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#18429 closed defect (can't reproduce)

Models with same ID in session

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

Description

The following bug report has been submitted:
Platform:        macOS-14.4-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope
> binning/MARV14_Fig.cxs"

Opened cryosparc_P662_J605_002_volume_map.mrc as #3, grid size 252,252,252,
pixel 1.6, shown at level 0.336, step 1, values float32  
Opened 250225-MARV-GP_MARV16.pdb map 4 as #5, grid size 46,55,60, pixel 2,
shown at level 0.0995, step 1, values float32  
Log from Wed Aug 13 15:36:20 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope
> binning/MARV14_Fig.cxs"

Opened cryosparc_P662_J605_002_volume_map.mrc as #3, grid size 252,252,252,
pixel 1.6, shown at level 0.336, step 1, values float32  
Opened 250225-MARV-GP_MARV16.pdb map 4 as #5, grid size 46,55,60, pixel 2,
shown at level 0.0995, step 1, values float32  
Log from Wed Aug 13 15:20:56 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV14/GP-
> MARV14-3.cxs

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened cryosparc_P662_J605_002_volume_map.mrc as #3, grid size 252,252,252,
pixel 1.6, shown at level 0.316, step 1, values float32  
Log from Tue Jul 29 16:02:53 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV14/cryosparc_P662_J603_005_volume_map.mrc

Opened cryosparc_P662_J603_005_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.0253, step 1, values float32  

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV14/cryosparc_P662_J604_002_volume_map.mrc

Opened cryosparc_P662_J604_002_volume_map.mrc as #2, grid size 252,252,252,
pixel 1.6, shown at level 0.038, step 1, values float32  

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV14/cryosparc_P662_J605_002_volume_map.mrc

Opened cryosparc_P662_J605_002_volume_map.mrc as #3, grid size 252,252,252,
pixel 1.6, shown at level 0.0608, step 1, values float32  

> hide #!2 models

> hide #!3 models

> volume #1 level 0.7408

> volume #1 level 0.3703

> volume #1 level 0.875

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/6BP2_GP.pdb

6BP2_GP.pdb title:  
Therapeutic human monoclonal antibody MR191 bound to A marburgvirus
glycoprotein [more info...]  
  
Chain information for 6BP2_GP.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
G M | No description available  
H N | No description available  
  
Non-standard residues in 6BP2_GP.pdb #4  
---  
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)  
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  

> hide atoms

> show cartoons

> ui mousemode right "translate selected models"

> select add #4

7320 atoms, 7481 bonds, 6 pseudobonds, 915 residues, 2 models selected  

> view matrix models #4,1,0,0,-79.334,0,1,0,112.12,0,0,1,114.37

> view matrix models #4,1,0,0,-4.8987,0,1,0,145.29,0,0,1,148.6

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.93851,-0.30592,0.16006,4.3835,-0.25205,-0.92389,-0.28791,289.62,0.23596,0.22986,-0.94419,262.74

> view matrix models
> #4,-0.21533,-0.95693,0.19472,255.68,-0.94989,0.25152,0.18562,346.06,-0.2266,-0.14499,-0.96314,370.41

> view matrix models
> #4,-0.70579,-0.7072,-0.04154,365.58,-0.70718,0.70681,-0.017574,298.91,0.041789,0.016973,-0.99898,314.01

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.70579,-0.7072,-0.04154,361.02,-0.70718,0.70681,-0.017574,312.04,0.041789,0.016973,-0.99898,286.45

> view matrix models
> #4,-0.70579,-0.7072,-0.04154,368.29,-0.70718,0.70681,-0.017574,316.91,0.041789,0.016973,-0.99898,287.03

> ui tool show "Fit in Map"

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J603_005_volume_map.mrc
(#1) using 7320 atoms  
average map value = 1.335, steps = 300  
shifted from previous position = 19.4  
rotated from previous position = 87.2 degrees  
atoms outside contour = 1699, contour level = 0.875  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J603_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.29143259 -0.91701277 -0.27231348 203.00955231  
-0.31453534 0.17698123 -0.93260129 330.13745437  
0.90340166 0.35744262 -0.23685482 26.49261354  
Axis 0.69864933 -0.63673227 0.32628382  
Axis point 0.00000000 235.62887688 105.27200708  
Rotation angle (degrees) 112.59535630  
Shift along axis -59.73257329  
  

> volume #1 color #b2b2b280

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.24928,-0.91639,-0.31317,214.99,-0.38948,0.20121,-0.89879,341.33,0.88666,0.34603,-0.30676,36.352

> view matrix models
> #4,-0.04818,-0.94695,0.31775,220.61,-0.8338,0.21329,0.50921,307.04,-0.54997,-0.24041,-0.79984,388.01

> view matrix models
> #4,0.69062,-0.71625,0.10015,83.406,-0.61594,-0.50992,0.6005,281.29,-0.37904,-0.4764,-0.79333,361.64

> view matrix models
> #4,0.94241,-0.2826,0.17891,10.619,-0.31842,-0.92176,0.22131,269.51,0.10237,-0.26553,-0.95865,272.13

> view matrix models
> #4,0.99728,-0.0505,0.05364,2.2643,-0.055165,-0.99447,0.089387,230.9,0.04883,-0.092103,-0.99455,279.78

> view matrix models
> #4,0.74992,-0.336,-0.56985,116.39,-0.22258,-0.93934,0.26095,247.49,-0.62296,-0.06885,-0.77922,394.69

> view matrix models
> #4,-0.033891,-0.99918,-0.022207,249.27,-0.95557,0.025886,0.29364,356.93,-0.29282,0.031172,-0.95566,340.4

> view matrix models
> #4,-0.031887,-0.99919,-0.024522,249.07,-0.95511,0.023232,0.29535,356.78,-0.29454,0.032839,-0.95507,340.64

> view matrix models
> #4,-0.28728,-0.95582,0.0623,291.09,-0.91636,0.29319,0.27263,341.36,-0.27885,0.021234,-0.9601,338.35

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.28728,-0.95582,0.0623,288.23,-0.91636,0.29319,0.27263,345.44,-0.27885,0.021234,-0.9601,334.16

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J603_005_volume_map.mrc
(#1) using 7320 atoms  
average map value = 1.335, steps = 280  
shifted from previous position = 5.5  
rotated from previous position = 68.8 degrees  
atoms outside contour = 1697, contour level = 0.875  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J603_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.32069767 -0.66843915 -0.67107533 342.07480289  
-0.56358529 -0.43476669 0.70238846 274.14654524  
-0.76126515 0.60346253 -0.23729381 351.14496966  
Axis -0.58176753 0.53039184 0.61662876  
Axis point 330.20086844 1.14100398 -0.00000000  
Rotation angle (degrees) 175.12271742  
Shift along axis 162.92316640  
  

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J603_005_volume_map.mrc
(#1) using 7320 atoms  
average map value = 1.335, steps = 280  
shifted from previous position = 5.5  
rotated from previous position = 68.8 degrees  
atoms outside contour = 1697, contour level = 0.875  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J603_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.32069767 -0.66843915 -0.67107533 342.07480289  
-0.56358529 -0.43476669 0.70238846 274.14654524  
-0.76126515 0.60346253 -0.23729381 351.14496966  
Axis -0.58176753 0.53039184 0.61662876  
Axis point 330.20086844 1.14100398 -0.00000000  
Rotation angle (degrees) 175.12271742  
Shift along axis 162.92316640  
  
Average map value = 1.335 for 7320 atoms, 1697 outside contour  

> view matrix models
> #4,-0.28728,-0.95582,0.0623,288.7,-0.91636,0.29319,0.27263,347.12,-0.27885,0.021234,-0.9601,326.46

> view matrix models
> #4,-0.28728,-0.95582,0.0623,288.29,-0.91636,0.29319,0.27263,338.56,-0.27885,0.021234,-0.9601,333.05

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.83982,-0.53961,0.059346,384.32,-0.54285,0.83383,-0.10021,276.97,0.0045897,-0.11637,-0.99319,284.09

> view matrix models
> #4,-0.99197,-0.030841,-0.12265,412.49,-0.034097,0.99912,0.024534,158.3,0.12178,0.028519,-0.99215,255.36

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.99197,-0.030841,-0.12265,414.64,-0.034097,0.99912,0.024534,163.42,0.12178,0.028519,-0.99215,259.34

> view matrix models
> #4,-0.99197,-0.030841,-0.12265,413.67,-0.034097,0.99912,0.024534,168.8,0.12178,0.028519,-0.99215,257.37

> volume #1 level 0.5492

> view matrix models
> #4,-0.99197,-0.030841,-0.12265,411.48,-0.034097,0.99912,0.024534,168.15,0.12178,0.028519,-0.99215,256.8

> select subtract #4

Nothing selected  

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J603_005_volume_map.mrc
(#1) using 7320 atoms  
average map value = 1.169, steps = 96  
shifted from previous position = 5.48  
rotated from previous position = 23.7 degrees  
atoms outside contour = 1708, contour level = 0.54918  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J603_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.93524537 0.35399792 0.00125607 375.50492340  
0.35399392 0.93524408 -0.00261042 94.63831101  
-0.00209882 -0.00199674 -0.99999580 277.97537979  
Axis 0.17993498 0.98367781 -0.00117096  
Axis point 179.21736561 0.00000000 138.89377969  
Rotation angle (degrees) 179.90229458  
Shift along axis 160.33457918  
  

> show #!2 models

> volume #2 color #929292

> volume #2 color #9292927a

> volume #2 level 0.9083

> hide #!1 models

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J603_005_volume_map.mrc
(#1) using 7320 atoms  
average map value = 1.169, steps = 28  
shifted from previous position = 0.0263  
rotated from previous position = 0.0354 degrees  
atoms outside contour = 1712, contour level = 0.54918  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J603_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.93546420 0.35341923 0.00125992 375.57129708  
0.35341523 0.93546291 -0.00261026 94.74549508  
-0.00210113 -0.00199653 -0.99999580 278.00217372  
Axis 0.17963068 0.98373342 -0.00117080  
Axis point 179.25611248 -0.00000000 138.90692141  
Rotation angle (degrees) 179.90212075  
Shift along axis 160.34295239  
  

> fitmap #4 inMap #2

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J604_002_volume_map.mrc
(#2) using 7320 atoms  
average map value = 1.465, steps = 184  
shifted from previous position = 3.42  
rotated from previous position = 48.9 degrees  
atoms outside contour = 2043, contour level = 0.9083  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J604_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.90494746 0.03768723 0.42385111 352.54721860  
-0.20643879 0.83211643 -0.51474778 248.07390814  
-0.37209289 -0.55331901 -0.74524154 353.56141913  
Axis -0.04627988 0.95501752 -0.29291586  
Axis point 226.60866985 0.00000000 173.91486692  
Rotation angle (degrees) 155.37251148  
Shift along axis 117.03533662  
  

> volume #2 level 0.8171

> volume #2 color darkgrey

> ui mousemode right "rotate selected models"

> select add #4

7320 atoms, 7481 bonds, 6 pseudobonds, 915 residues, 2 models selected  

> view matrix models
> #4,0.76488,0.62938,-0.1373,45.975,-0.5991,0.61668,-0.51066,334.05,-0.23673,0.47285,0.84875,150.73

> view matrix models
> #4,0.80422,0.55915,-0.20144,46.202,-0.56724,0.82329,0.020652,273.93,0.17739,0.097659,0.97928,69.822

> view matrix models
> #4,0.84385,0.53614,-0.021753,23.413,-0.52843,0.83738,0.13983,255.26,0.093186,-0.1065,0.98994,93.051

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.84385,0.53614,-0.021753,11.665,-0.52843,0.83738,0.13983,252.7,0.093186,-0.1065,0.98994,98.495

> view matrix models
> #4,0.84385,0.53614,-0.021753,11.002,-0.52843,0.83738,0.13983,263.55,0.093186,-0.1065,0.98994,108.74

> view matrix models
> #4,0.84385,0.53614,-0.021753,6.9264,-0.52843,0.83738,0.13983,264.83,0.093186,-0.1065,0.98994,103.94

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.12486,0.90265,0.41188,99.979,-0.26208,-0.37038,0.89114,189.1,0.95694,-0.21921,0.19032,4.7571

> view matrix models
> #4,0.73857,0.67358,0.028444,18.718,-0.66786,0.72524,0.16731,294.36,0.092066,-0.14257,0.98549,105.84

> fitmap #4 inMap #2

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J604_002_volume_map.mrc
(#2) using 7320 atoms  
average map value = 1.413, steps = 240  
shifted from previous position = 10.3  
rotated from previous position = 73.6 degrees  
atoms outside contour = 2112, contour level = 0.81712  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J604_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.43065815 0.90251164 -0.00250933 253.41394628  
-0.90251484 -0.43065858 0.00039244 399.32478478  
-0.00072648 0.00243371 0.99999678 125.67101449  
Axis 0.00113088 -0.00098771 -0.99999887  
Axis point 252.69355438 119.62383747 0.00000000  
Rotation angle (degrees) 115.50945134  
Shift along axis -125.77870924  
  

> volume #2 color #a9a9a98a

> fitmap #4 inMap #2

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J604_002_volume_map.mrc
(#2) using 7320 atoms  
average map value = 1.413, steps = 44  
shifted from previous position = 0.029  
rotated from previous position = 0.0239 degrees  
atoms outside contour = 2110, contour level = 0.81712  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J604_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.43028333 0.90269033 -0.00253388 253.33440976  
-0.90269357 -0.43028385 0.00036348 399.33839798  
-0.00076217 0.00244371 0.99999672 125.65056164  
Axis 0.00115224 -0.00098134 -0.99999885  
Axis point 252.71760875 119.61851769 0.00000000  
Rotation angle (degrees) 115.48566293  
Shift along axis -125.75040435  
  

> fitmap #4 inMap #2

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J604_002_volume_map.mrc
(#2) using 7320 atoms  
average map value = 1.413, steps = 44  
shifted from previous position = 0.0146  
rotated from previous position = 0.0228 degrees  
atoms outside contour = 2111, contour level = 0.81712  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J604_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.42993547 0.90285613 -0.00251107 253.25710199  
-0.90285923 -0.42993621 0.00026626 399.38004028  
-0.00083920 0.00238162 0.99999681 125.66678414  
Axis 0.00117147 -0.00092587 -0.99999889  
Axis point 252.74929224 119.63232299 0.00000000  
Rotation angle (degrees) 115.46358966  
Shift along axis -125.73973497  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.41504,0.89975,0.13489,72.176,-0.90613,0.39549,0.15004,357.47,0.081656,-0.1845,0.97943,117.62

> fitmap #4 inMap #2

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J604_002_volume_map.mrc
(#2) using 7320 atoms  
average map value = 1.413, steps = 164  
shifted from previous position = 1.42  
rotated from previous position = 50.9 degrees  
atoms outside contour = 2112, contour level = 0.81712  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J604_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.43032421 0.90267120 -0.00240722 253.33017808  
-0.90267426 -0.43032414 0.00057129 399.32386688  
-0.00052020 0.00241877 0.99999694 125.63266347  
Axis 0.00102334 -0.00104524 -0.99999893  
Axis point 252.69398523 119.61766300 0.00000000  
Rotation angle (degrees) 115.48823178  
Shift along axis -125.79067554  
  

> view matrix models
> #4,0.22927,0.97268,-0.036439,121.72,-0.97326,0.22964,0.0062788,389.38,0.014475,0.034025,0.99932,121.53

> view matrix models
> #4,0.54536,0.83731,0.038742,56.698,-0.83779,0.54306,0.056454,346.68,0.02623,-0.063245,0.99765,122.8

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.54536,0.83731,0.038742,57.044,-0.83779,0.54306,0.056454,342.87,0.02623,-0.063245,0.99765,121.47

> fitmap #4 inMap #2

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J604_002_volume_map.mrc
(#2) using 7320 atoms  
average map value = 1.413, steps = 196  
shifted from previous position = 2.19  
rotated from previous position = 58.6 degrees  
atoms outside contour = 2109, contour level = 0.81712  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J604_002_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.43006346 0.90279561 -0.00234758 253.27123891  
-0.90279831 -0.43006412 0.00024001 399.36837343  
-0.00079293 0.00222262 0.99999722 125.66634334  
Axis 0.00109803 -0.00086102 -0.99999903  
Axis point 252.73086843 119.64156807 0.00000000  
Rotation angle (degrees) 115.47169670  
Shift along axis -125.73198544  
  

> select subtract #4

Nothing selected  

> show #!3 models

> hide #!2 models

> volume #2 level 1.331

> hide #!2 models

> volume #3 level 0.5283

> volume #3 color darkgrey

> volume #3 color #a9a9a980

> fitmap #4 inMap #3

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J605_002_volume_map.mrc
(#3) using 7320 atoms  
average map value = 1.465, steps = 172  
shifted from previous position = 5.61  
rotated from previous position = 41 degrees  
atoms outside contour = 1084, contour level = 0.52835  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J605_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
0.96038777 0.27866476 0.00113158 -2.00269248  
-0.27866539 0.96038815 0.00044856 220.39466772  
-0.00096176 -0.00074613 0.99999926 118.97195063  
Axis -0.00214357 0.00375598 -0.99999065  
Axis point 775.66178941 118.35591513 0.00000000  
Rotation angle (degrees) 16.18070380  
Shift along axis -118.13874717  
  

> volume #3 level 0.3725

> volume #3 level 0.245

> fitmap #4 inMap #3

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J605_002_volume_map.mrc
(#3) using 7320 atoms  
average map value = 1.465, steps = 44  
shifted from previous position = 0.0304  
rotated from previous position = 0.0116 degrees  
atoms outside contour = 474, contour level = 0.24499  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J605_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
0.96039622 0.27863477 0.00132960 -1.99377596  
-0.27863553 0.96039683 0.00042300 220.40820901  
-0.00115908 -0.00077672 0.99999903 119.01463450  
Axis -0.00215283 0.00446577 -0.99998771  
Axis point 776.09325876 118.37750813 0.00000000  
Rotation angle (degrees) 16.17896721  
Shift along axis -118.02458644  
  

> volume #3 level 0.4646

> volume #3 level 0.3158

> show #!1 models

> hide #!3 models

> open
> /Users/aminaddetia/Downloads/cryosparc_P662_J608_class_00_00700_volume.mrc

Opened cryosparc_P662_J608_class_00_00700_volume.mrc as #5, grid size
128,128,128, pixel 3.15, shown at level 0.125, step 1, values float32  

> hide #!1 models

> volume #5 level 1.224

> volume #5 level 1.209

> volume #5 level 3.069

> volume #5 level 0.6669

> close #5

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV14/GP-
> MARV14-3.cxs

——— End of log from Tue Jul 29 16:02:53 2025 ———

opened ChimeraX session  

> show #!3 models

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/GP-
> MARV16_krios/250225-MARV-GP_MARV16.pdb

Chain information for 250225-MARV-GP_MARV16.pdb #1  
---  
Chain | Description  
A C G | No description available  
B D I | No description available  
E H J | No description available  
F K L | No description available  
  

> hide atoms

> show cartoons

> ui tool show Matchmaker

> matchmaker #!1 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6BP2_GP.pdb, chain A (#4) with 250225-MARV-GP_MARV16.pdb, chain C
(#1), sequence alignment score = 809.1  
RMSD between 129 pruned atom pairs is 0.644 angstroms; (across all 142 pairs:
1.417)  
  

> select #1/E,H,J,F,K,L

5211 atoms, 5328 bonds, 678 residues, 1 model selected  

> delete sel

> volume #3 level 0.3778

> volume #3 level 0.3365

> ui tool show "Segment Map"

Segmenting cryosparc_P662_J605_002_volume_map.mrc, density threshold 0.336468  
Showing 7 region surfaces  
13 watershed regions, grouped to 7 regions  
Showing cryosparc_P662_J605_002_volume_map.seg - 7 regions, 7 surfaces  
Smoothing and grouping, standard deviation 5 voxels  
No new groups smoothing 5 voxels  
No new groups smoothing 6 voxels  
Showing 4 region surfaces  
Got 4 regions after smoothing 7 voxels.  

> select add #2.1

1 model selected  

> color #2.1 #b7e0ca79

Simulating map res 4.000, grid 2.000  

> molmap #1 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 250225-MARV-GP_MARV16.pdb map 4 as #5, grid size 46,55,60, pixel 2,
shown at level 0.0995, step 1, values float32  
Opened cryosparc_P662_J605_002_volume_map_masked as #6, grid size 252,252,252,
pixel 1.6, shown at step 1, values float32  
Top score: 0.71593, z-score: 1.40362 (avg: 0.7093, stdev: 0.0047)  

> ui tool show Matchmaker

> matchmaker #!4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain C (#1) with 6BP2_GP.pdb, chain A
(#4), sequence alignment score = 809.1  
RMSD between 129 pruned atom pairs is 0.644 angstroms; (across all 142 pairs:
1.417)  
  

> hide #!1 models

> set bgColor white

> color #2.1 #bcbcbc72

> select subtract #2.1

Nothing selected  

> select add #2

5 models selected  

> select subtract #2

Nothing selected  

> lighting soft depthCue true depthCueStart 0.42 depthCueEnd 0.8

> graphics silhouettes true width 2

[Repeated 1 time(s)]

> lighting soft depthCue true depthCueStart 0.42 depthCueEnd 0.8

> lighting soft depthCue true depthCueStart 0.42 depthCueEnd 2

> cartoon style modeHelix default arrows false xsection round width 2
> thickness 2

> color #2.7 #fdee8cff

> color #2.6 #fdee8cff

> color #2.5 #fdee8cff

> cd "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope binning"

Current working directory is:
/Users/aminaddetia/Library/CloudStorage/GoogleDrive-aaddetia@uw.edu/Shared
drives/Veesler_lab/Amin Addetia/MARV/Paper/Revision/Supplemental
figures/Epitope binning  

> save "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope
> binning/MARV14_Fig.cxs"

> save MARV14-side.tif width 3000 height 3000 supersample 10

> save "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope
> binning/MARV14_Fig.cxs"

——— End of log from Wed Aug 13 15:20:56 2025 ———

opened ChimeraX session  
Showing cryosparc_P662_J605_002_volume_map.seg - 4 regions, 4 surfaces  

> color #2 #848686ff

> undo

> hide #2.1 models

> show #2.1 models

> hide #2.2 models

> hide #2.3 models

> show #2.3 models

> show #2.2 models

> hide #2.4 models

> show #2.4 models

> color #2.4 #84868672

> color #2.4 #84868680

> cd "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope binning"

Current working directory is:
/Users/aminaddetia/Library/CloudStorage/GoogleDrive-aaddetia@uw.edu/Shared
drives/Veesler_lab/Amin Addetia/MARV/Paper/Revision/Supplemental
figures/Epitope binning  

> save "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope
> binning/MARV14_Fig.cxs"

——— End of log from Wed Aug 13 15:36:20 2025 ———

opened ChimeraX session  
Showing cryosparc_P662_J605_002_volume_map.seg - 4 regions, 4 surfaces  

> open "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope
> binning/MARV7_Fig.cxs"

Opened cryosparc_P662_J528_002_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.515, step 1, values float32  
Opened 250225-MARV-GP_MARV16.pdb map 4 as #6, grid size 46,55,60, pixel 2,
shown at level 0.0995, step 1, values float32  
Opened 6BP2_GP.pdb map 4 as #7, grid size 52,50,61, pixel 2, shown at level
0.103, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 757, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 574, in restore_snapshot  
m.set_state_from_snapshot(session, data)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 397, in set_state_from_snapshot  
p.add([self])  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 314, in add  
om.add(models, parent = self)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 756, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 825, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
ValueError: Tried to add model 39 #5.2 with the same id as another model 39
#5.2  
  
Log from Wed Aug 13 16:46:18 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/GP-
> MARV7-v2.cxs

Opened cryosparc_P662_J528_002_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.52, step 1, values float32  
Log from Tue Jul 29 13:10:27 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/GP-
> MARV7.cxs

Opened cryosparc_P662_J528_002_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.52, step 1, values float32  
Log from Wed Jun 18 15:33:55 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV18/GP-
> MARV18.cxs

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Log from Wed Jun 18 14:42:12 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/aminaddetia/Downloads/cryosparc_P662_J524_005_volume_map
> (1).mrc"

Opened cryosparc_P662_J524_005_volume_map (1).mrc as #1, grid size
252,252,252, pixel 1.6, shown at level 0.0881, step 1, values float32  

> volume #1 level 0.3998

> open /Users/aminaddetia/Downloads/cryosparc_P662_J526_004_volume_map.mrc

Opened cryosparc_P662_J526_004_volume_map.mrc as #2, grid size 252,252,252,
pixel 1.6, shown at level 0.149, step 1, values float32  

> hide #!1 models

> volume #2 level 0.1033

> volume #2 color #ffffb282

> volume #2 color #929292

> volume #2 color #92929280

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/GP-
> MARV16_krios/250225-MARV-GP_MARV16.pdb

Chain information for 250225-MARV-GP_MARV16.pdb #3  
---  
Chain | Description  
A C G | No description available  
B D I | No description available  
E H J | No description available  
F K L | No description available  
  

> hide atoms

> show cartoons

> select /H:1-119

931 atoms, 952 bonds, 119 residues, 1 model selected  

> select /L:1-107

806 atoms, 824 bonds, 107 residues, 1 model selected  

> select #3/E,H,J,F,J,K

4405 atoms, 4504 bonds, 571 residues, 1 model selected  

> select #3/E,H,J,F,J,K,L

5211 atoms, 5328 bonds, 678 residues, 1 model selected  

> delsel

Unknown command: delsel  

> delete sel

> select add #3

6691 atoms, 6863 bonds, 6 pseudobonds, 823 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.53492,0.82857,0.16529,-110.76,0.74453,-0.36979,-0.55581,243.86,-0.39941,0.42038,-0.81471,351.96

> view matrix models
> #3,-0.71377,0.68499,0.14601,193.33,0.65631,0.72695,-0.20201,-43.032,-0.24452,-0.048365,-0.96844,449.79

> view matrix models
> #3,-0.60981,0.59858,0.51946,116.19,0.72755,0.68274,0.067355,-101.78,-0.31434,0.419,-0.85184,341.2

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.60981,0.59858,0.51946,102.77,0.72755,0.68274,0.067355,-103.14,-0.31434,0.419,-0.85184,378.21

> view matrix models
> #3,-0.60981,0.59858,0.51946,104.37,0.72755,0.68274,0.067355,-106.59,-0.31434,0.419,-0.85184,377.66

> volume #2 level 0.5917

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.090782,-0.99288,0.077084,383.22,-0.96222,-0.1074,-0.25021,490.62,0.25671,-0.051457,-0.96512,378.15

> view matrix models
> #3,-0.96447,-0.036395,0.26167,368.4,0.02512,0.97334,0.22797,-49.261,-0.26299,0.22644,-0.93785,424.99

> view matrix models
> #3,-0.98911,-0.12438,-0.078725,459.53,-0.13389,0.98242,0.13011,2.3048,0.061159,0.13923,-0.98837,383.79

> view matrix models
> #3,-0.97709,-0.15092,-0.15008,476.68,-0.18294,0.95591,0.22972,-0.9659,0.10879,0.25191,-0.96162,343.97

> view matrix models
> #3,-0.81942,0.17306,-0.54645,450.67,-0.53186,0.12593,0.83742,133.87,0.21374,0.97683,-0.011148,-21.622

> view matrix models
> #3,-0.83248,0.13518,-0.53731,459.86,-0.53801,0.034502,0.84223,153.96,0.13239,0.99022,0.044006,-17.795

> view matrix models
> #3,-0.68517,-0.47515,0.55207,345.7,-0.15899,0.83722,0.52325,-38.197,-0.71082,0.27074,-0.64917,455.35

> view matrix models
> #3,-0.86021,-0.50437,0.075165,483.42,-0.48723,0.85642,0.17074,97.705,-0.15049,0.11025,-0.98244,434.53

> view matrix models
> #3,-0.84724,-0.52178,-0.099607,518.71,-0.5273,0.80341,0.27656,96.992,-0.064281,0.28684,-0.95582,372.64

> view matrix models
> #3,-0.66168,-0.73564,-0.14495,533.69,-0.72799,0.58404,0.35907,171.37,-0.17949,0.34311,-0.92199,378.71

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.66168,-0.73564,-0.14495,520.77,-0.72799,0.58404,0.35907,162.13,-0.17949,0.34311,-0.92199,377.55

> view matrix models
> #3,-0.66168,-0.73564,-0.14495,522.97,-0.72799,0.58404,0.35907,161.36,-0.17949,0.34311,-0.92199,380.14

> view matrix models
> #3,-0.66168,-0.73564,-0.14495,525.35,-0.72799,0.58404,0.35907,157.02,-0.17949,0.34311,-0.92199,378.36

> view matrix models
> #3,-0.66168,-0.73564,-0.14495,525.27,-0.72799,0.58404,0.35907,162.98,-0.17949,0.34311,-0.92199,376.9

> ui tool show "Fit in Map"

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map (1).mrc (#1) using 6691 atoms  
average map value = 0.8912, steps = 308  
shifted from previous position = 53.1  
rotated from previous position = 39.4 degrees  
atoms outside contour = 1106, contour level = 0.39977  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map (1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.65528047 -0.56260308 0.50406872 361.60424167  
-0.52243342 0.81950854 0.23551871 93.10491594  
-0.54559218 -0.10901154 -0.83093060 479.77226669  
Axis -0.31165457 0.94950044 0.03633660  
Axis point 272.29234262 0.00000000 181.03413270  
Rotation angle (degrees) 146.44454843  
Shift along axis -6.85916455  
  

> fitmap #3 inMap #2

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J526_004_volume_map.mrc (#2) using 6691 atoms  
average map value = 1.028, steps = 132  
shifted from previous position = 7.92  
rotated from previous position = 27.9 degrees  
atoms outside contour = 1188, contour level = 0.59173  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J526_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.83650526 -0.54785406 -0.01071802 497.58325217  
-0.54788940 0.83655067 0.00043713 140.20757533  
0.00872668 0.00623795 -0.99994246 416.07806763  
Axis 0.28587362 -0.95826575 -0.00174148  
Axis point 268.60388216 0.00000000 209.22330262  
Rotation angle (degrees) 179.41868003  
Shift along axis 7.16521751  
  

> hide #!2 models

> show #!2 models

> volume #1 level 0.3712

> close #1

> volume #2 level 0.3764

> select subtract #3

Nothing selected  

> volume #2 level 0.4099

> color #2 #929292af models

> color #2 #929292ab models

> color #3 #212121ff

> color #3 #d4fb79ff

> color #3 #76d6ffff

> undo

[Repeated 2 time(s)]

> cartoon style modeHelix default arrows false xsection round width 2
> thickness 2

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/GP-
> MARV7.cxs

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV18/GP-
> MARV18.cxs

——— End of log from Wed Jun 18 14:42:12 2025 ———

opened ChimeraX session  

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV18/cryosparc_P662_J526_004_volume_map.mrc

Opened cryosparc_P662_J526_004_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.149, step 1, values float32  

> volume #1 level 0.3986

> color #1 #b2b2b2b8 models

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV23/GP-
> MARV23.png

Failed opening file
/Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV23/GP-
MARV23.png:  
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)  

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV23/cryosparc_P662_J527_002_volume_map.mrc

Opened cryosparc_P662_J527_002_volume_map.mrc as #2, grid size 252,252,252,
pixel 1.6, shown at level 0.0612, step 1, values float32  

> color #2 #ffffb280 models

> close #1-2

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV4/cryosparc_P662_J524_005_volume_map.mrc

Opened cryosparc_P662_J524_005_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.0881, step 1, values float32  

> volume #1 level 0.3714

> select add #3

6691 atoms, 6863 bonds, 6 pseudobonds, 823 residues, 2 models selected  

> color #1 #b2b2b290 models

> color #1 #b2b2b28f models

> volume #1 level 0.31

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.46989,-0.86665,0.16767,452.23,0.83476,-0.49803,-0.23483,175.82,0.28702,0.029614,0.95747,-33.061

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.46989,-0.86665,0.16767,453.95,0.83476,-0.49803,-0.23483,172.94,0.28702,0.029614,0.95747,-81.511

> ui tool show "Fit in Map"

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9054, steps = 112  
shifted from previous position = 6.29  
rotated from previous position = 20.1 degrees  
atoms outside contour = 830, contour level = 0.31005  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33555212 -0.81069086 0.47977610 351.83404151  
0.86174722 -0.46989303 -0.19129107 154.91510202  
0.38052137 0.34925759 0.85628420 -143.56260922  
Axis 0.30705591 0.05638114 0.95001991  
Axis point 150.10120181 194.14379491 0.00000000  
Rotation angle (degrees) 118.33203847  
Shift along axis -19.62032640  
  

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9054, steps = 40  
shifted from previous position = 0.0166  
rotated from previous position = 0.024 degrees  
atoms outside contour = 830, contour level = 0.31005  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33521935 -0.81090447 0.47964771 351.82373162  
0.86190326 -0.46954274 -0.19144814 154.83896434  
0.38046126 0.34923281 0.85632101 -143.53867410  
Axis 0.30706338 0.05632995 0.95002053  
Axis point 150.09441023 194.14915376 0.00000000  
Rotation angle (degrees) 118.30861136  
Shift along axis -19.61043153  
  

> view matrix models
> #3,-0.33522,-0.8109,0.47965,349.29,0.8619,-0.46954,-0.19145,159.87,0.38046,0.34923,0.85632,-142.32

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #3,-0.34818,-0.86285,0.36643,385.5,0.89234,-0.42484,-0.15249,136.02,0.28725,0.27389,0.91786,-118.04

> view matrix models
> #3,-0.34489,-0.87891,0.3295,395.5,0.93827,-0.33266,0.094754,57.732,0.026333,0.34184,0.93939,-80.632

> view matrix models
> #3,-0.10918,-0.93097,0.34839,352.17,0.91943,0.038623,0.39135,-76.44,-0.37779,0.36305,0.85174,19.167

> view matrix models
> #3,0.080115,-0.95144,0.29724,325.78,0.95376,-0.013495,-0.30027,63.094,0.2897,0.30755,0.90636,-123.57

> view matrix models
> #3,-0.31834,-0.89116,0.32327,393.63,0.94749,-0.31004,0.078367,54.081,0.030387,0.33124,0.94306,-79.941

> view matrix models
> #3,-0.58557,-0.24527,-0.77262,527.07,0.53744,-0.831,-0.14352,298.38,-0.60685,-0.49928,0.61843,300.26

> view matrix models
> #3,0.1787,-0.88558,0.42873,264.52,0.9271,0.0056508,-0.37476,79.334,0.32946,0.46445,0.82204,-149.43

> view matrix models
> #3,-0.24118,-0.95071,0.19487,415.02,0.94972,-0.27252,-0.15415,91.136,0.19966,0.14789,0.96864,-81.948

> view matrix models
> #3,0.60116,-0.59396,0.53462,89.748,0.72229,0.11763,-0.68151,159.56,0.34191,0.79585,0.49973,-160.31

> view matrix models
> #3,-0.64351,-0.7588,0.10061,478.93,0.75871,-0.64971,-0.047361,192.7,0.10131,0.045857,0.9938,-43.672

> view matrix models
> #3,-0.24029,-0.8479,0.47257,338.18,0.74839,-0.47187,-0.4661,238.75,0.6182,0.24167,0.74795,-149.15

> view matrix models
> #3,-0.75556,-0.64998,0.08157,483.38,0.6433,-0.7597,-0.094934,250.64,0.12367,-0.019254,0.99214,-34.135

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.75556,-0.64998,0.08157,485.85,0.6433,-0.7597,-0.094934,248.91,0.12367,-0.019254,0.99214,-40.051

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.8965, steps = 132  
shifted from previous position = 6.74  
rotated from previous position = 23.2 degrees  
atoms outside contour = 887, contour level = 0.31005  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.48462751 -0.85529227 0.18333389 451.26314999  
0.87351161 -0.48422443 0.05004175 109.42450221  
0.04597443 0.18439589 0.98177620 -59.16466869  
Axis 0.07723950 0.07896724 0.99388039  
Axis point 195.51999458 189.60891575 0.00000000  
Rotation angle (degrees) 119.57338183  
Shift along axis -15.30631207  
  

> volume #1 level 0.1901

> volume #1 level 0.5299

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.8965, steps = 40  
shifted from previous position = 0.00586  
rotated from previous position = 0.0599 degrees  
atoms outside contour = 1619, contour level = 0.52991  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.48505113 -0.85513673 0.18293873 451.39478033  
0.87332494 -0.48446459 0.05096674 109.32916872  
0.04504380 0.18448643 0.98180233 -58.99376148  
Axis 0.07677576 0.07929158 0.99389050  
Axis point 195.60578957 189.54335742 0.00000000  
Rotation angle (degrees) 119.59438767  
Shift along axis -15.30828063  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.59667,-0.80175,-0.034488,506.62,0.80174,-0.59741,0.017372,155.71,-0.034531,-0.017285,0.99925,-1.7552

> view matrix models
> #3,-0.74103,-0.66366,0.10211,481.19,0.66251,-0.7474,-0.049744,231.25,0.10933,0.030786,0.99353,-42.027

> view matrix models
> #3,-0.5539,-0.78771,0.26964,434.7,0.81639,-0.57741,-0.0097889,153.57,0.1634,0.21471,0.96291,-87.335

> view matrix models
> #3,-0.5117,-0.8361,0.19774,450.13,0.81593,-0.54499,-0.19298,182.62,0.26911,0.062597,0.96107,-76.984

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9054, steps = 96  
shifted from previous position = 3.09  
rotated from previous position = 19.3 degrees  
atoms outside contour = 1510, contour level = 0.52991  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33560634 -0.81096060 0.47928206 352.00699248  
0.86195297 -0.46961644 -0.19104314 154.78526324  
0.38000720 0.34900331 0.85661615 -143.47169997  
Axis 0.30671857 0.05638301 0.95012877  
Axis point 150.17369811 194.15561937 0.00000000  
Rotation angle (degrees) 118.31399841  
Shift along axis -19.62224685  
  

> view matrix models
> #3,-0.14299,-0.98272,-0.1175,464.58,0.9711,-0.11639,-0.20838,58.495,0.19111,-0.1439,0.97096,-18.901

> view matrix models
> #3,-0.47632,-0.83771,0.26714,429.75,0.87781,-0.47057,0.089512,96.522,0.050726,0.27714,0.95949,-77.134

> view matrix models
> #3,-0.084593,-0.89073,-0.44659,496.72,0.91497,0.10803,-0.38879,57.62,0.39455,-0.44151,0.80585,33.768

> view matrix models
> #3,-0.60366,-0.79606,-0.043412,509.18,0.79159,-0.60496,0.086115,144.76,-0.094815,0.01762,0.99534,3.1732

> view matrix models
> #3,-0.55741,-0.81824,0.14061,467.87,0.72992,-0.40228,0.55261,22.836,-0.3956,0.41067,0.82149,17.435

> view matrix models
> #3,-0.55352,-0.83154,0.046447,488.38,0.80349,-0.51852,0.29248,83.065,-0.21912,0.19921,0.95514,-1.2728

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9057, steps = 104  
shifted from previous position = 3.73  
rotated from previous position = 16.7 degrees  
atoms outside contour = 1507, contour level = 0.52991  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.42596765 -0.90181519 -0.07266993 497.96348202  
0.76826070 -0.40296436 0.49738841 28.08588364  
-0.47783582 0.15604193 0.86447895 78.12248504  
Axis -0.19482211 0.23124678 0.95318900  
Axis point 247.10702831 157.98045269 0.00000000  
Rotation angle (degrees) 118.83092151  
Shift along axis -16.05403432  
  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.42597,-0.90182,-0.07267,496.36,0.76826,-0.40296,0.49739,32.496,-0.47784,0.15604,0.86448,76.659

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.46198,-0.81178,-0.35721,540.54,0.63986,-0.58396,0.49957,98.786,-0.61413,0.0022254,0.7892,153.99

> view matrix models
> #3,-0.65076,-0.7563,0.067189,486.04,0.66175,-0.52156,0.53858,72.955,-0.37228,0.39495,0.83989,7.2118

> view matrix models
> #3,-0.63238,-0.76483,0.12301,472.96,0.69922,-0.49521,0.51561,63.7,-0.33344,0.41207,0.84795,-6.4407

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9057, steps = 108  
shifted from previous position = 5.8  
rotated from previous position = 18.2 degrees  
atoms outside contour = 1510, contour level = 0.52991  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.42598265 -0.90176785 -0.07316778 498.02941330  
0.76818101 -0.40322791 0.49729789 28.17172480  
-0.47795054 0.15563418 0.86448903 78.21681705  
Axis -0.19501962 0.23104760 0.95319691  
Axis point 247.13339927 158.01114059 0.00000000  
Rotation angle (degrees) 118.83970102  
Shift along axis -16.06047002  
  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.42598,-0.90177,-0.073168,497.78,0.76818,-0.40323,0.4973,25.083,-0.47795,0.15563,0.86449,81.726

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.25594,-0.94129,0.22014,412.07,0.88224,-0.13435,0.45122,-48.445,-0.39516,0.3097,0.86483,30.586

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9057, steps = 112  
shifted from previous position = 5.16  
rotated from previous position = 19.7 degrees  
atoms outside contour = 1507, contour level = 0.52991  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.42613018 -0.90170774 -0.07304947 498.02165290  
0.76804777 -0.40326640 0.49747246 28.16998997  
-0.47803316 0.15588255 0.86439859 78.19818993  
Axis -0.19499444 0.23118238 0.95316938  
Axis point 247.12799724 157.98109522 0.00000000  
Rotation angle (degrees) 118.84874258  
Shift along axis -16.06292797  
  

> volume #1 level 0.2781

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.42613,-0.90171,-0.073049,497.68,0.76805,-0.40327,0.49747,27.902,-0.47803,0.15588,0.8644,86.492

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.52777,-0.8293,-0.18361,525.69,0.82912,-0.54994,0.10067,124.21,-0.18446,-0.09911,0.97783,55.878

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.8959, steps = 80  
shifted from previous position = 5.26  
rotated from previous position = 4.89 degrees  
atoms outside contour = 814, contour level = 0.27807  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.48829215 -0.86456745 -0.11871773 511.28553532  
0.85629776 -0.50090703 0.12588208 102.33755111  
-0.16830009 -0.04019049 0.98491614 33.39960831  
Axis -0.09601952 0.02866744 0.99496655  
Axis point 227.54018717 198.24700364 0.00000000  
Rotation angle (degrees) 120.14178312  
Shift along axis -12.92814476  
  

> select subtract #3

Nothing selected  

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV4/GP-
> MARV4.cxs

> close #1

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/cryosparc_P662_J528_002_volume_map.mrc

Opened cryosparc_P662_J528_002_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.181, step 1, values float32  

> volume #1 color #b2b2b27d

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J528_002_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.807, steps = 112  
shifted from previous position = 2.14  
rotated from previous position = 28.3 degrees  
atoms outside contour = 152, contour level = 0.18087  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.06076214 -0.99814736 0.00313082 425.72158050  
0.99814570 -0.06077282 -0.00343797 3.30781971  
0.00362187 0.00291612 0.99998919 -13.36332519  
Axis 0.00318293 -0.00024598 0.99999490  
Axis point 211.32716592 201.96611681 0.00000000  
Rotation angle (degrees) 93.48417703  
Shift along axis -12.00902911  
  

> volume #1 color #b2b2b297

> volume #1 level 0.554

> volume #1 level 0.3505

> volume #1 level 0.5728

> volume #1 level 0.5427

> hide #!1 models

> open 6BP2 fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6BP2 fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
6BP2 bioassembly 1 title:  
Therapeutic human monoclonal antibody MR191 bound to a marburgvirus
glycoprotein [more info...]  
  
Chain information for 6BP2 bioassembly 1 #2  
---  
Chain | Description  
A AA AB | Envelope glycoprotein  
B BA BB | Envelope glycoprotein GP2  
C CA CB | MR191 Fab Heavy Chain  
D DA DB | MR191 Fab Light Chain  
  
Non-standard residues in 6BP2 bioassembly 1 #2  
---  
BMA — (BMA)  
MAN — (MAN)  
NAG — (NAG)  
  
6BP2 bioassembly 1 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Opened 1 biological assemblies for 6BP2  

> ui tool show Matchmaker

> matchmaker #!2 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain C (#3) with 6BP2 bioassembly 1,
chain A (#2), sequence alignment score = 720.5  
RMSD between 129 pruned atom pairs is 0.644 angstroms; (across all 142 pairs:
1.417)  
  

> hide atoms

> hide cartoons

> show cartoons

> show #!1 models

> hide #!2 models

> volume #1 level 0.7235

> volume #1 level 0.52

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/GP-
> MARV7.cxs

——— End of log from Wed Jun 18 15:33:55 2025 ———

opened ChimeraX session  

> ui tool show Matchmaker

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/6BP2_GP.pdb

6BP2_GP.pdb title:  
Therapeutic human monoclonal antibody MR191 bound to A marburgvirus
glycoprotein [more info...]  
  
Chain information for 6BP2_GP.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
G M | No description available  
H N | No description available  
  
Non-standard residues in 6BP2_GP.pdb #4  
---  
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)  
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  

> show #!3-4 atoms

> hide #!3-4 atoms

> show #!3-4 cartoons

> ui tool show Matchmaker

> matchmaker #!4 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain C (#3) with 6BP2_GP.pdb, chain A
(#4), sequence alignment score = 809.1  
RMSD between 129 pruned atom pairs is 0.644 angstroms; (across all 142 pairs:
1.417)  
  

> hide #!3 models

> hide #!1 models

> show #!1 models

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/GP-
> MARV7-v2.cxs

——— End of log from Tue Jul 29 13:10:27 2025 ———

opened ChimeraX session  

> close #2

> show #!3 models

> volume #1 level 0.1683

> volume #1 level 0.5913

> volume #1 level 0.4488

> ui tool show "Hide Dust"

> surface dust #1 size 9.6

> surface dust #1 size 9.19

> surface dust #1 size 16

> volume #1 level 0.4933

> volume #1 level 0.5022

> surface undust #1

> surface dust #1 size 16

> ui tool show "Segment Map"

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.502236  
Showing 9 region surfaces  
27 watershed regions, grouped to 9 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 9 regions, 9 surfaces  

> surface dust #1 size 16

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.502236  
Showing 6 region surfaces  
27 watershed regions, grouped to 6 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 6 regions, 6 surfaces  
Ungrouped to 6 regions  

> close #2

> ui tool show "Fit in Map"

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J528_002_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.807, steps = 28  
shifted from previous position = 0.0397  
rotated from previous position = 0.0644 degrees  
atoms outside contour = 815, contour level = 0.50224  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.06081217 -0.99814529 0.00280336 425.79711414  
0.99814602 -0.06081885 -0.00236378 3.14650160  
0.00252989 0.00265442 0.99999328 -13.07424453  
Axis 0.00251375 0.00013699 0.99999683  
Axis point 211.43390378 201.91011493 0.00000000  
Rotation angle (degrees) 93.48681636  
Shift along axis -12.00342273  
  

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J528_002_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.807, steps = 28  
shifted from previous position = 0.0312  
rotated from previous position = 0.0408 degrees  
atoms outside contour = 814, contour level = 0.50224  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.06077111 -0.99814594 0.00339861 425.69569753  
0.99814736 -0.06078056 -0.00275132 3.19412071  
0.00295279 0.00322511 0.99999044 -13.28725360  
Axis 0.00299375 0.00022332 0.99999549  
Axis point 211.36370090 201.89748100 0.00000000  
Rotation angle (degrees) 93.48462052  
Shift along axis -12.01205416  
  

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J528_002_volume_map.mrc
(#1) using 7320 atoms  
average map value = 0.7758, steps = 56  
shifted from previous position = 2.55  
rotated from previous position = 3.46 degrees  
atoms outside contour = 1105, contour level = 0.50224  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.54302390 0.83971724 0.00000249 60.19681128  
-0.83971722 0.54302390 0.00018627 349.14495949  
0.00015506 -0.00010324 0.99999998 114.02715980  
Axis -0.00017238 -0.00009085 -0.99999998  
Axis point 350.86502709 119.27798789 0.00000000  
Rotation angle (degrees) 57.11027354  
Shift along axis -114.06925385  
  

> color zone #1 near #4

> hide #!3 models

> color zone #1 near #4 distance 8

> color zone #1 near #4 distance 12

> color zone #1 near #4 distance 14

> color zone #1 near #4 distance 8

> color zone #1 near #4 distance 18

> color zone #1 near #4 distance 16

> color zone #1 near #4 distance 17

> color zone #1 near #4 distance 5

> color zone #1 near #4 distance 15

> volume #1 level 0.7131

> volume #1 level 0.4977

> color zone #1 near #4 distance 13

> color zone #1 near #4 distance 12

> volume splitbyzone #1

Opened cryosparc_P662_J528_002_volume_map.mrc 0 as #2.1, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 1 as #2.2, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 2 as #2.3, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 3 as #2.4, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 4 as #2.5, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 5 as #2.6, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 6 as #2.7, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 7 as #2.8, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  

> undo

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J528_002_volume_map.mrc
(#1) using 7320 atoms  
average map value = 0.7758, steps = 56  
shifted from previous position = 2.55  
rotated from previous position = 3.46 degrees  
atoms outside contour = 1081, contour level = 0.49765  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.54302390 0.83971724 0.00000249 60.19681128  
-0.83971722 0.54302390 0.00018627 349.14495949  
0.00015506 -0.00010324 0.99999998 114.02715980  
Axis -0.00017238 -0.00009085 -0.99999998  
Axis point 350.86502709 119.27798789 0.00000000  
Rotation angle (degrees) 57.11027354  
Shift along axis -114.06925385  
  

> hide #!4#!2.2-8 target m

> show #!2.2 models

> close #2

> show #!1 models

> color #1 #b2b2b29d models

> show #!4 models

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/GP-
> MARV16_krios/250225-MARV-GP_MARV16.pdb

Chain information for 250225-MARV-GP_MARV16.pdb #2  
---  
Chain | Description  
A C G | No description available  
B D I | No description available  
E H J | No description available  
F K L | No description available  
  

> hide #!2,4 atoms

> show #!2,4 cartoons

> select #2/A,C,G,B,D,I

6690 atoms, 6863 bonds, 6 pseudobonds, 822 residues, 2 models selected  

> delete sel

> select add #2

5212 atoms, 5328 bonds, 679 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-8.6904,0,1,0,-5.0575,0,0,1,-1.4875

> view matrix models #2,1,0,0,-6.5691,0,1,0,-8.393,0,0,1,1.0331

> view matrix models #2,1,0,0,-5.5704,0,1,0,-11.469,0,0,1,0.1517

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#2) to map
cryosparc_P662_J528_002_volume_map.mrc (#1) using 5212 atoms  
average map value = 0.847, steps = 200  
shifted from previous position = 5.6  
rotated from previous position = 0.89 degrees  
atoms outside contour = 1395, contour level = 0.49765  
  
Position of 250225-MARV-GP_MARV16.pdb (#2) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99987951 -0.01530886 0.00257182 -7.92126020  
0.01530779 0.99988273 0.00043370 -13.97061819  
-0.00257816 -0.00039428 0.99999660 -1.41324292  
Axis -0.02665950 0.16581924 0.98579575  
Axis point 870.68664672 -530.37555576 0.00000000  
Rotation angle (degrees) 0.88977629  
Shift along axis -3.49858927  
  

> color zone #1 near #2 distance 12

> color zone #1 near #2 distance 8

> color zone #1 near #2 distance 6

> color zone #1 near #2 distance 8

> color zone #1 near #2 distance 10

> select up

19223 atoms, 19672 bonds, 2417 residues, 5 models selected  

> volume splitbyzone #1

Opened cryosparc_P662_J528_002_volume_map.mrc 0 as #5.1, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 1 as #5.2, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 2 as #5.3, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 3 as #5.4, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  

> hide #!5.4 models

> hide #!5.1 models

> show #!5.1 models

> hide #!5 models

> show #!5 models

> hide #!5.1 models

> show #!5.1 models

> hide #!5.1 models

> show #!5.1 models

> hide #!5.2 models

> show #!5.2 models

> hide #!5.2 models

> show #!5.2 models

> hide #!5.3 models

> show #!5.3 models

> show #!5.4 models

> hide #!5.4 models

> hide #!5.3 models

> show #!5.3 models

> fitmap #2 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#2) to map
cryosparc_P662_J528_002_volume_map.mrc (#1) using 5212 atoms  
average map value = 0.847, steps = 200  
shifted from previous position = 5.6  
rotated from previous position = 0.89 degrees  
atoms outside contour = 1395, contour level = 0.49765  
  
Position of 250225-MARV-GP_MARV16.pdb (#2) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99987951 -0.01530886 0.00257182 -7.92126020  
0.01530779 0.99988273 0.00043370 -13.97061819  
-0.00257816 -0.00039428 0.99999660 -1.41324292  
Axis -0.02665950 0.16581924 0.98579575  
Axis point 870.68664672 -530.37555576 0.00000000  
Rotation angle (degrees) 0.88977629  
Shift along axis -3.49858927  
  

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J528_002_volume_map.mrc
(#1) using 7320 atoms  
average map value = 0.7758, steps = 56  
shifted from previous position = 2.55  
rotated from previous position = 3.46 degrees  
atoms outside contour = 1081, contour level = 0.49765  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.54302390 0.83971724 0.00000249 60.19681128  
-0.83971722 0.54302390 0.00018627 349.14495949  
0.00015506 -0.00010324 0.99999998 114.02715980  
Axis -0.00017238 -0.00009085 -0.99999998  
Axis point 350.86502709 119.27798789 0.00000000  
Rotation angle (degrees) 57.11027354  
Shift along axis -114.06925385  
  

> close #5

> select add #3

19223 atoms, 19672 bonds, 6 pseudobonds, 2417 residues, 6 models selected  

> select subtract #3

12532 atoms, 12809 bonds, 1594 residues, 4 models selected  

> select subtract #2

7320 atoms, 7481 bonds, 915 residues, 3 models selected  

> select subtract #1

7320 atoms, 7481 bonds, 915 residues, 1 model selected  

> show #!1 models

> ui tool show "Segment Map"

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 12 region surfaces  
28 watershed regions, grouped to 12 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 12 regions, 12 surfaces  

> select add #5

7320 atoms, 7481 bonds, 915 residues, 14 models selected  

> select add #4

7320 atoms, 7481 bonds, 6 pseudobonds, 915 residues, 15 models selected  

> select subtract #4

13 models selected  
0 or more than 1 volume model selected  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 12 region surfaces  
28 watershed regions, grouped to 12 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 12 regions, 12 surfaces  
Smoothing and grouping, standard deviation 4 voxels  
Showing 9 region surfaces  
Got 9 regions after smoothing 4 voxels.  
Smoothing and grouping, standard deviation 5 voxels  
Showing 6 region surfaces  
Got 6 regions after smoothing 5 voxels.  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 12 region surfaces  
28 watershed regions, grouped to 12 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 12 regions, 12 surfaces  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 12 region surfaces  
28 watershed regions, grouped to 12 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 12 regions, 12 surfaces  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 12 region surfaces  
28 watershed regions, grouped to 12 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 12 regions, 12 surfaces  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 9 region surfaces  
28 watershed regions, grouped to 9 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 9 regions, 9 surfaces  

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J528_002_volume_map.mrc
(#1) using 7320 atoms  
average map value = 0.7758, steps = 24  
shifted from previous position = 0.0192  
rotated from previous position = 0.0169 degrees  
atoms outside contour = 1078, contour level = 0.49765  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.54309135 0.83967361 -0.00008303 60.19055167  
-0.83967351 0.54309133 0.00045665 349.12841052  
0.00042853 -0.00017828 0.99999989 113.98672605  
Axis -0.00037808 -0.00030462 -0.99999988  
Axis point 350.84324665 119.27956931 0.00000000  
Rotation angle (degrees) 57.10567485  
Shift along axis -114.11582011  
  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 4 region surfaces  
28 watershed regions, grouped to 4 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 4 regions, 4 surfaces  

> hide #!2 models

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Only showing 4 of 4 regions.  
Showing 4 region surfaces  
28 watershed regions, grouped to 4 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 4 regions, 4 surfaces  

> surface dust #1 size 16

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Only showing 4 of 4 regions.  
Showing 4 region surfaces  
28 watershed regions, grouped to 4 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 4 regions, 4 surfaces  

> surface dust #5 size 16

> hide #!1 models

> show #!1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> surface dust #1 size 15.47

> surface dust #1 size 20.94

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> volume #1 level 0.5155

> ui tool show "Segment Map"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.515460  
Only showing 4 of 4 regions.  
Showing 4 region surfaces  
26 watershed regions, grouped to 4 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 4 regions, 4 surfaces  

> surface dust #5 size 16

> color #5.1 #f89ec17e

> select add #5.1

1 model selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 2 time(s)]Simulating map res 4.000, grid 2.000  

> molmap #3 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 250225-MARV-GP_MARV16.pdb map 4 as #6, grid size 46,55,60, pixel 2,
shown at level 0.0995, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map_masked as #7, grid size 252,252,252,
pixel 1.6, shown at step 1, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Simulating map res 4.000, grid 2.000  

> molmap #4 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 6BP2_GP.pdb map 4 as #7, grid size 52,50,61, pixel 2, shown at level
0.103, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map_masked as #8, grid size 252,252,252,
pixel 1.6, shown at step 1, values float32  
Top score: 0.76413, z-score: 2.15322 (avg: 0.7499, stdev: 0.0066)  

> ui tool show Matchmaker

> matchmaker #!4 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain F (#2) with 6BP2_GP.pdb, chain H
(#4), sequence alignment score = 38.5  
RMSD between 5 pruned atom pairs is 1.241 angstroms; (across all 48 pairs:
11.258)  
  

> matchmaker #!4 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain C (#3) with 6BP2_GP.pdb, chain A
(#4), sequence alignment score = 809.1  
RMSD between 129 pruned atom pairs is 0.644 angstroms; (across all 142 pairs:
1.417)  
  

> matchmaker #!4 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain C (#3) with 6BP2_GP.pdb, chain A
(#4), sequence alignment score = 809.1  
RMSD between 129 pruned atom pairs is 0.644 angstroms; (across all 142 pairs:
1.417)  
  

> close #2

> hide #!3 models

> set bgColor white

> color #5.1 #919191ff

> color #5.1 #9191917c

> lighting soft depthCue true depthCueStart 0.42 depthCueEnd 2

> graphics silhouettes true width 2

> cartoon style modeHelix default arrows false xsection round width 2
> thickness 2

> select subtract #5.1

Nothing selected  

> color #5.2 #3e4169ff

> color #5.3 #3e4169ff

> color #5.4 #3e4169ff

> cd "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope binning"

Current working directory is:
/Users/aminaddetia/Library/CloudStorage/GoogleDrive-aaddetia@uw.edu/Shared
drives/Veesler_lab/Amin Addetia/MARV/Paper/Revision/Supplemental
figures/Epitope binning  

> save "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope
> binning/MARV7_Fig.cxs"

——— End of log from Wed Aug 13 16:46:18 2025 ———

opened ChimeraX session  

> open "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope
> binning/MARV7_Fig.cxs"

Opened cryosparc_P662_J528_002_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.515, step 1, values float32  
Opened 250225-MARV-GP_MARV16.pdb map 4 as #6, grid size 46,55,60, pixel 2,
shown at level 0.0995, step 1, values float32  
Opened 6BP2_GP.pdb map 4 as #7, grid size 52,50,61, pixel 2, shown at level
0.103, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 757, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 574, in restore_snapshot  
m.set_state_from_snapshot(session, data)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 397, in set_state_from_snapshot  
p.add([self])  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 314, in add  
om.add(models, parent = self)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 756, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 825, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
ValueError: Tried to add model 39 #5.2 with the same id as another model 39
#5.2  
  
Log from Wed Aug 13 16:46:18 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/GP-
> MARV7-v2.cxs

Opened cryosparc_P662_J528_002_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.52, step 1, values float32  
Log from Tue Jul 29 13:10:27 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/GP-
> MARV7.cxs

Opened cryosparc_P662_J528_002_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.52, step 1, values float32  
Log from Wed Jun 18 15:33:55 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV18/GP-
> MARV18.cxs

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Log from Wed Jun 18 14:42:12 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/aminaddetia/Downloads/cryosparc_P662_J524_005_volume_map
> (1).mrc"

Opened cryosparc_P662_J524_005_volume_map (1).mrc as #1, grid size
252,252,252, pixel 1.6, shown at level 0.0881, step 1, values float32  

> volume #1 level 0.3998

> open /Users/aminaddetia/Downloads/cryosparc_P662_J526_004_volume_map.mrc

Opened cryosparc_P662_J526_004_volume_map.mrc as #2, grid size 252,252,252,
pixel 1.6, shown at level 0.149, step 1, values float32  

> hide #!1 models

> volume #2 level 0.1033

> volume #2 color #ffffb282

> volume #2 color #929292

> volume #2 color #92929280

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/GP-
> MARV16_krios/250225-MARV-GP_MARV16.pdb

Chain information for 250225-MARV-GP_MARV16.pdb #3  
---  
Chain | Description  
A C G | No description available  
B D I | No description available  
E H J | No description available  
F K L | No description available  
  

> hide atoms

> show cartoons

> select /H:1-119

931 atoms, 952 bonds, 119 residues, 1 model selected  

> select /L:1-107

806 atoms, 824 bonds, 107 residues, 1 model selected  

> select #3/E,H,J,F,J,K

4405 atoms, 4504 bonds, 571 residues, 1 model selected  

> select #3/E,H,J,F,J,K,L

5211 atoms, 5328 bonds, 678 residues, 1 model selected  

> delsel

Unknown command: delsel  

> delete sel

> select add #3

6691 atoms, 6863 bonds, 6 pseudobonds, 823 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.53492,0.82857,0.16529,-110.76,0.74453,-0.36979,-0.55581,243.86,-0.39941,0.42038,-0.81471,351.96

> view matrix models
> #3,-0.71377,0.68499,0.14601,193.33,0.65631,0.72695,-0.20201,-43.032,-0.24452,-0.048365,-0.96844,449.79

> view matrix models
> #3,-0.60981,0.59858,0.51946,116.19,0.72755,0.68274,0.067355,-101.78,-0.31434,0.419,-0.85184,341.2

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.60981,0.59858,0.51946,102.77,0.72755,0.68274,0.067355,-103.14,-0.31434,0.419,-0.85184,378.21

> view matrix models
> #3,-0.60981,0.59858,0.51946,104.37,0.72755,0.68274,0.067355,-106.59,-0.31434,0.419,-0.85184,377.66

> volume #2 level 0.5917

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.090782,-0.99288,0.077084,383.22,-0.96222,-0.1074,-0.25021,490.62,0.25671,-0.051457,-0.96512,378.15

> view matrix models
> #3,-0.96447,-0.036395,0.26167,368.4,0.02512,0.97334,0.22797,-49.261,-0.26299,0.22644,-0.93785,424.99

> view matrix models
> #3,-0.98911,-0.12438,-0.078725,459.53,-0.13389,0.98242,0.13011,2.3048,0.061159,0.13923,-0.98837,383.79

> view matrix models
> #3,-0.97709,-0.15092,-0.15008,476.68,-0.18294,0.95591,0.22972,-0.9659,0.10879,0.25191,-0.96162,343.97

> view matrix models
> #3,-0.81942,0.17306,-0.54645,450.67,-0.53186,0.12593,0.83742,133.87,0.21374,0.97683,-0.011148,-21.622

> view matrix models
> #3,-0.83248,0.13518,-0.53731,459.86,-0.53801,0.034502,0.84223,153.96,0.13239,0.99022,0.044006,-17.795

> view matrix models
> #3,-0.68517,-0.47515,0.55207,345.7,-0.15899,0.83722,0.52325,-38.197,-0.71082,0.27074,-0.64917,455.35

> view matrix models
> #3,-0.86021,-0.50437,0.075165,483.42,-0.48723,0.85642,0.17074,97.705,-0.15049,0.11025,-0.98244,434.53

> view matrix models
> #3,-0.84724,-0.52178,-0.099607,518.71,-0.5273,0.80341,0.27656,96.992,-0.064281,0.28684,-0.95582,372.64

> view matrix models
> #3,-0.66168,-0.73564,-0.14495,533.69,-0.72799,0.58404,0.35907,171.37,-0.17949,0.34311,-0.92199,378.71

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.66168,-0.73564,-0.14495,520.77,-0.72799,0.58404,0.35907,162.13,-0.17949,0.34311,-0.92199,377.55

> view matrix models
> #3,-0.66168,-0.73564,-0.14495,522.97,-0.72799,0.58404,0.35907,161.36,-0.17949,0.34311,-0.92199,380.14

> view matrix models
> #3,-0.66168,-0.73564,-0.14495,525.35,-0.72799,0.58404,0.35907,157.02,-0.17949,0.34311,-0.92199,378.36

> view matrix models
> #3,-0.66168,-0.73564,-0.14495,525.27,-0.72799,0.58404,0.35907,162.98,-0.17949,0.34311,-0.92199,376.9

> ui tool show "Fit in Map"

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map (1).mrc (#1) using 6691 atoms  
average map value = 0.8912, steps = 308  
shifted from previous position = 53.1  
rotated from previous position = 39.4 degrees  
atoms outside contour = 1106, contour level = 0.39977  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map (1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.65528047 -0.56260308 0.50406872 361.60424167  
-0.52243342 0.81950854 0.23551871 93.10491594  
-0.54559218 -0.10901154 -0.83093060 479.77226669  
Axis -0.31165457 0.94950044 0.03633660  
Axis point 272.29234262 0.00000000 181.03413270  
Rotation angle (degrees) 146.44454843  
Shift along axis -6.85916455  
  

> fitmap #3 inMap #2

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J526_004_volume_map.mrc (#2) using 6691 atoms  
average map value = 1.028, steps = 132  
shifted from previous position = 7.92  
rotated from previous position = 27.9 degrees  
atoms outside contour = 1188, contour level = 0.59173  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J526_004_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.83650526 -0.54785406 -0.01071802 497.58325217  
-0.54788940 0.83655067 0.00043713 140.20757533  
0.00872668 0.00623795 -0.99994246 416.07806763  
Axis 0.28587362 -0.95826575 -0.00174148  
Axis point 268.60388216 0.00000000 209.22330262  
Rotation angle (degrees) 179.41868003  
Shift along axis 7.16521751  
  

> hide #!2 models

> show #!2 models

> volume #1 level 0.3712

> close #1

> volume #2 level 0.3764

> select subtract #3

Nothing selected  

> volume #2 level 0.4099

> color #2 #929292af models

> color #2 #929292ab models

> color #3 #212121ff

> color #3 #d4fb79ff

> color #3 #76d6ffff

> undo

[Repeated 2 time(s)]

> cartoon style modeHelix default arrows false xsection round width 2
> thickness 2

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/GP-
> MARV7.cxs

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV18/GP-
> MARV18.cxs

——— End of log from Wed Jun 18 14:42:12 2025 ———

opened ChimeraX session  

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV18/cryosparc_P662_J526_004_volume_map.mrc

Opened cryosparc_P662_J526_004_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.149, step 1, values float32  

> volume #1 level 0.3986

> color #1 #b2b2b2b8 models

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV23/GP-
> MARV23.png

Failed opening file
/Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV23/GP-
MARV23.png:  
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)  

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV23/cryosparc_P662_J527_002_volume_map.mrc

Opened cryosparc_P662_J527_002_volume_map.mrc as #2, grid size 252,252,252,
pixel 1.6, shown at level 0.0612, step 1, values float32  

> color #2 #ffffb280 models

> close #1-2

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV4/cryosparc_P662_J524_005_volume_map.mrc

Opened cryosparc_P662_J524_005_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.0881, step 1, values float32  

> volume #1 level 0.3714

> select add #3

6691 atoms, 6863 bonds, 6 pseudobonds, 823 residues, 2 models selected  

> color #1 #b2b2b290 models

> color #1 #b2b2b28f models

> volume #1 level 0.31

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.46989,-0.86665,0.16767,452.23,0.83476,-0.49803,-0.23483,175.82,0.28702,0.029614,0.95747,-33.061

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.46989,-0.86665,0.16767,453.95,0.83476,-0.49803,-0.23483,172.94,0.28702,0.029614,0.95747,-81.511

> ui tool show "Fit in Map"

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9054, steps = 112  
shifted from previous position = 6.29  
rotated from previous position = 20.1 degrees  
atoms outside contour = 830, contour level = 0.31005  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33555212 -0.81069086 0.47977610 351.83404151  
0.86174722 -0.46989303 -0.19129107 154.91510202  
0.38052137 0.34925759 0.85628420 -143.56260922  
Axis 0.30705591 0.05638114 0.95001991  
Axis point 150.10120181 194.14379491 0.00000000  
Rotation angle (degrees) 118.33203847  
Shift along axis -19.62032640  
  

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9054, steps = 40  
shifted from previous position = 0.0166  
rotated from previous position = 0.024 degrees  
atoms outside contour = 830, contour level = 0.31005  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33521935 -0.81090447 0.47964771 351.82373162  
0.86190326 -0.46954274 -0.19144814 154.83896434  
0.38046126 0.34923281 0.85632101 -143.53867410  
Axis 0.30706338 0.05632995 0.95002053  
Axis point 150.09441023 194.14915376 0.00000000  
Rotation angle (degrees) 118.30861136  
Shift along axis -19.61043153  
  

> view matrix models
> #3,-0.33522,-0.8109,0.47965,349.29,0.8619,-0.46954,-0.19145,159.87,0.38046,0.34923,0.85632,-142.32

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #3,-0.34818,-0.86285,0.36643,385.5,0.89234,-0.42484,-0.15249,136.02,0.28725,0.27389,0.91786,-118.04

> view matrix models
> #3,-0.34489,-0.87891,0.3295,395.5,0.93827,-0.33266,0.094754,57.732,0.026333,0.34184,0.93939,-80.632

> view matrix models
> #3,-0.10918,-0.93097,0.34839,352.17,0.91943,0.038623,0.39135,-76.44,-0.37779,0.36305,0.85174,19.167

> view matrix models
> #3,0.080115,-0.95144,0.29724,325.78,0.95376,-0.013495,-0.30027,63.094,0.2897,0.30755,0.90636,-123.57

> view matrix models
> #3,-0.31834,-0.89116,0.32327,393.63,0.94749,-0.31004,0.078367,54.081,0.030387,0.33124,0.94306,-79.941

> view matrix models
> #3,-0.58557,-0.24527,-0.77262,527.07,0.53744,-0.831,-0.14352,298.38,-0.60685,-0.49928,0.61843,300.26

> view matrix models
> #3,0.1787,-0.88558,0.42873,264.52,0.9271,0.0056508,-0.37476,79.334,0.32946,0.46445,0.82204,-149.43

> view matrix models
> #3,-0.24118,-0.95071,0.19487,415.02,0.94972,-0.27252,-0.15415,91.136,0.19966,0.14789,0.96864,-81.948

> view matrix models
> #3,0.60116,-0.59396,0.53462,89.748,0.72229,0.11763,-0.68151,159.56,0.34191,0.79585,0.49973,-160.31

> view matrix models
> #3,-0.64351,-0.7588,0.10061,478.93,0.75871,-0.64971,-0.047361,192.7,0.10131,0.045857,0.9938,-43.672

> view matrix models
> #3,-0.24029,-0.8479,0.47257,338.18,0.74839,-0.47187,-0.4661,238.75,0.6182,0.24167,0.74795,-149.15

> view matrix models
> #3,-0.75556,-0.64998,0.08157,483.38,0.6433,-0.7597,-0.094934,250.64,0.12367,-0.019254,0.99214,-34.135

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.75556,-0.64998,0.08157,485.85,0.6433,-0.7597,-0.094934,248.91,0.12367,-0.019254,0.99214,-40.051

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.8965, steps = 132  
shifted from previous position = 6.74  
rotated from previous position = 23.2 degrees  
atoms outside contour = 887, contour level = 0.31005  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.48462751 -0.85529227 0.18333389 451.26314999  
0.87351161 -0.48422443 0.05004175 109.42450221  
0.04597443 0.18439589 0.98177620 -59.16466869  
Axis 0.07723950 0.07896724 0.99388039  
Axis point 195.51999458 189.60891575 0.00000000  
Rotation angle (degrees) 119.57338183  
Shift along axis -15.30631207  
  

> volume #1 level 0.1901

> volume #1 level 0.5299

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.8965, steps = 40  
shifted from previous position = 0.00586  
rotated from previous position = 0.0599 degrees  
atoms outside contour = 1619, contour level = 0.52991  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.48505113 -0.85513673 0.18293873 451.39478033  
0.87332494 -0.48446459 0.05096674 109.32916872  
0.04504380 0.18448643 0.98180233 -58.99376148  
Axis 0.07677576 0.07929158 0.99389050  
Axis point 195.60578957 189.54335742 0.00000000  
Rotation angle (degrees) 119.59438767  
Shift along axis -15.30828063  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.59667,-0.80175,-0.034488,506.62,0.80174,-0.59741,0.017372,155.71,-0.034531,-0.017285,0.99925,-1.7552

> view matrix models
> #3,-0.74103,-0.66366,0.10211,481.19,0.66251,-0.7474,-0.049744,231.25,0.10933,0.030786,0.99353,-42.027

> view matrix models
> #3,-0.5539,-0.78771,0.26964,434.7,0.81639,-0.57741,-0.0097889,153.57,0.1634,0.21471,0.96291,-87.335

> view matrix models
> #3,-0.5117,-0.8361,0.19774,450.13,0.81593,-0.54499,-0.19298,182.62,0.26911,0.062597,0.96107,-76.984

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9054, steps = 96  
shifted from previous position = 3.09  
rotated from previous position = 19.3 degrees  
atoms outside contour = 1510, contour level = 0.52991  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.33560634 -0.81096060 0.47928206 352.00699248  
0.86195297 -0.46961644 -0.19104314 154.78526324  
0.38000720 0.34900331 0.85661615 -143.47169997  
Axis 0.30671857 0.05638301 0.95012877  
Axis point 150.17369811 194.15561937 0.00000000  
Rotation angle (degrees) 118.31399841  
Shift along axis -19.62224685  
  

> view matrix models
> #3,-0.14299,-0.98272,-0.1175,464.58,0.9711,-0.11639,-0.20838,58.495,0.19111,-0.1439,0.97096,-18.901

> view matrix models
> #3,-0.47632,-0.83771,0.26714,429.75,0.87781,-0.47057,0.089512,96.522,0.050726,0.27714,0.95949,-77.134

> view matrix models
> #3,-0.084593,-0.89073,-0.44659,496.72,0.91497,0.10803,-0.38879,57.62,0.39455,-0.44151,0.80585,33.768

> view matrix models
> #3,-0.60366,-0.79606,-0.043412,509.18,0.79159,-0.60496,0.086115,144.76,-0.094815,0.01762,0.99534,3.1732

> view matrix models
> #3,-0.55741,-0.81824,0.14061,467.87,0.72992,-0.40228,0.55261,22.836,-0.3956,0.41067,0.82149,17.435

> view matrix models
> #3,-0.55352,-0.83154,0.046447,488.38,0.80349,-0.51852,0.29248,83.065,-0.21912,0.19921,0.95514,-1.2728

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9057, steps = 104  
shifted from previous position = 3.73  
rotated from previous position = 16.7 degrees  
atoms outside contour = 1507, contour level = 0.52991  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.42596765 -0.90181519 -0.07266993 497.96348202  
0.76826070 -0.40296436 0.49738841 28.08588364  
-0.47783582 0.15604193 0.86447895 78.12248504  
Axis -0.19482211 0.23124678 0.95318900  
Axis point 247.10702831 157.98045269 0.00000000  
Rotation angle (degrees) 118.83092151  
Shift along axis -16.05403432  
  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.42597,-0.90182,-0.07267,496.36,0.76826,-0.40296,0.49739,32.496,-0.47784,0.15604,0.86448,76.659

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.46198,-0.81178,-0.35721,540.54,0.63986,-0.58396,0.49957,98.786,-0.61413,0.0022254,0.7892,153.99

> view matrix models
> #3,-0.65076,-0.7563,0.067189,486.04,0.66175,-0.52156,0.53858,72.955,-0.37228,0.39495,0.83989,7.2118

> view matrix models
> #3,-0.63238,-0.76483,0.12301,472.96,0.69922,-0.49521,0.51561,63.7,-0.33344,0.41207,0.84795,-6.4407

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9057, steps = 108  
shifted from previous position = 5.8  
rotated from previous position = 18.2 degrees  
atoms outside contour = 1510, contour level = 0.52991  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.42598265 -0.90176785 -0.07316778 498.02941330  
0.76818101 -0.40322791 0.49729789 28.17172480  
-0.47795054 0.15563418 0.86448903 78.21681705  
Axis -0.19501962 0.23104760 0.95319691  
Axis point 247.13339927 158.01114059 0.00000000  
Rotation angle (degrees) 118.83970102  
Shift along axis -16.06047002  
  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.42598,-0.90177,-0.073168,497.78,0.76818,-0.40323,0.4973,25.083,-0.47795,0.15563,0.86449,81.726

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.25594,-0.94129,0.22014,412.07,0.88224,-0.13435,0.45122,-48.445,-0.39516,0.3097,0.86483,30.586

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.9057, steps = 112  
shifted from previous position = 5.16  
rotated from previous position = 19.7 degrees  
atoms outside contour = 1507, contour level = 0.52991  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.42613018 -0.90170774 -0.07304947 498.02165290  
0.76804777 -0.40326640 0.49747246 28.16998997  
-0.47803316 0.15588255 0.86439859 78.19818993  
Axis -0.19499444 0.23118238 0.95316938  
Axis point 247.12799724 157.98109522 0.00000000  
Rotation angle (degrees) 118.84874258  
Shift along axis -16.06292797  
  

> volume #1 level 0.2781

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.42613,-0.90171,-0.073049,497.68,0.76805,-0.40327,0.49747,27.902,-0.47803,0.15588,0.8644,86.492

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.52777,-0.8293,-0.18361,525.69,0.82912,-0.54994,0.10067,124.21,-0.18446,-0.09911,0.97783,55.878

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J524_005_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.8959, steps = 80  
shifted from previous position = 5.26  
rotated from previous position = 4.89 degrees  
atoms outside contour = 814, contour level = 0.27807  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J524_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.48829215 -0.86456745 -0.11871773 511.28553532  
0.85629776 -0.50090703 0.12588208 102.33755111  
-0.16830009 -0.04019049 0.98491614 33.39960831  
Axis -0.09601952 0.02866744 0.99496655  
Axis point 227.54018717 198.24700364 0.00000000  
Rotation angle (degrees) 120.14178312  
Shift along axis -12.92814476  
  

> select subtract #3

Nothing selected  

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV4/GP-
> MARV4.cxs

> close #1

> open
> /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/cryosparc_P662_J528_002_volume_map.mrc

Opened cryosparc_P662_J528_002_volume_map.mrc as #1, grid size 252,252,252,
pixel 1.6, shown at level 0.181, step 1, values float32  

> volume #1 color #b2b2b27d

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J528_002_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.807, steps = 112  
shifted from previous position = 2.14  
rotated from previous position = 28.3 degrees  
atoms outside contour = 152, contour level = 0.18087  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.06076214 -0.99814736 0.00313082 425.72158050  
0.99814570 -0.06077282 -0.00343797 3.30781971  
0.00362187 0.00291612 0.99998919 -13.36332519  
Axis 0.00318293 -0.00024598 0.99999490  
Axis point 211.32716592 201.96611681 0.00000000  
Rotation angle (degrees) 93.48417703  
Shift along axis -12.00902911  
  

> volume #1 color #b2b2b297

> volume #1 level 0.554

> volume #1 level 0.3505

> volume #1 level 0.5728

> volume #1 level 0.5427

> hide #!1 models

> open 6BP2 fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 6BP2 fetched from pdbe_bio  
---  
warning | Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
6BP2 bioassembly 1 title:  
Therapeutic human monoclonal antibody MR191 bound to a marburgvirus
glycoprotein [more info...]  
  
Chain information for 6BP2 bioassembly 1 #2  
---  
Chain | Description  
A AA AB | Envelope glycoprotein  
B BA BB | Envelope glycoprotein GP2  
C CA CB | MR191 Fab Heavy Chain  
D DA DB | MR191 Fab Light Chain  
  
Non-standard residues in 6BP2 bioassembly 1 #2  
---  
BMA — (BMA)  
MAN — (MAN)  
NAG — (NAG)  
  
6BP2 bioassembly 1 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Opened 1 biological assemblies for 6BP2  

> ui tool show Matchmaker

> matchmaker #!2 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain C (#3) with 6BP2 bioassembly 1,
chain A (#2), sequence alignment score = 720.5  
RMSD between 129 pruned atom pairs is 0.644 angstroms; (across all 142 pairs:
1.417)  
  

> hide atoms

> hide cartoons

> show cartoons

> show #!1 models

> hide #!2 models

> volume #1 level 0.7235

> volume #1 level 0.52

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/GP-
> MARV7.cxs

——— End of log from Wed Jun 18 15:33:55 2025 ———

opened ChimeraX session  

> ui tool show Matchmaker

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/6BP2_GP.pdb

6BP2_GP.pdb title:  
Therapeutic human monoclonal antibody MR191 bound to A marburgvirus
glycoprotein [more info...]  
  
Chain information for 6BP2_GP.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
G M | No description available  
H N | No description available  
  
Non-standard residues in 6BP2_GP.pdb #4  
---  
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)  
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  

> show #!3-4 atoms

> hide #!3-4 atoms

> show #!3-4 cartoons

> ui tool show Matchmaker

> matchmaker #!4 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain C (#3) with 6BP2_GP.pdb, chain A
(#4), sequence alignment score = 809.1  
RMSD between 129 pruned atom pairs is 0.644 angstroms; (across all 142 pairs:
1.417)  
  

> hide #!3 models

> hide #!1 models

> show #!1 models

> save /Users/aminaddetia/Documents/Veesler_Lab/MARV/MARV_Fabs_nsEM/MARV7/GP-
> MARV7-v2.cxs

——— End of log from Tue Jul 29 13:10:27 2025 ———

opened ChimeraX session  

> close #2

> show #!3 models

> volume #1 level 0.1683

> volume #1 level 0.5913

> volume #1 level 0.4488

> ui tool show "Hide Dust"

> surface dust #1 size 9.6

> surface dust #1 size 9.19

> surface dust #1 size 16

> volume #1 level 0.4933

> volume #1 level 0.5022

> surface undust #1

> surface dust #1 size 16

> ui tool show "Segment Map"

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.502236  
Showing 9 region surfaces  
27 watershed regions, grouped to 9 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 9 regions, 9 surfaces  

> surface dust #1 size 16

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.502236  
Showing 6 region surfaces  
27 watershed regions, grouped to 6 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 6 regions, 6 surfaces  
Ungrouped to 6 regions  

> close #2

> ui tool show "Fit in Map"

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J528_002_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.807, steps = 28  
shifted from previous position = 0.0397  
rotated from previous position = 0.0644 degrees  
atoms outside contour = 815, contour level = 0.50224  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.06081217 -0.99814529 0.00280336 425.79711414  
0.99814602 -0.06081885 -0.00236378 3.14650160  
0.00252989 0.00265442 0.99999328 -13.07424453  
Axis 0.00251375 0.00013699 0.99999683  
Axis point 211.43390378 201.91011493 0.00000000  
Rotation angle (degrees) 93.48681636  
Shift along axis -12.00342273  
  

> fitmap #3 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#3) to map
cryosparc_P662_J528_002_volume_map.mrc (#1) using 6691 atoms  
average map value = 0.807, steps = 28  
shifted from previous position = 0.0312  
rotated from previous position = 0.0408 degrees  
atoms outside contour = 814, contour level = 0.50224  
  
Position of 250225-MARV-GP_MARV16.pdb (#3) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.06077111 -0.99814594 0.00339861 425.69569753  
0.99814736 -0.06078056 -0.00275132 3.19412071  
0.00295279 0.00322511 0.99999044 -13.28725360  
Axis 0.00299375 0.00022332 0.99999549  
Axis point 211.36370090 201.89748100 0.00000000  
Rotation angle (degrees) 93.48462052  
Shift along axis -12.01205416  
  

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J528_002_volume_map.mrc
(#1) using 7320 atoms  
average map value = 0.7758, steps = 56  
shifted from previous position = 2.55  
rotated from previous position = 3.46 degrees  
atoms outside contour = 1105, contour level = 0.50224  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.54302390 0.83971724 0.00000249 60.19681128  
-0.83971722 0.54302390 0.00018627 349.14495949  
0.00015506 -0.00010324 0.99999998 114.02715980  
Axis -0.00017238 -0.00009085 -0.99999998  
Axis point 350.86502709 119.27798789 0.00000000  
Rotation angle (degrees) 57.11027354  
Shift along axis -114.06925385  
  

> color zone #1 near #4

> hide #!3 models

> color zone #1 near #4 distance 8

> color zone #1 near #4 distance 12

> color zone #1 near #4 distance 14

> color zone #1 near #4 distance 8

> color zone #1 near #4 distance 18

> color zone #1 near #4 distance 16

> color zone #1 near #4 distance 17

> color zone #1 near #4 distance 5

> color zone #1 near #4 distance 15

> volume #1 level 0.7131

> volume #1 level 0.4977

> color zone #1 near #4 distance 13

> color zone #1 near #4 distance 12

> volume splitbyzone #1

Opened cryosparc_P662_J528_002_volume_map.mrc 0 as #2.1, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 1 as #2.2, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 2 as #2.3, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 3 as #2.4, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 4 as #2.5, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 5 as #2.6, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 6 as #2.7, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 7 as #2.8, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  

> undo

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J528_002_volume_map.mrc
(#1) using 7320 atoms  
average map value = 0.7758, steps = 56  
shifted from previous position = 2.55  
rotated from previous position = 3.46 degrees  
atoms outside contour = 1081, contour level = 0.49765  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.54302390 0.83971724 0.00000249 60.19681128  
-0.83971722 0.54302390 0.00018627 349.14495949  
0.00015506 -0.00010324 0.99999998 114.02715980  
Axis -0.00017238 -0.00009085 -0.99999998  
Axis point 350.86502709 119.27798789 0.00000000  
Rotation angle (degrees) 57.11027354  
Shift along axis -114.06925385  
  

> hide #!4#!2.2-8 target m

> show #!2.2 models

> close #2

> show #!1 models

> color #1 #b2b2b29d models

> show #!4 models

> open /Users/aminaddetia/Documents/Veesler_Lab/MARV/GP-
> MARV16_krios/250225-MARV-GP_MARV16.pdb

Chain information for 250225-MARV-GP_MARV16.pdb #2  
---  
Chain | Description  
A C G | No description available  
B D I | No description available  
E H J | No description available  
F K L | No description available  
  

> hide #!2,4 atoms

> show #!2,4 cartoons

> select #2/A,C,G,B,D,I

6690 atoms, 6863 bonds, 6 pseudobonds, 822 residues, 2 models selected  

> delete sel

> select add #2

5212 atoms, 5328 bonds, 679 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-8.6904,0,1,0,-5.0575,0,0,1,-1.4875

> view matrix models #2,1,0,0,-6.5691,0,1,0,-8.393,0,0,1,1.0331

> view matrix models #2,1,0,0,-5.5704,0,1,0,-11.469,0,0,1,0.1517

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#2) to map
cryosparc_P662_J528_002_volume_map.mrc (#1) using 5212 atoms  
average map value = 0.847, steps = 200  
shifted from previous position = 5.6  
rotated from previous position = 0.89 degrees  
atoms outside contour = 1395, contour level = 0.49765  
  
Position of 250225-MARV-GP_MARV16.pdb (#2) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99987951 -0.01530886 0.00257182 -7.92126020  
0.01530779 0.99988273 0.00043370 -13.97061819  
-0.00257816 -0.00039428 0.99999660 -1.41324292  
Axis -0.02665950 0.16581924 0.98579575  
Axis point 870.68664672 -530.37555576 0.00000000  
Rotation angle (degrees) 0.88977629  
Shift along axis -3.49858927  
  

> color zone #1 near #2 distance 12

> color zone #1 near #2 distance 8

> color zone #1 near #2 distance 6

> color zone #1 near #2 distance 8

> color zone #1 near #2 distance 10

> select up

19223 atoms, 19672 bonds, 2417 residues, 5 models selected  

> volume splitbyzone #1

Opened cryosparc_P662_J528_002_volume_map.mrc 0 as #5.1, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 1 as #5.2, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 2 as #5.3, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map.mrc 3 as #5.4, grid size
252,252,252, pixel 1.6, shown at level 0.498, step 1, values float32  

> hide #!5.4 models

> hide #!5.1 models

> show #!5.1 models

> hide #!5 models

> show #!5 models

> hide #!5.1 models

> show #!5.1 models

> hide #!5.1 models

> show #!5.1 models

> hide #!5.2 models

> show #!5.2 models

> hide #!5.2 models

> show #!5.2 models

> hide #!5.3 models

> show #!5.3 models

> show #!5.4 models

> hide #!5.4 models

> hide #!5.3 models

> show #!5.3 models

> fitmap #2 inMap #1

Fit molecule 250225-MARV-GP_MARV16.pdb (#2) to map
cryosparc_P662_J528_002_volume_map.mrc (#1) using 5212 atoms  
average map value = 0.847, steps = 200  
shifted from previous position = 5.6  
rotated from previous position = 0.89 degrees  
atoms outside contour = 1395, contour level = 0.49765  
  
Position of 250225-MARV-GP_MARV16.pdb (#2) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99987951 -0.01530886 0.00257182 -7.92126020  
0.01530779 0.99988273 0.00043370 -13.97061819  
-0.00257816 -0.00039428 0.99999660 -1.41324292  
Axis -0.02665950 0.16581924 0.98579575  
Axis point 870.68664672 -530.37555576 0.00000000  
Rotation angle (degrees) 0.88977629  
Shift along axis -3.49858927  
  

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J528_002_volume_map.mrc
(#1) using 7320 atoms  
average map value = 0.7758, steps = 56  
shifted from previous position = 2.55  
rotated from previous position = 3.46 degrees  
atoms outside contour = 1081, contour level = 0.49765  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.54302390 0.83971724 0.00000249 60.19681128  
-0.83971722 0.54302390 0.00018627 349.14495949  
0.00015506 -0.00010324 0.99999998 114.02715980  
Axis -0.00017238 -0.00009085 -0.99999998  
Axis point 350.86502709 119.27798789 0.00000000  
Rotation angle (degrees) 57.11027354  
Shift along axis -114.06925385  
  

> close #5

> select add #3

19223 atoms, 19672 bonds, 6 pseudobonds, 2417 residues, 6 models selected  

> select subtract #3

12532 atoms, 12809 bonds, 1594 residues, 4 models selected  

> select subtract #2

7320 atoms, 7481 bonds, 915 residues, 3 models selected  

> select subtract #1

7320 atoms, 7481 bonds, 915 residues, 1 model selected  

> show #!1 models

> ui tool show "Segment Map"

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 12 region surfaces  
28 watershed regions, grouped to 12 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 12 regions, 12 surfaces  

> select add #5

7320 atoms, 7481 bonds, 915 residues, 14 models selected  

> select add #4

7320 atoms, 7481 bonds, 6 pseudobonds, 915 residues, 15 models selected  

> select subtract #4

13 models selected  
0 or more than 1 volume model selected  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 12 region surfaces  
28 watershed regions, grouped to 12 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 12 regions, 12 surfaces  
Smoothing and grouping, standard deviation 4 voxels  
Showing 9 region surfaces  
Got 9 regions after smoothing 4 voxels.  
Smoothing and grouping, standard deviation 5 voxels  
Showing 6 region surfaces  
Got 6 regions after smoothing 5 voxels.  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 12 region surfaces  
28 watershed regions, grouped to 12 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 12 regions, 12 surfaces  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 12 region surfaces  
28 watershed regions, grouped to 12 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 12 regions, 12 surfaces  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 12 region surfaces  
28 watershed regions, grouped to 12 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 12 regions, 12 surfaces  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 9 region surfaces  
28 watershed regions, grouped to 9 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 9 regions, 9 surfaces  

> fitmap #4 inMap #1

Fit molecule 6BP2_GP.pdb (#4) to map cryosparc_P662_J528_002_volume_map.mrc
(#1) using 7320 atoms  
average map value = 0.7758, steps = 24  
shifted from previous position = 0.0192  
rotated from previous position = 0.0169 degrees  
atoms outside contour = 1078, contour level = 0.49765  
  
Position of 6BP2_GP.pdb (#4) relative to
cryosparc_P662_J528_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.54309135 0.83967361 -0.00008303 60.19055167  
-0.83967351 0.54309133 0.00045665 349.12841052  
0.00042853 -0.00017828 0.99999989 113.98672605  
Axis -0.00037808 -0.00030462 -0.99999988  
Axis point 350.84324665 119.27956931 0.00000000  
Rotation angle (degrees) 57.10567485  
Shift along axis -114.11582011  
  
Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Showing 4 region surfaces  
28 watershed regions, grouped to 4 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 4 regions, 4 surfaces  

> hide #!2 models

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Only showing 4 of 4 regions.  
Showing 4 region surfaces  
28 watershed regions, grouped to 4 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 4 regions, 4 surfaces  

> surface dust #1 size 16

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.497652  
Only showing 4 of 4 regions.  
Showing 4 region surfaces  
28 watershed regions, grouped to 4 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 4 regions, 4 surfaces  

> surface dust #5 size 16

> hide #!1 models

> show #!1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> surface dust #1 size 15.47

> surface dust #1 size 20.94

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> volume #1 level 0.5155

> ui tool show "Segment Map"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Segmenting cryosparc_P662_J528_002_volume_map.mrc, density threshold 0.515460  
Only showing 4 of 4 regions.  
Showing 4 region surfaces  
26 watershed regions, grouped to 4 regions  
Showing cryosparc_P662_J528_002_volume_map.seg - 4 regions, 4 surfaces  

> surface dust #5 size 16

> color #5.1 #f89ec17e

> select add #5.1

1 model selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 2 time(s)]Simulating map res 4.000, grid 2.000  

> molmap #3 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 250225-MARV-GP_MARV16.pdb map 4 as #6, grid size 46,55,60, pixel 2,
shown at level 0.0995, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map_masked as #7, grid size 252,252,252,
pixel 1.6, shown at step 1, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Simulating map res 4.000, grid 2.000  

> molmap #4 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 6BP2_GP.pdb map 4 as #7, grid size 52,50,61, pixel 2, shown at level
0.103, step 1, values float32  
Opened cryosparc_P662_J528_002_volume_map_masked as #8, grid size 252,252,252,
pixel 1.6, shown at step 1, values float32  
Top score: 0.76413, z-score: 2.15322 (avg: 0.7499, stdev: 0.0066)  

> ui tool show Matchmaker

> matchmaker #!4 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain F (#2) with 6BP2_GP.pdb, chain H
(#4), sequence alignment score = 38.5  
RMSD between 5 pruned atom pairs is 1.241 angstroms; (across all 48 pairs:
11.258)  
  

> matchmaker #!4 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain C (#3) with 6BP2_GP.pdb, chain A
(#4), sequence alignment score = 809.1  
RMSD between 129 pruned atom pairs is 0.644 angstroms; (across all 142 pairs:
1.417)  
  

> matchmaker #!4 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 250225-MARV-GP_MARV16.pdb, chain C (#3) with 6BP2_GP.pdb, chain A
(#4), sequence alignment score = 809.1  
RMSD between 129 pruned atom pairs is 0.644 angstroms; (across all 142 pairs:
1.417)  
  

> close #2

> hide #!3 models

> set bgColor white

> color #5.1 #919191ff

> color #5.1 #9191917c

> lighting soft depthCue true depthCueStart 0.42 depthCueEnd 2

> graphics silhouettes true width 2

> cartoon style modeHelix default arrows false xsection round width 2
> thickness 2

> select subtract #5.1

Nothing selected  

> color #5.2 #3e4169ff

> color #5.3 #3e4169ff

> color #5.4 #3e4169ff

> cd "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope binning"

Current working directory is:
/Users/aminaddetia/Library/CloudStorage/GoogleDrive-aaddetia@uw.edu/Shared
drives/Veesler_lab/Amin Addetia/MARV/Paper/Revision/Supplemental
figures/Epitope binning  

> save "/Users/aminaddetia/Library/CloudStorage/GoogleDrive-
> aaddetia@uw.edu/Shared drives/Veesler_lab/Amin
> Addetia/MARV/Paper/Revision/Supplemental figures/Epitope
> binning/MARV7_Fig.cxs"

——— End of log from Wed Aug 13 16:46:18 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,11
      Model Number: MRW33LL/A
      Chip: Apple M3 Max
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 36 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4 (23E214)
      Kernel Version: Darwin 23.4.0
      Time since boot: 51 days, 3 hours, 44 minutes

Graphics/Displays:

    Apple M3 Max:

      Chipset Model: Apple M3 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      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
        HP 24f:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by pett, 2 months ago

Cc:	pett added
Component:	Unassigned → Sessions
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Models with same ID in session

Not really sure how this could happen

comment:2 by Tom Goddard, 2 months ago

Resolution:	→ can't reproduce
Status:	assigned → closed

I'm not sure what they are trying to report since the duplicate model ID error is about 100 commands before the end of the log.

I see they are using Segger and the duplicate model name is apparently "39". I'd guess the duplicate model number is somehow a Segger bug. Maybe on session restore Segger is regenerating a model that was saved in the session and thus gets 2 copies. Would need a session file to figure this out.

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