ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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

> open "C:\Users\sssmnb\OneDrive - University of Missouri\Vindya - Beamer lab
> - Ogrp\Vindya\Cryo-EM\PNCC\Essex_hexaglu_07152025\4.cxs" format session

Opened cryosparc_P9_J40_002_volume_map_sharp.mrc as #1, grid size 128,128,128,
pixel 2.02, shown at level 1.34, step 1, values float32  
Opened cryosparc_P8_J109_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.825, shown at level 0.141, step 1, values float32  
Opened cryosparc_P9_J76_007_volume_map_sharp.mrc as #6, grid size 512,512,512,
pixel 0.506, shown at level 0.104, step 1, values float32  
Opened cryosparc_P9_J76_007_volume_map_sharp.mrc z flip as #5, grid size
512,512,512, pixel 0.506, shown at level 0.149, step 1, values float32  
Opened cryosparc_P9_J76_007_volume_mask_refine.mrc as #7, grid size
512,512,512, pixel 0.506, shown at level 1, step 2, values float32  
Opened cryosparc_P9_J76_007_volume_mask_refine.mrc z flip as #8, grid size
512,512,512, pixel 0.506, shown at level 1, step 1, values float32  
Opened J76_flip_20_mask.mrc as #9, grid size 512,512,512, pixel 0.506, shown
at level 0.0867, step 1, values float32  
Opened cryosparc_P9_J83_010_volume_map_sharp.mrc as #10, grid size
512,512,512, pixel 0.506, shown at level 0.106, step 2, values float32  
Opened cryosparc_P9_J83_010_volume_map_sharp.mrc z flip as #11, grid size
512,512,512, pixel 0.506, shown at level 0.107, step 1, values float32  
Opened cryosparc_P9_J83_010_volume_map_sharp.mrc z flip gaussian as #12, grid
size 512,512,512, pixel 0.506, shown at level 0.0293, step 1, values float32  
Opened cryosparc_P8_J109_010_volume_map_sharp.mrc as #13, grid size
320,320,320, pixel 0.825, shown at level 0.105, step 1, values float32  
Opened cryosparc_P9_J123_006_volume_map_sharp.mrc as #14, grid size
512,512,512, pixel 0.506, shown at level 0.0731, step 1, values float32  
Opened cryosparc_P9_J124_006_volume_map_sharp.mrc as #15, grid size
512,512,512, pixel 0.506, shown at level 0.0894, step 1, values float32  
Log from Mon Oct 13 10:26:51 2025UCSF ChimeraX version: 1.8rc202406060152
(2024-06-06)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\sssmnb\OneDrive - University of Missouri\Vindya - Beamer lab
> - Ogrp\Vindya\Cryo-EM\PNCC\Essex_hexaglu_07152025\3.cxs" format session

Opened cryosparc_P9_J40_002_volume_map_sharp.mrc as #1, grid size 128,128,128,
pixel 2.02, shown at level 1.34, step 1, values float32  
Opened cryosparc_P8_J109_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.825, shown at level 0.141, step 1, values float32  
Opened cryosparc_P9_J76_007_volume_map_sharp.mrc as #6, grid size 512,512,512,
pixel 0.506, shown at level 0.104, step 1, values float32  
Opened cryosparc_P9_J76_007_volume_map_sharp.mrc z flip as #5, grid size
512,512,512, pixel 0.506, shown at level 0.149, step 1, values float32  
Opened cryosparc_P9_J76_007_volume_mask_refine.mrc as #7, grid size
512,512,512, pixel 0.506, shown at level 1, step 2, values float32  
Opened cryosparc_P9_J76_007_volume_mask_refine.mrc z flip as #8, grid size
512,512,512, pixel 0.506, shown at level 1, step 1, values float32  
Opened J76_flip_20_mask.mrc as #9, grid size 512,512,512, pixel 0.506, shown
at level 0.0867, step 1, values float32  
Opened cryosparc_P9_J83_010_volume_map_sharp.mrc as #10, grid size
512,512,512, pixel 0.506, shown at level 0.106, step 2, values float32  
Opened cryosparc_P9_J83_010_volume_map_sharp.mrc z flip as #11, grid size
512,512,512, pixel 0.506, shown at level 0.107, step 1, values float32  
Opened cryosparc_P9_J83_010_volume_map_sharp.mrc z flip gaussian as #12, grid
size 512,512,512, pixel 0.506, shown at level 0.0293, step 1, values float32  
Opened cryosparc_P8_J109_010_volume_map_sharp.mrc as #13, grid size
320,320,320, pixel 0.825, shown at level 0.105, step 1, values float32  
Opened cryosparc_P9_J123_006_volume_map_sharp.mrc as #14, grid size
512,512,512, pixel 0.506, shown at level 0.0731, step 1, values float32  
Log from Mon Oct 6 09:58:42 2025UCSF ChimeraX version: 1.8rc202406060152
(2024-06-06)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_hexaglu_07152025/2.cxs"

Opened cryosparc_P9_J40_002_volume_map_sharp.mrc as #1, grid size 128,128,128,
pixel 2.02, shown at level 1.34, step 1, values float32  
Opened cryosparc_P8_J109_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.825, shown at level 0.141, step 1, values float32  
Opened cryosparc_P9_J76_007_volume_map_sharp.mrc as #6, grid size 512,512,512,
pixel 0.506, shown at level 0.104, step 1, values float32  
Opened cryosparc_P9_J76_007_volume_map_sharp.mrc z flip as #5, grid size
512,512,512, pixel 0.506, shown at level 0.149, step 1, values float32  
Opened cryosparc_P9_J76_007_volume_mask_refine.mrc as #7, grid size
512,512,512, pixel 0.506, shown at level 1, step 2, values float32  
Opened cryosparc_P9_J76_007_volume_mask_refine.mrc z flip as #8, grid size
512,512,512, pixel 0.506, shown at level 1, step 1, values float32  
Log from Mon Sep 22 11:24:07 2025UCSF ChimeraX version: 1.8rc202406060152
(2024-06-06)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_hexaglu_07152025/1.cxs"

Opened cryosparc_P9_J40_002_volume_map_sharp.mrc as #1, grid size 128,128,128,
pixel 2.02, shown at level 0.272, step 1, values float32  
Opened cryosparc_P8_J109_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.825, shown at level 0.141, step 1, values float32  
Opened cryosparc_P9_J40_002_volume_map_sharp.mrc z flip as #5, grid size
128,128,128, pixel 2.02, shown at level 0.28, step 1, values float32  
Log from Fri Sep 19 14:00:52 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8rc202406060152 (2024-06-06)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 9gqu

Summary of feedback from opening 9gqu fetched from pdb  
---  
note | Fetching compressed mmCIF 9gqu from http://files.rcsb.org/download/9gqu.cif  
  
9gqu title:  
Crystal structure of NtcA from S. elongatus in apo form A2 [more info...]  
  
Chain information for 9gqu #1  
---  
Chain | Description | UniProt  
A B | Global nitrogen regulator | NTCA_SYNE7 1-222  
  

> set bgColor white

> set bgColor #ffffff00

> select /B:153

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

> select up

137 atoms, 138 bonds, 17 residues, 1 model selected  

> select up

952 atoms, 967 bonds, 136 residues, 1 model selected  

> select up

972 atoms, 986 bonds, 140 residues, 1 model selected  

> color #1 #ffaaffff

> select /A:19-220

1524 atoms, 1549 bonds, 1 pseudobond, 198 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> close

> close #

Expected a models specifier or a keyword  

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-
> EM/PNCC/Essex_hexaglu_07152025/cryosparc_P9_J40_002_volume_map_sharp.mrc"

Opened cryosparc_P9_J40_002_volume_map_sharp.mrc as #1, grid size 128,128,128,
pixel 2.02, shown at level 0.124, step 1, values float32  

> volume #1 level 0.1692

> color #1 #b2b2b201 models

> color #1 #b2b2b29b models

> open 8TQF fromDatabase pdb format mmcif

Summary of feedback from opening 8TQF fetched from pdb  
---  
note | Fetching compressed mmCIF 8tqf from http://files.rcsb.org/download/8tqf.cif  
  
8tqf title:  
Crystal structure of Soybean SHMT8 in complex with PLP-glycine and
diglutamylated 5-formyltetrahydrofolate [more info...]  
  
Chain information for 8tqf #2  
---  
Chain | Description | UniProt  
A B C D | Serine hydroxymethyltransferase | A0A0R0IK90_SOYBN 1-471  
  
Non-standard residues in 8tqf #2  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
PLG — N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane]
(N-pyridoxyl-glycine-5-monophosphate)  
S8R —
N-[4-({[(6R)-2-amino-5-formyl-4-hydroxy-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-
glutamyl-L-glutamic acid  
  
324 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select /D:221

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

42 atoms, 41 bonds, 7 residues, 1 model selected  

> select up

3613 atoms, 3697 bonds, 472 residues, 1 model selected  

> select up

4057 atoms, 3771 bonds, 846 residues, 1 model selected  

> select up

16194 atoms, 15047 bonds, 3387 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-0.26829,0,1,0,106.55,0,0,1,90.86

> view matrix models #2,1,0,0,0.70576,0,1,0,107.09,0,0,1,101.05

> view matrix models #2,1,0,0,1.9806,0,1,0,100.42,0,0,1,107.91

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.33279,-0.5291,-0.78058,46.655,0.69855,-0.41774,0.58096,97.04,-0.63346,-0.73862,0.23059,155.53

> view matrix models
> #2,0.35996,-0.57988,-0.73087,45.572,0.91727,0.076835,0.39079,90.902,-0.17046,-0.81107,0.55956,139.34

> view matrix models
> #2,0.22572,-0.96444,-0.13748,35.491,0.82377,0.11362,0.55543,86.341,-0.52005,-0.23863,0.82012,125.8

> view matrix models
> #2,0.29421,-0.95196,-0.084923,32.551,0.7965,0.19511,0.57229,84.728,-0.52823,-0.23602,0.81564,126.02

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.29421,-0.95196,-0.084923,32.935,0.7965,0.19511,0.57229,78.532,-0.52823,-0.23602,0.81564,124.42

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.29421,-0.95196,-0.084923,115.54,0.7965,0.19511,0.57229,141.13,-0.52823,-0.23602,0.81564,110.89

> view matrix models
> #2,0.29421,-0.95196,-0.084923,125.76,0.7965,0.19511,0.57229,89.593,-0.52823,-0.23602,0.81564,120.31

> view matrix models
> #2,0.29421,-0.95196,-0.084923,135.75,0.7965,0.19511,0.57229,83.502,-0.52823,-0.23602,0.81564,119.97

> view matrix models
> #2,0.29421,-0.95196,-0.084923,135.96,0.7965,0.19511,0.57229,83.259,-0.52823,-0.23602,0.81564,119.01

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.58394,0.62435,0.51884,83.606,0.72832,-0.68522,0.0048621,118.5,0.35856,0.37504,-0.85486,148.34

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.58394,0.62435,0.51884,91.453,0.72832,-0.68522,0.0048621,130.17,0.35856,0.37504,-0.85486,146.16

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.20475,0.95743,0.20349,107.34,0.85564,0.074115,0.51223,98.171,0.47534,0.279,-0.83439,145.5

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 8tqf (#2) to map cryosparc_P9_J40_002_volume_map_sharp.mrc (#1)
using 16194 atoms  
average map value = 0.1311, steps = 64  
shifted from previous position = 1.58  
rotated from previous position = 6.74 degrees  
atoms outside contour = 10374, contour level = 0.16924  
  
Position of 8tqf (#2) relative to cryosparc_P9_J40_002_volume_map_sharp.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.21148726 0.92487095 0.31604881 105.43412796  
0.86228095 0.02431623 0.50584608 98.15239138  
0.46015723 0.37950287 -0.80264118 142.67311156  
Axis -0.62666550 -0.71478139 -0.31044793  
Axis point 6.62863839 0.00000000 49.74958037  
Rotation angle (degrees) 174.21441793  
Shift along axis -180.52200576  
  

> show sel atoms

> hide sel cartoons

> view matrix models
> #2,-0.20918,0.92531,0.31629,105.38,0.85144,0.013269,0.52429,97.966,0.48094,0.37897,-0.79062,141.98

> select clear

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_042725/6UXH_tetramer.pdb"

18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Chain information for 6UXH_tetramer.pdb  
---  
Chain | Description  
3.1/A 3.1/B | No description available  
3.2/A 3.3/A 3.3/C | No description available  
3.2/B 3.3/B 3.3/D | No description available  
  
36 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #2 models

> select #3.2/B:453

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

112 atoms, 112 bonds, 16 residues, 1 model selected  

> select up

648 atoms, 659 bonds, 87 residues, 1 model selected  

> select up

680 atoms, 691 bonds, 92 residues, 1 model selected  

> select up

1468 atoms, 1496 bonds, 198 residues, 1 model selected  

> select up

1504 atoms, 1533 bonds, 203 residues, 1 model selected  

> select up

3511 atoms, 3590 bonds, 461 residues, 1 model selected  

> select up

3716 atoms, 3593 bonds, 663 residues, 1 model selected  

> select up

7399 atoms, 7174 bonds, 1306 residues, 1 model selected  

> select up

29596 atoms, 28696 bonds, 5224 residues, 3 models selected  

> select up

29596 atoms, 28696 bonds, 5224 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.98735,0.044735,-0.1521,15.835,-0.15643,0.11897,-0.9805,266.79,-0.025767,0.99189,0.12446,-12.289

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.1349,0.04834,0.98968,-22.983,0.99086,-0.0078374,-0.13468,20.485,0.001246,0.9988,-0.048956,6.1378

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.1349,0.04834,0.98968,-23.288,0.99086,-0.0078374,-0.13468,18.386,0.001246,0.9988,-0.048956,4.4594

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.98888,-0.12347,-0.082864,289.4,-0.079324,-0.033324,0.99629,13.676,-0.12577,0.99179,0.023159,12.63

> view matrix models
> #3,0.984,0.017414,0.17733,-24.018,0.17732,0.0019072,-0.98415,236.86,-0.017476,0.99985,-0.0012112,0.49402

> view matrix models
> #3,0.1702,0.031817,0.9849,-25.118,0.9854,-0.009598,-0.16997,24.181,0.0040449,0.99945,-0.032986,1.9012

> fitmap #3.1 inMap #1

Fit molecule 6UXH_tetramer.pdb (#3.1) to map
cryosparc_P9_J40_002_volume_map_sharp.mrc (#1) using 7399 atoms  
average map value = 0.1293, steps = 96  
shifted from previous position = 3.57  
rotated from previous position = 10 degrees  
atoms outside contour = 4731, contour level = 0.16924  
  
Position of 6UXH_tetramer.pdb (#3.1) relative to
cryosparc_P9_J40_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98533570 0.02124558 0.16929909 -24.79507763  
-0.02672607 0.99918776 0.03015863 -1.88827870  
-0.16852084 -0.03424108 0.98510318 26.63404195  
Axis -0.18546529 0.97289059 -0.13815397  
Axis point 143.16183567 0.00000000 159.86331558  
Rotation angle (degrees) 9.99816342  
Shift along axis -0.91806098  
  

> hide #!3 models

> show #!3 models

> hide #!1 models

> close #3.3

> close #3.2

> close #3.1

> hide #3 models

> show #3 models

> close #3

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_042725/6UXH_tetramer.pdb"

18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Chain information for 6UXH_tetramer.pdb  
---  
Chain | Description  
3.1/A 3.1/B | No description available  
3.2/A 3.3/A 3.3/C | No description available  
3.2/B 3.3/B 3.3/D | No description available  
  
36 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!3.3 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.3 models

> hide #!3.2 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.2 models

> hide #!3.2 models

> hide #!3.3 models

> show #!3.3 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.1,3 cartoons

> show #!3.1,3 atoms

> hide #!3.1,3 cartoons

> show #!3.2 models

> hide #!3.1 models

> hide #!3.2 models

> show #!1 models

> select up

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

> select up

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

> select up

3502 atoms, 3581 bonds, 462 residues, 1 model selected  

> select up

3683 atoms, 3581 bonds, 643 residues, 1 model selected  

> select up

14798 atoms, 14348 bonds, 2612 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3.3,0.98782,-0.15504,-0.013395,23.916,0.015267,0.01089,0.99982,-3.0051,-0.15486,-0.98785,0.013125,281.63

> view matrix models
> #3.3,0.99121,-0.13002,-0.02451,21.622,0.02583,0.0084788,0.99963,-4.0544,-0.12977,-0.99147,0.011763,278.97

> view matrix models
> #3.3,0.99377,-0.097694,-0.053696,20.856,0.05448,0.0053724,0.9985,-7.2752,-0.097259,-0.9952,0.010661,275.32

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #3.3,-0.33645,-0.087269,0.93765,64.148,-0.93991,-0.03035,-0.34008,305.47,0.058137,-0.99572,-0.071814,265.77

> fitmap #3.3 inMap #1

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P9_J40_002_volume_map_sharp.mrc (#1) using 14798 atoms  
average map value = 0.1309, steps = 100  
shifted from previous position = 4.57  
rotated from previous position = 13.6 degrees  
atoms outside contour = 9419, contour level = 0.16924  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P9_J40_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.53739851 -0.00355002 0.84332094 89.31186090  
-0.84324887 -0.01147282 -0.53740087 313.29017427  
0.01158306 -0.99992787 0.00317192 260.40610943  
Axis -0.36443031 0.65533578 -0.66160831  
Axis point 57.60193874 261.40674043 0.00000000  
Rotation angle (degrees) 140.61048444  
Shift along axis 0.47546643  
  

> select clear

> hide #!3.3 models

> show #2 models

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-
> EM/PNCC/Essex_042725/cryosparc_P8_J109_010_volume_map_sharp.mrc"

Opened cryosparc_P8_J109_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.825, shown at level 0.052, step 2, values float32  

> volume #4 level 0.1152

> hide #!1 models

> volume #4 level 0.08191

> volume #4 step 1

> volume #4 level 0.141

> fitmap #3.3 inMap #4

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) using 14798 atoms  
average map value = 0.01967, steps = 92  
shifted from previous position = 0.637  
rotated from previous position = 2.26 degrees  
atoms outside contour = 12978, contour level = 0.14099  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.51668865 0.00472659 0.85616031 83.32262294  
-0.85554143 -0.04126371 -0.51608735 315.66402916  
0.03288902 -0.99913710 0.02536428 254.34953754  
Axis -0.37592004 0.64068799 -0.66947966  
Axis point 55.89564711 256.83641729 0.00000000  
Rotation angle (degrees) 140.02225369  
Shift along axis 0.63766695  
  

> fitmap #3.3 inMap #4

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) using 14798 atoms  
average map value = 0.01967, steps = 64  
shifted from previous position = 0.00324  
rotated from previous position = 0.00893 degrees  
atoms outside contour = 12980, contour level = 0.14099  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.51671100 0.00466417 0.85614716 83.33472281  
-0.85553133 -0.04112353 -0.51611528 315.64804333  
0.03280054 -0.99914317 0.02523932 254.37539464  
Axis -0.37590551 0.64075086 -0.66942766  
Axis point 55.89283024 256.85712128 0.00000000  
Rotation angle (degrees) 140.02257131  
Shift along axis 0.63984807  
  

> volume #4 color #ffffb29b

> hide #2 cartoons

> show #2 atoms

> hide #2 atoms

> hide #2 cartoons

> show #2 cartoons

> show #2 atoms

> hide #2 cartoons

> select clear

> select #2/A:164@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

95 atoms, 97 bonds, 12 residues, 1 model selected  

> select up

3580 atoms, 3664 bonds, 472 residues, 1 model selected  

> select up

4013 atoms, 3744 bonds, 829 residues, 1 model selected  

> select up

16194 atoms, 15047 bonds, 3387 residues, 1 model selected  

> view matrix models
> #2,-0.29359,0.93307,0.20782,109.92,0.81523,0.13086,0.56417,95.208,0.49921,0.33505,-0.79908,142.74

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.29359,0.93307,0.20782,109.61,0.81523,0.13086,0.56417,97.272,0.49921,0.33505,-0.79908,144.78

> view matrix models
> #2,-0.29359,0.93307,0.20782,109.79,0.81523,0.13086,0.56417,96.608,0.49921,0.33505,-0.79908,144.52

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.29359,0.93307,0.20782,112.66,0.81523,0.13086,0.56417,96.762,0.49921,0.33505,-0.79908,142.75

> view matrix models
> #2,-0.29359,0.93307,0.20782,112.64,0.81523,0.13086,0.56417,97.77,0.49921,0.33505,-0.79908,143.77

> view matrix models
> #2,-0.29359,0.93307,0.20782,113.2,0.81523,0.13086,0.56417,97.952,0.49921,0.33505,-0.79908,143.6

> fitmap #3.3 inMap #4

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) using 14798 atoms  
average map value = 0.01966, steps = 48  
shifted from previous position = 0.0129  
rotated from previous position = 0.00957 degrees  
atoms outside contour = 12982, contour level = 0.14099  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.51673504 0.00459766 0.85613301 83.34519489  
-0.85552044 -0.04097319 -0.51614528 315.64095345  
0.03270544 -0.99914966 0.02510567 254.39945025  
Axis -0.37588978 0.64081823 -0.66937200  
Axis point 55.89066609 256.88224600 0.00000000  
Rotation angle (degrees) 140.02289933  
Shift along axis 0.65200169  
  

> fitmap #3.3 inMap #4

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) using 14798 atoms  
average map value = 0.01967, steps = 76  
shifted from previous position = 0.0148  
rotated from previous position = 0.0166 degrees  
atoms outside contour = 12979, contour level = 0.14099  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.51669562 0.00470163 0.85615624 83.32662632  
-0.85553753 -0.04123946 -0.51609575 315.66156736  
0.03288093 -0.99913822 0.02533067 254.35499373  
Axis -0.37592007 0.64070083 -0.66946736  
Axis point 55.89392941 256.84137244 0.00000000  
Rotation angle (degrees) 140.02298190  
Shift along axis 0.63811266  
  

> fitmap #3.3 inMap #4

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) using 14798 atoms  
average map value = 0.01966, steps = 48  
shifted from previous position = 0.0116  
rotated from previous position = 0.0053 degrees  
atoms outside contour = 12981, contour level = 0.14099  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.51670111 0.00468544 0.85615302 83.32898731  
-0.85553688 -0.04114876 -0.51610407 315.66063038  
0.03281147 -0.99914203 0.02527018 254.36690485  
Axis -0.37590794 0.64073769 -0.66943890  
Axis point 55.89516319 256.85543180 0.00000000  
Rotation angle (degrees) 140.02188002  
Shift along axis 0.64853435  
  

> fitmap #3.3 inMap #4

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) using 14798 atoms  
average map value = 0.01967, steps = 48  
shifted from previous position = 0.00875  
rotated from previous position = 0.0134 degrees  
atoms outside contour = 12973, contour level = 0.14099  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.51667284 0.00490481 0.85616885 83.29637836  
-0.85555587 -0.04122157 -0.51606677 315.67103867  
0.03276142 -0.99913798 0.02549440 254.35120263  
Axis -0.37587113 0.64068212 -0.66951274  
Axis point 55.91083031 256.83596010 -0.00000000  
Rotation angle (degrees) 140.01386845  
Shift along axis 0.64471415  
  

> fitmap #3.3 inMap #4

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) using 14798 atoms  
average map value = 0.01967, steps = 76  
shifted from previous position = 0.0027  
rotated from previous position = 0.0103 degrees  
atoms outside contour = 12977, contour level = 0.14099  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.51669061 0.00473124 0.85615910 83.32304126  
-0.85554025 -0.04126638 -0.51608909 315.67516298  
0.03288885 -0.99913697 0.02536972 254.35064015  
Axis -0.37591830 0.64068671 -0.66948187  
Axis point 55.89799488 256.84125297 0.00000000  
Rotation angle (degrees) 140.02221810  
Shift along axis 0.64308259  
  
Average map value = 0.01967 for 14798 atoms, 12977 outside contour  

> fitmap #3.3 inMap #4

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) using 14798 atoms  
average map value = 0.01967, steps = 76  
shifted from previous position = 0.00948  
rotated from previous position = 0.0102 degrees  
atoms outside contour = 12980, contour level = 0.14099  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.51671465 0.00465285 0.85614502 83.33742648  
-0.85552937 -0.04110919 -0.51611966 315.64829450  
0.03279400 -0.99914381 0.02522238 254.37977449  
Axis -0.37590479 0.64075800 -0.66942122  
Axis point 55.89261460 256.86107406 0.00000000  
Rotation angle (degrees) 140.02285064  
Shift along axis 0.64001420  
  

> hide #2 models

> show #2 models

> show #!3.3 models

> hide #!3.3 models

> fitmap #2 inMap #4

Fit molecule 8tqf (#2) to map cryosparc_P8_J109_010_volume_map_sharp.mrc (#4)
using 16194 atoms  
average map value = 0.2292, steps = 92  
shifted from previous position = 1.08  
rotated from previous position = 9.27 degrees  
atoms outside contour = 6678, contour level = 0.14099  
  
Position of 8tqf (#2) relative to cryosparc_P8_J109_010_volume_map_sharp.mrc
(#4) coordinates:  
Matrix rotation and translation  
-0.19174364 0.92349373 0.33225543 107.23745411  
0.85810196 -0.00655856 0.51343744 100.92862903  
0.47633537 0.38355740 -0.79119423 143.72805548  
Axis -0.63447567 -0.70384351 -0.31944474  
Axis point 5.04302085 0.00000000 48.59100163  
Rotation angle (degrees) 174.12535997  
Shift along axis -184.99068706  
  

> show #!1 models

> select #1

2 models selected  

> hide #!4 models

> show #!4 models

> hide #!4 models

> select clear

> show #!4 models

> show #!3.3 models

> hide #!1 models

> hide #2 models

> select up

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

> select up

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

> select up

3511 atoms, 3590 bonds, 461 residues, 1 model selected  

> select up

3716 atoms, 3593 bonds, 663 residues, 1 model selected  

> select up

14798 atoms, 14348 bonds, 2612 residues, 1 model selected  

> view matrix models
> #3.3,-0.51669,0.0047312,0.85616,82.78,-0.85554,-0.041266,-0.51609,318.77,0.032889,-0.99914,0.02537,254.55

> ui mousemode right "rotate selected models"

> view matrix models
> #3.3,0.14513,-0.088186,0.98548,-9.3427,-0.98941,-0.0097211,0.14484,244.99,-0.0031925,-0.99606,-0.088662,273.96

> ui mousemode right "translate selected models"

> view matrix models
> #3.3,0.14513,-0.088186,0.98548,-9.5637,-0.98941,-0.0097211,0.14484,245.45,-0.0031925,-0.99606,-0.088662,272.25

> fitmap #3.3 inMap #4

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) using 14798 atoms  
average map value = 0.02261, steps = 92  
shifted from previous position = 1.22  
rotated from previous position = 1.81 degrees  
atoms outside contour = 12734, contour level = 0.14099  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.12473862 -0.09459051 0.98767044 -5.60017810  
-0.99182195 0.01521002 0.12671962 245.84198222  
-0.02700896 -0.99540005 -0.09191966 275.82933794  
Axis -0.63796447 0.57688090 -0.51010760  
Axis point 0.00000000 250.31512227 26.61265132  
Rotation angle (degrees) 118.42353627  
Shift along axis 4.69161518  
  

> show #!1 models

> select #1

2 models selected  

> select up

16194 atoms, 15047 bonds, 3387 residues, 6 models selected  

> select up

16194 atoms, 15047 bonds, 3387 residues, 6 models selected  

> select clear

> select #1

2 models selected  

> select #1

2 models selected  

> hide #!3.3 models

> hide #!4 models

> show #!3.3 models

> hide #!3.3 models

> show #!4 models

> show #!3.3 models

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99972,0.010829,0.020997,-4.1585,-0.0082457,0.99281,-0.11943,17.637,-0.02214,0.11923,0.99262,-12.145

> view matrix models
> #1,0.99924,0.0033342,0.038852,-5.4137,0.0012276,0.99315,-0.1168,15.989,-0.038975,0.11676,0.99239,-9.5469

> view matrix models
> #1,0.965,0.25995,0.034731,-34.87,-0.25609,0.96256,-0.088901,50.665,-0.05654,0.076895,0.99543,-2.2421

> view matrix models
> #1,0.98659,0.15809,0.04068,-24.804,-0.15375,0.98364,-0.093916,34.881,-0.054862,0.086401,0.99475,-3.6554

> view matrix models
> #1,0.99453,0.10441,0.00092792,-13.449,-0.10375,0.98919,-0.10366,28.76,-0.011741,0.103,0.99461,-11.602

> view matrix models
> #1,0.99644,0.06368,0.055258,-15.304,-0.058121,0.99359,-0.096964,21.23,-0.061079,0.093408,0.99375,-3.6425

> view matrix models
> #1,0.98134,0.072623,0.17804,-30.511,-0.055855,0.99367,-0.09745,20.981,-0.18399,0.085687,0.97919,15.63

> view matrix models
> #1,0.9823,0.070418,0.17356,-29.758,-0.057067,0.9951,-0.080758,18.774,-0.17839,0.069425,0.98151,16.773

> fitmap #1 inMap #4

Fit map cryosparc_P9_J40_002_volume_map_sharp.mrc in map
cryosparc_P8_J109_010_volume_map_sharp.mrc using 17046 points  
correlation = 0.1402, correlation about mean = 0.03028, overlap = 136  
steps = 96, shift = 0.622, angle = 1.41 degrees  
  
Position of cryosparc_P9_J40_002_volume_map_sharp.mrc (#1) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98656353 0.05937609 0.15220662 -26.64222569  
-0.04810364 0.99589280 -0.07670442 16.69801946  
-0.15613589 0.06835209 0.98536772 13.41386804  
Axis 0.40597152 0.86296208 -0.30080487  
Axis point 68.20371566 0.00000000 179.88398436  
Rotation angle (degrees) 10.29134385  
Shift along axis -0.44118394  
  

> select clear

> hide #!4 models

> hide #!3 models

> show #2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #!3 models

> hide #!3 models

> volume #1 level 0.2721

> hide #!1 models

> show #!1 models

> volume flip #1

Opened cryosparc_P9_J40_002_volume_map_sharp.mrc z flip as #5, grid size
128,128,128, pixel 2.02, shown at step 1, values float32  

> show #!3 models

> hide #!3.3 models

> show #!3.2 models

> close #3.2

> show #!3.1 models

> close #3.1

> show #!3.3 models

> fitmap #3.3 inMap #5

Fit molecule 6UXH_tetramer.pdb (#3.3) to map
cryosparc_P9_J40_002_volume_map_sharp.mrc z flip (#5) using 14798 atoms  
average map value = 0.3042, steps = 84  
shifted from previous position = 4.11  
rotated from previous position = 10.5 degrees  
atoms outside contour = 6851, contour level = 0.27214  
  
Position of 6UXH_tetramer.pdb (#3.3) relative to
cryosparc_P9_J40_002_volume_map_sharp.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.02464196 -0.00028542 0.99969630 -5.98689032  
-0.99950843 0.01938093 0.02464287 255.68551656  
-0.01938208 -0.99981213 0.00019231 261.96193766  
Axis -0.58312475 0.58006435 -0.56876258  
Axis point 0.00000000 259.18723649 4.42304207  
Rotation angle (degrees) 118.54784159  
Shift along axis 2.81100981  
  

> select clear

> show #!3.3 cartoons

> hide #!3.3 atoms

> show #2 models

> fitmap #2 inMap #5

Fit molecule 8tqf (#2) to map cryosparc_P9_J40_002_volume_map_sharp.mrc z flip
(#5) using 16194 atoms  
average map value = 0.2983, steps = 84  
shifted from previous position = 6.68  
rotated from previous position = 10.2 degrees  
atoms outside contour = 7528, contour level = 0.27214  
  
Position of 8tqf (#2) relative to cryosparc_P9_J40_002_volume_map_sharp.mrc z
flip (#5) coordinates:  
Matrix rotation and translation  
-0.21275976 0.92207154 0.32329145 105.12186949  
0.84582258 0.00814761 0.53340207 97.79178669  
0.48920082 0.38693371 -0.78164242 138.14664958  
Axis -0.62572293 -0.70877623 -0.32574079  
Axis point 6.10199479 0.00000000 46.28830282  
Rotation angle (degrees) 173.27873649  
Shift along axis -180.08965760  
  

> hide atoms

> show cartoons

> hide #!3 models

> show #2 atoms

> hide #2 cartoons

> select ::name="HOH"

2242 atoms, 2242 residues, 2 models selected  

> hide sel & #2 atoms

> view sel

No displayed objects specified.  

> ui tool show "Side View"

> volume #5 level 0.1734

> volume #5 level 0.2433

> volume #5 level 0.161

> view

> volume #5 level 0.1569

> volume #5 level 0.2804

> save "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_hexaglu_07152025/1.cxs"

——— End of log from Fri Sep 19 14:00:52 2025 ———

opened ChimeraX session  

> select ::name="S8R"

172 atoms, 180 bonds, 4 residues, 1 model selected  

> hide #* target a

> show sel target ab

> ui tool show "Surface Zone"

> surface zone #5 nearAtoms #2 distance 12.15

> surface zone #5 nearAtoms sel distance 12.15

> volume #1 level -0.2274

> surface zone #5 nearAtoms sel distance 12.15

[Repeated 1 time(s)]

> volume #1 level 0.432

> ui tool show "Side View"

> surface zone #5 nearAtoms sel distance 12.15

[Repeated 2 time(s)]

> surface unzone #5

> surface zone #5 nearAtoms sel distance 12.15

> volume #1 level 0.2059

> surface unzone #5

[Repeated 1 time(s)]

> volume #1 level 0.3519

> volume #1 level 0.8088

> surface zone #5 nearAtoms sel distance 12.15

> surface unzone #5

> show sel target ab

> select clear

> show #1-2,5 target ab

> hide : HOH

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!5 models

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-
> EM/PNCC/Essex_hexaglu_07152025/cryosparc_P9_J76_007_volume_map_sharp.mrc"

Opened cryosparc_P9_J76_007_volume_map_sharp.mrc as #6, grid size 512,512,512,
pixel 0.506, shown at level 0.0451, step 2, values float32  

> volume #5 level 0.3039

> volume #5 step 2

> volume #5 step 1

> hide #!5 models

> close #5

> hide #!6 models

> show #!6 models

> volume #6 level 0.07127

> volume #6 step 1

> volume #6 level 0.1042

> volume flip #6

Opened cryosparc_P9_J76_007_volume_map_sharp.mrc z flip as #5, grid size
512,512,512, pixel 0.506, shown at step 1, values float32  

> ui tool show "Fit in Map"

> fitmap #2 inMap #5

Fit molecule 8tqf (#2) to map cryosparc_P9_J76_007_volume_map_sharp.mrc z flip
(#5) using 16194 atoms  
average map value = 0.1155, steps = 140  
shifted from previous position = 2.61  
rotated from previous position = 8.93 degrees  
atoms outside contour = 8869, contour level = 0.10417  
  
Position of 8tqf (#2) relative to cryosparc_P9_J76_007_volume_map_sharp.mrc z
flip (#5) coordinates:  
Matrix rotation and translation  
-0.17787800 0.93348110 0.31140396 105.19916563  
0.85811348 -0.00775138 0.51340155 98.52023890  
0.48166445 0.35854278 -0.79965393 141.48442947  
Axis -0.63944210 -0.70303885 -0.31120762  
Axis point 4.10937327 0.00000000 48.49325291  
Rotation angle (degrees) 173.04504569  
Shift along axis -180.56336292  
  

> color #5 #b2b2b29b models

> select :SRS

Nothing selected  

> select :S8R

172 atoms, 180 bonds, 4 residues, 1 model selected  

> hide #* target a

> show sel target ab

> ui tool show "Surface Zone"

> surface zone #5 nearAtoms sel distance 3.04

[Repeated 3 time(s)]

> select :377,378,379,380,381,382,383,384,385,386,387,PLP, S8R

604 atoms, 616 bonds, 4 pseudobonds, 76 residues, 3 models selected  

> hide #* target a

> show (#2 & sel) target ab

> surface zone #5 nearAtoms sel distance 3.04

> select clear

> select :377,378,379,380,381,382,383,384,385,386,387,PLG, S8R

684 atoms, 696 bonds, 4 pseudobonds, 80 residues, 3 models selected  

> hide #* target a

> show (#2 & sel) target ab

> surface zone #5 nearAtoms sel distance 3.04

> select clear

> volume #1 level 1.341

> surface unzone #5

No atoms selected for zoning  

[Repeated 1 time(s)]

> select :377,378,379,380,381,382,383,384,385,386,387,PLG, S8R

684 atoms, 696 bonds, 4 pseudobonds, 80 residues, 3 models selected  

> surface zone #5 nearAtoms sel distance 3.04

> select clear

> surface unzone #5

> show #2,5 target ab

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-
> EM/PNCC/Essex_hexaglu_07152025/cryosparc_P9_J76_007_volume_mask_refine.mrc"

Opened cryosparc_P9_J76_007_volume_mask_refine.mrc as #7, grid size
512,512,512, pixel 0.506, shown at level 1, step 2, values float32  

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!5 models

> show #!5 models

> volume #7 level 1

> volume flip #7

Opened cryosparc_P9_J76_007_volume_mask_refine.mrc z flip as #8, grid size
512,512,512, pixel 0.506, shown at step 1, values float32  

> volume #5 level 0.1494

> volume #8 level 0.9815

> volume #8 level 1

> hide #!8 models

> show #!8 models

> color #8 #b2ffff9b models

> save "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_hexaglu_07152025/2.cxs"

——— End of log from Mon Sep 22 11:24:07 2025 ———

opened ChimeraX session  

> hide #!8 models

> molmap #2 and 12

Missing or invalid "resolution" argument: Expected a number  

> molmap 12 and #2

Missing or invalid "atoms" argument: invalid atoms specifier  

> molmap #2 12 onGrid #5

Opened 8tqf map 12 as #9, grid size 512,512,512, pixel 0.506, shown at level
0.0858, step 1, values float32  

> color #9 #ffb2ff0f models

> color #9 #ffb2ff01 models

> color #9 #ffb2ff73 models

> color #9 #ffb2ff01 models

> color #9 #ffb2ff9b models

> molmap #2 16 onGrid #5

Opened 8tqf map 16 as #9, grid size 512,512,512, pixel 0.506, shown at level
0.0679, step 1, values float32  

> color #9 #ffb2b29b models

> hide #!5 models

> show #!5 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> molmap #2 20 onGrid #5

Opened 8tqf map 20 as #9, grid size 512,512,512, pixel 0.506, shown at level
0.0555, step 1, values float32  

> color #9 #b2ffb29b models

> color #9 #b2ffb201 models

> color #9 #b2ffb20f models

> hide #!5 models

> show #!5 models

> hide #!9 models

> show #!9 models

> save "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_hexaglu_07152025/J76_flip_20_mask.mrc"
> models #9

> save "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_hexaglu_07152025/2.cxs"

> show #!8 models

> hide #!9 models

> show #!9 models

> color #9 #9bffb20f models

> color #9 #9affb20f models

> color #9 #9bffb20f models

> color #9 #9b9bb20f models

> color #9 #9b9b9b0f models

> color #9 #9b9b9b9b models

> hide #!9 models

> show #!9 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> hide #!8 models

> show #!8 models

> show #!9 models

> color #9 #aaffff9b models

> color #8 #9bffff9b models

> color #8 #9b9bff9b models

> color #8 #9b9b9b9b models

> hide #!9 models

> volume #9 level 0.275

> hide #!8 models

> volume #9 level 0.1259

> volume #9 level 0.08673

> hide #!9 models

> show #!8 models

> hide #!8 models

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-
> EM/PNCC/Essex_hexaglu_07152025/cryosparc_P9_J83_010_volume_map_sharp.mrc"

Opened cryosparc_P9_J83_010_volume_map_sharp.mrc as #10, grid size
512,512,512, pixel 0.506, shown at level 0.0499, step 2, values float32  

> volume flip #10

Opened cryosparc_P9_J83_010_volume_map_sharp.mrc z flip as #11, grid size
512,512,512, pixel 0.506, shown at step 1, values float32  

> volume #11 level 0.1073

> volume #11 step 2

> volume #11 step 4

> volume #11 step 1

> ui tool show "Fit in Map"

> fitmap #2 inMap #11

Fit molecule 8tqf (#2) to map cryosparc_P9_J83_010_volume_map_sharp.mrc z flip
(#11) using 16194 atoms  
average map value = 0.06565, steps = 44  
shifted from previous position = 0.0385  
rotated from previous position = 0.188 degrees  
atoms outside contour = 11364, contour level = 0.1073  
  
Position of 8tqf (#2) relative to cryosparc_P9_J83_010_volume_map_sharp.mrc z
flip (#11) coordinates:  
Matrix rotation and translation  
-0.17544553 0.93455024 0.30957178 105.19228725  
0.85800728 -0.00904125 0.51355792 98.54212507  
0.48274460 0.35571629 -0.80026467 141.50144574  
Axis -0.64033444 -0.70253022 -0.31052068  
Axis point 3.92525095 0.00000000 48.51465640  
Rotation angle (degrees) 172.92032961  
Shift along axis -180.52619083  
  

> hide #!5 models

> color #11 #e5bf9bff models

> color #11 #e5bf9b9b models

> color #11 #e59b9b9b models

> color #11 #9b9b9b9b models

> hide : HOH

> volume gaussian #11 sDev 1

Opened cryosparc_P9_J83_010_volume_map_sharp.mrc z flip gaussian as #12, grid
size 512,512,512, pixel 0.506, shown at step 1, values float32  

> volume #10 level 0.1064

> volume #12 level -0.02313

> volume #12 level 0.02925

> hide #!10 models

> color #12 #cccc999b models

> show #!11 models

> hide #!12 models

> lighting full

> lighting soft

> lighting simple

> fitmap #2 inMap #11

Fit molecule 8tqf (#2) to map cryosparc_P9_J83_010_volume_map_sharp.mrc z flip
(#11) using 16194 atoms  
average map value = 0.06565, steps = 40  
shifted from previous position = 0.00279  
rotated from previous position = 0.00341 degrees  
atoms outside contour = 11363, contour level = 0.1073  
  
Position of 8tqf (#2) relative to cryosparc_P9_J83_010_volume_map_sharp.mrc z
flip (#11) coordinates:  
Matrix rotation and translation  
-0.17540282 0.93456626 0.30954761 105.19274191  
0.85802575 -0.00905327 0.51352686 98.54302109  
0.48272730 0.35567388 -0.80029396 141.50077494  
Axis -0.64035102 -0.70252580 -0.31049650  
Axis point 3.92324509 -0.00000000 48.51558556  
Rotation angle (degrees) 172.92000265  
Shift along axis -180.52478949  
  

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-
> EM/PNCC/Essex_042725/cryosparc_P8_J109_010_volume_map_sharp.mrc"

Opened cryosparc_P8_J109_010_volume_map_sharp.mrc as #13, grid size
320,320,320, pixel 0.825, shown at level 0.052, step 2, values float32  

> volume #13 step 1

> volume #13 level 0.1048

> hide #!11 models

> fitmap #2 inMap #13

Fit molecule 8tqf (#2) to map cryosparc_P8_J109_010_volume_map_sharp.mrc (#13)
using 16194 atoms  
average map value = 0.02835, steps = 72  
shifted from previous position = 1.57  
rotated from previous position = 2.01 degrees  
atoms outside contour = 13138, contour level = 0.10477  
  
Position of 8tqf (#2) relative to cryosparc_P8_J109_010_volume_map_sharp.mrc
(#13) coordinates:  
Matrix rotation and translation  
-0.19947502 0.92844145 0.31337863 105.04054470  
0.84253187 -0.00079278 0.53864589 99.19741149  
0.50034962 0.37147788 -0.78208338 139.82271711  
Axis -0.63055897 -0.70525596 -0.32405157  
Axis point 4.35157943 0.00000000 46.67767166  
Rotation angle (degrees) 172.38271499  
Shift along axis -181.50359386  
  

> color #13 #b2b2b29b models

> hide #2 models

> show #2 models

> select #2/A:377@CG

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

76 atoms, 77 bonds, 12 residues, 1 model selected  

> select up

3580 atoms, 3664 bonds, 472 residues, 1 model selected  

> select up

4013 atoms, 3744 bonds, 829 residues, 1 model selected  

> select up

16194 atoms, 15047 bonds, 3387 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.19948,0.92844,0.31338,107.95,0.84253,-0.00079278,0.53865,98.992,0.50035,0.37148,-0.78208,143.3

> view matrix models
> #2,-0.19948,0.92844,0.31338,107.86,0.84253,-0.00079278,0.53865,100.29,0.50035,0.37148,-0.78208,143.66

> select clear

> fitmap #2 inMap #13

Fit molecule 8tqf (#2) to map cryosparc_P8_J109_010_volume_map_sharp.mrc (#13)
using 16194 atoms  
average map value = 0.2292, steps = 72  
shifted from previous position = 0.418  
rotated from previous position = 1.87 degrees  
atoms outside contour = 5688, contour level = 0.10477  
  
Position of 8tqf (#2) relative to cryosparc_P8_J109_010_volume_map_sharp.mrc
(#13) coordinates:  
Matrix rotation and translation  
-0.19174410 0.92348811 0.33227081 107.23648237  
0.85799690 -0.00665127 0.51361178 100.92651081  
0.47652439 0.38356936 -0.79107460 143.72099072  
Axis -0.63447237 -0.70380811 -0.31952927  
Axis point 5.03826357 0.00000000 48.58014976  
Rotation angle (degrees) 174.11795841  
Shift along axis -184.99454553  
  

> show #!11 models

> hide #!13 models

> select #2/B:6@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

53 atoms, 55 bonds, 7 residues, 1 model selected  

> select up

3613 atoms, 3697 bonds, 472 residues, 1 model selected  

> select up

4056 atoms, 3768 bonds, 848 residues, 1 model selected  

> select up

16194 atoms, 15047 bonds, 3387 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.19174,0.92349,0.33227,105.59,0.858,-0.0066513,0.51361,101.14,0.47652,0.38357,-0.79107,142.17

> view matrix models
> #2,-0.19174,0.92349,0.33227,105.44,0.858,-0.0066513,0.51361,98.692,0.47652,0.38357,-0.79107,141

> select clear

> fitmap #11 inMap #13

Fit map cryosparc_P9_J83_010_volume_map_sharp.mrc z flip in map
cryosparc_P8_J109_010_volume_map_sharp.mrc using 489224 points  
correlation = 0.1655, correlation about mean = 0.03257, overlap = 2621  
steps = 128, shift = 3.06, angle = 5.58 degrees  
  
Position of cryosparc_P9_J83_010_volume_map_sharp.mrc z flip (#11) relative to
cryosparc_P8_J109_010_volume_map_sharp.mrc (#13) coordinates:  
Matrix rotation and translation  
0.99529163 -0.02519224 -0.09359450 18.67380626  
0.02583888 0.99964985 0.00570332 -5.37754098  
0.09341805 -0.00809485 0.99559406 -10.04198034  
Axis -0.07099994 -0.96229288 0.26258602  
Axis point 120.07046565 0.00000000 194.39736187  
Rotation angle (degrees) 5.57624634  
Shift along axis 1.21204664  
  

> show #!13 models

> fitmap #2 inMap #11

Fit molecule 8tqf (#2) to map cryosparc_P9_J83_010_volume_map_sharp.mrc z flip
(#11) using 16194 atoms  
average map value = 0.06483, steps = 116  
shifted from previous position = 2.22  
rotated from previous position = 2.15 degrees  
atoms outside contour = 11426, contour level = 0.1073  
  
Position of 8tqf (#2) relative to cryosparc_P9_J83_010_volume_map_sharp.mrc z
flip (#11) coordinates:  
Matrix rotation and translation  
-0.12913944 0.96353252 0.23436737 105.79737078  
0.85881825 -0.00947964 0.51219266 98.61444925  
0.49573601 0.26742325 -0.82627513 143.27159346  
Axis -0.65607279 -0.70056487 -0.28067306  
Axis point 0.46967651 0.00000000 51.11256512  
Rotation angle (degrees) 169.24898993  
Shift along axis -178.70907078  
  

> hide #!13 models

> hide #!11 models

> show #!11 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!11 models

> select #13

2 models selected  

> view matrix models #13,1,0,0,0.64469,0,1,0,-5.8811,0,0,1,-2.5886

> fitmap #13 inMap #11

Fit map cryosparc_P8_J109_010_volume_map_sharp.mrc in map
cryosparc_P9_J83_010_volume_map_sharp.mrc z flip using 117002 points  
correlation = 0.3703, correlation about mean = 0.1736, overlap = 1915  
steps = 128, shift = 2.24, angle = 1.87 degrees  
  
Position of cryosparc_P8_J109_010_volume_map_sharp.mrc (#13) relative to
cryosparc_P9_J83_010_volume_map_sharp.mrc z flip (#11) coordinates:  
Matrix rotation and translation  
0.99365619 -0.00001185 0.11246059 -16.41861677  
0.00000803 1.00000000 0.00003440 -2.33460293  
-0.11246059 -0.00003328 0.99365619 12.76913618  
Axis -0.00030092 0.99999995 0.00008836  
Axis point 104.97522208 0.00000000 151.92220321  
Rotation angle (degrees) 6.45717773  
Shift along axis -2.32853381  
  

> show #!11 models

> select clear

> color #11 #ffaaff9b models

[Repeated 1 time(s)]

> color #11 #ffaa9b9b models

> hide #!11 models

> show #!11 models

> hide #!13 models

> select #2/A:170@CZ

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

107 atoms, 108 bonds, 13 residues, 1 model selected  

> select up

3580 atoms, 3664 bonds, 472 residues, 1 model selected  

> select up

4013 atoms, 3744 bonds, 829 residues, 1 model selected  

> select up

16194 atoms, 15047 bonds, 3387 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.19657,0.93421,0.2977,106.96,0.85801,0.016945,0.51336,96.325,0.47454,0.35633,-0.80489,140.92

> view matrix models
> #2,-0.19657,0.93421,0.2977,106.38,0.85801,0.016945,0.51336,96.535,0.47454,0.35633,-0.80489,140.3

> view matrix models
> #2,-0.19657,0.93421,0.2977,106.95,0.85801,0.016945,0.51336,96.294,0.47454,0.35633,-0.80489,140.55

> view matrix models
> #2,-0.19657,0.93421,0.2977,108.34,0.85801,0.016945,0.51336,95.8,0.47454,0.35633,-0.80489,142.2

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.23594,0.90523,0.35341,107.77,0.87205,0.036757,0.48804,96.003,0.4288,0.42333,-0.79807,141.54

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.23594,0.90523,0.35341,107.41,0.87205,0.036757,0.48804,96.295,0.4288,0.42333,-0.79807,142.85

> view matrix models
> #2,-0.23594,0.90523,0.35341,107.8,0.87205,0.036757,0.48804,96.179,0.4288,0.42333,-0.79807,143.54

> view matrix models
> #2,-0.23594,0.90523,0.35341,106.9,0.87205,0.036757,0.48804,96.583,0.4288,0.42333,-0.79807,143.38

> view matrix models
> #2,-0.23594,0.90523,0.35341,107.05,0.87205,0.036757,0.48804,96.479,0.4288,0.42333,-0.79807,143.03

> view matrix models
> #2,-0.23594,0.90523,0.35341,106.15,0.87205,0.036757,0.48804,97.977,0.4288,0.42333,-0.79807,143.61

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.44896,0.85346,0.26466,113.42,0.79892,0.25074,0.54668,93.476,0.40021,0.45688,-0.79442,143.36

> view matrix models
> #2,-0.38958,0.87628,0.28347,111.43,0.82395,0.19409,0.53239,94.534,0.4115,0.44097,-0.79763,143.56

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.38958,0.87628,0.28347,112.83,0.82395,0.19409,0.53239,92.323,0.4115,0.44097,-0.79763,142.39

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.38857,0.88105,0.26975,113.15,0.81068,0.18775,0.55457,91.962,0.43796,0.43417,-0.7872,141.74

> fitmap #2 inMap #11

Fit molecule 8tqf (#2) to map cryosparc_P9_J83_010_volume_map_sharp.mrc z flip
(#11) using 16194 atoms  
average map value = 0.06564, steps = 144  
shifted from previous position = 1.51  
rotated from previous position = 10.4 degrees  
atoms outside contour = 11364, contour level = 0.1073  
  
Position of 8tqf (#2) relative to cryosparc_P9_J83_010_volume_map_sharp.mrc z
flip (#11) coordinates:  
Matrix rotation and translation  
-0.17560754 0.93445322 0.30977273 105.18869292  
0.85796297 -0.00903676 0.51363202 98.54052513  
0.48276444 0.35597120 -0.80013935 141.49852583  
Axis -0.64027466 -0.70253474 -0.31063370  
Axis point 3.93378210 -0.00000000 48.50640520  
Rotation angle (degrees) 172.92781727  
Shift along axis -180.53200797  
  

> select clear

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-
> EM/PNCC/Essex_hexaglu_07152025/cryosparc_P9_J123_006_volume_map_sharp.mrc"

Opened cryosparc_P9_J123_006_volume_map_sharp.mrc as #14, grid size
512,512,512, pixel 0.506, shown at level 0.0357, step 2, values float32  

> volume #14 level 0.06579

> volume #14 step 1

> volume #14 level 0.07309

> hide #!11 models

> select #14

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #14,1,0,0,3.6122,0,1,0,0.95229,0,0,1,-2.2452

> show #!11 models

> hide #!14 models

> show #!14 models

> hide #!11 models

> color #14 #ffffb20f models

> color #14 #ffffb29b models

> color #14 #ff01b29b models

> color #14 #ffb1b29b models

> color #14 #ff01b29b models

> color #14 #ff9bb29b models

> color #14 #9b9bb29b models

> select clear

> volume flip #14

Opened cryosparc_P9_J123_006_volume_map_sharp.mrc z flip as #15, grid size
512,512,512, pixel 0.506, shown at step 1, values float32  

> volume flip #14

Opened cryosparc_P9_J123_006_volume_map_sharp.mrc z flip as #16, grid size
512,512,512, pixel 0.506, shown at step 1, values float32  

> volume flip #14

Opened cryosparc_P9_J123_006_volume_map_sharp.mrc z flip as #17, grid size
512,512,512, pixel 0.506, shown at step 1, values float32  

> close #17

> close #16

> close #15

> show #!14 models

> fitmap #2 inMap #14

Fit molecule 8tqf (#2) to map cryosparc_P9_J123_006_volume_map_sharp.mrc (#14)
using 16194 atoms  
average map value = 0.06228, steps = 120  
shifted from previous position = 1.27  
rotated from previous position = 8.02 degrees  
atoms outside contour = 10174, contour level = 0.073087  
  
Position of 8tqf (#2) relative to cryosparc_P9_J123_006_volume_map_sharp.mrc
(#14) coordinates:  
Matrix rotation and translation  
-0.13593155 0.93738889 0.32066284 103.69240557  
0.83505116 -0.06576264 0.54622781 97.72208531  
0.53311552 0.34201948 -0.77382846 142.97535698  
Axis -0.65462758 -0.68105633 -0.32806252  
Axis point 0.07196541 0.00000000 47.08639624  
Rotation angle (degrees) 171.02677368  
Shift along axis -181.33900834  
  

> save "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_hexaglu_07152025/3.cxs"

——— End of log from Mon Oct 6 09:58:42 2025 ———

opened ChimeraX session  

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-
> EM/PNCC/Essex_hexaglu_07152025/cryosparc_P9_J124_006_volume_map_sharp.mrc"

Opened cryosparc_P9_J124_006_volume_map_sharp.mrc as #15, grid size
512,512,512, pixel 0.506, shown at level 0.0367, step 2, values float32  

> hide #2 models

> volume #15 step 1

> volume #15 level 0.08937

> lighting soft

> graphics silhouettes true

> show #!14 models

> volume #14 color #9b9bb2

> save "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_hexaglu_07152025/4.cxs"

——— End of log from Mon Oct 13 10:26:51 2025 ———

> view name session-start

opened ChimeraX session  

> show #2 models

> color #14 #9b9bb20f models

> color #14 #9b9bb29b models

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-
> EM/PNCC/Essex_hexaglu_07152025/cryosparc_P9_J128_006_volume_map_sharp.mrc"

Opened cryosparc_P9_J128_006_volume_map_sharp.mrc as #16, grid size
512,512,512, pixel 0.506, shown at level 0.044, step 2, values float32  

> volume #16 level 0.1312

> volume #16 level 0.1245

> select #16

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.99985,-0.017346,-0.0010921,2.4015,0.017345,0.99985,-0.0015911,-2.0265,0.0011196,0.0015719,1,-0.34815

> view matrix models
> #16,0.57001,0.49505,0.65576,-93.03,-0.51116,0.83852,-0.18869,111.67,-0.64328,-0.22764,0.73101,147.76

> view matrix models
> #16,-0.84266,-0.23614,0.4839,207.1,-0.45432,-0.17051,-0.87437,323.41,0.28898,-0.95664,0.036405,210.83

> view matrix models
> #16,0.91074,0.19274,0.36524,-60.604,-0.39889,0.18154,0.89885,41.104,0.10694,-0.96431,0.24221,208.8

> view matrix models
> #16,0.92476,-0.12377,0.35986,-20.848,-0.3325,0.19719,0.92226,27.43,-0.18511,-0.97252,0.1412,260.86

> view matrix models
> #16,0.40445,-0.067178,0.91209,-32.111,-0.90244,0.13252,0.40993,176.14,-0.14841,-0.9889,-0.0070272,277.41

> view matrix models
> #16,0.37607,-0.050603,0.92521,-32.265,-0.79622,0.49305,0.35061,123.46,-0.47392,-0.86853,0.14513,284.42

> view matrix models
> #16,0.40073,-0.06582,0.91383,-32.028,-0.89633,0.17844,0.4059,169.93,-0.18978,-0.98175,0.01251,279.33

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.40073,-0.06582,0.91383,-25.889,-0.89633,0.17844,0.4059,170.44,-0.18978,-0.98175,0.01251,281.07

> hide #!14 models

> select up

16194 atoms, 15047 bonds, 3387 residues, 30 models selected  

> select up

16194 atoms, 15047 bonds, 3387 residues, 30 models selected  

> select up

16194 atoms, 15047 bonds, 3387 residues, 30 models selected  

> volume flip #16

Opened cryosparc_P9_J128_006_volume_map_sharp.mrc z flip as #17, grid size
512,512,512, pixel 0.506, shown at step 1, values float32  

> view matrix models
> #1,0.98656,0.059376,0.15221,-26.976,-0.048104,0.99589,-0.076704,17.826,-0.15614,0.068352,0.98537,11.591,#2,-0.13593,0.93739,0.32066,106.97,0.83505,-0.065763,0.54623,99.802,0.53312,0.34202,-0.77383,138.91,#3,1,0,0,-0.33336,0,1,0,1.1279,0,0,1,-1.8228,#4,1,0,0,-0.33336,0,1,0,1.1279,0,0,1,-1.8228,#6,1,0,0,-0.33336,0,1,0,1.1279,0,0,1,-1.8228,#5,1,0,0,-0.33336,0,1,0,1.1279,0,0,1,-1.8228,#7,1,0,0,-0.33336,0,1,0,1.1279,0,0,1,-1.8228,#8,1,0,0,-0.33336,0,1,0,1.1279,0,0,1,-1.8228,#9,1,0,0,-0.33336,0,1,0,1.1279,0,0,1,-1.8228,#10,1,0,0,-0.33336,0,1,0,1.1279,0,0,1,-1.8228,#11,0.99529,-0.025192,-0.093595,18.34,0.025839,0.99965,0.0057033,-4.2496,0.093418,-0.0080948,0.99559,-11.865,#12,1,0,0,-0.33336,0,1,0,1.1279,0,0,1,-1.8228,#13,0.9995,-0.025201,0.018929,0.86283,0.025042,0.99965,0.0086074,-6.9348,-0.01914,-0.0081291,0.99978,-0.66684,#14,1,0,0,3.2789,0,1,0,2.0802,0,0,1,-4.0681,#15,1,0,0,-0.33336,0,1,0,1.1279,0,0,1,-1.8228,#16,0.40073,-0.06582,0.91383,-26.223,-0.89633,0.17844,0.4059,171.57,-0.18978,-0.98175,0.01251,279.24

> hide #2 models

> show #2 models

> hide #!17 models

> view matrix models
> #1,0.98656,0.059376,0.15221,-24.641,-0.048104,0.99589,-0.076704,13.71,-0.15614,0.068352,0.98537,10.292,#2,-0.13593,0.93739,0.32066,109.31,0.83505,-0.065763,0.54623,95.687,0.53312,0.34202,-0.77383,137.61,#3,1,0,0,2.0013,0,1,0,-2.9878,0,0,1,-3.1218,#4,1,0,0,2.0013,0,1,0,-2.9878,0,0,1,-3.1218,#6,1,0,0,2.0013,0,1,0,-2.9878,0,0,1,-3.1218,#5,1,0,0,2.0013,0,1,0,-2.9878,0,0,1,-3.1218,#7,1,0,0,2.0013,0,1,0,-2.9878,0,0,1,-3.1218,#8,1,0,0,2.0013,0,1,0,-2.9878,0,0,1,-3.1218,#9,1,0,0,2.0013,0,1,0,-2.9878,0,0,1,-3.1218,#10,1,0,0,2.0013,0,1,0,-2.9878,0,0,1,-3.1218,#11,0.99529,-0.025192,-0.093595,20.675,0.025839,0.99965,0.0057033,-8.3653,0.093418,-0.0080948,0.99559,-13.164,#12,1,0,0,2.0013,0,1,0,-2.9878,0,0,1,-3.1218,#13,0.9995,-0.025201,0.018929,3.1974,0.025042,0.99965,0.0086074,-11.051,-0.01914,-0.0081291,0.99978,-1.9658,#14,1,0,0,5.6135,0,1,0,-2.0355,0,0,1,-5.367,#15,1,0,0,2.0013,0,1,0,-2.9878,0,0,1,-3.1218,#16,0.40073,-0.06582,0.91383,-23.888,-0.89633,0.17844,0.4059,167.46,-0.18978,-0.98175,0.01251,277.95

> ui mousemode right "rotate selected models"

> show #!17 models

> view matrix models
> #1,0.70672,-0.70487,-0.060825,139.11,0.69492,0.70773,-0.12732,-41.142,0.13279,0.04771,0.99,-26.024,#2,-0.81497,0.57904,-0.023223,137.89,0.3736,0.55561,0.74278,85.934,0.443,0.59666,-0.66914,131.21,#3,0.64612,-0.73131,-0.21846,171.46,0.70822,0.68116,-0.18558,-31.158,0.28452,-0.034811,0.95804,-30.713,#4,0.64612,-0.73131,-0.21846,171.46,0.70822,0.68116,-0.18558,-31.158,0.28452,-0.034811,0.95804,-30.713,#6,0.64612,-0.73131,-0.21846,171.46,0.70822,0.68116,-0.18558,-31.158,0.28452,-0.034811,0.95804,-30.713,#5,0.64612,-0.73131,-0.21846,171.46,0.70822,0.68116,-0.18558,-31.158,0.28452,-0.034811,0.95804,-30.713,#7,0.64612,-0.73131,-0.21846,171.46,0.70822,0.68116,-0.18558,-31.158,0.28452,-0.034811,0.95804,-30.713,#8,0.64612,-0.73131,-0.21846,171.46,0.70822,0.68116,-0.18558,-31.158,0.28452,-0.034811,0.95804,-30.713,#9,0.64612,-0.73131,-0.21846,171.46,0.70822,0.68116,-0.18558,-31.158,0.28452,-0.034811,0.95804,-30.713,#10,0.64612,-0.73131,-0.21846,171.46,0.70822,0.68116,-0.18558,-31.158,0.28452,-0.034811,0.95804,-30.713,#11,0.60377,-0.74556,-0.28214,189.66,0.70515,0.66458,-0.24716,-19.732,0.37178,-0.049721,0.92699,-34.834,#12,0.64612,-0.73131,-0.21846,171.46,0.70822,0.68116,-0.18558,-31.158,0.28452,-0.034811,0.95804,-30.713,#13,0.63167,-0.74556,-0.21248,177.88,0.72848,0.66458,-0.16627,-36.017,0.26517,-0.049757,0.96292,-28.985,#14,0.64612,-0.73131,-0.21846,173.59,0.70822,0.68116,-0.18558,-27.534,0.28452,-0.034811,0.95804,-31.87,#15,0.64612,-0.73131,-0.21846,171.46,0.70822,0.68116,-0.18558,-31.158,0.28452,-0.034811,0.95804,-30.713,#16,0.95586,0.04145,0.29087,-31.311,-0.29152,0.25713,0.92136,14.446,-0.036599,-0.96549,0.25786,225.26

> hide #2 models

> show #2 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> select clear

> color #17 #b2b2b20f models

> color #17 #b2b2b29b models

> show #!16 models

> hide #!17 models

> select #16

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.70334,-0.11717,-0.70113,150.43,-0.69168,-0.34034,-0.63698,345.38,-0.16399,0.93297,-0.32042,71.484

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.70334,-0.11717,-0.70113,150.67,-0.69168,-0.34034,-0.63698,346.08,-0.16399,0.93297,-0.32042,68.724

> view matrix models
> #16,0.70334,-0.11717,-0.70113,149.29,-0.69168,-0.34034,-0.63698,345,-0.16399,0.93297,-0.32042,68.406

> select clear

> ui tool show "Fit in Map"

> fitmap #2 inMap #16

Fit molecule 8tqf (#2) to map cryosparc_P9_J128_006_volume_map_sharp.mrc (#16)
using 16194 atoms  
average map value = 0.1057, steps = 152  
shifted from previous position = 1.97  
rotated from previous position = 8.46 degrees  
atoms outside contour = 10883, contour level = 0.12448  
  
Position of 8tqf (#2) relative to cryosparc_P9_J128_006_volume_map_sharp.mrc
(#16) coordinates:  
Matrix rotation and translation  
-0.85340036 0.01768483 -0.52095616 160.52270985  
0.49767656 0.32483801 -0.80423783 142.47935043  
0.15500355 -0.94560440 -0.28601814 153.58174916  
Axis -0.16809139 -0.80374737 0.57073238  
Axis point 40.08357589 0.00000000 148.15218009  
Rotation angle (degrees) 155.13352190  
Shift along axis -53.84581213  
  

> color #16 #b2b2b20f models

> color #16 #b2b2b29b models

> lighting soft

> lighting full

> show #!15 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!15 models

> select #15

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,-0.54548,-0.3598,0.75697,151.33,-0.73475,-0.22925,-0.63843,332.49,0.40324,-0.90443,-0.13931,208.8

> view matrix models
> #15,0.26927,0.25425,0.9289,-56.099,-0.94569,-0.11256,0.30495,222.46,0.18209,-0.96057,0.21014,199.44

> view matrix models
> #15,0.28336,-0.1081,0.9529,-14.079,-0.92472,0.23253,0.30136,175.49,-0.25415,-0.96656,-0.034074,288.4

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.28336,-0.1081,0.9529,-5.9717,-0.92472,0.23253,0.30136,178.46,-0.25415,-0.96656,-0.034074,289.01

> hide #!16 models

> volume #15 level 0.06592

> select clear

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> volume flip #15

Opened cryosparc_P9_J124_006_volume_map_sharp.mrc z flip as #18, grid size
512,512,512, pixel 0.506, shown at step 1, values float32  

> select #18

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #18,0.57906,-0.064502,0.81273,-31.847,-0.79234,0.1903,0.57964,130.86,-0.19205,-0.9796,0.059087,270.62

> view matrix models
> #18,0.58077,-0.13209,0.80328,-22.089,-0.76703,0.24178,0.59432,119.01,-0.27273,-0.9613,0.039101,281.29

> view matrix models
> #18,0.81225,-0.1276,0.56918,-22.451,-0.54984,0.15829,0.82014,72.536,-0.19474,-0.97911,0.058409,271

> view matrix models
> #18,0.42053,-0.11507,-0.89995,216.33,-0.90078,-0.17151,-0.39898,318.12,-0.10844,0.97844,-0.17578,36.367

> fitmap #2 inMap #18

Fit molecule 8tqf (#2) to map cryosparc_P9_J124_006_volume_map_sharp.mrc z
flip (#18) using 16194 atoms  
average map value = 0.01583, steps = 68  
shifted from previous position = 1.91  
rotated from previous position = 1.25 degrees  
atoms outside contour = 12756, contour level = 0.065924  
  
Position of 8tqf (#2) relative to cryosparc_P9_J124_006_volume_map_sharp.mrc z
flip (#18) coordinates:  
Matrix rotation and translation  
-0.66736885 -0.21464751 -0.71312346 166.50614993  
0.59187204 0.42830936 -0.68281654 136.54979625  
0.45200236 -0.87776841 -0.15879650 147.33390875  
Axis -0.13629339 -0.81455461 0.56384830  
Axis point 26.34921769 0.00000000 162.16289920  
Rotation angle (degrees) 134.34106329  
Shift along axis -50.84697830  
  

> show #!15 models

> hide #!18 models

> fitmap #2 inMap #15

Fit molecule 8tqf (#2) to map cryosparc_P9_J124_006_volume_map_sharp.mrc (#15)
using 16194 atoms  
average map value = 0.01656, steps = 96  
shifted from previous position = 1.4  
rotated from previous position = 1.84 degrees  
atoms outside contour = 12714, contour level = 0.065924  
  
Position of 8tqf (#2) relative to cryosparc_P9_J124_006_volume_map_sharp.mrc
(#15) coordinates:  
Matrix rotation and translation  
-0.64462044 -0.38369230 -0.66124477 168.13990635  
-0.40859301 -0.55812946 0.72217947 120.94297464  
-0.64615491 0.73571166 0.20300766 113.54904714  
Axis 0.42146947 -0.46998423 -0.77555033  
Axis point 115.36964807 25.03441655 0.00000000  
Rotation angle (degrees) 179.08015808  
Shift along axis -74.03845485  
  

> fitmap #2 inMap #15

Fit molecule 8tqf (#2) to map cryosparc_P9_J124_006_volume_map_sharp.mrc (#15)
using 16194 atoms  
average map value = 0.01656, steps = 28  
shifted from previous position = 0.00631  
rotated from previous position = 0.00452 degrees  
atoms outside contour = 12710, contour level = 0.065924  
  
Position of 8tqf (#2) relative to cryosparc_P9_J124_006_volume_map_sharp.mrc
(#15) coordinates:  
Matrix rotation and translation  
-0.64457301 -0.38373610 -0.66126559 168.13497188  
-0.40862543 -0.55810369 0.72218104 120.94019212  
-0.64618173 0.73570836 0.20293425 113.55196967  
Axis 0.42149765 -0.46999798 -0.77552668  
Axis point 115.37078979 25.03051312 0.00000000  
Rotation angle (degrees) 179.08055066  
Shift along axis -74.03573163  
  

> hide #!15 models

> show #!17 models

> hide #!17 models

> show #!16 models

> close #17

> fitmap #2 inMap #16

Fit molecule 8tqf (#2) to map cryosparc_P9_J128_006_volume_map_sharp.mrc (#16)
using 16194 atoms  
average map value = 0.1057, steps = 72  
shifted from previous position = 2.86  
rotated from previous position = 2.69 degrees  
atoms outside contour = 10885, contour level = 0.12448  
  
Position of 8tqf (#2) relative to cryosparc_P9_J128_006_volume_map_sharp.mrc
(#16) coordinates:  
Matrix rotation and translation  
-0.85341548 0.01767819 -0.52093162 160.52218344  
0.49765548 0.32481395 -0.80426060 142.48148454  
0.15498798 -0.94561280 -0.28599883 153.58103778  
Axis -0.16808288 -0.80374067 0.57074433  
Axis point 40.08510632 0.00000000 148.15310773  
Rotation angle (degrees) 155.13487638  
Shift along axis -53.84368800  
  

> view matrix models
> #18,0.42053,-0.11507,-0.89995,216.33,-0.90078,-0.17151,-0.39898,318.12,-0.10844,0.97844,-0.17578,36.367

> select ::name="S8R"

172 atoms, 180 bonds, 4 residues, 1 model selected  

> color sel forest green

> color sel byhetero

> select clear

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> volume #16 level 0.09987

> volume #16 step 1

> volume #16 level 0.1272

> volume gaussian #16 sDev 1

Opened cryosparc_P9_J128_006_volume_map_sharp.mrc gaussian as #17, grid size
512,512,512, pixel 0.506, shown at step 1, values float32  

> color #17 #b2b2ff0f models

> color #17 #b2b2ff9b models

> hide #!17 models

> show #!16 models

> open "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-
> EM/PNCC/Essex_hexaglu_07152025/cryosparc_P9_J129_006_volume_map_sharp.mrc"

Opened cryosparc_P9_J129_006_volume_map_sharp.mrc as #19, grid size
512,512,512, pixel 0.506, shown at level 0.0476, step 2, values float32  

> volume #19 level 0.1173

> color #19 #ffb2ff0f models

> color #19 #ffb2ff9b models

> select #19

2 models selected  

> select clear

> select #19

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #19,-0.073955,0.52637,0.84704,-38.804,-0.087541,-0.84951,0.52026,183.6,0.99341,-0.035674,0.1089,-8.6359

> view matrix models
> #19,0.10697,-0.50871,0.85427,70.945,-0.17986,-0.85492,-0.48658,326.74,0.97786,-0.1016,-0.18295,39.742

> view matrix models
> #19,0.064307,-0.51225,0.85643,76.653,-0.19099,-0.84866,-0.49326,328.23,0.97948,-0.13185,-0.15241,39.496

> view matrix models
> #19,-0.19856,0.83635,-0.51097,113.15,0.20155,-0.47536,-0.85639,276.05,-0.95914,-0.27303,-0.074182,298.87

> select clear

> select #19

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #19,-0.17233,-0.29167,-0.94087,311.64,0.3216,-0.91948,0.22614,177.76,-0.93106,-0.26361,0.25225,251.71

> view matrix models
> #19,0.38177,-0.29673,-0.87533,232,0.10171,-0.92782,0.35888,190.13,-0.91864,-0.22604,-0.32404,319.91

> view matrix models
> #19,-0.12032,-0.29121,-0.94906,305.9,0.30503,-0.9206,0.24381,177.76,-0.94471,-0.26016,0.1996,259.86

> ui mousemode right "translate selected models"

> view matrix models
> #19,-0.12032,-0.29121,-0.94906,303.47,0.30503,-0.9206,0.24381,174.64,-0.94471,-0.26016,0.1996,261.81

> ui mousemode right "rotate selected models"

> view matrix models
> #19,-0.17229,-0.29455,-0.93998,309.46,0.24714,-0.93665,0.24821,183.66,-0.95354,-0.18954,0.23417,249.32

> ui mousemode right "translate selected models"

> view matrix models
> #19,-0.17229,-0.29455,-0.93998,311.13,0.24714,-0.93665,0.24821,186.52,-0.95354,-0.18954,0.23417,249.17

> ui mousemode right "rotate selected models"

> view matrix models
> #19,-0.20671,0.69757,-0.68606,154.12,-0.18371,0.66106,0.7275,-26.797,0.961,0.27642,-0.008498,-27.861

> view matrix models
> #19,0.010823,0.68336,-0.73,133.46,-0.40885,0.66925,0.62044,15.19,0.91254,0.29174,0.28664,-61.813

> view matrix models
> #19,-0.077089,0.68873,-0.7209,142.98,-0.32369,0.6666,0.67147,-2.115,0.94302,0.28511,0.17155,-49.989

> ui mousemode right "translate selected models"

> view matrix models
> #19,-0.077089,0.68873,-0.7209,144.46,-0.32369,0.6666,0.67147,-1.7791,0.94302,0.28511,0.17155,-53.803

> view matrix models
> #19,-0.077089,0.68873,-0.7209,146.42,-0.32369,0.6666,0.67147,-3.451,0.94302,0.28511,0.17155,-54.905

> fitmap #2 inMap #19

Fit molecule 8tqf (#2) to map cryosparc_P9_J129_006_volume_map_sharp.mrc (#19)
using 16194 atoms  
average map value = 0.139, steps = 72  
shifted from previous position = 2.36  
rotated from previous position = 2 degrees  
atoms outside contour = 9100, contour level = 0.11726  
  
Position of 8tqf (#2) relative to cryosparc_P9_J129_006_volume_map_sharp.mrc
(#19) coordinates:  
Matrix rotation and translation  
0.47709725 0.38189645 -0.79153861 141.34273263  
-0.18971396 0.92417046 0.33153836 104.85959250  
0.85812992 -0.00801009 0.51337026 98.56194456  
Axis -0.19090711 -0.92750666 -0.32138121  
Axis point 17.07633603 0.00000000 129.68130542  
Rotation angle (degrees) 62.78576028  
Shift along axis -155.91725866  
  

> select clear

> hide #!16 models

> color #19 #afb2ff9b models

> color #19 #afafff9b models

> color #19 #afafaf9b models

> volume #19 step 1

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> volume gaussian #19 sDev 0.5

Opened cryosparc_P9_J129_006_volume_map_sharp.mrc gaussian as #20, grid size
512,512,512, pixel 0.506, shown at step 1, values float32  

> volume #20 level 0.05916

> select : 377,378

120 atoms, 120 bonds, 16 residues, 2 models selected  

> select : 377,378,379,380,381,382,383,384,385

368 atoms, 372 bonds, 4 pseudobonds, 56 residues, 3 models selected  

> color #20 #ffb2b201 models

> color #20 #ffb2b20f models

> color #20 #ffb2b29b models

> show #!19 models

> hide #!20 models

> select : 377,378,379,380,381,382,383,384,385,PLG,LLP,S8R

716 atoms, 728 bonds, 4 pseudobonds, 68 residues, 3 models selected  

> hide #* target a

> show (#2 & sel) target ab

> ui tool show "Surface Zone"

> surface zone #19 nearAtoms sel distance 3.04

> volume #19 level 0.1929

> volume #19 level 0.1002

> hide #!19 models

> view matrix models
> #2,-0.78607,0.61284,-0.08073,137.47,0.29531,0.48706,0.82193,87.66,0.54303,0.62225,-0.56384,126.99,#3.3,-0.037986,-0.15131,0.98776,24.074,-0.9951,0.096005,-0.023562,251.43,-0.091264,-0.98381,-0.15421,291.36

> undo

> surface unzone #19

> show (#2 & sel) target ab

> select clear

> show #2,19 target ab

> save "C:/Users/sssmnb/OneDrive - University of Missouri/Vindya - Beamer lab
> - Ogrp/Vindya/Cryo-EM/PNCC/Essex_hexaglu_07152025/6.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1058, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save  
fserialize(stream, data)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\safesave.py", line 151, in write  
self._f.write(buf)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 740, in write  
compressed = self._compressor.compress(data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
^^^^^^^^^^^^^^^  
MemoryError  
  
MemoryError  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\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 "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1058, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save  
fserialize(stream, data)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\safesave.py", line 151, in write  
self._f.write(buf)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 740, in write  
compressed = self._compressor.compress(data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
^^^^^^^^^^^^^^^  
MemoryError  
  
MemoryError  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2125
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

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

Manufacturer: Dell Inc.
Model: OptiPlex 5090
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 16,899,969,024
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    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: 2025.7.14
    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
    comtypes: 1.4.10
    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
    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: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    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
    pywin32: 310
    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
    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
    WMI: 1.5.1