Opened 5 months ago

Closed 5 months ago

#17885 closed defect (fixed)

Meeting: can not serialize 'numpy.uint8' object

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: VR Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Error processing trigger "vr update":
TypeError: can not serialize 'numpy.uint8' object

File "msgpack\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack

See log for complete Python traceback.


Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Meeting

> meeting join sars

Joining meeting"sars" at chimeraxmeeting.net port 52195  
Log from Tue Jun 3 14:08:51 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "Z:\ChimeraX Content\ChimeraX VR
> sessions\SARS_CoV2_spike\6vxx_6vsb_down_up.cxs" format session

Log from Thu May 8 13:49:54 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "Z:/ChimeraX Content/ChimeraX VR
> sessions/SARS_CoV2_spike/6vxx_6vsb_down_up.cxs"

Log from Wed May 7 17:39:33 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6vxx fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6vxx fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 6vxx bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6vxx-assembly-1.cif.gz  
  
6vxx bioassembly 1 title:  
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]  
  
Chain information for 6vxx bioassembly 1 #1  
---  
Chain | Description  
A B C | Spike glycoprotein  
  
Non-standard residues in 6vxx bioassembly 1 #1  
---  
NAG — (NAG)  
  
Computing secondary structure  
Opened 1 biological assemblies for 6vxx  

> open 6vsb fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6vsb fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 6vsb bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6vsb-assembly-1.cif.gz  
  
6vsb bioassembly 1 title:  
Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain
up [more info...]  
  
Chain information for 6vsb bioassembly 1 #2  
---  
Chain | Description  
A | Spike glycoprotein  
B | Spike glycoprotein  
C | Spike glycoprotein  
  
Non-standard residues in 6vsb bioassembly 1 #2  
---  
NAG — (NAG)  
  
Opened 1 biological assemblies for 6vsb  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain A (#1) with 6vsb bioassembly 1, chain C
(#2), sequence alignment score = 4499.5  
RMSD between 878 pruned atom pairs is 0.752 angstroms; (across all 954 pairs:
1.451)  
  

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain A (#1) with 6vsb bioassembly 1, chain A
(#2), sequence alignment score = 4269.7  
RMSD between 697 pruned atom pairs is 0.850 angstroms; (across all 942 pairs:
9.211)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> hide #!1 models

> select #2/A:27

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

> select #2/A:27-300

1715 atoms, 1759 bonds, 5 pseudobonds, 222 residues, 2 models selected  

> select sequence sdldr

Nothing selected  

> select sequence gnpvi

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select sequence aytns

228 atoms, 228 bonds, 30 residues, 2 models selected  

> select
> #1/A:28-30,47-55,61-65,83-85,90-96,101-107,117-122,125-129,169-171,188-197,200-209,224-230,237-242,265-269,271-279,285-290,311-319,325-328,354-358,376-379,394-403,431-437,451-453,493-495,507-516,538-543,546-554,565-567,573-577,584-588,592-599,609-613,642-645,648-651,664-667,670-675,691-696,711-728,733-736,858-861,1047-1056,1059-1069,1071-1078,1088-1090,1094-1097,1102-1105,1120-1122

2368 atoms, 2392 bonds, 290 residues, 1 model selected  

> select #1/A:295

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

> select #1/A:295-302

59 atoms, 59 bonds, 8 residues, 1 model selected  

> show #!1 models

> hide #!2 models

> select sequence csvk

Nothing selected  

> select #2/A:27

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

> select #2/A:27

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

> select
> #2/A:28-31,48-51,60-65,90-94,101-107,116-120,126-129,169-172,188-197,200-209,238-242,265-269,275-279,285-290,311-319,354-358,376-379,394-402,432-437,508-516,538-540,549-554,575-577,584-588,592-599,609-612,711-715,717-728,733-736,788-790,858-861,1047-1054,1059-1070,1072-1078,1081-1083,1086-1090,1094-1098,1101-1105,1120-1122

1843 atoms, 1862 bonds, 227 residues, 1 model selected  

> select #2/A:27

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

> select #2/A:27-28

17 atoms, 17 bonds, 2 residues, 1 model selected  

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> color (#!1 & sel) blue

> ui tool show "Color Actions"

> color sel dodger blue

> color sel cornflower blue

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel forest green

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> ui tool show Matchmaker

> matchmaker #2/B to #1/B pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain B (#1) with 6vsb bioassembly 1, chain B
(#2), sequence alignment score = 4427.3  
RMSD between 818 pruned atom pairs is 0.898 angstroms; (across all 948 pairs:
1.719)  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> select clear

> show #!2 models

> hide #!1 models

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> show sel & #!2 surfaces

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> ui tool show "Color Actions"

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> show #!1 models

> hide #!2 models

> hide #2.2 models

> show #2.2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!2 models

> select clear

> hide #!1 models

> show #!1 models

> hide #!2 models

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> show sel & #!1 surfaces

> show #!2 models

> hide #!2 models

> select clear

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> select clear

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Desktop/6vxx_6vsb_down_up.cxs

——— End of log from Wed May 7 17:39:33 2025 ———

opened ChimeraX session  

> vr true

started SteamVR rendering  

> vr false

> select #1/335-521

Nothing selected  

> select #1:335-521

3819 atoms, 3924 bonds, 12 pseudobonds, 471 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel lime green

[Repeated 1 time(s)]

> color sel spring green

> color sel pale green

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> save "Z:/ChimeraX Content/ChimeraX VR
> sessions/SARS_CoV2_spike/6vxx_6vsb_down_up.cxs"

——— End of log from Thu May 8 13:49:54 2025 ———

opened ChimeraX session  

> xr true

started OpenXR rendering SteamVR/OpenXR : oculus  

> hide #!1 models

> ui tool show meeting

> meeting start sars

Meeting "sars" started at chimeraxmeeting.net port 52195  
Participants can join with command "meeting sars"  
Connection from ::ffff:127.0.0.1 port 63608 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 63608  
Connection from ::ffff:127.0.0.1 port 63624 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 63624  

——— End of log from Tue Jun 3 14:08:51 2025 ———

> vr true

Failed to initialize OpenVR.  
Possibly SteamVR is not installed or it failed to start.  
  

> vr true

started SteamVR rendering  
Disconnected from 18.144.20.53 port 52195  

> meeting close

> meeting join sars

Joining meeting"sars" at chimeraxmeeting.net port 52195  
Disconnected from 18.144.20.53 port 52195  

> meeting join sars2

Joining meeting"sars2" at chimeraxmeeting.net port 52196  
Log from Tue Jun 3 14:33:37 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "Z:/ChimeraX Content/ChimeraX VR
> sessions/SARS_CoV2_spike/6vxx_6vsb_down_up.cxs"

Log from Thu May 8 13:49:54 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "Z:/ChimeraX Content/ChimeraX VR
> sessions/SARS_CoV2_spike/6vxx_6vsb_down_up.cxs"

Log from Wed May 7 17:39:33 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6vxx fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6vxx fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 6vxx bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6vxx-assembly-1.cif.gz  
  
6vxx bioassembly 1 title:  
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]  
  
Chain information for 6vxx bioassembly 1 #1  
---  
Chain | Description  
A B C | Spike glycoprotein  
  
Non-standard residues in 6vxx bioassembly 1 #1  
---  
NAG — (NAG)  
  
Computing secondary structure  
Opened 1 biological assemblies for 6vxx  

> open 6vsb fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6vsb fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 6vsb bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6vsb-assembly-1.cif.gz  
  
6vsb bioassembly 1 title:  
Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain
up [more info...]  
  
Chain information for 6vsb bioassembly 1 #2  
---  
Chain | Description  
A | Spike glycoprotein  
B | Spike glycoprotein  
C | Spike glycoprotein  
  
Non-standard residues in 6vsb bioassembly 1 #2  
---  
NAG — (NAG)  
  
Opened 1 biological assemblies for 6vsb  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain A (#1) with 6vsb bioassembly 1, chain C
(#2), sequence alignment score = 4499.5  
RMSD between 878 pruned atom pairs is 0.752 angstroms; (across all 954 pairs:
1.451)  
  

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain A (#1) with 6vsb bioassembly 1, chain A
(#2), sequence alignment score = 4269.7  
RMSD between 697 pruned atom pairs is 0.850 angstroms; (across all 942 pairs:
9.211)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> hide #!1 models

> select #2/A:27

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

> select #2/A:27-300

1715 atoms, 1759 bonds, 5 pseudobonds, 222 residues, 2 models selected  

> select sequence sdldr

Nothing selected  

> select sequence gnpvi

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select sequence aytns

228 atoms, 228 bonds, 30 residues, 2 models selected  

> select
> #1/A:28-30,47-55,61-65,83-85,90-96,101-107,117-122,125-129,169-171,188-197,200-209,224-230,237-242,265-269,271-279,285-290,311-319,325-328,354-358,376-379,394-403,431-437,451-453,493-495,507-516,538-543,546-554,565-567,573-577,584-588,592-599,609-613,642-645,648-651,664-667,670-675,691-696,711-728,733-736,858-861,1047-1056,1059-1069,1071-1078,1088-1090,1094-1097,1102-1105,1120-1122

2368 atoms, 2392 bonds, 290 residues, 1 model selected  

> select #1/A:295

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

> select #1/A:295-302

59 atoms, 59 bonds, 8 residues, 1 model selected  

> show #!1 models

> hide #!2 models

> select sequence csvk

Nothing selected  

> select #2/A:27

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

> select #2/A:27

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

> select
> #2/A:28-31,48-51,60-65,90-94,101-107,116-120,126-129,169-172,188-197,200-209,238-242,265-269,275-279,285-290,311-319,354-358,376-379,394-402,432-437,508-516,538-540,549-554,575-577,584-588,592-599,609-612,711-715,717-728,733-736,788-790,858-861,1047-1054,1059-1070,1072-1078,1081-1083,1086-1090,1094-1098,1101-1105,1120-1122

1843 atoms, 1862 bonds, 227 residues, 1 model selected  

> select #2/A:27

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

> select #2/A:27-28

17 atoms, 17 bonds, 2 residues, 1 model selected  

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> color (#!1 & sel) blue

> ui tool show "Color Actions"

> color sel dodger blue

> color sel cornflower blue

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel forest green

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> ui tool show Matchmaker

> matchmaker #2/B to #1/B pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain B (#1) with 6vsb bioassembly 1, chain B
(#2), sequence alignment score = 4427.3  
RMSD between 818 pruned atom pairs is 0.898 angstroms; (across all 948 pairs:
1.719)  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> select clear

> show #!2 models

> hide #!1 models

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> show sel & #!2 surfaces

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> ui tool show "Color Actions"

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> show #!1 models

> hide #!2 models

> hide #2.2 models

> show #2.2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!2 models

> select clear

> hide #!1 models

> show #!1 models

> hide #!2 models

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> show sel & #!1 surfaces

> show #!2 models

> hide #!2 models

> select clear

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> select clear

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Desktop/6vxx_6vsb_down_up.cxs

——— End of log from Wed May 7 17:39:33 2025 ———

opened ChimeraX session  

> vr true

started SteamVR rendering  

> vr false

> select #1/335-521

Nothing selected  

> select #1:335-521

3819 atoms, 3924 bonds, 12 pseudobonds, 471 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel lime green

[Repeated 1 time(s)]

> color sel spring green

> color sel pale green

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> save "Z:/ChimeraX Content/ChimeraX VR
> sessions/SARS_CoV2_spike/6vxx_6vsb_down_up.cxs"

——— End of log from Thu May 8 13:49:54 2025 ———

opened ChimeraX session  

> ui tool show meeting

> meeting start sars

meeting: Meeting name "sars" already in use  

> meeting start sars

meeting: Meeting name "sars" already in use  

> meeting start sars2

Meeting "sars2" started at chimeraxmeeting.net port 52196  
Participants can join with command "meeting sars2"  
Connection from ::ffff:127.0.0.1 port 64449 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64449  
Connection from ::ffff:127.0.0.1 port 64472 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64472  
Disconnected from ::ffff:127.0.0.1 port 64449  
Connection from ::ffff:127.0.0.1 port 64490 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64490  
Disconnected from ::ffff:127.0.0.1 port 64472  
Connection from ::ffff:127.0.0.1 port 64517 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64517  
Disconnected from ::ffff:127.0.0.1 port 64490  
Connection from ::ffff:127.0.0.1 port 64556 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64556  
Connection from ::ffff:127.0.0.1 port 64621 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64621  

——— End of log from Tue Jun 3 14:33:37 2025 ———

> vr true

[Repeated 2 time(s)]

> xr true

Failed to initialize OpenXR.  
  
The call was made without having made a previously required call.  

> xr true

Failed to initialize OpenXR.  
  
The call was made without having made a previously required call.  

> vr false

> xr true

started OpenXR rendering SteamVR/OpenXR : oculus  
Socket error for message stream to 18.144.20.53 port 52196: Unable to write  
Disconnected from 18.144.20.53 port 52196  

> meeting close

> meeting join sars2 color #1034ff

Joining meeting"sars2" at chimeraxmeeting.net port 52200  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 1747, in _vr_tracking_cb  
self._participant._send_message(msg)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 976, in _send_message  
msg_bytes = MessageStream.message_as_bytes(msg)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 1310, in message_as_bytes  
bytes = packb(message)  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\msgpack\\__init__.py", line 36, in packb  
return Packer(**kwargs).pack(o)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\\\_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack  
TypeError: can not serialize 'numpy.uint8' object  
  
Error processing trigger "vr update":  
TypeError: can not serialize 'numpy.uint8' object  
  
File "msgpack\\\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Log from Tue Jun 3 14:43:00 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "Z:\ChimeraX Content\ChimeraX VR
> sessions\SARS_CoV2_spike\6vxx_6vsb_down_up.cxs" format session

Log from Thu May 8 13:49:54 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "Z:/ChimeraX Content/ChimeraX VR
> sessions/SARS_CoV2_spike/6vxx_6vsb_down_up.cxs"

Log from Wed May 7 17:39:33 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6vxx fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6vxx fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 6vxx bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6vxx-assembly-1.cif.gz  
  
6vxx bioassembly 1 title:  
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]  
  
Chain information for 6vxx bioassembly 1 #1  
---  
Chain | Description  
A B C | Spike glycoprotein  
  
Non-standard residues in 6vxx bioassembly 1 #1  
---  
NAG — (NAG)  
  
Computing secondary structure  
Opened 1 biological assemblies for 6vxx  

> open 6vsb fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6vsb fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 6vsb bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6vsb-assembly-1.cif.gz  
  
6vsb bioassembly 1 title:  
Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain
up [more info...]  
  
Chain information for 6vsb bioassembly 1 #2  
---  
Chain | Description  
A | Spike glycoprotein  
B | Spike glycoprotein  
C | Spike glycoprotein  
  
Non-standard residues in 6vsb bioassembly 1 #2  
---  
NAG — (NAG)  
  
Opened 1 biological assemblies for 6vsb  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain A (#1) with 6vsb bioassembly 1, chain C
(#2), sequence alignment score = 4499.5  
RMSD between 878 pruned atom pairs is 0.752 angstroms; (across all 954 pairs:
1.451)  
  

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain A (#1) with 6vsb bioassembly 1, chain A
(#2), sequence alignment score = 4269.7  
RMSD between 697 pruned atom pairs is 0.850 angstroms; (across all 942 pairs:
9.211)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> hide #!1 models

> select #2/A:27

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

> select #2/A:27-300

1715 atoms, 1759 bonds, 5 pseudobonds, 222 residues, 2 models selected  

> select sequence sdldr

Nothing selected  

> select sequence gnpvi

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select sequence aytns

228 atoms, 228 bonds, 30 residues, 2 models selected  

> select
> #1/A:28-30,47-55,61-65,83-85,90-96,101-107,117-122,125-129,169-171,188-197,200-209,224-230,237-242,265-269,271-279,285-290,311-319,325-328,354-358,376-379,394-403,431-437,451-453,493-495,507-516,538-543,546-554,565-567,573-577,584-588,592-599,609-613,642-645,648-651,664-667,670-675,691-696,711-728,733-736,858-861,1047-1056,1059-1069,1071-1078,1088-1090,1094-1097,1102-1105,1120-1122

2368 atoms, 2392 bonds, 290 residues, 1 model selected  

> select #1/A:295

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

> select #1/A:295-302

59 atoms, 59 bonds, 8 residues, 1 model selected  

> show #!1 models

> hide #!2 models

> select sequence csvk

Nothing selected  

> select #2/A:27

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

> select #2/A:27

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

> select
> #2/A:28-31,48-51,60-65,90-94,101-107,116-120,126-129,169-172,188-197,200-209,238-242,265-269,275-279,285-290,311-319,354-358,376-379,394-402,432-437,508-516,538-540,549-554,575-577,584-588,592-599,609-612,711-715,717-728,733-736,788-790,858-861,1047-1054,1059-1070,1072-1078,1081-1083,1086-1090,1094-1098,1101-1105,1120-1122

1843 atoms, 1862 bonds, 227 residues, 1 model selected  

> select #2/A:27

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

> select #2/A:27-28

17 atoms, 17 bonds, 2 residues, 1 model selected  

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> color (#!1 & sel) blue

> ui tool show "Color Actions"

> color sel dodger blue

> color sel cornflower blue

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel forest green

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> ui tool show Matchmaker

> matchmaker #2/B to #1/B pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain B (#1) with 6vsb bioassembly 1, chain B
(#2), sequence alignment score = 4427.3  
RMSD between 818 pruned atom pairs is 0.898 angstroms; (across all 948 pairs:
1.719)  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> select clear

> show #!2 models

> hide #!1 models

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> show sel & #!2 surfaces

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> ui tool show "Color Actions"

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> show #!1 models

> hide #!2 models

> hide #2.2 models

> show #2.2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!2 models

> select clear

> hide #!1 models

> show #!1 models

> hide #!2 models

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> show sel & #!1 surfaces

> show #!2 models

> hide #!2 models

> select clear

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> select clear

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Desktop/6vxx_6vsb_down_up.cxs

——— End of log from Wed May 7 17:39:33 2025 ———

opened ChimeraX session  

> vr true

started SteamVR rendering  

> vr false

> select #1/335-521

Nothing selected  

> select #1:335-521

3819 atoms, 3924 bonds, 12 pseudobonds, 471 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel lime green

[Repeated 1 time(s)]

> color sel spring green

> color sel pale green

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> save "Z:/ChimeraX Content/ChimeraX VR
> sessions/SARS_CoV2_spike/6vxx_6vsb_down_up.cxs"

——— End of log from Thu May 8 13:49:54 2025 ———

opened ChimeraX session  

> ui tool show meeting

> meeting start sars2

Meeting "sars2" started at chimeraxmeeting.net port 52200  
Participants can join with command "meeting sars2"  
Connection from ::ffff:127.0.0.1 port 64814 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64814  

——— End of log from Tue Jun 3 14:43:00 2025 ———

> vr false

[Repeated 1 time(s)]

> xr true

started OpenXR rendering SteamVR/OpenXR : oculus  

> ui tool show meeting

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 1747, in _vr_tracking_cb  
self._participant._send_message(msg)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 976, in _send_message  
msg_bytes = MessageStream.message_as_bytes(msg)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 1310, in message_as_bytes  
bytes = packb(message)  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\msgpack\\__init__.py", line 36, in packb  
return Packer(**kwargs).pack(o)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\\\_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack  
TypeError: can not serialize 'numpy.uint8' object  
  
Error processing trigger "vr update":  
TypeError: can not serialize 'numpy.uint8' object  
  
File "msgpack\\\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> xr false

> meeting join sars2

To join another meeting you must exit the meeting you are currently in using
command "meeting close"  

> meeting close

> meeting join sars2

Joining meeting"sars2" at chimeraxmeeting.net port 52200  

> vr true

started SteamVR rendering  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 1747, in _vr_tracking_cb  
self._participant._send_message(msg)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 976, in _send_message  
msg_bytes = MessageStream.message_as_bytes(msg)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 1310, in message_as_bytes  
bytes = packb(message)  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\msgpack\\__init__.py", line 36, in packb  
return Packer(**kwargs).pack(o)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\\\_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack  
TypeError: can not serialize 'numpy.uint8' object  
  
Error processing trigger "vr update":  
TypeError: can not serialize 'numpy.uint8' object  
  
File "msgpack\\\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Log from Tue Jun 3 14:45:04 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "Z:\ChimeraX Content\ChimeraX VR
> sessions\SARS_CoV2_spike\6vxx_6vsb_down_up.cxs" format session

Log from Thu May 8 13:49:54 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "Z:/ChimeraX Content/ChimeraX VR
> sessions/SARS_CoV2_spike/6vxx_6vsb_down_up.cxs"

Log from Wed May 7 17:39:33 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6vxx fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6vxx fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 6vxx bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6vxx-assembly-1.cif.gz  
  
6vxx bioassembly 1 title:  
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]  
  
Chain information for 6vxx bioassembly 1 #1  
---  
Chain | Description  
A B C | Spike glycoprotein  
  
Non-standard residues in 6vxx bioassembly 1 #1  
---  
NAG — (NAG)  
  
Computing secondary structure  
Opened 1 biological assemblies for 6vxx  

> open 6vsb fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6vsb fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Fetching compressed 6vsb bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6vsb-assembly-1.cif.gz  
  
6vsb bioassembly 1 title:  
Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain
up [more info...]  
  
Chain information for 6vsb bioassembly 1 #2  
---  
Chain | Description  
A | Spike glycoprotein  
B | Spike glycoprotein  
C | Spike glycoprotein  
  
Non-standard residues in 6vsb bioassembly 1 #2  
---  
NAG — (NAG)  
  
Opened 1 biological assemblies for 6vsb  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain A (#1) with 6vsb bioassembly 1, chain C
(#2), sequence alignment score = 4499.5  
RMSD between 878 pruned atom pairs is 0.752 angstroms; (across all 954 pairs:
1.451)  
  

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain A (#1) with 6vsb bioassembly 1, chain A
(#2), sequence alignment score = 4269.7  
RMSD between 697 pruned atom pairs is 0.850 angstroms; (across all 942 pairs:
9.211)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> hide #!1 models

> select #2/A:27

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

> select #2/A:27-300

1715 atoms, 1759 bonds, 5 pseudobonds, 222 residues, 2 models selected  

> select sequence sdldr

Nothing selected  

> select sequence gnpvi

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select sequence aytns

228 atoms, 228 bonds, 30 residues, 2 models selected  

> select
> #1/A:28-30,47-55,61-65,83-85,90-96,101-107,117-122,125-129,169-171,188-197,200-209,224-230,237-242,265-269,271-279,285-290,311-319,325-328,354-358,376-379,394-403,431-437,451-453,493-495,507-516,538-543,546-554,565-567,573-577,584-588,592-599,609-613,642-645,648-651,664-667,670-675,691-696,711-728,733-736,858-861,1047-1056,1059-1069,1071-1078,1088-1090,1094-1097,1102-1105,1120-1122

2368 atoms, 2392 bonds, 290 residues, 1 model selected  

> select #1/A:295

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

> select #1/A:295-302

59 atoms, 59 bonds, 8 residues, 1 model selected  

> show #!1 models

> hide #!2 models

> select sequence csvk

Nothing selected  

> select #2/A:27

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

> select #2/A:27

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

> select
> #2/A:28-31,48-51,60-65,90-94,101-107,116-120,126-129,169-172,188-197,200-209,238-242,265-269,275-279,285-290,311-319,354-358,376-379,394-402,432-437,508-516,538-540,549-554,575-577,584-588,592-599,609-612,711-715,717-728,733-736,788-790,858-861,1047-1054,1059-1070,1072-1078,1081-1083,1086-1090,1094-1098,1101-1105,1120-1122

1843 atoms, 1862 bonds, 227 residues, 1 model selected  

> select #2/A:27

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

> select #2/A:27-28

17 atoms, 17 bonds, 2 residues, 1 model selected  

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> color (#!1 & sel) blue

> ui tool show "Color Actions"

> color sel dodger blue

> color sel cornflower blue

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel forest green

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> ui tool show Matchmaker

> matchmaker #2/B to #1/B pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vxx bioassembly 1, chain B (#1) with 6vsb bioassembly 1, chain B
(#2), sequence alignment score = 4427.3  
RMSD between 818 pruned atom pairs is 0.898 angstroms; (across all 948 pairs:
1.719)  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> select clear

> show #!2 models

> hide #!1 models

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> show sel & #!2 surfaces

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> ui tool show "Color Actions"

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> show #!1 models

> hide #!2 models

> hide #2.2 models

> show #2.2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!2 models

> select clear

> hide #!1 models

> show #!1 models

> hide #!2 models

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> show sel & #!1 surfaces

> show #!2 models

> hide #!2 models

> select clear

> select /B,C

29897 atoms, 30545 bonds, 48 pseudobonds, 3890 residues, 4 models selected  

> select :27-305

10353 atoms, 10620 bonds, 27 pseudobonds, 1318 residues, 4 models selected  

> color sel dodger blue

> select :853-907

2475 atoms, 2535 bonds, 327 residues, 2 models selected  

> color sel red

> select :687-815

5790 atoms, 5886 bonds, 3 pseudobonds, 759 residues, 3 models selected  

> color sel red

> select :1076-1141

3102 atoms, 3192 bonds, 396 residues, 2 models selected  

> color sel purple

> select :908-985

3480 atoms, 3492 bonds, 468 residues, 2 models selected  

> color sel yellow

> select :335-521

7197 atoms, 7392 bonds, 23 pseudobonds, 935 residues, 4 models selected  

> color sel green

> select :986-1035

2280 atoms, 2292 bonds, 300 residues, 2 models selected  

> color sel orange

> select :816-828

624 atoms, 630 bonds, 75 residues, 2 models selected  

> color sel cyan

> select clear

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Desktop/6vxx_6vsb_down_up.cxs

——— End of log from Wed May 7 17:39:33 2025 ———

opened ChimeraX session  

> vr true

started SteamVR rendering  

> vr false

> select #1/335-521

Nothing selected  

> select #1:335-521

3819 atoms, 3924 bonds, 12 pseudobonds, 471 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel lime green

[Repeated 1 time(s)]

> color sel spring green

> color sel pale green

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> save "Z:/ChimeraX Content/ChimeraX VR
> sessions/SARS_CoV2_spike/6vxx_6vsb_down_up.cxs"

——— End of log from Thu May 8 13:49:54 2025 ———

opened ChimeraX session  

> ui tool show meeting

> meeting start sars2

Meeting "sars2" started at chimeraxmeeting.net port 52200  
Participants can join with command "meeting sars2"  
Connection from ::ffff:127.0.0.1 port 64814 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64814  
Connection from ::ffff:127.0.0.1 port 64825 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64825  

> xr true

Could not find VR headset.  
  
The active OpenXR runtime is Oculus.  
  
Perhaps the Oculus application is not running, or the headset is not connected
by Quest Link (cable) or Air Link (wifi). Check in the "Devices" section of
the Oculus application to see if the headset is connected. If you want instead
to use SteamVR then press "Set SteamVR as OpenXR Runtime" in the SteamVR
application under Settings / OpenXR.  

> ui tool show meeting

> xr true

Could not find VR headset.  
  
The active OpenXR runtime is Oculus.  
  
Perhaps the Oculus application is not running, or the headset is not connected
by Quest Link (cable) or Air Link (wifi). Check in the "Devices" section of
the Oculus application to see if the headset is connected. If you want instead
to use SteamVR then press "Set SteamVR as OpenXR Runtime" in the SteamVR
application under Settings / OpenXR.  

> xr false

Connection from ::ffff:127.0.0.1 port 64856 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64856  
Disconnected from ::ffff:127.0.0.1 port 64814  
Connection from ::ffff:127.0.0.1 port 64860 established, waiting for join
message  
Connection accepted from ::ffff:127.0.0.1 port 64860  

——— End of log from Tue Jun 3 14:45:04 2025 ———

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 1747, in _vr_tracking_cb  
self._participant._send_message(msg)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 976, in _send_message  
msg_bytes = MessageStream.message_as_bytes(msg)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 1310, in message_as_bytes  
bytes = packb(message)  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\msgpack\\__init__.py", line 36, in packb  
return Packer(**kwargs).pack(o)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\\\_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack  
TypeError: can not serialize 'numpy.uint8' object  
  
Error processing trigger "vr update":  
TypeError: can not serialize 'numpy.uint8' object  
  
File "msgpack\\\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> hide #!1 models

> show #!1 models

> hide #!2 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 1747, in _vr_tracking_cb  
self._participant._send_message(msg)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 976, in _send_message  
msg_bytes = MessageStream.message_as_bytes(msg)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\meeting\meeting.py", line 1310, in message_as_bytes  
bytes = packb(message)  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\msgpack\\__init__.py", line 36, in packb  
return Packer(**kwargs).pack(o)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\\\_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack  
TypeError: can not serialize 'numpy.uint8' object  
  
Error processing trigger "vr update":  
TypeError: can not serialize 'numpy.uint8' object  
  
File "msgpack\\\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 576.02
OpenGL renderer: NVIDIA GeForce RTX 3080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D30
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 68,497,039,360
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700K
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
    zipp: 3.19.2

Change History (5)

comment:1 by Eric Pettersen, 5 months ago

Component: Unassigned → VR
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Meeting: can not serialize 'numpy.uint8' object

comment:2 by Tom Goddard, 5 months ago

ChimeraX 1.9 joined a VR meeting and is trying to send head and hand positions and possibly other info like name, color, face image, button assignments, scene move, gui panels and images. Somewhere in the message is a numpy uint8 value which can't be encoded by msgpack. No info reveals what part of the message has the uint8 value. The error happened immediately on opening a session

open "Z:/ChimeraX Content/ChimeraX VR sessions/SARS_CoV2_spike/6vxx_6vsb_down_up.cxs"

comment:3 by Tom Goddard, 5 months ago

My guess would be the pointer color was changed from the default value and it set it to RGBA values that were uint8. It looks like from the code that is what would happen if the color is specified with the meeting join or meeting start command. The meeting join in this report did not specify a color, but the color is saved in settings so the color could be set previously. I'm not sure if settings would preserve uint8 color as a numpy integer. No the settings file saves just integers. Aha, there is a "meeting join sars2 color #1034ff" command. That looks like the problem.

comment:4 by Tom Goddard, 5 months ago

I suspect this bug report is from Phil Cruz since I see cruzp in a file path in the log.

comment:5 by Tom Goddard, 5 months ago

Resolution: → fixed
Status: assigned → closed

Fixed in 1.10 and 1.11.

The color option to the meeting start and meeting join command set uint8 color components that would cause this error. I didn't try to reproduce it with VR because that is pretty time consuming, but I think it is most likely the culprit.

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