find_close_points: NumPy array is not contiguous

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/leileifeng/Documents/BA.5_CR9/RBD/session/density.cxs

Opened density.mrc zone as #3, grid size 256,256,256, pixel 1.04, shown at
level 0.105, step 1, values float32  
Log from Thu May 23 21:50:21 2024UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/leileifeng/Documents/BA.5_CR9/RBD/figure/density.mrc

Opened density.mrc as #1, grid size 256,256,256, pixel 1.04, shown at level
5.66e-05, step 1, values float32  

> open /Users/leileifeng/Documents/BA.5_CR9/RBD/figure/map.pdb

Summary of feedback from opening
/Users/leileifeng/Documents/BA.5_CR9/RBD/figure/map.pdb  
---  
warnings | CONECT record for nonexistent atom: 1172  
Start residue of secondary structure not found: HELIX 1 1 PRO A 335 PHE A 340
1 6  
Start residue of secondary structure not found: HELIX 2 2 TYR A 363 ASN A 368
1 6  
Start residue of secondary structure not found: HELIX 3 3 ASN A 415 ASP A 418
1 4  
Start residue of secondary structure not found: HELIX 4 4 TYR A 447 TYR A 449
1 3  
Start residue of secondary structure not found: HELIX 5 5 VAL A 501 HIS A 503
1 3  
20 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (334 )  
Cannot find LINK/SSBOND residue CYS (377 )  
Cannot find LINK/SSBOND residue CYS (389 )  
Cannot find LINK/SSBOND residue CYS (478 )  
Cannot find LINK/SSBOND residue CYS (22 )  
1 messages similar to the above omitted  
  
Chain information for map.pdb #2  
---  
Chain | Description  
A | No description available  
H | No description available  
L | No description available  
  

> set bgColor white

> hide #!2 models

> show #!2 models

> volume #1 level 0.0414

> volume #1 level 0.08651

> volume #1 level 0.1316

> show #2 atoms

> ui mousemode right "map eraser"

[Repeated 1 time(s)]

> hide #3 models

> transparency #1 30

> transparency #1 40

> volume #1 style mesh

> close #3

Drag select of 1 density.mrc , 10 atoms, 4 residues, 8 bonds  

> select clear

> hide #!2 models

> select #1

2 models selected  

> select #1

2 models selected  

> select #1

2 models selected  

> select clear

> surface dust #1 size 10.4

> show #!2 models

> vop gaussian #1 sdev 3.12

Opened density.mrc gaussian as #3, grid size 256,256,256, pixel 1.04, shown at
step 1, values float32  

> vop gaussian #3 sdev 3.12

Opened density.mrc gaussian as #4, grid size 256,256,256, pixel 1.04, shown at
step 1, values float32  

> vop gaussian #4 sdev 3.12

Opened density.mrc gaussian as #5, grid size 256,256,256, pixel 1.04, shown at
step 1, values float32  

> hide #!5 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> close #3

> close #4

> close #5

> show #!1 models

> surface dust #1 size 10.4

> close #1

Drag select of 10 atoms, 4 residues, 8 bonds  

> close #2

> open /Users/leileifeng/Documents/BA.5_CR9/RBD/figure/density.mrc

Opened density.mrc as #1, grid size 256,256,256, pixel 1.04, shown at level
6.6e-06, step 1, values float32  

> open /Users/leileifeng/Documents/BA.5_CR9/RBD/figure/map.pdb

Summary of feedback from opening
/Users/leileifeng/Documents/BA.5_CR9/RBD/figure/map.pdb  
---  
warnings | CONECT record for nonexistent atom: 1172  
Start residue of secondary structure not found: HELIX 1 1 PRO A 335 PHE A 340
1 6  
Start residue of secondary structure not found: HELIX 2 2 TYR A 363 ASN A 368
1 6  
Start residue of secondary structure not found: HELIX 3 3 ASN A 415 ASP A 418
1 4  
Start residue of secondary structure not found: HELIX 4 4 TYR A 447 TYR A 449
1 3  
Start residue of secondary structure not found: HELIX 5 5 VAL A 501 HIS A 503
1 3  
20 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (334 )  
Cannot find LINK/SSBOND residue CYS (377 )  
Cannot find LINK/SSBOND residue CYS (389 )  
Cannot find LINK/SSBOND residue CYS (478 )  
Cannot find LINK/SSBOND residue CYS (22 )  
1 messages similar to the above omitted  
  
Chain information for map.pdb #2  
---  
Chain | Description  
A | No description available  
H | No description available  
L | No description available  
  

> volume #1 level 0.1563

> transparency #1 40

> volume #1 style mesh

> show #2 atoms

> surface dust #1 size 10.4

> select /H:33@CD2

1 atom, 1 residue, 1 model selected  
Drag select of 11 atoms, 2 residues, 13 bonds  

> hide sel

> hide pseudobonds

> select /A:485

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

> select add /A:484

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

> hide sel

> hide sel cartoons

> volume #1 level 0.1144

> undo

> show sel

> select clear

> show #2 atoms

> close #2

> close #1

> open /Users/leileifeng/Documents/BA.5_CR9/RBD/figure/density.mrc

Opened density.mrc as #1, grid size 256,256,256, pixel 1.04, shown at level
6.6e-06, step 1, values float32  

> open /Users/leileifeng/Documents/BA.5_CR9/RBD/figure/map.pdb

Summary of feedback from opening
/Users/leileifeng/Documents/BA.5_CR9/RBD/figure/map.pdb  
---  
warnings | CONECT record for nonexistent atom: 1172  
Start residue of secondary structure not found: HELIX 1 1 PRO A 335 PHE A 340
1 6  
Start residue of secondary structure not found: HELIX 2 2 TYR A 363 ASN A 368
1 6  
Start residue of secondary structure not found: HELIX 3 3 ASN A 415 ASP A 418
1 4  
Start residue of secondary structure not found: HELIX 4 4 TYR A 447 TYR A 449
1 3  
Start residue of secondary structure not found: HELIX 5 5 VAL A 501 HIS A 503
1 3  
20 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (334 )  
Cannot find LINK/SSBOND residue CYS (377 )  
Cannot find LINK/SSBOND residue CYS (389 )  
Cannot find LINK/SSBOND residue CYS (478 )  
Cannot find LINK/SSBOND residue CYS (22 )  
1 messages similar to the above omitted  
  
Chain information for map.pdb #2  
---  
Chain | Description  
A | No description available  
H | No description available  
L | No description available  
  

> volume #1 level 0.4213

Drag select of 14 atoms, 14 bonds  

> show #2 cartoons

> show #2

> volume #1 level 0.1639

> select clear

> volume #1 style mesh

> surface dust #1 size 10.4

> volume #1 level 0.08006

> volume #1 level 0.1068

> volume #1 level 0.0896

> volume

> surface smoothing

Expected an atoms specifier or a keyword  

> surfaceSmoothing t

Unknown command: surfaceSmoothing t  

> volume #1 surfaceSmoothing true

> volume #1 surfaceIterations 2

Expected a keyword  

> volume #1 surfaceIterations 3

Expected a keyword  

> volume #1 smothingIterations 3

Expected a keyword  

> volume #1 smoothingIterations 3

> volume #1 level 0.1029

> volume #1 level 0.122

> hide #!1 models

> select /A:498

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> hide sel

> show #!1 models

> hide #2 models

> show #2 models

> hide #!1 models

> select /L:28

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

> hide sel

> hide sel cartoons

> show #!1 models

> vop zone #2 3.5

> volume zone #2 3.5

Expected a keyword  

> vop zone #2 #1 3.5

> volume zone #2 #1 3.5

Expected a keyword  

> select #2

208 atoms, 212 bonds, 26 residues, 1 model selected  

> vop zone #2 sel #1 3.5

> volume zone #2 sel #1 3.5

Expected a keyword  

> vop zone #2 sel #1 3.55

> volume zone #2 sel #1 3.55

Expected a keyword  

> volume zone #1 nearAtoms #2 sel 3.0

Expected a keyword  

> volume zone #1 nearAtoms #2 sel range 3

Expected a keyword  

> volume zone #1 nearAtoms #2 sel

Expected a keyword  

> hide #!1 models

> select clear

Drag select of 124 atoms, 24 residues, 108 bonds  

> show #!1 models

> volume zone #1 nearAtoms #2

> hide #!1 models

> show #!1 models

> hide #2 models

> show #2 models

> hide #!1 models

> show #2 cartoons

> select clear

> select /L:28

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

> select add /A:498

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

> delete sel

> volume zone #1 nearAtoms #2

> show #!1 models

> volume zone #1 nearAtoms #2 range 2.5

> volume #1 style surface

> volume #1 style mesh

> volume #1 level 0.1506

> surface dust #1 size 10.4

> volume #1 level 0.1239

> volume zone #1 nearAtoms #2 range 2.5

> surface dust #1

> volume zone #1 nearAtoms #2 range 2.5

> volume zone #1 nearAtoms #2 range 2.5 newMap true

Opened density.mrc zone as #3, grid size 256,256,256, pixel 1.04, shown at
step 1, values float32  

> hide #!3 models

> show #!3 models

> show #!1 models

> hide #2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #2 models

> hide #!1 models

> volume #3 level 0.1055

> surface dust #3

> volume #3 level 0.111

> volume #3 color #d6d6d6

> surfacesmoothing

Unknown command: surfacesmoothing  

> volume #3 smoothingIterations 3

> volume #3 smoothingFactor 0.3

> volume #3 smoothingFactor 0.5

> volume #3 smoothingFactor 0.1

> volume #3 smoothingFactor 0.6

> volume #3 smoothingFactor 1

> volume #3 smoothingFactor 0.4

> volume #3 subdivideSurface true

> volume #3 subdivisionLevels 4

> volume #3 subdivisionLevels 1

> volume #3 subdivisionLevels 0.8

Invalid "subdivisionLevels" argument: Expected an integer  

> volume #3 subdivisionLevels 2

> volume #3 subdivisionLevels 1

> volume #3 meshLighting false

> volume #3 twoSlideLighting 1

Expected a keyword  

> volume #3 twoSlideLighting t

Expected a keyword  

> volume #3 twoSlidedLighting t

Expected a keyword  

> volume #3 twoSidedLighting true

> volume #3 twoSidedLighting false

> volume #3 meshLighting true

> volume #3 twoSidedLighting true

> volume #3 meshLighting false

> volume #3 squareMesh true

> volume #3 ssubdivisionLevels 3

Expected a keyword  

> volume #3 subdivisionLevels 3

> volume #3 subdivisionLevels 1

> hide #!3 models

> show #!1 models

> show #!3 models

> hide #!1 models

> hide #!3 models

Drag select of 17 atoms, 6 residues, 12 bonds  

> select clear

> select /L:34

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

> select #2/L

46 atoms, 46 bonds, 6 residues, 1 model selected  

> color sel

> color sel deeppink

> color #2/A #b2b2ff

> color #2/A

> color #2/H lightblue

> color byhetero

> show #!3 models

> color

> color zone #3 near #2/L deeppink

Expected a keyword  

> color zone #3 near #2/L distance 3deeppink

Invalid "distance" argument: Expected a number  

> color zone #3 near #2/L distance 3 deeppink

Expected a keyword  

> color zone #3 near #2/L distance 3 deeppink

Expected a keyword  

> color zone #3 near #2/L distance 3 farColor deeppink

> select clear

> color zone #3 near #2/L: 29-34 distance 3 farColor deeppink

> color zone #3 near #2/L: 29-34 distance 2 farColor deeppink

> color zone #3 near #2/L:29-34 distance 2 farColor deeppink

> color zone #3 near #2/L:29-34 distance 4 farColor deeppink

> color zone #3 near #2/L:29-34 distance 5 farColor deeppink

> color single #3

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #1 level 0.1811

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> volume #1 level 0.0915

> volume #1 level 0.1506

> show #!3 models

> hide #!1 models

> hide #2 models

> select #3

2 models selected  

> select #3

2 models selected  

> select clear

> select #3

2 models selected  

> select clear

> show #2 models

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide #!3 models

> select up

46 atoms, 46 bonds, 6 residues, 1 model selected  

> show #!3 models

> color zone #3 near sel distance 3 farColor deeppink

> color zone #3 near sel distance 3

> color sel deeppink

> color zone #3 near sel distance 3

> color zone #3 near sel distance 2.5

> color zone #3 near sel distance 2.5-2.8

Invalid "distance" argument: Expected a number  

> color zone #3 near sel distance 2.8

> color zone #3 near sel distance 2.7

> select clear

> hide #!3 models

> select /H:102

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

> select up

30 atoms, 29 bonds, 4 residues, 1 model selected  

> select up

195 atoms, 199 bonds, 24 residues, 1 model selected  

> select down

30 atoms, 29 bonds, 4 residues, 1 model selected  

> color sel lighskyblue

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

> color sel light skyblue

> color zone #3 near sel distance 2.7

> show #!3 models

> select clear

> hide #2 models

> show #2 models

> hide #!3 models

> select /A:487

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

29 atoms, 30 bonds, 3 residues, 1 model selected  

> select up

119 atoms, 124 bonds, 14 residues, 1 model selected  

> color sel #b2b2ff

> color zone #3 near sel distance 2.7

> show #!3 models

> select clear

> color #2 byhetero

> show #!3 models

> select clear

> color zone #3 near sel distance 2.7

color zone: No atoms specified.  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

29 atoms, 30 bonds, 3 residues, 1 model selected  

> select up

119 atoms, 124 bonds, 14 residues, 1 model selected  

> color zone #3 near sel distance 2.7

> close #1

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> select up

30 atoms, 29 bonds, 4 residues, 1 model selected  

> color zone #3 near sel distance 2.7 update false

> color zone #3 near sel distance 2.7 update false sharpEdges true

> color zone #3 near sel distance 2.7 update false

> color zone #3 near #2/L distance 2.7 update false

> color zone #3 near #2 distance 2.7 update false

> volume #3 level 0.0834

> color zone #3 near #2 distance 2.7 update false

> volume #3 level 0.1055

> color zone #3 near #2 distance 2.7 update false

> select clear

> color byhetero

> save density format session

——— End of log from Thu May 23 21:50:21 2024 ———

opened ChimeraX session  

> hide #2 models

> show #2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #3

2 models selected  

> select clear

> select /H:101

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

> select up

30 atoms, 29 bonds, 4 residues, 1 model selected  

> select

195 atoms, 199 bonds, 24 residues, 3 models selected  

> select clear

> select #3

2 models selected  

> select clear

> hide #!3 models

> select /H:102

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

> select up

30 atoms, 29 bonds, 4 residues, 1 model selected  

> show #!3 models

> select zone #2/B #3 2

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 63, in select_zone  
sa, ss = zone_items(na, ns, range, fa, fs, extend, residues)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
TypeError: NumPy array is not contiguous  
  
TypeError: NumPy array is not contiguous  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
  
See log for complete Python traceback.  
  

> hide #!3 models

> show #!3 models

> select clear

> select zone #2/B #3 2.5

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 63, in select_zone  
sa, ss = zone_items(na, ns, range, fa, fs, extend, residues)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
TypeError: NumPy array is not contiguous  
  
TypeError: NumPy array is not contiguous  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: Z1250003LCH/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 1天19小时5分钟

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL SE2723DS:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 75.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[pett]

Probably long ago fixed

[Tom Goddard]

Not able to reproduce this error. Maybe the code has changed since ChimeraX 1.5. In current code the zonesel command uses just atoms.scene_coords and surface.vertices in the find_close_points_sets() call. I don't see how either of these could be non-contiguous. The surface appears to be from a volume (MRC). The tried hide dust and color zone (including sharp edges) and volume zone. Still I can't think of any way to make the surface vertices non-contiguous.