Find Cavities not disposing of deleted structures

[mdooley302@…]

The following bug report has been submitted:
Platform:        macOS-15.7.3-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
I am trying to save a session file after running kvfinder.

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs

Log from Wed Jun 24 12:28:31 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs
> format session

Log from Wed Jun 24 12:20:33 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/morgandooley/Documents/GltPh_Oligomerization/cavity_figure_base.cxs
> format session

Log from Mon Jun 22 18:10:19 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/morgandooley/Documents/GltPh_Oligomerization/gltph_wCavity.cif

Summary of feedback from opening
/Users/morgandooley/Documents/GltPh_Oligomerization/gltph_wCavity.cif  
---  
warnings | Unknown polymer entity '1' on line 36  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Atom XP is not in the residue template for CAV /X:6  
  
Chain information for gltph_wCavity.cif  
---  
Chain | Description  
1.1/A 1.1/B 1.1/C | No description available  
  
Computing secondary structure  

> select protein & cavity :< 4.5

Expected a keyword  

> select #2:CAV :< 4.5

Nothing selected  

> select #1:CAV :< 4.5

1501 atoms, 234 bonds, 31 residues, 2 models selected  

> name contacts sel

> name list

contacts sel  

> name delete contacts sel

Expected fewer arguments  

> name delete contacts

> name list

There are no user-defined specifier names.  

> name contacts_cav sel

> name list

contacts_cav sel  

> ~select #2:CAV

1501 atoms, 234 bonds, 31 residues, 2 models selected  

> ~select #1:CAV

249 atoms, 234 bonds, 30 residues, 1 model selected  

> name contacts_only sel

> select clear

> select contacts_only

Nothing selected  

> name delete

Missing or invalid "name" argument: Expected a text string  

> name delete contacts_only

> name delete contacts_cav

> select #1:CAV :< 4.5 ~sel #1:CAV

Expected a keyword  

> select #1:CAV :< 4.5

1501 atoms, 234 bonds, 31 residues, 2 models selected  

> ~select #1:CAV

249 atoms, 234 bonds, 30 residues, 1 model selected  

> namesel contacts_only sel

Unknown command: namesel contacts_only sel  

> name frozen contacts_only sel

> select clear

> select contacts_only

249 atoms, 234 bonds, 30 residues, 1 model selected  

> select #1

10738 atoms, 9666 bonds, 1249 residues, 3 models selected  

> ~select ~contacts_only

249 atoms, 234 bonds, 30 residues, 1 model selected  

> select #1

10738 atoms, 9666 bonds, 1249 residues, 3 models selected  

> ~select ~contacts_only

249 atoms, 234 bonds, 30 residues, 1 model selected  

> color contacts_only red

> color all gray 80

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

> color #1 gray 80

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

> color #1:all gray 80

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

> color #1 all gray 80

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

> color all gray 80

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

> select #1:CAV

1252 atoms, 1 residue, 1 model selected  

> surface #1:CAV

> name cavity surface #1:CAV

"surface #1:CAV": invalid atom specifier  

> name cavity #1:CAV

> select clear

> surface cavity

> select cavity

1252 atoms, 1 residue, 1 model selected  

> transparency cavity 50

> name list

cavity #1:CAV  
contacts_only [249 atoms, 468 bonds]  

> show contacts_only atoms

> style contacts_only stick

Changed 249 atom styles  

> color concacts_only bypolymer

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

> color concacts_only byatom

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

> color concacts_only bymodel

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

> color contacts_only bymodel

> color contacts_only byatom

> color contacts_only bymodel

> color contacts_only byatom

> label contacts_only residues

> hide #1 atoms

> show #1 cartoons

> color #1 gray80

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

> color #1 gray 80

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

> hide #!1.2 models

> show #!1.2 models

> hide #!1.1 models

> show #!1.1 models

> color #1 gray

> transparency #1 cartoons 30

Missing or invalid "percent" argument: Expected a number  

> transparency #1 30

> show contacts_only atoms

> color contacts_only red

> color contacts_only byatom

> select ~contacts_only

10489 atoms, 9384 bonds, 1219 residues, 4 models selected  

> select #1:CAV :< 4.5

1501 atoms, 234 bonds, 31 residues, 2 models selected  

> ~select #1:CAV :< 4.5

1 model selected  

> select #1:CAV :< 4.5

1501 atoms, 234 bonds, 31 residues, 2 models selected  

> name cav_n_contacts #1:CAV :< 4.5

> ~select cav_n_contacts

1 model selected  

> transparency #1 70 cartoons

> transparency contacts_only 0 cartoons

> transparency contacts_only 0 atoms

> select cavity

1252 atoms, 1 residue, 1 model selected  

> color cavity green

> color cavity blue

> transparency cavity 80

> select contacts_only :> 15

6417 atoms, 6528 bonds, 846 residues, 1 model selected  

> transparency sel 40 All

> transparency sel 90 All

> transparency sel 100 All

> select contacts_only :> 10

7400 atoms, 7520 bonds, 985 residues, 1 model selected  

> select contacts_only :> 10, ~sel contacts_only :> 15

Expected a keyword  

> select contacts_only :> 10, ~sel contacts_only :> 15

Expected a keyword  

> select contacts_only :> 10

7400 atoms, 7520 bonds, 985 residues, 1 model selected  

> ~select contacts_only :> 15

983 atoms, 944 bonds, 139 residues, 1 model selected  

> transparency sel 80 All

> select clear

> set bgColor white

> lighting soft

> lighting full

> lighting simple

> set bgColor black

> save
> /Users/morgandooley/Documents/GltPh_Oligomerization/cavity_figure_base.cxs

——— End of log from Mon Jun 22 18:10:19 2026 ———

> view name session-start

opened ChimeraX session  

> close session

> open 6X15 format mmcif fromDatabase pdb

6x15 title:  
Inward-facing state of the glutamate transporter homologue GltPh in complex
with L-aspartate and sodium ions [more info...]  
  
Chain information for 6x15 #1  
---  
Chain | Description  
A B C | Glutamate transporter homologue GltPh  
  
Non-standard residues in 6x15 #1  
---  
6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-
propan-2-yl] (~{Z})-octadec-9-enoate  
ASP — aspartic acid  
HG — mercury (II) ion  
NA — sodium ion  
  

> save
> /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs

——— End of log from Wed Jun 24 12:20:33 2026 ———

> view name session-start

opened ChimeraX session  

> select add #1.1

51 pseudobonds, 1 model selected  

> hide sel

> select subtract #1.1

Nothing selected  

> select add #1

10026 atoms, 10146 bonds, 51 pseudobonds, 1320 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select /a-c

10026 atoms, 10146 bonds, 51 pseudobonds, 1320 residues, 2 models selected  

> select :6OU,NA,HG

654 atoms, 603 bonds, 51 residues, 1 model selected  

> hide sel

> select /a-c

10026 atoms, 10146 bonds, 51 pseudobonds, 1320 residues, 2 models selected  

> hide atoms

> select :1-75,120-220

4065 atoms, 4161 bonds, 528 residues, 1 model selected  

> select :1-70,120-220

3969 atoms, 4062 bonds, 513 residues, 1 model selected  

> select :1-70,125-220

3834 atoms, 3921 bonds, 498 residues, 1 model selected  

> select :1-75,125-220

3930 atoms, 4020 bonds, 513 residues, 1 model selected  

> name frozen scaffold sel

> select ~sel & ##selected

6096 atoms, 6126 bonds, 51 pseudobonds, 807 residues, 2 models selected  

> name frozen transport sel

> save
> /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs

> color (#!1 & sel) light gray

> select ~sel & ##selected

3930 atoms, 4020 bonds, 513 residues, 1 model selected  

> color sel cornflower blue

> select clear

> save
> /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs

——— End of log from Wed Jun 24 12:28:31 2026 ———

> view name session-start

opened ChimeraX session  

> name list

scaffold [3930 atoms, 4020 bonds]  
transport [6096 atoms, 6126 bonds, 2 models]  

> ui tool show "Find Cavities"

> kvfinder gridSpacing 0.7 probeIn 1.2 probeOut 5.5

99 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.45 |  | 1335.99 | 899.35 | 3895 | 0 | 0  
1.2.33 |  | 1001.9 | 883.06 | 2921 | 6.96 | 1.54  
1.2.58 |  | 995.39 | 854.89 | 2902 | 7.03 | 1.52  
1.2.8 |  | 945.99 | 827.7 | 2758 | 6.93 | 1.55  
1.2.27 |  | 747.05 | 573.24 | 2178 | 8.1 | 2.09  
1.2.70 |  | 664.05 | 455.94 | 1936 | 9.8 | 2.13  
1.2.44 |  | 648.27 | 450.94 | 1890 | 9.1 | 2.3  
1.2.79 |  | 133.77 | 109.63 | 390 | 2.89 | 0.78  
1.2.20 |  | 127.25 | 117.26 | 371 | 2.21 | 0.6  
1.2.49 |  | 126.91 | 127.16 | 370 | 2.32 | 0.73  
1.2.7 |  | 120.05 | 152.62 | 350 | 0 | 0  
1.2.85 |  | 117.31 | 124.38 | 342 | 6.93 | 3.75  
1.2.61 |  | 116.62 | 124.05 | 340 | 0 | 0  
1.2.16 |  | 115.25 | 124.32 | 336 | 0 | 0  
1.2.72 |  | 114.22 | 144.44 | 333 | 0 | 0  
1.2.78 |  | 113.88 | 140.31 | 332 | 0 | 0  
1.2.55 |  | 104.96 | 95.02 | 306 | 2.1 | 0.46  
1.2.89 |  | 85.41 | 123.8 | 249 | 0 | 0  
1.2.17 |  | 85.06 | 132.43 | 248 | 0 | 0  
1.2.53 |  | 77.52 | 118.11 | 226 | 0 | 0  
1.2.83 |  | 77.52 | 122.53 | 226 | 6.06 | 2.34  
1.2.38 |  | 65.51 | 83.36 | 191 | 2.1 | 0.8  
1.2.93 |  | 64.14 | 69.56 | 187 | 2.89 | 0.9  
1.2.12 |  | 62.77 | 64.07 | 183 | 2.89 | 0.97  
1.2.47 |  | 56.25 | 60.53 | 164 | 2.62 | 0.93  
1.2.77 |  | 37.04 | 57.78 | 108 | 0 | 0  
1.2.43 |  | 34.3 | 59.26 | 100 | 0 | 0  
1.2.80 |  | 34.3 | 55.77 | 100 | 4.48 | 1.55  
1.2.60 |  | 33.96 | 59.15 | 99 | 0 | 0  
1.2.41 |  | 32.58 | 53.45 | 95 | 0 | 0  
1.2.84 |  | 31.9 | 49.67 | 93 | 3.77 | 1.33  
1.2.29 |  | 31.21 | 52.45 | 91 | 0 | 0  
1.2.30 |  | 30.53 | 47.8 | 89 | 0 | 0  
1.2.69 |  | 30.53 | 49.56 | 89 | 0 | 0  
1.2.24 |  | 28.13 | 55.57 | 82 | 4.7 | 1.75  
1.2.76 |  | 27.78 | 42.74 | 81 | 1.4 | 0.4  
1.2.48 |  | 26.75 | 49.29 | 78 | 0 | 0  
1.2.31 |  | 25.72 | 38.12 | 75 | 1.57 | 0.34  
1.2.5 |  | 25.04 | 42.19 | 73 | 0 | 0  
1.2.90 |  | 19.55 | 36.76 | 57 | 0 | 0  
1.2.99 |  | 19.55 | 33.23 | 57 | 0 | 0  
1.2.62 |  | 19.21 | 37.64 | 56 | 0 | 0  
1.2.92 |  | 19.21 | 45.85 | 56 | 0 | 0  
1.2.9 |  | 17.15 | 35.89 | 50 | 0 | 0  
1.2.39 |  | 17.15 | 27.86 | 50 | 0.7 | 0.2  
1.2.73 |  | 17.15 | 33.07 | 50 | 1.4 | 0.32  
1.2.52 |  | 16.81 | 29.07 | 49 | 0.7 | 0.1  
1.2.37 |  | 16.12 | 39.37 | 47 | 0 | 0  
1.2.57 |  | 16.12 | 35.42 | 47 | 0 | 0  
1.2.14 |  | 15.78 | 31.43 | 46 | 1.57 | 0.34  
1.2.3 |  | 15.43 | 25.17 | 45 | 0.7 | 0.22  
1.2.11 |  | 15.09 | 29.18 | 44 | 0 | 0  
1.2.54 |  | 15.09 | 29.18 | 44 | 0 | 0  
1.2.68 |  | 14.75 | 24.39 | 43 | 0.7 | 0.2  
1.2.66 |  | 14.06 | 31.51 | 41 | 0 | 0  
1.2.2 |  | 13.72 | 20.49 | 40 | 1.57 | 0.5  
1.2.88 |  | 13.72 | 20.95 | 40 | 0.99 | 0.22  
1.2.23 |  | 13.38 | 20.27 | 39 | 1.4 | 0.28  
1.2.34 |  | 13.38 | 28.48 | 39 | 0 | 0  
1.2.56 |  | 13.38 | 28.48 | 39 | 0 | 0  
1.2.82 |  | 13.03 | 28.47 | 38 | 0 | 0  
1.2.71 |  | 12.35 | 30.77 | 36 | 0 | 0  
1.2.67 |  | 12 | 24.8 | 35 | 0 | 0  
1.2.63 |  | 10.98 | 20.44 | 32 | 1.71 | 0.9  
1.2.1 |  | 9.95 | 24.86 | 29 | 1.71 | 0.78  
1.2.19 |  | 9.6 | 21.06 | 28 | 0 | 0  
1.2.22 |  | 9.6 | 21.06 | 28 | 0 | 0  
1.2.28 |  | 9.6 | 21.06 | 28 | 0 | 0  
1.2.46 |  | 9.6 | 21.06 | 28 | 0 | 0  
1.2.75 |  | 9.6 | 21.06 | 28 | 0 | 0  
1.2.35 |  | 9.26 | 17.59 | 27 | 0.7 | 0.13  
1.2.15 |  | 8.92 | 11.44 | 26 | 0.7 | 0.11  
1.2.36 |  | 8.23 | 21.46 | 24 | 0.99 | 0.37  
1.2.86 |  | 7.89 | 17.5 | 23 | 1.98 | 0.89  
1.2.4 |  | 7.2 | 14.18 | 21 | 1.4 | 0.58  
1.2.98 |  | 6.86 | 13.59 | 20 | 0.99 | 0.34  
1.2.6 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.10 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.13 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.18 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.21 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.25 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.40 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.42 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.50 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.51 |  | 6.52 | 11.65 | 19 | 0.7 | 0.26  
1.2.59 |  | 6.52 | 13.56 | 19 | 0 | 0  
1.2.64 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.65 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.74 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.81 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.87 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.91 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.94 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.95 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.96 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.97 |  | 6.52 | 18.31 | 19 | 0 | 0  
1.2.26 |  | 5.83 | 12.83 | 17 | 0.7 | 0.16  
1.2.32 |  | 5.49 | 12.83 | 16 | 0.7 | 0.09  
  

Populating font family aliases took 132 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.  

> view #1.2.45 @< 3.5

> zoom 0.75

moved plane near -29.545798891320946 [-0.00277775 -0.01561962 0.99987415]  
moved plane far -29.545798891320946 [-0.00277775 -0.01561962 0.99987415]  

> surface #1.2.1-99 probeRadius 1.2 transparency 50

> ~surface #1.2

> surface #1.2.45 probeRadius 1.2

> select #1.2.45

3895 atoms, 1 residue, 1 model selected  

> kvfinder probeIn 1.2 probeOut 5.5

119 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.53 |  | 1452.6 | 986.2 | 6725 | 0 | 0  
1.2.36 |  | 1282.61 | 1010.48 | 5938 | 8.09 | 1.82  
1.2.9 |  | 1234.87 | 969.38 | 5717 | 7.78 | 1.78  
1.2.67 |  | 1225.8 | 969.93 | 5675 | 7.73 | 1.77  
1.2.81 |  | 773.93 | 491.7 | 3583 | 9.6 | 2.27  
1.2.26 |  | 758.16 | 509.2 | 3510 | 9.6 | 2.27  
1.2.54 |  | 753.41 | 498.41 | 3488 | 9.08 | 2.32  
1.2.100 |  | 213.62 | 237.53 | 989 | 0 | 0  
1.2.16 |  | 201.1 | 162.73 | 931 | 2.68 | 0.63  
1.2.66 |  | 200.45 | 129.13 | 928 | 2.81 | 0.66  
1.2.94 |  | 193.97 | 146.98 | 898 | 3.23 | 0.78  
1.2.59 |  | 158.33 | 136.56 | 733 | 3.06 | 0.94  
1.2.18 |  | 118.58 | 120.07 | 549 | 0 | 0  
1.2.45 |  | 116.64 | 142.22 | 540 | 6.21 | 1.94  
1.2.8 |  | 116.42 | 135.11 | 539 | 0 | 0  
1.2.73 |  | 116.21 | 114.79 | 538 | 0 | 0  
1.2.82 |  | 115.78 | 133.7 | 536 | 0 | 0  
1.2.93 |  | 114.26 | 136.42 | 529 | 0 | 0  
1.2.11 |  | 92.02 | 89.95 | 426 | 3.93 | 1.17  
1.2.111 |  | 91.15 | 89.25 | 422 | 3.5 | 1.07  
1.2.19 |  | 90.5 | 115.36 | 419 | 0 | 0  
1.2.64 |  | 81 | 105.96 | 375 | 0 | 0  
1.2.57 |  | 79.7 | 84.23 | 369 | 3.7 | 1.02  
1.2.101 |  | 68.69 | 87.05 | 318 | 4.53 | 1.32  
1.2.35 |  | 65.88 | 83.86 | 305 | 3.06 | 0.95  
1.2.92 |  | 54.65 | 73.8 | 253 | 4.87 | 1.81  
1.2.34 |  | 46.66 | 54.94 | 216 | 2.4 | 0.55  
1.2.102 |  | 44.71 | 65.15 | 207 | 4.53 | 1.55  
1.2.72 |  | 39.74 | 58.58 | 184 | 0 | 0  
1.2.1 |  | 36.29 | 52.69 | 168 | 4.02 | 1.16  
1.2.10 |  | 35.64 | 54.18 | 165 | 3.45 | 0.97  
1.2.25 |  | 34.78 | 52.69 | 161 | 1.7 | 0.33  
1.2.91 |  | 31.97 | 45.94 | 148 | 0 | 0  
1.2.31 |  | 31.75 | 46.4 | 147 | 0 | 0  
1.2.22 |  | 30.67 | 37.43 | 142 | 1.7 | 0.45  
1.2.117 |  | 30.24 | 46.36 | 140 | 3.65 | 0.82  
1.2.32 |  | 30.02 | 45.33 | 139 | 0 | 0  
1.2.78 |  | 28.3 | 37.68 | 131 | 1.2 | 0.31  
1.2.109 |  | 28.08 | 42.49 | 130 | 0 | 0  
1.2.90 |  | 27.43 | 40 | 127 | 1.8 | 0.43  
1.2.118 |  | 27.22 | 40.43 | 126 | 0 | 0  
1.2.15 |  | 26.57 | 39.09 | 123 | 1.9 | 0.45  
1.2.44 |  | 26.57 | 39.16 | 123 | 1.2 | 0.25  
1.2.63 |  | 26.14 | 37.52 | 121 | 1.2 | 0.29  
1.2.105 |  | 25.49 | 31.17 | 118 | 1.34 | 0.38  
1.2.58 |  | 25.06 | 38.23 | 116 | 0 | 0  
1.2.4 |  | 24.62 | 32.12 | 114 | 1.34 | 0.4  
1.2.6 |  | 24.62 | 37.04 | 114 | 0 | 0  
1.2.68 |  | 21.82 | 38.38 | 101 | 0 | 0  
1.2.99 |  | 20.3 | 32.08 | 94 | 2.81 | 1.07  
1.2.12 |  | 20.09 | 34.05 | 93 | 0 | 0  
1.2.76 |  | 20.09 | 32.25 | 93 | 3.12 | 1.52  
1.2.85 |  | 19.66 | 35.41 | 91 | 1.8 | 0.51  
1.2.62 |  | 19.44 | 29.35 | 90 | 1.2 | 0.29  
1.2.119 |  | 17.93 | 28.88 | 83 | 0.85 | 0.31  
1.2.13 |  | 16.63 | 28.37 | 77 | 0 | 0  
1.2.38 |  | 16.42 | 29.42 | 76 | 0 | 0  
1.2.65 |  | 16.2 | 27.33 | 75 | 0 | 0  
1.2.107 |  | 16.2 | 27.01 | 75 | 0 | 0  
1.2.110 |  | 15.77 | 27.01 | 73 | 0 | 0  
1.2.20 |  | 15.55 | 26.2 | 72 | 0 | 0  
1.2.2 |  | 14.26 | 26.44 | 66 | 2.08 | 0.71  
1.2.70 |  | 14.26 | 26.1 | 66 | 0 | 0  
1.2.103 |  | 14.04 | 25.79 | 65 | 1.99 | 0.67  
1.2.79 |  | 13.18 | 23.81 | 61 | 0 | 0  
1.2.48 |  | 12.96 | 23.79 | 60 | 0.6 | 0.18  
1.2.49 |  | 12.96 | 25.2 | 60 | 0 | 0  
1.2.52 |  | 12.74 | 19.36 | 59 | 1.2 | 0.35  
1.2.104 |  | 12.1 | 20.14 | 56 | 0.6 | 0.18  
1.2.39 |  | 11.66 | 22.63 | 54 | 0 | 0  
1.2.74 |  | 11.66 | 21.34 | 54 | 0 | 0  
1.2.98 |  | 11.66 | 21.02 | 54 | 0 | 0  
1.2.80 |  | 11.02 | 20.14 | 51 | 0 | 0  
1.2.112 |  | 11.02 | 20.14 | 51 | 0 | 0  
1.2.41 |  | 10.37 | 17.27 | 48 | 0.6 | 0.14  
1.2.89 |  | 10.37 | 20.05 | 48 | 0 | 0  
1.2.83 |  | 10.15 | 19.57 | 47 | 1.47 | 0.47  
1.2.108 |  | 9.94 | 15.03 | 46 | 1.34 | 0.37  
1.2.87 |  | 9.72 | 18.43 | 45 | 0 | 0  
1.2.75 |  | 9.29 | 14.57 | 43 | 1.47 | 0.43  
1.2.40 |  | 8.64 | 16.75 | 40 | 0.6 | 0.11  
1.2.106 |  | 8.64 | 15.84 | 40 | 1.8 | 0.61  
1.2.96 |  | 7.99 | 13.44 | 37 | 0.85 | 0.26  
1.2.21 |  | 7.78 | 15.52 | 36 | 0 | 0  
1.2.23 |  | 7.78 | 15.52 | 36 | 0 | 0  
1.2.27 |  | 7.78 | 15.52 | 36 | 0 | 0  
1.2.30 |  | 7.78 | 15.52 | 36 | 0 | 0  
1.2.50 |  | 7.78 | 15.52 | 36 | 0 | 0  
1.2.56 |  | 7.78 | 15.52 | 36 | 0 | 0  
1.2.60 |  | 7.78 | 15.52 | 36 | 0 | 0  
1.2.114 |  | 7.78 | 15.52 | 36 | 0 | 0  
1.2.115 |  | 7.78 | 15.52 | 36 | 0 | 0  
1.2.3 |  | 7.56 | 14.41 | 35 | 1.47 | 0.62  
1.2.5 |  | 7.34 | 14.46 | 34 | 1.8 | 0.88  
1.2.47 |  | 7.34 | 13.03 | 34 | 0.6 | 0.16  
1.2.55 |  | 7.13 | 12.71 | 33 | 0.85 | 0.38  
1.2.61 |  | 7.13 | 12.05 | 33 | 0.6 | 0.22  
1.2.69 |  | 7.13 | 14.87 | 33 | 0.6 | 0.05  
1.2.37 |  | 6.48 | 11.65 | 30 | 0.6 | 0.2  
1.2.113 |  | 6.48 | 12.75 | 30 | 0.6 | 0.12  
1.2.24 |  | 6.26 | 11.56 | 29 | 0.6 | 0.19  
1.2.7 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.14 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.17 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.28 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.29 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.33 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.43 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.46 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.51 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.71 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.84 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.86 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.88 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.95 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.97 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.116 |  | 5.83 | 12.3 | 27 | 0 | 0  
1.2.42 |  | 5.62 | 11.73 | 26 | 1.8 | 0.88  
1.2.77 |  | 5.18 | 10.51 | 24 | 0.6 | 0.08  
  

> view #1.2.53 @< 3.5

> zoom 0.75

moved plane near -34.0078564350414 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -34.0078564350414 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-119 probeRadius 1.2 transparency 50

> ~surface #1.2

> surface #1.2.53 probeRadius 1.2

> select #1.2.53

6725 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.5

105 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.32 |  | 1482.75 | 1191.35 | 2896 | 7.96 | 1.73  
1.2.46 |  | 1480.7 | 992.57 | 2892 | 0 | 0  
1.2.9 |  | 1402.37 | 1084.63 | 2739 | 7.07 | 1.6  
1.2.56 |  | 1333.25 | 1065.59 | 2604 | 7.55 | 1.68  
1.2.67 |  | 904.7 | 560.43 | 1767 | 9.6 | 2.27  
1.2.23 |  | 869.38 | 584.26 | 1698 | 9.6 | 2.22  
1.2.35 |  | 826.37 | 547.66 | 1614 | 10.4 | 2.3  
1.2.54 |  | 284.16 | 197.04 | 555 | 3.3 | 0.7  
1.2.75 |  | 282.62 | 200.95 | 552 | 3.3 | 0.82  
1.2.15 |  | 270.85 | 187.44 | 529 | 2.99 | 0.67  
1.2.17 |  | 224.26 | 261.35 | 438 | 0 | 0  
1.2.49 |  | 202.24 | 165.99 | 395 | 2.77 | 1  
1.2.8 |  | 137.73 | 179.02 | 269 | 0 | 0  
1.2.62 |  | 136.7 | 141.34 | 267 | 0 | 0  
1.2.69 |  | 128.51 | 150.88 | 251 | 0 | 0  
1.2.74 |  | 127.49 | 142.35 | 249 | 0 | 0  
1.2.83 |  | 125.44 | 131.31 | 245 | 0 | 0  
1.2.84 |  | 122.37 | 162.55 | 239 | 6.5 | 2.46  
1.2.99 |  | 111.62 | 103.14 | 218 | 3.75 | 1.2  
1.2.36 |  | 102.4 | 126.99 | 200 | 4.08 | 1.19  
1.2.12 |  | 100.35 | 93.03 | 196 | 3.67 | 1.19  
1.2.47 |  | 95.74 | 99.25 | 187 | 3.67 | 0.96  
1.2.52 |  | 86.02 | 121.15 | 168 | 0 | 0  
1.2.31 |  | 85.5 | 106.14 | 167 | 2.65 | 1.05  
1.2.76 |  | 65.54 | 85.2 | 128 | 5.12 | 1.76  
1.2.30 |  | 61.95 | 80.86 | 121 | 4 | 0.78  
1.2.89 |  | 60.93 | 80.18 | 119 | 0 | 0  
1.2.80 |  | 59.9 | 93.82 | 117 | 5.12 | 1.91  
1.2.21 |  | 45.57 | 68.06 | 89 | 1.13 | 0.18  
1.2.2 |  | 45.06 | 72.49 | 88 | 4.08 | 1.37  
1.2.51 |  | 45.06 | 55.03 | 88 | 1.39 | 0.35  
1.2.20 |  | 44.54 | 48.97 | 87 | 2.26 | 0.5  
1.2.73 |  | 43.52 | 67.76 | 85 | 0 | 0  
1.2.27 |  | 37.89 | 57.45 | 74 | 0 | 0  
1.2.60 |  | 35.33 | 54.21 | 69 | 0 | 0  
1.2.7 |  | 33.79 | 49.17 | 66 | 0 | 0  
1.2.42 |  | 33.28 | 51.17 | 65 | 0 | 0  
1.2.45 |  | 33.28 | 56 | 65 | 0 | 0  
1.2.103 |  | 33.28 | 44.53 | 65 | 1.79 | 0.43  
1.2.28 |  | 32.77 | 54.5 | 64 | 0 | 0  
1.2.70 |  | 31.23 | 47.94 | 61 | 1.6 | 0.39  
1.2.72 |  | 30.21 | 45.98 | 59 | 1.6 | 0.39  
1.2.87 |  | 30.21 | 33.5 | 59 | 1.6 | 0.37  
1.2.104 |  | 30.21 | 47.91 | 59 | 0 | 0  
1.2.48 |  | 29.18 | 51.75 | 57 | 0 | 0  
1.2.14 |  | 28.67 | 41.42 | 56 | 1.6 | 0.39  
1.2.82 |  | 28.16 | 43.91 | 55 | 3.49 | 1.7  
1.2.10 |  | 27.65 | 47.81 | 54 | 0 | 0  
1.2.37 |  | 27.14 | 46.63 | 53 | 3.58 | 1.17  
1.2.16 |  | 26.62 | 42.83 | 52 | 3.39 | 1.26  
1.2.41 |  | 26.62 | 37.98 | 52 | 1.6 | 0.42  
1.2.53 |  | 25.09 | 31.86 | 49 | 1.13 | 0.35  
1.2.91 |  | 24.58 | 40.25 | 48 | 0.8 | 0.08  
1.2.92 |  | 24.58 | 36.56 | 48 | 1.79 | 0.43  
1.2.65 |  | 23.55 | 41.54 | 46 | 3.49 | 1.92  
1.2.90 |  | 23.55 | 37.36 | 46 | 0 | 0  
1.2.6 |  | 22.02 | 29.22 | 43 | 0.8 | 0.26  
1.2.58 |  | 20.99 | 41.3 | 41 | 0 | 0  
1.2.97 |  | 19.46 | 42.8 | 38 | 0 | 0  
1.2.57 |  | 17.41 | 31.94 | 34 | 0.8 | 0.19  
1.2.66 |  | 16.38 | 37.59 | 32 | 0 | 0  
1.2.105 |  | 16.38 | 30.33 | 32 | 0.8 | 0.12  
1.2.3 |  | 15.36 | 25.11 | 30 | 1.6 | 0.64  
1.2.63 |  | 15.36 | 32.54 | 30 | 0 | 0  
1.2.95 |  | 15.36 | 32.54 | 30 | 0 | 0  
1.2.13 |  | 14.34 | 27.51 | 28 | 0 | 0  
1.2.55 |  | 14.34 | 27.51 | 28 | 0 | 0  
1.2.11 |  | 13.31 | 21.48 | 26 | 1.39 | 0.54  
1.2.50 |  | 13.31 | 21.49 | 26 | 1.39 | 0.39  
1.2.102 |  | 13.31 | 31.52 | 26 | 3.39 | 1.76  
1.2.100 |  | 12.8 | 20.65 | 25 | 0.8 | 0.16  
1.2.29 |  | 12.29 | 17.9 | 24 | 0 | 0  
1.2.64 |  | 11.78 | 18.64 | 23 | 1.39 | 0.54  
1.2.5 |  | 11.26 | 20.6 | 22 | 0.8 | 0.18  
1.2.1 |  | 10.75 | 17.06 | 21 | 0.8 | 0.19  
1.2.33 |  | 10.75 | 16.52 | 21 | 0.8 | 0.27  
1.2.4 |  | 10.24 | 18.57 | 20 | 0 | 0  
1.2.25 |  | 10.24 | 17.92 | 20 | 0.8 | 0.04  
1.2.18 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.19 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.22 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.24 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.26 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.34 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.39 |  | 9.73 | 16.04 | 19 | 0.8 | 0.08  
1.2.43 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.59 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.68 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.71 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.79 |  | 9.73 | 16.33 | 19 | 0.8 | 0.21  
1.2.81 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.88 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.101 |  | 9.73 | 23.91 | 19 | 0 | 0  
1.2.38 |  | 8.19 | 14.91 | 16 | 0 | 0  
1.2.78 |  | 8.19 | 13.26 | 16 | 0.8 | 0.2  
1.2.86 |  | 8.19 | 13.77 | 16 | 0 | 0  
1.2.96 |  | 7.68 | 15.82 | 15 | 0.8 | 0.43  
1.2.61 |  | 7.17 | 12.54 | 14 | 0 | 0  
1.2.77 |  | 6.14 | 11.47 | 12 | 0.8 | 0.07  
1.2.85 |  | 5.63 | 9.78 | 11 | 0.8 | 0.15  
1.2.40 |  | 5.12 | 9.16 | 10 | 0 | 0  
1.2.44 |  | 5.12 | 10.46 | 10 | 0.8 | 0.16  
1.2.93 |  | 5.12 | 8.76 | 10 | 0 | 0  
1.2.94 |  | 5.12 | 10.21 | 10 | 0 | 0  
1.2.98 |  | 5.12 | 7.45 | 10 | 0 | 0  
  

> view #1.2.46 @< 3.5

> zoom 0.75

moved plane near -32.39149791328405 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -32.39149791328405 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-105 probeRadius 1.2 transparency 50

> ~surface #1.2

> surface #1.2.46 probeRadius 1.2

> select #1.2.46

2892 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.5 volumeCutoff 900

5 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.2 |  | 1482.75 | 1191.35 | 2896 | 7.96 | 1.73  
1.2.3 |  | 1480.7 | 992.57 | 2892 | 0 | 0  
1.2.1 |  | 1402.37 | 1084.63 | 2739 | 7.07 | 1.6  
1.2.4 |  | 1333.25 | 1065.59 | 2604 | 7.55 | 1.68  
1.2.5 |  | 904.7 | 560.43 | 1767 | 9.6 | 2.27  
  

> view #1.2.3 @< 3.5

> zoom 0.75

moved plane near -32.39149791328405 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -32.39149791328405 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-5 probeRadius 1.2 transparency 50

> ~surface #1.2

> surface #1.2.3 probeRadius 1.2

> select #1.2.3

2892 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.4 volumeCutoff 900

4 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.3 |  | 1565.7 | 1112.59 | 3058 | 0 | 0  
1.2.2 |  | 1387.52 | 1082.76 | 2710 | 7.96 | 1.77  
1.2.4 |  | 1288.7 | 1025.31 | 2517 | 7.63 | 1.68  
1.2.1 |  | 1260.54 | 986.31 | 2462 | 7.07 | 1.64  
  

> view #1.2.3 @< 3.5

> zoom 0.75

moved plane near -34.221898520410825 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -34.221898520410825 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-4 probeRadius 1.2 transparency 50

> ~surface #1.2

> surface #1.2.3 probeRadius 1.2

> select #1.2.3

3058 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.6 volumeCutoff 900

6 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.2 |  | 1545.22 | 1218.6 | 3018 | 7.92 | 1.72  
1.2.1 |  | 1498.62 | 1139.68 | 2927 | 7.71 | 1.67  
1.2.4 |  | 1492.48 | 1015.74 | 2915 | 0 | 0  
1.2.5 |  | 1458.18 | 1156.63 | 2848 | 7.71 | 1.64  
1.2.3 |  | 927.23 | 583.74 | 1811 | 9.6 | 2.42  
1.2.6 |  | 920.58 | 572.46 | 1798 | 9.6 | 2.23  
  

> view #1.2.4 @< 3.5

> zoom 0.75

moved plane near -30.619789271527594 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -30.619789271527594 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-6 probeRadius 1.2 transparency 50

> ~surface #1.2

> surface #1.2.4 probeRadius 1.2

> select #1.2.4

2915 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.6 volumeCutoff 900

6 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.2 |  | 1545.22 | 1218.6 | 3018 | 7.92 | 1.72  
1.2.1 |  | 1498.62 | 1139.68 | 2927 | 7.71 | 1.67  
1.2.4 |  | 1492.48 | 1015.74 | 2915 | 0 | 0  
1.2.5 |  | 1458.18 | 1156.63 | 2848 | 7.71 | 1.64  
1.2.3 |  | 927.23 | 583.74 | 1811 | 9.6 | 2.42  
1.2.6 |  | 920.58 | 572.46 | 1798 | 9.6 | 2.23  
  

> view #1.2.1 @< 3.5

> zoom 0.75

moved plane near -46.651350154162884 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -46.651350154162884 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-6 probeRadius 1.2 transparency 50

> ~surface #1.2

> surface #1.2.1 probeRadius 1.2

> select #1.2.1

2927 atoms, 1 residue, 1 model selected  

> view #!1.2.2 @< 3.5

> zoom 0.75

moved plane near -46.99354999206374 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -46.99354999206374 [ 0.11252654 -0.05074317 0.99235221]  

> ~surface #1.2

> surface #!1.2.2 probeRadius 1.2

> select #!1.2.2

3018 atoms, 1 residue, 1 model selected  

> view #!1.2.4 @< 3.5

> zoom 0.75

moved plane near -30.619789271527594 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -30.619789271527594 [ 0.11252654 -0.05074317 0.99235221]  

> ~surface #1.2

> surface #!1.2.4 probeRadius 1.2

> select #!1.2.4

2915 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.3 volumeCutoff 900

5 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.3 |  | 1472 | 957.8 | 2875 | 0 | 0  
1.2.2 |  | 1357.82 | 1074.91 | 2652 | 7.96 | 1.74  
1.2.1 |  | 1310.72 | 1054.59 | 2560 | 7.02 | 1.65  
1.2.4 |  | 1305.6 | 1063.38 | 2550 | 7.59 | 1.71  
1.2.5 |  | 927.74 | 631.71 | 1812 | 8.65 | 2.09  
  

> view #1.2.3 @< 3.5

> zoom 0.75

moved plane near -30.3815091799255 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -30.3815091799255 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-5 probeRadius 1.2 transparency 50

> ~surface #1.2

> surface #1.2.3 probeRadius 1.2

> select #1.2.3

2875 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.2 volumeCutoff 900

4 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.3 |  | 1474.05 | 974 | 2879 | 0 | 0  
1.2.2 |  | 1281.02 | 1010.48 | 2502 | 7.96 | 1.72  
1.2.1 |  | 1243.14 | 1004.12 | 2428 | 6.97 | 1.62  
1.2.4 |  | 1183.74 | 947.83 | 2312 | 7.59 | 1.66  
  

> view #1.2.3 @< 3.5

> zoom 0.75

moved plane near -31.01868138775968 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -31.01868138775968 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-4 probeRadius 1.2 transparency 50

> ~surface #1.2

> surface #1.2.3 probeRadius 1.2

> select #1.2.3

2879 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5 volumeCutoff 900

4 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.3 |  | 1541.12 | 1046.49 | 3010 | 0 | 0  
1.2.2 |  | 1272.83 | 987.49 | 2486 | 7.71 | 1.68  
1.2.1 |  | 1171.97 | 950.57 | 2289 | 6.88 | 1.58  
1.2.4 |  | 1166.85 | 918.55 | 2279 | 7.2 | 1.61  
  

> view #1.2.3 @< 3.5

> zoom 0.75

moved plane near -33.50697070131426 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -33.50697070131426 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-4 probeRadius 1.2 transparency 50

> ~surface #1.2

> surface #1.2.3 probeRadius 1.2

> select #1.2.3

3010 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.3 probeOut 5 volumeCutoff 900

3 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.2 |  | 1277.44 | 787.49 | 2495 | 0 | 0  
1.2.1 |  | 1125.38 | 907.04 | 2198 | 7.71 | 1.65  
1.2.3 |  | 1029.12 | 851.68 | 2010 | 5.99 | 1.48  
  

> view #1.2.2 @< 3.5

> zoom 0.75

moved plane near -25.94895592629877 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -25.94895592629877 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-3 probeRadius 1.3 transparency 50

> ~surface #1.2

> surface #1.2.2 probeRadius 1.3

> select #1.2.2

2495 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.3 probeOut 4.8 volumeCutoff 900

0 cavities found for 6x15 #1  

> kvfinder gridSpacing 0.8 probeIn 1.3 probeOut 4.9 volumeCutoff 900

2 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.2 |  | 1277.95 | 792.67 | 2496 | 0 | 0  
1.2.1 |  | 1039.87 | 848.06 | 2031 | 6.84 | 1.6  
  

> view #1.2.2 @< 3.5

> zoom 0.75

moved plane near -26.20204210646268 [ 0.11252654 -0.05074317 0.99235221]  
moved plane far -26.20204210646268 [ 0.11252654 -0.05074317 0.99235221]  

> surface #1.2.1-2 probeRadius 1.3 transparency 50

> ~surface #1.2

> surface #1.2.2 probeRadius 1.3

> select #1.2.2

2496 atoms, 1 residue, 1 model selected  

> view #!1.2.1 @< 3.5

> zoom 0.75

moved plane near -40.1437939466313 [-0.02399375 0.07662399 0.99677132]  
moved plane far -40.1437939466313 [-0.02399375 0.07662399 0.99677132]  

> ~surface #1.2

> surface #!1.2.1 probeRadius 1.3

> select #!1.2.1

2031 atoms, 1 residue, 1 model selected  

> view #!1.2.2 @< 3.5

> zoom 0.75

moved plane near -26.37070356607748 [-0.02399375 0.07662399 0.99677132]  
moved plane far -26.37070356607748 [-0.02399375 0.07662399 0.99677132]  

> ~surface #1.2

> surface #!1.2.2 probeRadius 1.3

> select #!1.2.2

2496 atoms, 1 residue, 1 model selected  

> kvfinder gridSpacing 0.8 probeIn 1.3 probeOut 4.9 volumeCutoff 900

2 cavities found for 6x15 #1  
6x15 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.2.2 |  | 1277.95 | 792.67 | 2496 | 0 | 0  
1.2.1 |  | 1039.87 | 848.06 | 2031 | 6.84 | 1.6  
  

> view #1.2.2 @< 3.5

> zoom 0.75

moved plane near -26.37070356607748 [-0.02399375 0.07662399 0.99677132]  
moved plane far -26.37070356607748 [-0.02399375 0.07662399 0.99677132]  

> surface #1.2.1-2 probeRadius 1.3 transparency 50

> ~surface #1.2

> surface #1.2.2 probeRadius 1.3

> select #1.2.2

2496 atoms, 1 residue, 1 model selected  

> select #!1 & (#!1.2.2 @< 3.5)

186 atoms, 154 bonds, 38 residues, 1 model selected  

> ~select #!1.2.2

186 atoms, 154 bonds, 38 residues, 1 model selected  

> ~surface #1.2

> view #1

> view #!1.2.2 @< 3.5

> zoom 0.75

moved plane near -25.504779775329137 [0.03552242 0.01945198 0.99917955]  
moved plane far -25.504779775329137 [0.03552242 0.01945198 0.99917955]  

> show
> #!1/A,C:60,63,142-143,146-147,157,161,183,186-187,190/B:60,63-64,142-143,146-147,157,161,183,186-187,190

> hide
> #!1/A,C:60,63,142-143,146-147,157,161,183,186-187,190/B:60,63-64,142-143,146-147,157,161,183,186-187,190

> show
> #!1/A,C:60,63,142-143,146-147,157,161,183,186-187,190/B:60,63-64,142-143,146-147,157,161,183,186-187,190

> hide
> #!1/A,C:60,63,142-143,146-147,157,161,183,186-187,190/B:60,63-64,142-143,146-147,157,161,183,186-187,190

> ~select #!1 & (#!1.2.2 @< 3.5)

Nothing selected  

> select #!1 & (#!1.2.2 @< 3.5)

186 atoms, 154 bonds, 38 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> ~select #!1 & (#!1.2.2 @< 3.5)

Nothing selected  

> select #!1.2.2

2496 atoms, 1 residue, 1 model selected  

> ~surface #1.2

> surface #!1.2.2 probeRadius 1.3

> color byattribute a:kvfinder_depth #!1.2.1

2031 atoms, 1 residues, 1 surfaces, atom kvfinder_depth range 0 to 6.84  

> select subtract #1.2.2

1 model selected  

> select add #1.2.1

2031 atoms, 1 residue, 1 model selected  

> delete sel

> view #!1.2.2 @< 3.5

> zoom 0.75

moved plane near -25.504779775329137 [0.03552242 0.01945198 0.99917955]  
moved plane far -25.504779775329137 [0.03552242 0.01945198 0.99917955]  

> ~surface #1.2

> surface #!1.2.2 probeRadius 1.3

> select #!1.2.2

2496 atoms, 1 residue, 1 model selected  

> save
> /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 226, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 373, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x32e07fa90>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90>,
<chimerax.cmd_line.tool.CommandLine object at 0x32e023150>,
<chimerax.log.tool.Log object at 0x32e07c950>,
<chimerax.toolbar.tool.ToolbarTool object at 0x32e035190>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90> ->
<chimerax.atomic.structure.Structure object at 0x35126fc90> 'cavity 1'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1058, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x32e07fa90>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90>,
<chimerax.cmd_line.tool.CommandLine object at 0x32e023150>,
<chimerax.log.tool.Log object at 0x32e07c950>,
<chimerax.toolbar.tool.ToolbarTool object at 0x32e035190>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90> ->
<chimerax.atomic.structure.Structure object at 0x35126fc90> 'cavity 1': Error
while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x32e07fa90>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90>,
<chimerax.cmd_line.tool.CommandLine object at 0x32e023150>,
<chimerax.log.tool.Log object at 0x32e07c950>,
<chimerax.toolbar.tool.ToolbarTool object at 0x32e035190>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90> ->
<chimerax.atomic.structure.Structure object at 0x35126fc90> 'cavity 1'  
  
ValueError: error processing: 'tools' -> [, , , , ] -> -> 'cavity 1': Error
while saving session data for 'tools' -> [, , , , ] -> -> 'cavity 1'  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 226, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 373, in take_snapshot  
'positions': self.positions.array(),  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x32e07fa90>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90>,
<chimerax.cmd_line.tool.CommandLine object at 0x32e023150>,
<chimerax.log.tool.Log object at 0x32e07c950>,
<chimerax.toolbar.tool.ToolbarTool object at 0x32e035190>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90> ->
<chimerax.atomic.structure.Structure object at 0x35126fc90> 'cavity 1'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1058, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x32e07fa90>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90>,
<chimerax.cmd_line.tool.CommandLine object at 0x32e023150>,
<chimerax.log.tool.Log object at 0x32e07c950>,
<chimerax.toolbar.tool.ToolbarTool object at 0x32e035190>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90> ->
<chimerax.atomic.structure.Structure object at 0x35126fc90> 'cavity 1': Error
while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x32e07fa90>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90>,
<chimerax.cmd_line.tool.CommandLine object at 0x32e023150>,
<chimerax.log.tool.Log object at 0x32e07c950>,
<chimerax.toolbar.tool.ToolbarTool object at 0x32e035190>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x350cb9d90> ->
<chimerax.atomic.structure.Structure object at 0x35126fc90> 'cavity 1'  
  
ValueError: error processing: 'tools' -> [, , , , ] -> -> 'cavity 1': Error
while saving session data for 'tools' -> [, , , , ] -> -> 'cavity 1'  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/bug_reporter/tool.py", line 253, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/post_form.py", line 45, in
post_multipart_formdata  
return r.status, r.msg, r.getheaders(), r.read()  
^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 482, in read  
s = self._safe_read(self.length)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 633, in _safe_read  
raise IncompleteRead(data, amt-len(data))  
http.client.IncompleteRead: IncompleteRead(666 bytes read, 6446 more expected)  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,7
      Model Number: MX2Y3LL/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 48 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.3 (24G419)
      Kernel Version: Darwin 24.6.0
      Time since boot: 54 days, 6 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.6.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    narwhals: 2.22.1
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 2.4.6
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    plotly: 6.7.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.9.2
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tomlkit: 0.15.0
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[Eric Pettersen]

Hi Morgan,

Thanks for reporting this problem. It has been fixed in later releases of ChimeraX, so if you update your version then it will not happen to you again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab