ISOLDE: _populate_platform_combo_box: tuple.index(x): x not in tuple

[jing.16.liu@…]

The following bug report has been submitted:
Platform:        macOS-13.3.1-arm64-arm-64bit
ChimeraX Version: 1.6rc202305021906 (2023-05-02 19:06:00 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6rc202305021906 (2023-05-02)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/CMV-related/Chimerax/CMV/gB113_ITC88_density-
> model_202305.cxs format session

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "ClipCap" returned None  

[Repeated 1 time(s)]Opened cryosparc_P2_J169_008_volume_map_sharp.mrc as #1,
grid size 208,208,208, pixel 1.86, shown at level 0.625, step 1, values
float32  
Opened cryosparc_P2_J182_004_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.21, shown at level 0.278, step 2, values float32  
Opened cryosparc_P2_J183_010_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 1.21, shown at level 0.509, step 1, values float32  
Opened cryosparc_P2_J191_008_volume_map_sharp.mrc as #7, grid size
320,320,320, pixel 1.21, shown at level 0.268, step 1, values float32  
Opened cryosparc_P11_J49_003_volume_map_sharp.mrc as #8, grid size
144,144,144, pixel 1.76, shown at level 0.731, step 1, values float32  
Opened cryosparc_P2_J112_008_volume_map_sharp.mrc as #9, grid size
256,256,256, pixel 1.16, shown at level 0.456, step 1, values float32  
Opened cryosparc_P2_J118_007_volume_map_sharp (1).mrc as #10, grid size
256,256,256, pixel 1.16, shown at level 0.454, step 1, values float32  
Opened cryosparc_P2_J193_008_volume_map_sharp.mrc as #12, grid size
320,320,320, pixel 1.21, shown at level 0.443, step 1, values float32  
Log from Mon May 1 16:26:37 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/CMV-related/Chimerax/CMV/gB113_ITC88_density-
> model_20230427.cxs format session

Opened cryosparc_P2_J169_008_volume_map_sharp.mrc as #1, grid size
208,208,208, pixel 1.86, shown at level 1.02, step 1, values float32  
Log from Fri Apr 28 10:53:44 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113_ITC88_density-model_20230427.cxs" format session

Opened cryosparc_P2_J165_map.mrc as #3, grid size 208,208,208, pixel 1.86,
shown at level 0.696, step 1, values float32  
Log from Fri Apr 28 09:58:39 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jl209164/Downloads/cryosparc_P2_J109_007_volume_map_sharp.mrc

Opened cryosparc_P2_J109_007_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.16, shown at level 0.222, step 1, values float32  

> volume #1 level 0.4309

> open /Users/jl209164/Downloads/cryosparc_P2_J112_008_volume_map_sharp.mrc

Opened cryosparc_P2_J112_008_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.16, shown at level 0.2, step 1, values float32  

> volume #2 level 0.1999

> volume #2 level 0.6215

> volume #2 level 0.3881

> volume #2 level 0.501

> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/CMV-related/CMV/prefusiongB-gsk/gB-
> dDV_Nov2022/gBdDV_465_C2_I.pdb

Chain information for gBdDV_465_C2_I.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> select #3

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.69291,-0.72084,0.016069,137.45,-0.71045,-0.68638,-0.1554,344.93,0.12305,0.09626,-0.98772,222.08

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.69291,-0.72084,0.016069,144.63,-0.71045,-0.68638,-0.1554,345.22,0.12305,0.09626,-0.98772,251.32

> view matrix models
> #3,0.69291,-0.72084,0.016069,147.65,-0.71045,-0.68638,-0.1554,348.43,0.12305,0.09626,-0.98772,253.68

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.92852,-0.36364,0.074938,59.111,-0.36637,-0.9301,0.026295,308.41,0.060138,-0.051871,-0.99684,283.48

> view matrix models
> #3,0.81912,-0.57345,0.014265,110.28,-0.57358,-0.81911,0.008129,325.66,0.0070229,-0.014841,-0.99987,286.56

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.81912,-0.57345,0.014265,111.58,-0.57358,-0.81911,0.008129,338.57,0.0070229,-0.014841,-0.99987,286.4

> ui tool show "Fit in Map"

Fit molecule gBdDV_465_C2_I.pdb (#3) to map
cryosparc_P2_J109_007_volume_map_sharp.mrc (#1) using 27645 atoms  
average map value = 0.1325, steps = 96  
shifted from previous position = 8.92  
rotated from previous position = 1.57 degrees  
atoms outside contour = 23936, contour level = 0.43087  
  
Position of gBdDV_465_C2_I.pdb (#3) relative to
cryosparc_P2_J109_007_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.80721293 -0.59019337 0.00889229 117.66221757  
-0.59012227 -0.80725835 -0.00946878 342.05856737  
0.01276679 0.00239579 -0.99991563 274.45035995  
Axis 0.95058167 -0.31042235 0.00569632  
Axis point 0.00000000 189.79080824 137.43773961  
Rotation angle (degrees) 179.64243254  
Shift along axis 7.22828033  
  
Fit molecule gBdDV_465_C2_I.pdb (#3) to map
cryosparc_P2_J112_008_volume_map_sharp.mrc (#2) using 27645 atoms  
average map value = 0.4421, steps = 96  
shifted from previous position = 8.19  
rotated from previous position = 11.9 degrees  
atoms outside contour = 16797, contour level = 0.50104  
  
Position of gBdDV_465_C2_I.pdb (#3) relative to
cryosparc_P2_J112_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.91113215 -0.41211431 -0.00000876 80.30496050  
-0.41211431 -0.91113214 -0.00010916 330.45245128  
0.00003701 0.00010306 -0.99999999 284.71111342  
Axis 0.97753035 -0.21079470 0.00000712  
Axis point 0.00000000 173.87680497 142.36448986  
Rotation angle (degrees) 179.99378055  
Shift along axis 8.84493619  
  

> volume #2 color #ffffb2be

> volume #2 level 0.4064

> volume #2 level 0.3184

> volume #2 level 0.7851

> volume #2 level 0.5687

> volume #2 level 0.7513

> volume #2 level 0.3117

> volume #2 level 0.6904

> volume #2 level 0.3658

> open
> /Users/jl209164/Downloads/cryosparc_P2_J108_class_02_00124_volume_sharp.mrc

Opened cryosparc_P2_J108_class_02_00124_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.33, shown at level 0.597, step 1, values float32  

> open
> /Users/jl209164/Downloads/cryosparc_P2_J108_class_01_00124_volume_sharp.mrc

Opened cryosparc_P2_J108_class_01_00124_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.33, shown at level 0.597, step 1, values float32  

> hide #3 models

> ~select #3

Nothing selected  

> open
> /Users/jl209164/Downloads/cryosparc_P2_J108_class_00_00124_volume_sharp.mrc

Opened cryosparc_P2_J108_class_00_00124_volume_sharp.mrc as #6, grid size
128,128,128, pixel 2.33, shown at level 0.567, step 1, values float32  

> select #4

2 models selected  

> view matrix models #4,1,0,0,29.86,0,1,0,-127.25,0,0,1,-1.4684

> select #6

2 models selected  

> view matrix models #6,1,0,0,-20.644,0,1,0,95.068,0,0,1,10.144

> view matrix models #6,1,0,0,-33.268,0,1,0,147.04,0,0,1,8.404

> select #4

2 models selected  

> view matrix models #4,1,0,0,31.551,0,1,0,-132.16,0,0,1,1.4181

> set bgColor white

> select clear

> volume #4 level 0.8453

> volume #4 level 0.5318

> volume #4 level 1.051

> volume #5 level 0.6854

> volume #5 level 0.8456

> volume #6 level 0.8033

> open /Users/jl209164/Downloads/cryosparc_P2_J135_class_00_final_volume.mrc

Opened cryosparc_P2_J135_class_00_final_volume.mrc as #7, grid size
128,128,128, pixel 2.62, shown at level 0.757, step 1, values float32  

> volume #7 level 0.7536

> volume #7 level 0.5826

> volume #7 level 0.3378

> volume #7 level 0.2339

> select #7

2 models selected  

> view matrix models #7,1,0,0,-11.138,0,1,0,-17.056,0,0,1,-64.959

> volume #7 color #ffb2b292

> volume #7 level 0.4484

> view matrix models #7,1,0,0,-12.395,0,1,0,-16.116,0,0,1,-53.757

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.85844,-0.5072,-0.076342,104.02,0.50605,0.86179,-0.035139,-73.59,0.083614,-0.0084677,0.99646,-65.894

> view matrix models
> #7,0.87678,-0.47943,-0.037418,90.05,0.47725,0.87706,-0.054733,-67.872,0.059059,0.030131,0.9978,-68.064

> view matrix models
> #7,0.86922,-0.4921,-0.048019,95.09,0.49323,0.86978,0.014736,-81.036,0.034515,-0.036493,0.99874,-53.607

> open 7kdd

7kdd title:  
HCMV postfusion gB in complex with SM5-1 Fab [more info...]  
  
Chain information for 7kdd #8  
---  
Chain | Description | UniProt  
A B C | Envelope glycoprotein B | GB_HCMVT  
D F H | SM5-1 Fab antibody heavy chain |  
E G I | SM5-1 Fab antibody light chain |  
  
Non-standard residues in 7kdd #8  
---  
CA — calcium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> select #8

19741 atoms, 20211 bonds, 9 pseudobonds, 2467 residues, 3 models selected  

> view matrix models
> #8,0.99739,0.072264,0.00026426,-13.312,-0.072265,0.99737,0.0046271,12.731,7.0807e-05,-0.0046341,0.99999,0.87005

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.99739,0.072264,0.00026426,-10.858,-0.072265,0.99737,0.0046271,-15.767,7.0807e-05,-0.0046341,0.99999,-79.731

> view matrix models
> #8,0.99739,0.072264,0.00026426,-28.686,-0.072265,0.99737,0.0046271,-0.054646,7.0807e-05,-0.0046341,0.99999,-83.827

> view matrix models
> #8,0.99739,0.072264,0.00026426,-56.561,-0.072265,0.99737,0.0046271,-31.358,7.0807e-05,-0.0046341,0.99999,-76.941

> volume #7 level 0.2875

> ~select #8

Nothing selected  

> hide #!8 models

> volume #4 level 0.8231

> close session

> open
> /Users/jl209164/Downloads/cryosparc_P11_J170_class_00_00082_volume_sharp.mrc

Opened cryosparc_P11_J170_class_00_00082_volume_sharp.mrc as #1, grid size
128,128,128, pixel 1.83, shown at level 0.172, step 1, values float32  

> open /Users/jl209164/Downloads/cryosparc_P2_J112_008_volume_map_sharp.mrc

Opened cryosparc_P2_J112_008_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.16, shown at level 0.2, step 1, values float32  

> volume #2 level 0.4259

> close #2

> open
> /Users/jl209164/Downloads/cryosparc_P11_J170_class_01_00082_volume_sharp.mrc

Opened cryosparc_P11_J170_class_01_00082_volume_sharp.mrc as #2, grid size
128,128,128, pixel 1.83, shown at level 0.155, step 1, values float32  

> select #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99998,-0.0034125,-0.0059812,1.1184,0.0035512,0.99972,0.023332,-3.1059,0.0058999,-0.023352,0.99971,2.1985

> view matrix models
> #2,0.55248,0.83246,-0.042269,-44.52,-0.8099,0.52414,-0.26333,183.5,-0.19706,0.17972,0.96378,5.2847

> view matrix models
> #2,0.43244,0.83042,0.35127,-76.217,-0.80168,0.53242,-0.27175,182.52,-0.41269,-0.16409,0.89597,80.405

> open
> /Users/jl209164/Downloads/cryosparc_P11_J170_class_01_00082_volume_sharp.mrc

Opened cryosparc_P11_J170_class_01_00082_volume_sharp.mrc as #3, grid size
128,128,128, pixel 1.83, shown at level 0.155, step 1, values float32  

> select #3

2 models selected  

> view matrix models
> #3,0.90663,-0.3906,-0.15955,77.274,0.41194,0.90122,0.13453,-51.757,0.091247,-0.18769,0.97798,14.851

> view matrix models
> #3,0.4678,0.8227,0.32301,-76.102,-0.86292,0.50417,-0.034392,165.4,-0.19114,-0.26264,0.94577,60.755

> hide #!2 models

> show #!2 models

> close #3

> open
> /Users/jl209164/Downloads/cryosparc_P11_J170_class_01_00082_volume_sharp.mrc

Opened cryosparc_P11_J170_class_01_00082_volume_sharp.mrc as #3, grid size
128,128,128, pixel 1.83, shown at level 0.155, step 1, values float32  

> close #3

> open /Users/jl209164/Downloads/cryosparc_P11_J171_map.mrc

Opened cryosparc_P11_J171_map.mrc as #3, grid size 128,128,128, pixel 1.83,
shown at level 0.163, step 1, values float32  

> close #2

> close #3

> open /Users/jl209164/Downloads/cryosparc_P11_J171_map.mrc

Opened cryosparc_P11_J171_map.mrc as #2, grid size 128,128,128, pixel 1.83,
shown at level 0.163, step 1, values float32  

> close #2

> open /Users/jl209164/Downloads/cryosparc_P11_J172_map.mrc

Opened cryosparc_P11_J172_map.mrc as #2, grid size 128,128,128, pixel 1.83,
shown at level 0.148, step 1, values float32  

> select #2

2 models selected  

> view matrix models
> #2,0.4228,-0.89891,0.11486,163.84,0.90419,0.40998,-0.11979,-19.522,0.060592,0.1545,0.98613,-24.337

> ~select #2

Nothing selected  

> ui tool show "Fit in Map"

Fit map cryosparc_P11_J170_class_00_00082_volume_sharp.mrc in map
cryosparc_P11_J172_map.mrc using 20966 points  
correlation = 0.9885, correlation about mean = 0.5965, overlap = 718.2  
steps = 92, shift = 5.89, angle = 10.9 degrees  
  
Position of cryosparc_P11_J170_class_00_00082_volume_sharp.mrc (#1) relative
to cryosparc_P11_J172_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.49999807 0.86602652 -0.00004695 -42.72715681  
-0.86602644 0.49999805 0.00040334 159.50932112  
0.00037278 -0.00016101 0.99999992 -0.02456268  
Axis -0.00032583 -0.00024233 -0.99999992  
Axis point 116.77519623 116.75737211 0.00000000  
Rotation angle (degrees) 60.00013109  
Shift along axis -0.00016980  
  

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #2 level 0.1102

> volume #1 level 0.09338

> volume #2 level 0.08742

> open /Users/jl209164/Downloads/cryosparc_P2_J118_007_volume_map_sharp.mrc

Opened cryosparc_P2_J118_007_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.16, shown at level 0.196, step 1, values float32  

> volume #3 level 0.4111

> volume #3 level 0.6449

> open /Users/jl209164/Downloads/cryosparc_P2_J145_class_01_final_volume.mrc

Opened cryosparc_P2_J145_class_01_final_volume.mrc as #4, grid size
128,128,128, pixel 2.09, shown at level 0.284, step 1, values float32  

> volume #4 level 0.7642

> volume #4 level 0.1875

> volume #4 level 0.07079

> close #4

> open /Users/jl209164/Downloads/cryosparc_P6_J61_004_volume_map_sharp.mrc

Opened cryosparc_P6_J61_004_volume_map_sharp.mrc as #4, grid size 180,180,180,
pixel 1.74, shown at level 0.542, step 1, values float32  

> volume #4 level 1.25

> volume #4 level 0.2255

> volume #4 level 0.4841

> close #4

> open /Users/jl209164/Downloads/cryosparc_P6_J61_004_volume_map_sharp.mrc

Opened cryosparc_P6_J61_004_volume_map_sharp.mrc as #4, grid size 180,180,180,
pixel 1.74, shown at level 0.542, step 1, values float32  

> volume #4 level 1.528

> volume #4 level 1.107

> volume #4 level 0.6565

> open /Users/jl209164/Downloads/cryosparc_P2_J147_006_volume_map_sharp.mrc

Opened cryosparc_P2_J147_006_volume_map_sharp.mrc as #5, grid size
180,180,180, pixel 1.86, shown at level 0.613, step 1, values float32  

> volume #5 level 0.4865

> volume #5 level 0.3819

> volume #5 level 0.5086

> volume #5 level 0.6765

> volume #5 level 0.5593

> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/CMV-related/CMV/prefusiongB-gsk/gB-
> dDV_Nov2022/gBdDV_465_C2_I.pdb

Chain information for gBdDV_465_C2_I.pdb #6  
---  
Chain | Description  
A B C | No description available  
  

> select #6

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> view matrix models
> #6,0.94356,0.32848,0.042275,-40.83,-0.32867,0.94444,-0.0025213,54.724,-0.040755,-0.011516,0.9991,7.4731

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.94356,0.32848,0.042275,-13.898,-0.32867,0.94444,-0.0025213,91.466,-0.040755,-0.011516,0.9991,8.0782

> view matrix models
> #6,0.94356,0.32848,0.042275,-10.649,-0.32867,0.94444,-0.0025213,78.242,-0.040755,-0.011516,0.9991,5.7973

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.58287,0.81255,0.0033736,148.6,-0.81073,-0.58184,0.064637,341,0.054484,0.03494,0.9979,-13.838

> view matrix models
> #6,-0.35921,0.90275,0.23665,75.002,-0.93149,-0.3624,-0.031446,341.4,0.057375,-0.23174,0.97108,24.5

> view matrix models
> #6,-0.35875,0.90184,0.2408,74.532,-0.93154,-0.36231,-0.030937,341.33,0.059344,-0.23541,0.97008,24.833

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.35875,0.90184,0.2408,69.114,-0.93154,-0.36231,-0.030937,351.43,0.059344,-0.23541,0.97008,19.724

> close #1-5

> open /Users/jl209164/Downloads/cryosparc_P2_J148_map.mrc

Opened cryosparc_P2_J148_map.mrc as #1, grid size 180,180,180, pixel 1.86,
shown at level 0.574, step 1, values float32  

> view matrix models
> #6,-0.35875,0.90184,0.2408,72.172,-0.93154,-0.36231,-0.030937,347.19,0.059344,-0.23541,0.97008,27.614

Fit molecule gBdDV_465_C2_I.pdb (#6) to map cryosparc_P2_J148_map.mrc (#1)
using 27645 atoms  
average map value = 0.6302, steps = 92  
shifted from previous position = 13.5  
rotated from previous position = 16 degrees  
atoms outside contour = 10523, contour level = 0.57448  
  
Position of gBdDV_465_C2_I.pdb (#6) relative to cryosparc_P2_J148_map.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.48594939 0.87398694 -0.00013635 114.13877305  
-0.87398690 -0.48594941 -0.00026418 354.12474939  
-0.00029715 -0.00000921 0.99999996 -4.28142352  
Axis 0.00014587 0.00009199 -0.99999999  
Axis point 161.21126643 143.49601318 0.00000000  
Rotation angle (degrees) 119.07469463  
Shift along axis 4.33064930  
  

> color #1 #b2b2ff96 models

> color #1 #b2b2ff78 models

[Repeated 1 time(s)]

> volume #1 level 0.4889

> volume #1 level 0.3009

> volume #1 level 0.4066

> select clear

> volume #1 level 0.2774

> volume #1 level 0.3479

> volume #1 level 0.561

> volume #1 level 0.4654

> volume #1 level 0.3462

Window position QRect(3788,462 658x459) outside any known screen, using
primary screen  

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113_ITC88_density-model_20230427.cxs"

> open
> /Users/jl209164/Downloads/cryosparc_P2_J146_class_00_00122_volume_sharp.mrc

Opened cryosparc_P2_J146_class_00_00122_volume_sharp.mrc as #2, grid size
128,128,128, pixel 2.09, shown at level 0.401, step 1, values float32  

> open
> /Users/jl209164/Downloads/cryosparc_P2_J146_class_01_00122_volume_sharp.mrc

Opened cryosparc_P2_J146_class_01_00122_volume_sharp.mrc as #3, grid size
128,128,128, pixel 2.09, shown at level 0.371, step 1, values float32  

> hide #!2 models

> hide #!1 models

> hide #6 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> select #2

2 models selected  

> select #3

2 models selected  

> show #!2 models

> close #2

> open
> /Users/jl209164/Downloads/cryosparc_P2_J160_class_01_00062_volume_sharp.mrc

Opened cryosparc_P2_J160_class_01_00062_volume_sharp.mrc as #2, grid size
128,128,128, pixel 3.02, shown at level 1.07, step 1, values float32  

> volume #2 level 1.598

> volume #2 level 0.986

> volume #2 level 0.4863

> close #3

> select #2

2 models selected  

> view matrix models #2,1,0,0,-21.327,0,1,0,-16.616,0,0,1,-35.503

> show #6 models

> volume #2 level 1.238

> volume #2 level 0.9579

> close #2

> open /Users/jl209164/Downloads/cryosparc_P2_J164_map.mrc

Opened cryosparc_P2_J164_map.mrc as #2, grid size 128,128,128, pixel 3.02,
shown at level 1.06, step 1, values float32  

> volume #2 level 0.7786

> volume #2 level 0.6132

> select #2

2 models selected  

> view matrix models #2,1,0,0,-21.77,0,1,0,-6.3479,0,0,1,-15.441

> view matrix models #2,1,0,0,-26.249,0,1,0,-6.5048,0,0,1,-19.762

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.92251,0.36587,-0.12294,-55.617,-0.35127,0.92784,0.1254,48.713,0.15995,-0.072497,0.98446,-33.439

Fit map cryosparc_P2_J164_map.mrc in map cryosparc_P2_J148_map.mrc using 43109
points  
correlation = 0.9758, correlation about mean = 0.8151, overlap = 2.691e+04  
steps = 112, shift = 19.7, angle = 13.7 degrees  
  
Position of cryosparc_P2_J164_map.mrc (#2) relative to
cryosparc_P2_J148_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.94876351 0.31178428 -0.05136507 -66.55799530  
-0.31547076 0.94390345 -0.09759343 63.41133395  
0.01805558 0.10879726 0.99389997 -49.05563298  
Axis 0.31084020 -0.10455282 -0.94469417  
Axis point 161.26557857 258.94202093 0.00000000  
Rotation angle (degrees) 19.38950870  
Shift along axis 19.02383640  
  

> volume #2 color #e5bf9992

> volume #2 color #e5bf9991

> volume #2 level 0.503

> volume #2 level 0.7362

> volume #2 level 0.6048

> volume #2 level 1.381

> volume #2 level 1.109

> open /Users/jl209164/Downloads/cryosparc_P2_J165_map.mrc

Opened cryosparc_P2_J165_map.mrc as #3, grid size 208,208,208, pixel 1.86,
shown at level 0.511, step 1, values float32  

> select #3

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-17.9,0,1,0,-36.072,0,0,1,-33.699

> view matrix models #3,1,0,0,-21.568,0,1,0,-30.251,0,0,1,-28.72

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.9567,0.28862,-0.037831,-58.062,-0.28914,0.95724,-0.0090545,33.16,0.0336,0.019601,0.99924,-38.37

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.9567,0.28862,-0.037831,-65.514,-0.28914,0.95724,-0.0090545,38.227,0.0336,0.019601,0.99924,-34.926

Fit map cryosparc_P2_J165_map.mrc in map cryosparc_P2_J148_map.mrc using 89973
points  
correlation = 0.9774, correlation about mean = 0.6604, overlap = 4.304e+04  
steps = 64, shift = 1.6, angle = 5.48 degrees  
  
Position of cryosparc_P2_J165_map.mrc (#3) relative to
cryosparc_P2_J148_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.94783531 0.31456592 -0.05154124 -66.89863032  
-0.31826644 0.94291175 -0.09810149 64.19181666  
0.01773946 0.10938790 0.99384083 -49.11127375  
Axis 0.30988299 -0.10346992 -0.94512777  
Axis point 161.56528202 258.22240927 0.00000000  
Rotation angle (degrees) 19.55956606  
Shift along axis 19.04375863  
  

> hide #!2 models

Fit molecule gBdDV_465_C2_I.pdb (#6) to map cryosparc_P2_J165_map.mrc (#3)
using 27645 atoms  
average map value = 0.6741, steps = 72  
shifted from previous position = 0.639  
rotated from previous position = 3.48 degrees  
atoms outside contour = 7406, contour level = 0.51061  
  
Position of gBdDV_465_C2_I.pdb (#6) relative to cryosparc_P2_J165_map.mrc (#3)
coordinates:  
Matrix rotation and translation  
-0.19011744 0.98014745 0.05627011 76.20245809  
-0.97909321 -0.19351181 0.06268705 342.75466752  
0.07233149 -0.04317578 0.99644569 17.82365008  
Axis -0.05395207 -0.00818554 -0.99850998  
Axis point 178.61159146 140.48874318 0.00000000  
Rotation angle (degrees) 101.16247103  
Shift along axis -24.71400562  
  

> close #1

> close #2

> volume #3 color #99bfe5b1

> volume #3 color #99bfe5b0

> volume #3 level 0.6067

> volume #3 level 0.3386

> volume #3 color #99bfe567

> volume #3 level 0.6111

> volume #3 level 0.2493

> volume #3 level 0.772

> volume #3 level 0.696

Window position QRect(2293,317 658x459) outside any known screen, using
primary screen  

Window position QRect(2069,591 100x30) outside any known screen, using primary
screen  

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113_ITC88_density-model_20230427.cxs"

——— End of log from Fri Apr 28 09:58:39 2023 ———

opened ChimeraX session  

> open /Users/jl209164/Downloads/cryosparc_P2_J169_008_volume_map_sharp.mrc

Opened cryosparc_P2_J169_008_volume_map_sharp.mrc as #1, grid size
208,208,208, pixel 1.86, shown at level 0.479, step 1, values float32  

> select #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-32.623,0,1,0,-26.251,0,0,1,-27.11

> ui tool show "Fit in Map"

Fit map cryosparc_P2_J169_008_volume_map_sharp.mrc in map
cryosparc_P2_J165_map.mrc using 89856 points  
correlation = 0.9309, correlation about mean = 0.5399, overlap = 5.385e+04  
steps = 64, shift = 6.6, angle = 0.065 degrees  
  
Position of cryosparc_P2_J169_008_volume_map_sharp.mrc (#1) relative to
cryosparc_P2_J165_map.mrc (#3) coordinates:  
Matrix rotation and translation  
0.94806214 -0.31760243 0.01751804 67.61772799  
0.31397183 0.94321015 0.10851865 -69.40809375  
-0.05098898 -0.09738225 0.99394005 29.41501295  
Axis -0.30832111 0.10258412 0.94573495  
Axis point 252.04309278 171.53869259 0.00000000  
Rotation angle (degrees) 19.50606168  
Shift along axis -0.14933498  
  
Fit molecule gBdDV_465_C2_I.pdb (#6) to map
cryosparc_P2_J169_008_volume_map_sharp.mrc (#1) using 27645 atoms  
average map value = 0.7796, steps = 52  
shifted from previous position = 0.751  
rotated from previous position = 3.48 degrees  
atoms outside contour = 7826, contour level = 0.47924  
  
Position of gBdDV_465_C2_I.pdb (#6) relative to
cryosparc_P2_J169_008_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.48434008 0.87487981 0.00005399 139.82100522  
-0.87487979 -0.48434008 0.00020174 380.00285517  
0.00020265 0.00005047 0.99999998 21.69634265  
Axis -0.00008645 -0.00008496 -0.99999999  
Axis point 181.89711094 148.79535002 0.00000000  
Rotation angle (degrees) 118.96924634  
Shift along axis -21.74071369  
  

> close #3

> volume #1 color #ffffb2a4

> volume #1 color #929292

> volume #1 color #92929294

> volume #1 color #92929280

> color #6 #ff85ff transparency 0

> color #6 #ff40ff transparency 0

> color #6 #00fdff transparency 0

> color #6 #73fdff transparency 0

> color #6 #76d6ff transparency 0

> color #6 #0433ff transparency 0

> volume #1 level 1.091

> volume #1 level 0.8448

> volume #1 level 0.726

> volume #1 level 0.6346

> volume #1 level 0.5067

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 6/A  

> open /Users/jl209164/Downloads/cryosparc_P2_J172_006_volume_map_sharp.mrc

Opened cryosparc_P2_J172_006_volume_map_sharp.mrc as #2, grid size
208,208,208, pixel 1.86, shown at level 0.666, step 1, values float32  

> select #2

2 models selected  

> view matrix models #2,1,0,0,-30.517,0,1,0,-21.013,0,0,1,-32.739

> view matrix models #2,1,0,0,-32.674,0,1,0,-22.798,0,0,1,-31.344

> view matrix models #2,1,0,0,-113.13,0,1,0,60.354,0,0,1,-18.451

> volume #2 level 0.982

> volume #2 level 0.6012

> close #2

> volume #1 level 1.018

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113_ITC88_density-model_20230427.cxs"

——— End of log from Fri Apr 28 10:53:44 2023 ———

opened ChimeraX session  

> volume #1 level 0.625

> open /Users/jl209164/Downloads/cryosparc_P2_J182_004_volume_map_sharp.mrc

Opened cryosparc_P2_J182_004_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.21, shown at level 0.264, step 2, values float32  

> select #2,6

27645 atoms, 27963 bonds, 1749 residues, 3 models selected  

> select #1,6

27645 atoms, 27963 bonds, 1749 residues, 3 models selected  

> view matrix models
> #6,-0.48494,0.87455,-0.00043429,141.19,-0.87455,-0.48494,-0.0005572,376.55,-0.0006979,0.0001096,1,25.353,#1,1,0.00068617,-0.00048842,1.1237,-0.00068654,1,-0.0007589,-3.3365,0.0004879,0.00075923,1,3.2996

> view matrix models
> #6,-0.48494,0.87455,-0.00043429,140.02,-0.87455,-0.48494,-0.0005572,375.19,-0.0006979,0.0001096,1,25.522,#1,1,0.00068617,-0.00048842,-0.048228,-0.00068654,1,-0.0007589,-4.697,0.0004879,0.00075923,1,3.4687

> ui tool show "Fit in Map"

Fit map cryosparc_P2_J169_008_volume_map_sharp.mrc in map
cryosparc_P2_J182_004_volume_map_sharp.mrc using 56588 points  
correlation = 0.7253, correlation about mean = 0.1441, overlap = 1.4e+04  
steps = 92, shift = 7.39, angle = 2.53 degrees  
  
Position of cryosparc_P2_J169_008_volume_map_sharp.mrc (#1) relative to
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99976596 -0.00581272 0.02083858 2.84875715  
0.00502904 0.99928531 0.03746430 -11.43383293  
-0.02104146 -0.03735073 0.99908067 10.79126811  
Axis -0.86569379 0.48459905 0.12545132  
Axis point 0.00000000 305.72634325 224.96616563  
Rotation angle (degrees) 2.47658022  
Shift along axis -6.65319709  
  
Fit molecule gBdDV_465_C2_I.pdb (#6) to map
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) using 27645 atoms  
average map value = 0.2682, steps = 96  
shifted from previous position = 5.11  
rotated from previous position = 14.1 degrees  
atoms outside contour = 14274, contour level = 0.26375  
  
Position of gBdDV_465_C2_I.pdb (#6) relative to
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.68299306 0.73042471 0.00046854 187.25936214  
-0.73042404 -0.68299119 -0.00194027 387.85675489  
-0.00109721 -0.00166742 0.99999801 26.34136707  
Axis 0.00018677 0.00107181 -0.99999941  
Axis point 177.80379602 153.30581660 0.00000000  
Rotation angle (degrees) 133.07798100  
Shift along axis -25.89066793  
  

> volume #2 color #ffffb2ae

> volume #2 color #ffffb2ad

> volume #1 color #92929280

Fit molecule gBdDV_465_C2_I.pdb (#6) to map
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) using 27645 atoms  
average map value = 0.2682, steps = 44  
shifted from previous position = 0.0248  
rotated from previous position = 0.0194 degrees  
atoms outside contour = 14287, contour level = 0.26375  
  
Position of gBdDV_465_C2_I.pdb (#6) relative to
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.68287409 0.73053587 0.00056399 187.21456190  
-0.73053504 -0.68287160 -0.00222203 387.91957161  
-0.00123814 -0.00192938 0.99999737 26.39535301  
Axis 0.00020030 0.00123343 -0.99999922  
Axis point 177.81490235 153.33996701 0.00000000  
Rotation angle (degrees) 133.06865014  
Shift along axis -25.87936269  
  

> select #1

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.53276,-0.8363,-0.12949,283.05,0.84426,0.53577,0.013387,-79.378,0.058182,-0.11646,0.99149,12.25

Fit map cryosparc_P2_J169_008_volume_map_sharp.mrc in map
cryosparc_P2_J182_004_volume_map_sharp.mrc using 56588 points  
correlation = 0.9463, correlation about mean = 0.5803, overlap = 2.801e+04  
steps = 92, shift = 6.78, angle = 7.74 degrees  
  
Position of cryosparc_P2_J169_008_volume_map_sharp.mrc (#1) relative to
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.49887824 -0.86666768 -0.00276459 265.03078814  
0.86667090 0.49888029 -0.00006438 -70.75884577  
0.00143500 -0.00236387 0.99999618 0.14781774  
Axis -0.00132662 -0.00242283 0.99999618  
Axis point 193.70316217 193.80193712 0.00000000  
Rotation angle (degrees) 60.07424596  
Shift along axis -0.03234133  
  

> select #6

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> view matrix models
> #6,-0.99494,-0.055769,0.083586,325.55,0.070192,-0.98097,0.18101,289.56,0.071902,0.18596,0.97992,-6.4261

Fit molecule gBdDV_465_C2_I.pdb (#6) to map
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) using 27645 atoms  
average map value = 0.379, steps = 120  
shifted from previous position = 5.75  
rotated from previous position = 12.5 degrees  
atoms outside contour = 8106, contour level = 0.26375  
  
Position of gBdDV_465_C2_I.pdb (#6) relative to
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99979675 0.02010187 0.00153960 327.58636280  
-0.02010562 -0.99979484 -0.00245979 333.61254335  
0.00148984 -0.00249024 0.99999579 21.81317023  
Axis -0.00075744 0.00123764 -0.99999895  
Axis point 165.46194302 165.17325477 0.00000000  
Rotation angle (degrees) 178.84806167  
Shift along axis -21.64838319  
  
Fit molecule gBdDV_465_C2_I.pdb (#6) to map
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) using 27645 atoms  
average map value = 0.379, steps = 40  
shifted from previous position = 0.00325  
rotated from previous position = 0.0103 degrees  
atoms outside contour = 8106, contour level = 0.26375  
  
Position of gBdDV_465_C2_I.pdb (#6) relative to
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99979927 0.01997699 0.00152652 327.60388828  
-0.01998052 -0.99979765 -0.00233220 333.57530993  
0.00147962 -0.00236223 0.99999611 21.79720602  
Axis -0.00075161 0.00117373 -0.99999903  
Axis point 165.46015413 165.16408210 0.00000000  
Rotation angle (degrees) 178.85522424  
Shift along axis -21.65188949  
  

> volume #2 level 0.1972

> select #6:64-85

1017 atoms, 1023 bonds, 66 residues, 1 model selected  

> color sel red

> select ::name="ASN"

1722 atoms, 1602 bonds, 123 residues, 1 model selected  

> color sel lime

> style sel sphere

Changed 1722 atom styles  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> hide sel target a

> volume #2 level 0.278

> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/CMV-related/CMV/prefusiongB-gsk/gB-
> dDV_Nov2022/gBdDV_Nov28.pdb

Chain information for gBdDV_Nov28.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/CMV-related/CMV/prefusiongB-gsk/gB-
> dDV_Nov2022/gBdDV_465_C2_I.pdb

Chain information for gBdDV_465_C2_I.pdb #4  
---  
Chain | Description  
A B C | No description available  
  

> close #3

> select #4

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> view matrix models
> #4,-0.54844,0.8318,-0.085591,122.23,0.83585,0.54827,-0.027512,-56.26,0.024043,-0.086629,-0.99595,261.53

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.54844,0.8318,-0.085591,132.99,0.83585,0.54827,-0.027512,-57.166,0.024043,-0.086629,-0.99595,394.07

> view matrix models
> #4,-0.54844,0.8318,-0.085591,174.77,0.83585,0.54827,-0.027512,0.20291,0.024043,-0.086629,-0.99595,369.8

> view matrix models
> #4,-0.54844,0.8318,-0.085591,164.72,0.83585,0.54827,-0.027512,1.9206,0.024043,-0.086629,-0.99595,372.37

Fit molecule gBdDV_465_C2_I.pdb (#4) to map
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) using 27645 atoms  
average map value = 0.3887, steps = 84  
shifted from previous position = 5.75  
rotated from previous position = 7.7 degrees  
atoms outside contour = 8650, contour level = 0.278  
  
Position of gBdDV_465_C2_I.pdb (#4) relative to
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.48419881 0.87473348 0.01982040 137.01596982  
0.87494707 0.48418172 0.00597194 6.14237847  
-0.00437283 0.02023340 -0.99978572 362.88154023  
Axis 0.50780304 0.86143963 0.00760542  
Axis point 68.17407385 -0.00000000 181.01590745  
Rotation angle (degrees) 179.19540771  
Shift along axis 77.62828109  
  

> select #6:64-85

1017 atoms, 1023 bonds, 66 residues, 1 model selected  

> color sel cyan

> select clear

> color #4 #d783ff transparency 0

> select #6:64-85

1017 atoms, 1023 bonds, 66 residues, 1 model selected  

> color #4 #ff2600 transparency 0

> color #4 #ff40ff transparency 0

> select #6:64-85

1017 atoms, 1023 bonds, 66 residues, 1 model selected  

> color #4 #941100 transparency 0

> color #4 #ff40ff transparency 0

> select clear

> select #6:64-85

1017 atoms, 1023 bonds, 66 residues, 1 model selected  

> color #4 #941100 transparency 0

> select #6

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> select #4

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> select #2

2 models selected  

> select #2

2 models selected  

> select #4

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> color #4 #0096ff transparency 0

> select clear

> select #6:64-85

1017 atoms, 1023 bonds, 66 residues, 1 model selected  

> color sel magenta

> show #!1 models

> select #4:64-85

1017 atoms, 1023 bonds, 66 residues, 1 model selected  

> color sel magenta

> select #2

2 models selected  

> select clear

> hide #!2 models

> show #!2 models

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113_ITC88_density-model_20230427.cxs"

> hide #!1 models

> open /Users/jl209164/Downloads/cryosparc_P2_J183_007_volume_map_sharp.mrc

Opened cryosparc_P2_J183_007_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 1.21, shown at level 0.252, step 2, values float32  

> volume #3 level 0.3831

> volume #3 level 0.3085

> volume #3 level 0.2481

> volume #3 step 1

> volume #3 level 0.3522

> volume #3 level 0.2332

> volume #3 level 0.2146

> volume #3 color #b2ffffb5

> volume #3 level 0.3151

> volume #3 level 0.5568

> volume #3 level 0.4787

> volume #3 level 0.3746

> volume #3 level 0.2667

> volume #3 level 0.2295

> volume #3 level 0.2035

> select ::name="ASN"

3444 atoms, 3204 bonds, 246 residues, 2 models selected  

> color sel forest green

> color sel orange red

> ui tool show "Side View"

> open /Users/jl209164/Downloads/cryosparc_P2_J183_010_volume_map_sharp.mrc

Opened cryosparc_P2_J183_010_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 1.21, shown at level 0.249, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.3259

> volume #5 level 0.28

> volume #5 level 0.4752

> volume #5 color #b2b2ffb4

> volume #5 color #b2b2ffb5

> volume #5 level 0.3719

> volume #5 level 0.3068

> volume #5 level 0.3451

> volume #5 level 0.3221

> volume #5 level 0.2455

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113_ITC88_density-model_20230427.cxs"

> volume #5 level 0.4063

> volume #5 level 0.4216

> volume #5 level 0.6016

> select ::name="ASN"

3444 atoms, 3204 bonds, 246 residues, 2 models selected  

> cartoon sel

> select clear

> save
> /Users/jl209164/Documents/ushpc/CMV/gB113-ITC88/gB113-ITC88/input/CMVgB113_dimer.pdb
> relModel #5

> volume #5 level 0.4446

> volume #5 level 0.3527

> volume #5 level 0.4446

> volume #5 level 0.3221

> volume #5 level 0.3565

> volume #5 level 0.2225

> volume #5 level 0.2264

> open /Users/jl209164/Downloads/cryosparc_P2_J187_007_volume_map_sharp.mrc

Opened cryosparc_P2_J187_007_volume_map_sharp.mrc as #7, grid size
320,320,320, pixel 1.21, shown at level 0.251, step 2, values float32  

> volume #7 level 0.1893

> volume #7 level 0.3346

> volume #7 step 1

> volume #7 level 0.246

> volume #7 level 0.647

> close #7

> open /Users/jl209164/Downloads/cryosparc_P2_J191_008_volume_map_sharp.mrc

Opened cryosparc_P2_J191_008_volume_map_sharp.mrc as #7, grid size
320,320,320, pixel 1.21, shown at level 0.251, step 2, values float32  

> volume #7 step 1

> volume #7 level 0.3851

> volume #7 level 0.3307

> volume #7 level 0.5402

> volume #7 level 0.3851

> volume #7 level 0.3307

> volume #7 level 0.5611

> volume #7 level 0.2678

> hide #!7 models

> show #!5 models

> volume #5 level 0.3029

> open /Users/jl209164/Downloads/cryosparc_P11_J49_003_volume_map_sharp.mrc

Opened cryosparc_P11_J49_003_volume_map_sharp.mrc as #8, grid size
144,144,144, pixel 1.76, shown at level 0.731, step 1, values float32  

> open /Users/jl209164/Downloads/cryosparc_P11_J49_003_volume_map_sharp.mrc

Opened cryosparc_P11_J49_003_volume_map_sharp.mrc as #9, grid size
144,144,144, pixel 1.76, shown at level 0.731, step 1, values float32  

> view #9

> open /Users/jl209164/Downloads/cryosparc_P11_J161_008_volume_map_sharp.mrc

Opened cryosparc_P11_J161_008_volume_map_sharp.mrc as #10, grid size
320,320,320, pixel 0.73, shown at level 0.0448, step 2, values float32  

> volume #10 level 0.02622

> volume #10 level 0.04851

> close #9

> hide #6 models

> hide #4 models

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/EBV/EBVgB210_dimer_J161.tif" width 861 height 782
> supersample 3 transparentBackground true

> open /Users/jl209164/Downloads/cryosparc_P11_J175_map_locres.mrc

Opened cryosparc_P11_J175_map_locres.mrc as #9, grid size 320,320,320, pixel
0.73, shown at level 9.48, step 2, values float32  

> ui tool show "Surface Color"

> color sample #10.1 map #9 palette #0000ff:#7f7fff:#ffffff:#ff7f7f:#ff0000

Map values for surface "surface": minimum 4.159, mean 5.24, maximum 7.329  

> color sample #10.1 map #9 palette
> 4,#0000ff:4.6,#7f7fff:5.2,#ffffff:6,#ff7f7f:7,#ff0000

Map values for surface "surface": minimum 4.159, mean 5.24, maximum 7.329  

> key blue:4.0 #7f7fff:4.6 white:5.2 #ff7f7f:6.0 red:7.0 showTool true

> ui mousemode right "color key"

> ui mousemode right "translate selected models"

> color single #10.1

> color sample #10.1 map #9 palette #0000ff:#7f7fff:#ffffff:#ff7f7f:#ff0000

Map values for surface "surface": minimum 4.159, mean 5.24, maximum 7.329  

> color sample #10.1 map #9 palette
> 4.1,#0000ff:4.9,#7f7fff:5.7,#ffffff:6.5,#ff7f7f:7.3,#ff0000

Map values for surface "surface": minimum 4.159, mean 5.24, maximum 7.329  

> color sample #10.1 map #9 palette
> 4.1,#0000ff:4.9,#7f7fff:5.7,#ffffff:6.5,#ff7f7f:7.3,#ff0000

Map values for surface "surface": minimum 4.159, mean 5.24, maximum 7.329  

> key blue:4.1 #7f7fff:4.9 white:5.7 #ff7f7f:6.5 red:7.3 showTool true

> ui mousemode right "color key"

> key pos 0.69000,0.08000

> key pos 0.68000,0.08000

> key pos 0.67000,0.08000

> key pos 0.66000,0.08000

> key pos 0.65000,0.08000

> key pos 0.65000,0.07000

> key pos 0.65000,0.06000

> key pos 0.65000,0.05000

> key size 0.24000,0.05000

> key size 0.23000,0.05000

> key size 0.22000,0.05000

> key size 0.23000,0.05000

> key size 0.24000,0.05000

> key size 0.25000,0.05000

> key size 0.26000,0.05000

> key size 0.26000,0.04000

> key size 0.26000,0.03000

> key pos 0.66000,0.05000

> key pos 0.65000,0.05000

> key pos 0.64000,0.05000

> key pos 0.63000,0.05000

> key pos 0.62000,0.05000

> key size 0.27000,0.03000

> key size 0.27000,0.04000

> key pos 0.62000,0.04000

> key pos 0.61000,0.04000

> key pos 0.60000,0.04000

> key pos 0.59000,0.04000

> key pos 0.58000,0.04000

> key pos 0.57000,0.04000

> key pos 0.56000,0.04000

> key pos 0.55000,0.04000

> key pos 0.54000,0.04000

> key pos 0.53000,0.04000

> key pos 0.52000,0.04000

> key pos 0.51000,0.04000

> key pos 0.50000,0.04000

> key pos 0.49000,0.04000

> key pos 0.48000,0.04000

> key pos 0.47000,0.04000

> key pos 0.46000,0.04000

> key pos 0.45000,0.04000

> key pos 0.44000,0.04000

> key pos 0.43000,0.04000

> key pos 0.42000,0.04000

> key pos 0.41000,0.04000

> key pos 0.40000,0.04000

> key pos 0.39000,0.04000

> key pos 0.38000,0.04000

> key pos 0.37000,0.04000

> key pos 0.36000,0.04000

> key pos 0.35000,0.04000

> key pos 0.34000,0.04000

> key pos 0.33000,0.04000

> key pos 0.32000,0.04000

> key pos 0.31000,0.04000

> key pos 0.30000,0.04000

> key pos 0.30000,0.03000

> key pos 0.30000,0.02000

> key pos 0.30000,0.03000

> key pos 0.30000,0.04000

> key pos 0.30000,0.05000

> key pos 0.30000,0.06000

> ui mousemode right "translate selected models"

Window position QRect(3756,573 654x459) outside any known screen, using
primary screen  

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/EBV/gB210_dimer_localres.tif" width 861 height 782
> supersample 3 transparentBackground true

> close #9

> close #10

> ui tool show "Surface Color"

> key red-white-blue :0.0 :0.5 :1.0 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right "translate selected models"

> open /Users/jl209164/Downloads/cryosparc_P2_J112_008_volume_map_sharp.mrc

Opened cryosparc_P2_J112_008_volume_map_sharp.mrc as #9, grid size
256,256,256, pixel 1.16, shown at level 0.2, step 1, values float32  

> volume #9 level 0.488

> open "/Users/jl209164/Downloads/cryosparc_P2_J118_007_volume_map_sharp
> (1).mrc"

Opened cryosparc_P2_J118_007_volume_map_sharp (1).mrc as #10, grid size
256,256,256, pixel 1.16, shown at level 0.196, step 1, values float32  

> volume #10 level 0.3612

> volume #10 level 0.4537

> volume #9 level 0.584

> show #4 models

> select #9

3 models selected  

> seelct #9,10

Unknown command: seelct #9,10  

> select #9,10

5 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #9,1,0,0,-14.032,0,1,0,25.267,0,0,1,86.808,#10,1,0,0,-14.032,0,1,0,25.267,0,0,1,86.808

> view matrix models
> #9,1,0,0,43.434,0,1,0,36.435,0,0,1,83.735,#10,1,0,0,43.434,0,1,0,36.435,0,0,1,83.735

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.95746,-0.28855,-0.0014009,91.54,0.28801,0.95594,-0.056777,12.264,0.017722,0.053958,0.99839,73.765,#10,0.95746,-0.28855,-0.0014009,91.54,0.28801,0.95594,-0.056777,12.264,0.017722,0.053958,0.99839,73.765

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.95746,-0.28855,-0.0014009,89.298,0.28801,0.95594,-0.056777,14.685,0.017722,0.053958,0.99839,69.797,#10,0.95746,-0.28855,-0.0014009,89.298,0.28801,0.95594,-0.056777,14.685,0.017722,0.053958,0.99839,69.797

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.89711,-0.44162,0.013255,118.88,0.44169,0.89575,-0.050374,2.3118,0.010373,0.051045,0.99864,71.187,#10,0.89711,-0.44162,0.013255,118.88,0.44169,0.89575,-0.050374,2.3118,0.010373,0.051045,0.99864,71.187

Fit map cryosparc_P2_J118_007_volume_map_sharp (1).mrc in map
cryosparc_P2_J182_004_volume_map_sharp.mrc using 61399 points  
correlation = 0.9179, correlation about mean = 0.3588, overlap = 2.341e+04  
steps = 64, shift = 4.85, angle = 4.47 degrees  
  
Position of cryosparc_P2_J118_007_volume_map_sharp (1).mrc (#10) relative to
cryosparc_P2_J182_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.91983203 -0.39186317 -0.01876957 117.59156660  
0.39184558 0.92001869 -0.00475931 -1.03120118  
0.01913336 -0.00297700 0.99981251 77.81820277  
Axis 0.00227154 -0.04830695 0.99882995  
Axis point 51.99795423 288.99300633 0.00000000  
Rotation angle (degrees) 23.09852261  
Shift along axis 78.04407991  
  
Fit map cryosparc_P2_J118_007_volume_map_sharp (1).mrc in map
cryosparc_P2_J191_008_volume_map_sharp.mrc using 61399 points  
correlation = 0.9427, correlation about mean = 0.6378, overlap = 2.916e+04  
steps = 48, shift = 0.065, angle = 1.11 degrees  
  
Position of cryosparc_P2_J118_007_volume_map_sharp (1).mrc (#10) relative to
cryosparc_P2_J191_008_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.91966536 -0.39270297 0.00009659 115.01083125  
0.39270298 0.91966532 -0.00025234 -1.78654089  
0.00001026 0.00026999 0.99999996 80.20998096  
Axis 0.00066504 0.00010991 0.99999977  
Axis point 61.86692102 280.07779460 0.00000000  
Rotation angle (degrees) 23.12279660  
Shift along axis 80.28625373  
  
Fit map cryosparc_P2_J118_007_volume_map_sharp (1).mrc in map
cryosparc_P2_J183_010_volume_map_sharp.mrc using 61399 points  
correlation = 0.9486, correlation about mean = 0.6458, overlap = 2.839e+04  
steps = 28, shift = 0.031, angle = 0.0185 degrees  
  
Position of cryosparc_P2_J118_007_volume_map_sharp (1).mrc (#10) relative to
cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.91978659 -0.39241892 0.00014722 114.95650087  
0.39241894 0.91978657 -0.00017150 -1.79113897  
-0.00006812 0.00021552 0.99999997 80.25195566  
Axis 0.00049311 0.00027438 0.99999984  
Axis point 61.89365564 280.19086843 0.00000000  
Rotation angle (degrees) 23.10510037  
Shift along axis 80.30813780  
  
Fit map cryosparc_P2_J112_008_volume_map_sharp.mrc in map
cryosparc_P2_J183_010_volume_map_sharp.mrc using 41998 points  
correlation = 0.9476, correlation about mean = 0.5678, overlap = 2.412e+04  
steps = 72, shift = 4.87, angle = 4.1 degrees  
  
Position of cryosparc_P2_J112_008_volume_map_sharp.mrc (#9) relative to
cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.91777685 -0.39709648 0.00018632 115.93479574  
0.39709652 0.91777681 -0.00028910 -2.15934882  
-0.00005620 0.00033932 0.99999994 80.41775312  
Axis 0.00079128 0.00030537 0.99999964  
Axis point 63.20923362 278.70765447 0.00000000  
Rotation angle (degrees) 23.39680070  
Shift along axis 80.50880111  
  

> ~select #10

3 models selected  

> show #!10 models

> hide #!10 models

> select clear

Fit molecule gBdDV_465_C2_I.pdb (#4) to map
cryosparc_P2_J112_008_volume_map_sharp.mrc (#9) using 27645 atoms  
average map value = 0.4421, steps = 52  
shifted from previous position = 0.145  
rotated from previous position = 1.21 degrees  
atoms outside contour = 18969, contour level = 0.58403  
  
Position of gBdDV_465_C2_I.pdb (#4) relative to
cryosparc_P2_J112_008_volume_map_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
-0.09880370 0.99510692 -0.00019992 25.78725653  
0.99510692 0.09880373 0.00016999 -1.37666541  
0.00018891 -0.00018215 -0.99999996 284.73553123  
Axis -0.67126974 -0.74121315 0.00000389  
Axis point 13.49181758 -0.00000000 142.36907603  
Rotation angle (degrees) 179.98497164  
Shift along axis -16.28869418  
  
Fit molecule gBdDV_465_C2_I.pdb (#4) to map
cryosparc_P2_J112_008_volume_map_sharp.mrc (#9) using 27645 atoms  
average map value = 0.4421, steps = 24  
shifted from previous position = 0.00204  
rotated from previous position = 0.00655 degrees  
atoms outside contour = 18974, contour level = 0.58403  
  
Position of gBdDV_465_C2_I.pdb (#4) relative to
cryosparc_P2_J112_008_volume_map_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
-0.09880362 0.99510694 -0.00009398 25.77116324  
0.99510692 0.09880364 0.00021273 -1.38196214  
0.00022098 -0.00007250 -0.99999997 284.71746819  
Axis -0.67127064 -0.74121234 -0.00004756  
Axis point 13.49095818 -0.00000000 142.35984165  
Rotation angle (degrees) 179.98782694  
Shift along axis -16.28863794  
  

> volume #9 level 0.4082

> volume #9 level 0.4961

> volume #9 color #b2b2b2b3

> select clear

> volume #9 color #b2b2b2b3

> volume #9 level 0.4556

> select #4/A

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel cornflower blue

> select #4/B

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> select #9

4 models selected  

> ui tool show "Color Zone"

> color zone #9 near #4 distance 6.98

> select #4/A

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel cornflower blue

> select #4/B

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel gray

> select #4/C

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel dim gray

> color zone #9 near #4 distance 6.98

> select #4/B

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel light gray

> color zone #9 near #4 distance 6.98

> color sel gray

> color zone #9 near #4 distance 6.98

> select #4/C

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel dim gray

> color zone #9 near #4 distance 6.98

[Repeated 1 time(s)]

> select #4/B

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel dark gray

> color zone #9 near #4 distance 6.98

> select clear

> volume #9 color #b2b2b299

> volume #9 color #b2b2b2af

> color zone #9 near #4 distance 6.98

> volume #9 color #b2b2b2b0

> transparency #9 70 surfaces

> transparency #9 50 surfaces

[Repeated 1 time(s)]

> transparency #9 40 surfaces

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/CMVgB113_withmodel_job112.tif" width 1692 height 1089
> supersample 3 transparentBackground true

> hide #!9 models

> hide #4 models

> show #4 models

> show #!5 models

Fit map cryosparc_P2_J183_010_volume_map_sharp.mrc in map
cryosparc_P2_J112_008_volume_map_sharp.mrc using 236152 points  
correlation = 0.6266, correlation about mean = 0.3766, overlap = 3.005e+04  
steps = 2000, shift = 0.304, angle = 0.257 degrees  
  
Position of cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) relative to
cryosparc_P2_J112_008_volume_map_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.91820378 0.39609338 -0.00344219 -104.56319879  
-0.39608413 0.91820907 0.00307644 47.17604095  
0.00437920 -0.00146140 0.99998934 -81.24135229  
Axis -0.00572795 -0.00987264 -0.99993486  
Axis point 64.12969657 276.05280051 0.00000000  
Rotation angle (degrees) 23.33550431  
Shift along axis 81.36924059  
  
Fit map cryosparc_P2_J183_010_volume_map_sharp.mrc in map
cryosparc_P2_J112_008_volume_map_sharp.mrc using 236152 points  
correlation = 0.6265, correlation about mean = 0.3765, overlap = 3.004e+04  
steps = 2000, shift = 0.426, angle = 0.531 degrees  
  
Position of cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) relative to
cryosparc_P2_J112_008_volume_map_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.91822422 0.39604404 0.00366015 -106.35585152  
-0.39603536 0.91823074 -0.00288240 48.35662595  
-0.00450242 0.00119714 0.99998915 -80.04000735  
Axis 0.00515009 0.01030456 -0.99993364  
Axis point 61.72780309 282.33128425 0.00000000  
Rotation angle (degrees) 23.33247297  
Shift along axis 79.98524817  
  
Fit map cryosparc_P2_J183_010_volume_map_sharp.mrc in map
cryosparc_P2_J112_008_volume_map_sharp.mrc using 236152 points  
correlation = 0.6266, correlation about mean = 0.3766, overlap = 3.005e+04  
steps = 2000, shift = 0.426, angle = 0.532 degrees  
  
Position of cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) relative to
cryosparc_P2_J112_008_volume_map_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.91820397 0.39609136 -0.00361890 -104.52756089  
-0.39608278 0.91821032 0.00287026 47.22762709  
0.00445980 -0.00120210 0.99998933 -81.30734332  
Axis -0.00514039 -0.01019747 -0.99993479  
Axis point 64.31298545 276.12290471 0.00000000  
Rotation angle (degrees) 23.33540094  
Shift along axis 81.35775182  
  

> select #6

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> show #6 models

> ~select #6

Nothing selected  

> select #6

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> color sel yellow

Fit molecule gBdDV_465_C2_I.pdb (#6) to map
cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) using 27645 atoms  
average map value = 0.422, steps = 48  
shifted from previous position = 0.551  
rotated from previous position = 0.401 degrees  
atoms outside contour = 10302, contour level = 0.30293  
  
Position of gBdDV_465_C2_I.pdb (#6) relative to
cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.99986056 0.01669934 0.00003273 328.39885217  
-0.01669934 -0.99986055 0.00007710 332.97555675  
0.00003401 0.00007655 1.00000000 21.69142470  
Axis -0.00001669 -0.00003841 -1.00000000  
Axis point 165.58945645 165.11625675 0.00000000  
Rotation angle (degrees) 179.04315390  
Shift along axis -21.70969565  
  
Fit molecule gBdDV_465_C2_I.pdb (#4) to map
cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) using 27645 atoms  
average map value = 0.422, steps = 48  
shifted from previous position = 0.267  
rotated from previous position = 0.272 degrees  
atoms outside contour = 10297, contour level = 0.30293  
  
Position of gBdDV_465_C2_I.pdb (#4) relative to
cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.48539922 0.87429261 -0.00017188 140.08645362  
0.87429262 0.48539919 -0.00017439 6.80068410  
-0.00006904 -0.00023493 -0.99999997 365.21522736  
Axis -0.50726621 -0.86178940 0.00010555  
Axis point 68.03539671 -0.00000000 182.60977989  
Rotation angle (degrees) 179.99658126  
Shift along axis -76.88333458  
  

> color zone #5 near #4 distance 7.25

> color zone #5 near #6 distance 7.25

> color zone #5 near #4 distance 7.25

> select #4,6

55290 atoms, 55926 bonds, 3498 residues, 2 models selected  

> color #5 surface near sel

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

> color #5 surface near 7.25 sel

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

> color #5 surface sel

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

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/CMV/CMVgB113/gBdDV_dimer.pdb" relModel #5

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/CMV/CMVgB113/CMVgB113.cxs"

> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/CMV-related/CMV/CMVgB113/gBdDV_dimer.pdb

Chain information for gBdDV_dimer.pdb  
---  
Chain | Description  
11.1/A 11.2/A 11.1/B 11.2/B 11.1/C 11.2/C | No description available  
  

> color #11.2 #fffb00 transparency 0

> seelct #11.1/A

Unknown command: seelct #11.1/A  

> select #11.1/A

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel cornflower blue

> select #11.1/B

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel light gray

> select #11.1/C

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel dim gray

> color zone #5 near #11.1 distance 7.25

> color zone #5 near #11.2 distance 7.25

> select #11.1

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> close #11

> open /Users/jl209164/Library/CloudStorage/OneDrive-
> GSK/OneDrive_Documents/CMV-related/CMV/CMVgB113/gB113_dimer.pdb

Chain information for gB113_dimer.pdb #11  
---  
Chain | Description  
A B C D E F | No description available  
  

> select #11

55290 atoms, 55926 bonds, 3498 residues, 1 model selected  

> hide sel target a

> cartoon sel

> select #11

55290 atoms, 55926 bonds, 3498 residues, 1 model selected  

> select #11/D,E,F

27645 atoms, 27963 bonds, 1749 residues, 1 model selected  

> color sel yellow

> select #11/A

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel cornflower blue

> select #11/B

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel light gray

> select #11/C

9215 atoms, 9321 bonds, 583 residues, 1 model selected  

> color sel dim gray

> color zone #5 near #11 distance 7.25

> turn #5 y 90

Expected an axis vector or a keyword  

> turn y #5 90

Expected a number or a keyword  

> select #5

4 models selected  

> turn y 90

[Repeated 1 time(s)]

> turn x 90

[Repeated 5 time(s)]

> turn y 90

> transparency #5.1 0

> select clear

> volume #5 level 0.3259

> color zone #5 near #11 distance 7.25

> select #5

4 models selected  

> transparency #5 0 surfaces

> select clear

> volume #5 color #b2b2ffb5

> volume #5 color #ff2f92

> color zone #5 near #11 distance 7.25

> hide #4 models

> hide #6 models

> hide #11 models

> volume #5 level 0.4409

> volume #5 level 0.2684

> volume #5 level 0.4333

> volume #5 level 0.4831

> volume #5 level 0.5291

> volume #5 level 0.51

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113_ITC88_density-model_20230427.cxs"

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113_dimer_density183.tif" width 696 height 782
> supersample 3 transparentBackground true

> volume #5 level 0.3796

> volume #5 level 0.3374

> volume #5 level 0.2608

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113-ITC88_dimer_density183_Fab.tif" width 835 height
> 782 supersample 3

> transparency #5 50 surfaces

> show #11 models

> ui tool show "Side View"

> volume #5 level 0.2468

> color zone #5 near #11 distance 7.25

> transparency #5 50 surfaces

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113-ITC88_interface_20230501.tif" width 835 height
> 782 supersample 3 transparentBackground true

[Repeated 1 time(s)]

> transparency #5 0 surfaces

> volume #5 level 0.5

> color zone #5 near #11 distance 7.25

> volume #5 level 0.309

> volume #5 level 0.2438

[Repeated 1 time(s)]

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113-ITC88_dimer_density183_Fab.tif" width 835 height
> 782 supersample 3 transparentBackground true

> open /Users/jl209164/Downloads/cryosparc_P2_J193_008_volume_map_sharp.mrc

Opened cryosparc_P2_J193_008_volume_map_sharp.mrc as #12, grid size
320,320,320, pixel 1.21, shown at level 0.226, step 2, values float32  
Fit map cryosparc_P2_J193_008_volume_map_sharp.mrc in map
cryosparc_P2_J183_010_volume_map_sharp.mrc using 40924 points  
correlation = 0.6555, correlation about mean = 0.1452, overlap = 3996  
steps = 84, shift = 6.46, angle = 1.47 degrees  
  
Position of cryosparc_P2_J193_008_volume_map_sharp.mrc (#12) relative to
cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99990292 0.00096769 0.01390007 -8.59712027  
-0.00062492 0.99969612 -0.02464300 1.55236674  
-0.01391969 0.02463192 0.99959968 -1.82340803  
Axis 0.87045489 0.49144356 -0.02813383  
Axis point -0.00000000 84.81195139 194.94916069  
Rotation angle (degrees) 1.62192326  
Shift along axis -6.66920531  
  

> select #12

2 models selected  

> view matrix models
> #12,-0.99297,-0.0035041,-0.11833,403.5,-0.00998,-0.99353,0.11317,337.35,-0.11796,0.11355,0.9865,4.5209

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.99297,-0.0035041,-0.11833,406.68,-0.00998,-0.99353,0.11317,366.53,-0.11796,0.11355,0.9865,0.22052

Fit map cryosparc_P2_J193_008_volume_map_sharp.mrc in map
cryosparc_P2_J183_010_volume_map_sharp.mrc using 40924 points  
correlation = 0.9863, correlation about mean = 0.9348, overlap = 9352  
steps = 124, shift = 4.07, angle = 9.21 degrees  
  
Position of cryosparc_P2_J193_008_volume_map_sharp.mrc (#12) relative to
cryosparc_P2_J183_010_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.99999999 -0.00000203 -0.00011571 386.90092015  
0.00000204 -0.99999999 -0.00004715 386.88925920  
-0.00011571 -0.00004714 0.99999998 0.04057009  
Axis 0.00024908 -0.00029037 0.99999993  
Axis point 193.45025835 193.44483217 0.00000000  
Rotation angle (degrees) 179.99988350  
Shift along axis 0.02459921  
  

> ~select #12

Nothing selected  

> volume #12 step 1

> volume #12 level 0.3217

> volume #12 level 0.4427

> transparency #5 50 surfaces

> volume #5 level 0.5088

> color zone #12 near #11 distance 7.25

[Repeated 1 time(s)]

> color zone #10 near #11 distance 6.98

> color zone #5 near #11 distance 7.25

> save "/Users/jl209164/OneDrive - GSK/OneDrive_Documents/CMV-
> related/Chimerax/CMV/gB113_ITC88_density-model_202305.cxs"

——— End of log from Mon May 1 16:26:37 2023 ———

opened ChimeraX session  

> ui tool show ISOLDE

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jl209164/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/tool.py", line 42, in _launch_main_gui  
tw = self.tool_window = IsoldeMainWin(self)  
File "/Users/jl209164/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/main_win.py", line 54, in __init__  
self.general_tab = GeneralTab(self.session, self.isolde, self, tabw)  
File "/Users/jl209164/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/ui_base.py", line 226, in __init__  
self.populate()  
File "/Users/jl209164/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/__init__.py", line 26, in populate  
self.addWidget(ComputationalPlatformPanel(session, isolde, parent, gui))  
File "/Users/jl209164/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/platform.py", line 14, in __init__  
cpd = self.content = ComputationalPlatformDialog(session, isolde, gui, self)  
File "/Users/jl209164/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/platform.py", line 26, in __init__  
self._populate_platform_combo_box()  
File "/Users/jl209164/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/platform.py", line 36, in
_populate_platform_combo_box  
platform_names = list(sorted(platform_names, key=lambda
p:sim_params.platforms.index(p)))  
File "/Users/jl209164/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/platform.py", line 36, in <lambda>  
platform_names = list(sorted(platform_names, key=lambda
p:sim_params.platforms.index(p)))  
ValueError: tuple.index(x): x not in tuple  
  
Error processing trigger "new frame":  
ValueError: tuple.index(x): x not in tuple  
  
File "/Users/jl209164/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/platform.py", line 36, in  
platform_names = list(sorted(platform_names, key=lambda
p:sim_params.platforms.index(p)))  
  
See log for complete Python traceback.  
  
Done loading forcefield  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14X000HQLL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3.1 (22E261)
      Kernel Version: Darwin 22.4.0
      Time since boot: 9 days, 14 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.20.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202305021906
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Eric Pettersen]

Reported by Jing Liu

[Tristan Croll]

I should have seen this one coming. :)

The good news is that the change causing this should make ISOLDE simulations about 40-60% faster on your machine (there's now a native Metal platform implementation for OpenMM). I'll work on future-proofing ISOLDE's code so this doesn't happen again (and add that to the new release scheduled for a week or two from now), but for now you can get yourself working again by doing the following:

• open the ChimeraX shell (Tools/General/Shell). In the window that comes up, do:

from chimerax.isolde import constants

constants.__file__

This should print the full path to the file constants.py. Open that in a text editor, and change line 63 from:

        'OPENMM_PLATFORMS':           ('CUDA', 'OpenCL', 'CPU', 'Reference'), 

to:

        'OPENMM_PLATFORMS':           ('CUDA', 'HIP', 'Metal', 'OpenCL', 'CPU', 'Reference'), 

After you restart ChimeraX, things should once again work correctly.

[Tristan Croll]

Fixed in the ISOLDE 1.6 release.