :166 byhetero

> select :21,50

15 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel

> color sel cyan

> color sel byhetero

> select clear

> open 7rfw fromDatabase eds

Summary of feedback from opening 7rfw fetched from eds  
---  
note | Fetching map 7rfw from http://www.ebi.ac.uk/pdbe/coordinates/files/7rfw.ccp4  
  
Opened eds 7rfw as #2, grid size 200,96,80, pixel 0.573,0.553,0.568, shown at
level 0.885, step 1, values float32  

> select :4WI :<5

276 atoms, 276 bonds, 7 pseudobonds, 28 residues, 2 models selected  

> volume cover #2 near sel

Expected a keyword  

> volume cover #2 atomBox sel

Extended map eds 7rfw to box of size (58, 57, 47),  
cell size (200, 96, 80) grid points, 4 symmetry operations,  
0 points not covered by any symmetry,  
maximum value difference where symmetric map copies overlap = 1.4156e-06  
  
Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at step 1, values float32  

> volume #3 level 0.6537

> volume #3 level 0.5574

> volume zone #3 nearAtoms sel & #1 range 3.44

> volume #3 level 0.4804

> select clear

> volume #3 color #ffffb24e

> volume #3 color #ffffb27f

> save paxlovid.cxs

> sym #1 assembly 1

Made 2 copies for 7rfw assembly 1  

> view

> hide #!4.2 models

> show #!4.2 models

> color #4.2 cornflowerblue ribbons

> color #4.2 cornflowerblue

> color #4.2:4WI pink

> color #4.2:21,50 lime

> color #4.2:166 orange lime

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #4.2:166 orange

> color #4.1:21,50 lime

> color #4 byhetero

> save paxlovid.cxs

> volume #3 color #ffffff7f

> volume #3 color #ffffff80

[Repeated 1 time(s)]

> save paxlovid.cxs

> save paxlovid.glb

> ui tool show "Send to Quest"

> save /Users/goddard/Desktop/paxlovid.glb

Running command: "/opt/homebrew/bin/adb" push
/Users/goddard/Desktop/paxlovid.glb /sdcard/Android/data/com.UCSF.Lookie/files  
stdout:  
adb: error: failed to get feature set: no devices/emulators found  
  
stderr:  
  

> save /Users/goddard/Desktop/paxlovid.glb

Running command: "/opt/homebrew/bin/adb" push
/Users/goddard/Desktop/paxlovid.glb
/sdcard/Android/data/com.UCSF.LookieAR/files  
stdout:  
adb: error: failed to get feature set: no devices/emulators found  
  
stderr:  
  

> save /Users/goddard/Desktop/paxlovid.glb

Running command: "/opt/homebrew/bin/adb" push
/Users/goddard/Desktop/paxlovid.glb
/sdcard/Android/data/com.UCSF.LookieAR/files  

> volume cover #2 atomBox #4.2:4WI :< 5

Extended map eds 7rfw to box of size (58, 57, 47),  
cell size (200, 96, 80) grid points, 4 symmetry operations,  
0 points not covered by any symmetry,  
maximum value difference where symmetric map copies overlap = 1.4156e-06  
  
Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at step 1, values float32  

> select #4.2:4WI :< 5

288 atoms, 286 bonds, 7 pseudobonds, 30 residues, 4 models selected  

> volume #5 color #feffff

> volume #5 color #feffff7c

> volume #5 color #feffff7d

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

> hide #!4.1 models

> volume zone #5 nearAtoms sel & #4.2 range 3.44

> volume #2 level 0.4977

> volume #5 level 0.4783

> show #!4.1 models

> select clear

> save paxlovid.cxs

[Repeated 1 time(s)]

> save /Users/goddard/Desktop/paxlovid.glb

Running command: "/opt/homebrew/bin/adb" push
/Users/goddard/Desktop/paxlovid.glb
/sdcard/Android/data/com.UCSF.LookieAR/files  

> save paxlovid.cxs

——— End of log from Mon Mar 20 10:30:55 2023 ———

> view name session-start

opened ChimeraX session  

> save paxlovid.cxs

——— End of log from Tue Mar 11 13:22:41 2025 ———

> view name session-start

opened ChimeraX session  

> xr true

> mousemode setting zoom speed 0.2

started OpenXR rendering SpatialLabs Display Driver, render size 1920 by 1080  




OpenGL version: 3.3.0 NVIDIA 576.57
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7000
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 68,393,086,976
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700K
OSLanguage: en-US

Installed Packages:
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    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
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    ChimeraX-Struts: 1.0.1
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    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.5.1
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.14.1
    typing_extensions: 4.12.2
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1
    zipp: 3.19.2

[Tom Goddard]

The front center mode uses the center of the scene bounding box if the camera.view_width(at center of scene) >= (scene width). So my guess is that the camera.view_width() is giving an incorrect large value.

[Tom Goddard]

The ChimeraX OpenXR camera computes view_width() assuming a field of view
of 100 degrees that is hard-coded. The camera has an actual field of view
from the last rendering and should use that instead.

[Tom Goddard]

Fixed.

Used the actual openxr reported field of view which was 45 degrees for the Acer 3D display.