'clear log' missing from session restore options

[ruchi.sharma@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/ruchigautamsharma/Desktop/Chimera/S1 with Mava120523.cxs"

[Repeated 1 time(s)]Error opening map
"/Users/ruchigautamsharma/Desktop/Chimera/S1 with Mava120523.cxs": File S1
with Mava120523.cxs, format mrc  
MRC header value nsymbt (1953787962) is invalid  
  

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_P20_J956_class_00_final_volume.mrc as #4, grid size
128,128,128, pixel 1.64, shown at level 0.0659, step 1, values float32  
Opened cryosparc_P16_J181_002_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 0.94, shown at level 0.0844, step 1, values float32  
Opened cryosparc_P20_J374_004_volume_map_sharp (1).mrc as #6, grid size
256,256,256, pixel 0.82, shown at level 0.0584, step 1, values float32  
Opened cryosparc_P16_J196_001_volume_map_sharp.mrc as #7, grid size
130,130,130, pixel 3, shown at level 0.984, step 1, values float32  
Opened cryosparc_P20_J1196_005_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 0.82, shown at level 0.0649, step 1, values float32  
Opened cryosparc_P20_J1214_map_sharp.mrc as #9, grid size 256,256,256, pixel
0.82, shown at level 0.00911, step 1, values float32  
Opened cryosparc_P20_J1219_map.mrc as #10, grid size 256,256,256, pixel 0.82,
shown at level 0.0232, step 1, values float32  
Opened cryosparc_P20_J1220_map.mrc as #11, grid size 256,256,256, pixel 0.82,
shown at level 0.0166, step 1, values float32  

restore_snapshot for "Redust" returned None  

[Repeated 1 time(s)]Log from Wed Dec 6 12:06:25 2023UCSF ChimeraX version:
1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/ruchigautamsharma/Desktop/S1E525K_oct.cxs format session

Opened cryosparc_P20_J783_004_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.82, shown at level 0.275, step 1, values float32  
Opened denmod_map.ccp4 as #3, grid size 77,88,125, pixel 0.82, shown at level
0.219, step 1, values float32  
Opened cryosparc_P20_J956_class_00_final_volume.mrc as #4, grid size
128,128,128, pixel 1.64, shown at level 0.0659, step 1, values float32  
Log from Mon Nov 27 09:12:11 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/ruchigautamsharma/Desktop/pdbs/S!E525Kdm/S1 E525K.cxs" format
> session

Opened cryosparc_P20_J783_004_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.82, shown at level 0.275, step 1, values float32  
Opened denmod_map.ccp4 as #3, grid size 77,88,125, pixel 0.82, shown at level
0.219, step 1, values float32  
Log from Wed Oct 25 17:37:00 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/ruchigautamsharma/Desktop/pdbs/S1E525K/cryosparc_P20_J783_004_volume_map_sharp.mrc

Opened cryosparc_P20_J783_004_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.82, shown at level 0.0488, step 1, values float32  

> surface dust #1 size 8.2

> open "/Users/ruchigautamsharma/Downloads/5n69 (1).pdb"

5n69 (1).pdb title:  
Cardiac muscle myosin S1 fragment In the pre-powerstroke state Co-
crystallized with the activator omecamtiv mecarbil [more info...]  
  
Chain information for 5n69 (1).pdb #2  
---  
Chain | Description | UniProt  
A B | myosin-7 | MYH7_BOVIN 1-828  
G H | myosin light chain 3 | MYL3_BOVIN 1-199  
  
Non-standard residues in 5n69 (1).pdb #2  
---  
2OW — methyl
4-(2-fluoro-3-{[(6-methylpyridin-3-yl)carbamoyl]amino}benzyl)piperazine-1-carboxylate
(omecamtiv mercarbil)  
ADP — adenosine-5'-diphosphate  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
TCE — 3,3',3''-phosphanetriyltripropanoic acid
(3-[bis(2-carboxyethyl)phosphanyl]propanoic acid)  
VO4 — vanadate ion  
  

> select /G

1279 atoms, 1252 bonds, 2 pseudobonds, 201 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select /B

6651 atoms, 6424 bonds, 12 pseudobonds, 1122 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,7.5243,0,1,0,-42.508,0,0,1,14.07

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.61548,0.721,-0.31834,11.332,-0.78625,-0.58977,0.18436,-38.657,-0.054828,0.36376,0.92988,13.85

> view matrix models
> #2,-0.66163,-0.41006,-0.62777,29.668,0.1277,-0.88661,0.44454,-44.306,-0.73887,0.21396,0.63897,23.936

> view matrix models
> #2,-0.19767,-0.88337,-0.42495,26.646,0.50315,-0.46348,0.7294,-56.47,-0.84129,-0.069634,0.53608,29.282

> view matrix models
> #2,-0.18793,-0.6606,-0.72683,35.36,0.59523,-0.66524,0.45072,-45.484,-0.78127,-0.34793,0.51823,31.901

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.18793,-0.6606,-0.72683,72.409,0.59523,-0.66524,0.45072,96.24,-0.78127,-0.34793,0.51823,60.896

> view matrix models
> #2,-0.18793,-0.6606,-0.72683,129.19,0.59523,-0.66524,0.45072,79.578,-0.78127,-0.34793,0.51823,82.527

> view matrix models
> #2,-0.18793,-0.6606,-0.72683,125.36,0.59523,-0.66524,0.45072,85.909,-0.78127,-0.34793,0.51823,84.685

> transparency 50

> fitmap #2 inMap #1

Fit molecule 5n69 (1).pdb (#2) to map
cryosparc_P20_J783_004_volume_map_sharp.mrc (#1) using 15954 atoms  
average map value = 0.02253, steps = 100  
shifted from previous position = 2.06  
rotated from previous position = 1.11 degrees  
atoms outside contour = 13068, contour level = 0.048772  
  
Position of 5n69 (1).pdb (#2) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.19291703 -0.66656530 -0.72005120 124.53603557  
0.58318061 -0.66804952 0.46217985 87.29141838  
-0.78910291 -0.33075753 0.51760608 84.30343050  
Axis -0.53516016 0.04660358 0.84346411  
Axis point 66.18454417 75.23248632 0.00000000  
Rotation angle (degrees) 132.19687865  
Shift along axis 8.52828559  
  

> view matrix models
> #2,-0.19292,-0.66657,-0.72005,131.58,0.58318,-0.66805,0.46218,78.098,-0.7891,-0.33076,0.51761,80.763

> ui mousemode right translate

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.46415,-0.50295,-0.72911,130.42,0.52729,-0.8183,0.22881,87.004,-0.71171,-0.27825,0.64501,76.164

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.46415,-0.50295,-0.72911,128.58,0.52729,-0.8183,0.22881,94.912,-0.71171,-0.27825,0.64501,75.168

> fitmap #2 inMap #1

Fit molecule 5n69 (1).pdb (#2) to map
cryosparc_P20_J783_004_volume_map_sharp.mrc (#1) using 15954 atoms  
average map value = 0.06183, steps = 252  
shifted from previous position = 4.34  
rotated from previous position = 15.5 degrees  
atoms outside contour = 10731, contour level = 0.048772  
  
Position of 5n69 (1).pdb (#2) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.65223123 -0.39006087 -0.64995918 125.75157441  
0.33999218 -0.91689298 0.20907553 93.36046818  
-0.67749519 -0.08461545 0.73064389 72.79967220  
Axis -0.37299090 0.03497105 0.92717572  
Axis point 67.28356376 60.20262318 0.00000000  
Rotation angle (degrees) 156.81525069  
Shift along axis 23.85881003  
  

> view matrix models
> #2,-0.65223,-0.39006,-0.64996,125.93,0.33999,-0.91689,0.20908,93.374,-0.6775,-0.084615,0.73064,72.559

> fitmap #2 inMap #1

Fit molecule 5n69 (1).pdb (#2) to map
cryosparc_P20_J783_004_volume_map_sharp.mrc (#1) using 15954 atoms  
average map value = 0.06183, steps = 80  
shifted from previous position = 0.303  
rotated from previous position = 0.00326 degrees  
atoms outside contour = 10731, contour level = 0.048772  
  
Position of 5n69 (1).pdb (#2) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.65221901 -0.39004483 -0.64998107 125.75548489  
0.33994947 -0.91690298 0.20910111 93.35492813  
-0.67752839 -0.08458101 0.73061709 72.80621861  
Axis -0.37300682 0.03498796 0.92716868  
Axis point 67.28897691 60.19860605 0.00000000  
Rotation angle (degrees) 156.81703890  
Shift along axis 23.86228967  
  

> ui mousemode right translate

> volume #1 level 0.1066

> open /Users/ruchigautamsharma/Desktop/pdbs/S!E525Kdm/denmod_map.ccp4

Opened denmod_map.ccp4 as #3, grid size 77,88,125, pixel 0.82, shown at level
1.55, step 1, values float32  

> volume #3 level 0.1753

> surface dust #1 size 8.2

> surface dust #3 size 8.2

> transparency 0

> select ::name="ADP"

54 atoms, 58 bonds, 2 residues, 1 model selected  

> style sel stick

Changed 54 atom styles  

> transparency 50

> volume #3 level 0.5263

> volume #1 level 0.275

> select ::name="VO4"

10 atoms, 8 bonds, 2 residues, 1 model selected  

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show sel atoms

> select add #2

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 3 models selected  

> show sel atoms

> hide sel atoms

> volume #3 level 0.2191

> fitmap #2 inMap #3

Fit molecule 5n69 (1).pdb (#2) to map denmod_map.ccp4 (#3) using 15954 atoms  
average map value = 0.3878, steps = 80  
shifted from previous position = 0.0777  
rotated from previous position = 0.308 degrees  
atoms outside contour = 12046, contour level = 0.21914  
  
Position of 5n69 (1).pdb (#2) relative to denmod_map.ccp4 (#3) coordinates:  
Matrix rotation and translation  
-0.65226034 -0.39379620 -0.64767353 125.62031492  
0.34040567 -0.91562605 0.21389933 93.17812535  
-0.67725950 -0.08095369 0.73127701 72.82120329  
Axis -0.37240733 0.03736787 0.92731679  
Axis point 67.16525857 60.10369391 0.00000000  
Rotation angle (degrees) 156.67948348  
Shift along axis 24.22826606  
  

> save "/Users/ruchigautamsharma/Desktop/pdbs/S!E525Kdm/S1 E525K.cxs"
> includeMaps true

> select add #3

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 5 models selected  

> save "/Users/ruchigautamsharma/Desktop/pdbs/S!E525Kdm/S1 E525K.cxs"

——— End of log from Wed Oct 25 17:37:00 2023 ———

opened ChimeraX session  

> open
> /Users/ruchigautamsharma/Downloads/cryosparc_P20_J956_class_00_final_volume.mrc

Opened cryosparc_P20_J956_class_00_final_volume.mrc as #4, grid size
128,128,128, pixel 1.64, shown at level 0.0956, step 1, values float32  

> hide #!4 models

> show #!4 models

> select add #4

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 5 models selected  

> transparency sel 50

> surface dust #4 size 16.4

> volume #4 level 0.05191

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.65226,-0.3938,-0.64767,125.03,0.34041,-0.91563,0.2139,91.17,-0.67726,-0.080954,0.73128,79.637,#4,1,0,0,-0.5863,0,1,0,-2.0079,0,0,1,6.8154

> select subtract #2

2 models selected  

> view matrix models #4,1,0,0,19.578,0,1,0,72.525,0,0,1,-16.281

> volume #4 level 0.06591

> view matrix models #4,1,0,0,12.021,0,1,0,-7.4143,0,0,1,-3.581

> hide #!4 models

> select subtract #4

Nothing selected  

> select add #2

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select add #2

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 3 models selected  

> view matrix models
> #2,-0.65226,-0.3938,-0.64767,123.89,0.34041,-0.91563,0.2139,93.029,-0.67726,-0.080954,0.73128,71.915

> fitmap #2 inMap #3

Fit molecule 5n69 (1).pdb (#2) to map denmod_map.ccp4 (#3) using 15954 atoms  
average map value = 0.3879, steps = 84  
shifted from previous position = 1.97  
rotated from previous position = 0.00229 degrees  
atoms outside contour = 12049, contour level = 0.21914  
  
Position of 5n69 (1).pdb (#2) relative to denmod_map.ccp4 (#3) coordinates:  
Matrix rotation and translation  
-0.65223922 -0.39380192 -0.64769132 125.63289236  
0.34043044 -0.91562036 0.21388425 93.17942306  
-0.67726739 -0.08099014 0.73126567 72.81677218  
Axis -0.37241745 0.03735368 0.92731329  
Axis point 67.17033404 60.10672558 0.00000000  
Rotation angle (degrees) 156.67836480  
Shift along axis 24.21667322  
  

> select up

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 3 models selected  

> save /Users/ruchigautamsharma/Desktop/S1E525K_oct.cxs

——— End of log from Mon Nov 27 09:12:11 2023 ———

opened ChimeraX session  

> hide #!3 models

> show #!3 models

> show #!1 models

> hide #!1 models

> open
> /Users/ruchigautamsharma/Downloads/cryosparc_P16_J181_002_volume_map_sharp.mrc

Opened cryosparc_P16_J181_002_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 0.94, shown at level 0.0982, step 1, values float32  

> surface dust #3 size 8.2

> surface dust #5 size 9.4

> select add #5

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 5 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.65224,-0.3938,-0.64769,120.28,0.34043,-0.91562,0.21388,72.733,-0.67727,-0.08099,0.73127,121.63,#5,1,0,0,-5.3573,0,1,0,-20.447,0,0,1,48.817

> undo

> hide #!3 models

> show #!3 models

> select subtract #2

2 models selected  

> view matrix models #5,1,0,0,-13.666,0,1,0,-65.347,0,0,1,88.458

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.61763,-0.47779,0.6247,195.35,-0.0046531,-0.79208,-0.61041,216.32,0.78646,-0.37991,0.48698,82.932

> view matrix models
> #5,0.46555,-0.38745,0.7957,10.04,0.24243,-0.80886,-0.5357,174.01,0.85117,0.4423,-0.28263,72.728

> view matrix models
> #5,0.93089,0.19099,0.3114,-63.808,0.35531,-0.67145,-0.65031,156.08,0.084887,0.71601,-0.69291,200.15

> view matrix models
> #5,0.76763,0.62136,-0.15704,-33.117,0.33086,-0.59406,-0.73322,160.74,-0.54889,0.51088,-0.6616,310.12

> view matrix models
> #5,0.94378,0.21045,-0.25492,1.133,-0.15949,-0.38558,-0.90879,227.84,-0.28955,0.89835,-0.33033,188.2

> view matrix models
> #5,0.90251,0.19431,-0.38434,24.637,-0.13507,-0.71969,-0.68103,235.13,-0.40893,0.66655,-0.62328,267.6

> view matrix models
> #5,0.92568,0.3783,0.0034475,-47.132,0.31556,-0.76705,-0.55862,161.58,-0.20868,0.51819,-0.82942,281.35

> view matrix models
> #5,0.87123,0.48583,-0.070206,-42.809,0.37203,-0.74681,-0.55124,150.32,-0.32024,0.45414,-0.83139,304.84

> view matrix models
> #5,0.88715,0.43531,-0.1532,-29.134,0.39028,-0.88488,-0.25429,127.45,-0.24626,0.16581,-0.95492,342.62

> view matrix models
> #5,0.8667,0.49765,-0.034194,-47.917,0.35851,-0.6691,-0.65098,155.44,-0.34684,0.55194,-0.75833,288.44

> view matrix models
> #5,-0.39141,-0.63846,0.66269,177.07,0.089355,-0.74311,-0.66317,203.74,0.91587,-0.20036,0.34792,60.775

> view matrix models
> #5,-0.34556,-0.70708,0.61695,184.03,-0.16494,-0.60145,-0.7817,238.02,0.92379,-0.37189,0.091213,110.71

> view matrix models
> #5,-0.94804,-0.20942,0.23952,258.34,-0.12676,-0.44187,-0.88808,227.15,0.29182,-0.87229,0.39237,221.58

> view matrix models
> #5,-0.92533,-0.30178,0.22954,266.97,-0.059113,-0.48317,-0.87353,220.52,0.37452,-0.82187,0.42925,199.51

> view matrix models
> #5,-0.8964,-0.30676,0.31994,252.42,-0.13132,-0.50562,-0.85271,230.84,0.42334,-0.80638,0.41295,192.77

> view matrix models
> #5,-0.93711,0.32258,-0.13331,240.89,-0.152,-0.72097,-0.67608,237.08,-0.3142,-0.6133,0.72466,237.41

> view matrix models
> #5,-0.9616,0.10484,-0.25365,284.14,0.22287,-0.24109,-0.94456,161.16,-0.16018,-0.96482,0.20847,318.94

> view matrix models
> #5,-0.96519,0.16066,-0.20638,272.45,0.12604,-0.40569,-0.90528,189.12,-0.22917,-0.89978,0.37132,301.41

> view matrix models
> #5,-0.96498,0.16952,-0.20017,270.65,0.11073,-0.42854,-0.89671,192.89,-0.23779,-0.88748,0.39476,298.36

> view matrix models
> #5,-0.9772,0.16795,-0.12992,264,0.021175,-0.53171,-0.84666,211.42,-0.21128,-0.83011,0.51603,273.2

> volume #5 level 0.1121

> volume #5 level 0.1029

> transparency sel 50

> view matrix models
> #5,0.72213,0.48931,-0.48898,29.202,0.12708,-0.78867,-0.60154,195.83,-0.67999,0.37225,-0.6317,342.44

> view matrix models
> #5,-0.22774,-0.88914,0.39695,213.84,-0.23779,-0.34453,-0.90816,234.4,0.94424,-0.30122,-0.13296,127.41

> view matrix models
> #5,-0.86886,-0.49342,-0.040171,313.14,0.19684,-0.26989,-0.94256,168.21,0.45424,-0.82686,0.33162,200.57

> view matrix models
> #5,-0.58877,-0.80194,0.10119,291.28,0.31254,-0.34132,-0.88646,153.07,0.74543,-0.4903,0.4516,106.1

> view matrix models
> #5,0.22271,-0.94131,0.25363,173.14,0.27185,-0.18988,-0.94342,148.51,0.93622,0.27906,0.21361,20.113

> view matrix models
> #5,-0.81791,-0.52906,0.2261,277.53,0.092269,-0.50852,-0.8561,199.81,0.5679,-0.67934,0.46473,151.34

> open
> "/Users/ruchigautamsharma/Downloads/cryosparc_P20_J374_004_volume_map_sharp
> (1).mrc"

Opened cryosparc_P20_J374_004_volume_map_sharp (1).mrc as #6, grid size
256,256,256, pixel 0.82, shown at level 0.0584, step 1, values float32  

> hide #!3 models

> hide #!5 models

> show #!5 models

> hide #!2 models

> surface dust #5 size 9.4

> select add #6

4 models selected  

> surface dust #5 size 9.4

> surface dust #6 size 8.2

> select subtract #5

2 models selected  

> view matrix models
> #6,0.32426,-0.78954,0.52104,98.724,0.029573,-0.54207,-0.83981,252.57,0.9455,0.28773,-0.15242,-5.0166

> view matrix models
> #6,-0.22167,-0.97383,0.050238,226.22,0.26332,-0.10939,-0.95849,194.7,0.9389,-0.19924,0.28068,1.0191

> view matrix models
> #6,-0.28854,-0.95423,0.078624,228.04,-0.083284,-0.056791,-0.99491,229.16,0.95384,-0.29362,-0.063086,46.669

> view matrix models
> #6,-0.28206,-0.95405,0.10111,224.92,0.17968,-0.15605,-0.97127,209.8,0.94242,-0.25579,0.21544,13.745

> select add #5

4 models selected  

> select subtract #6

2 models selected  

> view matrix models
> #5,-0.88706,-0.27413,0.37147,240.57,-0.14084,-0.60559,-0.78322,235.19,0.43966,-0.74707,0.49858,173.2

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.88706,-0.27413,0.37147,202.34,-0.14084,-0.60559,-0.78322,289.51,0.43966,-0.74707,0.49858,103.13

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.27686,-0.88461,0.37524,184.72,-0.012347,-0.3872,-0.92191,263.19,0.96083,-0.25988,0.09628,22.337

> view matrix models
> #5,-0.19866,-0.91773,0.34396,181.18,-0.16995,-0.31338,-0.9343,278.7,0.96522,-0.24407,-0.093707,43.044

> view matrix models
> #5,-0.19689,-0.91826,0.34357,181.04,-0.16929,-0.31333,-0.93443,278.62,0.9657,-0.24214,-0.093758,42.763

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.19689,-0.91826,0.34357,82.628,-0.16929,-0.31333,-0.93443,242.53,0.9657,-0.24214,-0.093758,-1.1543

> view matrix models
> #5,-0.19689,-0.91826,0.34357,76.505,-0.16929,-0.31333,-0.93443,252.51,0.9657,-0.24214,-0.093758,-0.91163

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.054829,-0.95404,0.29462,66.332,-0.3226,-0.26232,-0.90946,265.47,0.94495,-0.14491,-0.29339,15.255

> view matrix models
> #5,-0.65898,-0.46809,0.58875,61.029,-0.094888,-0.72476,-0.68243,258.2,0.74615,-0.50558,0.43319,-3.7686

> select subtract #5

Nothing selected  

> select add #6

2 models selected  

> view matrix models
> #6,0.41572,-0.90638,0.075165,149.82,0.28553,0.051598,-0.95698,175,0.86351,0.4193,0.28025,-57.249

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.41572,-0.90638,0.075165,34.882,0.28553,0.051598,-0.95698,142.61,0.86351,0.4193,0.28025,-64.088

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.41572,-0.90638,0.075165,18.092,0.28553,0.051598,-0.95698,143.5,0.86351,0.4193,0.28025,-88.073

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.53828,-0.84276,-0.0026382,119.21,0.4464,-0.28246,-0.84909,150.81,0.71484,-0.45822,0.52825,-5.4475

> view matrix models
> #6,-0.52077,-0.71126,0.47213,52.064,0.51273,-0.70277,-0.49317,150.44,0.68257,-0.014749,0.73067,-71.383

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.52077,-0.71126,0.47213,59.911,0.51273,-0.70277,-0.49317,153.75,0.68257,-0.014749,0.73067,-61.312

> view matrix models
> #6,-0.52077,-0.71126,0.47213,67.068,0.51273,-0.70277,-0.49317,161.95,0.68257,-0.014749,0.73067,-71.328

> view matrix models
> #6,-0.52077,-0.71126,0.47213,67.97,0.51273,-0.70277,-0.49317,161.2,0.68257,-0.014749,0.73067,-75.025

> view matrix models
> #6,-0.52077,-0.71126,0.47213,70.816,0.51273,-0.70277,-0.49317,158.11,0.68257,-0.014749,0.73067,-68.355

> fitmap #6 inMap #5

Fit map cryosparc_P20_J374_004_volume_map_sharp (1).mrc in map
cryosparc_P16_J181_002_volume_map_sharp.mrc using 167594 points  
correlation = 0.7525, correlation about mean = 0.2043, overlap = 1891  
steps = 124, shift = 7.24, angle = 15.3 degrees  
  
Position of cryosparc_P20_J374_004_volume_map_sharp (1).mrc (#6) relative to
cryosparc_P16_J181_002_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.81964767 0.57175415 0.03570568 -28.64788678  
-0.56063645 0.81339839 -0.15514455 109.82229550  
-0.11774748 0.10714596 0.98724631 14.18765792  
Axis 0.22371036 0.13088182 -0.96582795  
Axis point 164.07249817 99.61468910 0.00000000  
Rotation angle (degrees) 35.88978388  
Shift along axis -5.73792317  
  

> save "/Users/ruchigautamsharma/Desktop/S1NS with Cryo E525K with Mava.cxs"

> volume #5 level 0.0675

> surface dust #6 size 8.2

> select add #5

4 models selected  

> surface dust #5 size 9.4

> surface dust #6 size 8.2

> surface dust #5 size 9.4

> surface dust #6 size 8.2

> volume #5 level 0.07518

> volume #5 level 0.08441

> save "/Users/ruchigautamsharma/Desktop/S1NS with Cryo E525K with Mava.cxs"

> open
> /Users/ruchigautamsharma/Downloads/cryosparc_P16_J196_001_volume_map_sharp.mrc

Opened cryosparc_P16_J196_001_volume_map_sharp.mrc as #7, grid size
130,130,130, pixel 3, shown at level 2.13, step 1, values float32  

> volume #7 level 2.844

> volume #7 level 7.476

> select add #7

6 models selected  

> select subtract #6

4 models selected  

> select subtract #5

2 models selected  

> view matrix models #7,1,0,0,-146.41,0,1,0,-108.11,0,0,1,-186.14

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.36312,0.7304,0.5785,-271.54,-0.8708,0.045173,0.48956,156.06,0.33144,-0.68153,0.65243,-53.862

> view matrix models
> #7,-0.18989,0.73704,-0.64862,67.12,-0.83694,0.22387,0.49941,112.92,0.5133,0.63769,0.57435,-330.55

> view matrix models
> #7,-0.76942,0.37991,-0.51347,224.92,-0.4375,0.27226,0.85701,-42.416,0.46539,0.88405,-0.043273,-252.53

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.76942,0.37991,-0.51347,191.18,-0.4375,0.27226,0.85701,-54.071,0.46539,0.88405,-0.043273,-165.75

> view matrix models
> #7,-0.76942,0.37991,-0.51347,164.82,-0.4375,0.27226,0.85701,-65.562,0.46539,0.88405,-0.043273,-171.43

> view matrix models
> #7,-0.76942,0.37991,-0.51347,173.02,-0.4375,0.27226,0.85701,-76.567,0.46539,0.88405,-0.043273,-167.99

> volume #7 level 0.9837

> hide #!5 models

> select subtract #7

Nothing selected  

> select add #7

2 models selected  

> transparency sel 50

> save "/Users/ruchigautamsharma/Desktop/S1NS with Cryo E525K with Mava.cxs"

> hide #!6 models

> show #!6 models

> select subtract #7

Nothing selected  

> select add #6

2 models selected  

> view matrix models
> #6,-0.34703,-0.69444,0.63034,51.121,0.40891,-0.71689,-0.56468,133.27,0.84402,0.061792,0.53274,-53.287

> view matrix models
> #6,-0.34703,-0.69444,0.63034,47.871,0.40891,-0.71689,-0.56468,175.19,0.84402,0.061792,0.53274,-55.382

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.62792,0.71922,-0.29737,-104.94,-0.31512,0.58432,0.74784,-30.184,0.71163,-0.37588,0.59355,-1.3062

> view matrix models
> #6,0.98671,0.15686,0.042483,-118.89,-0.13657,0.65872,0.73989,-55.912,0.088072,-0.73585,0.67139,93.859

> view matrix models
> #6,0.97851,0.12676,0.16261,-127.79,-0.20618,0.60001,0.77296,-45.94,0.00041729,-0.78988,0.61326,115.06

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.97851,0.12676,0.16261,-109.8,-0.20618,0.60001,0.77296,-114.39,0.00041729,-0.78988,0.61326,114.27

> view matrix models
> #6,0.97851,0.12676,0.16261,-103.49,-0.20618,0.60001,0.77296,-114.19,0.00041729,-0.78988,0.61326,121.43

> view matrix models
> #6,0.97851,0.12676,0.16261,-99.006,-0.20618,0.60001,0.77296,-112.08,0.00041729,-0.78988,0.61326,113.26

> view matrix models
> #6,0.97851,0.12676,0.16261,-109.22,-0.20618,0.60001,0.77296,-119.21,0.00041729,-0.78988,0.61326,112.29

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.71015,-0.084902,0.69891,-116.47,-0.69427,0.080471,0.7152,-6.4689,-0.11696,-0.99313,-0.0017985,212.68

> view matrix models
> #6,-0.95008,-0.042737,0.30907,94.311,0.28514,0.28326,0.91567,-151.99,-0.12668,0.95809,-0.25693,32.476

> open
> /Users/ruchigautamsharma/Downloads/cryosparc_P20_J1196_005_volume_map_sharp.mrc

Opened cryosparc_P20_J1196_005_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 0.82, shown at level 0.0511, step 1, values float32  

> open /Users/ruchigautamsharma/Downloads/cryosparc_P20_J1214_map_sharp.mrc

Opened cryosparc_P20_J1214_map_sharp.mrc as #9, grid size 256,256,256, pixel
0.82, shown at level 0.00164, step 1, values float32  

> hide #!6 models

> hide #!7 models

> select subtract #6

Nothing selected  

> show #!2 models

> surface dust #8 size 8.2

> surface dust #9 size 8.2

> volume #9 level 0.009113

> hide #!9 models

> show #!9 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> select add #9

2 models selected  

> view matrix models
> #9,-0.21063,-0.80377,-0.55641,267.34,0.45235,0.42444,-0.78437,95.538,0.86661,-0.4169,0.27418,30.025

> view matrix models
> #9,-0.86516,-0.2997,0.4021,181.03,-0.42256,0.0038242,-0.90633,242.21,0.27009,-0.95403,-0.12995,189.97

> view matrix models
> #9,0.97416,0.15336,-0.16583,5.6009,0.042553,-0.84563,-0.53207,236.97,-0.22183,0.51126,-0.8303,172.5

> view matrix models
> #9,0.95655,0.28662,-0.053415,-18.076,0.2112,-0.8075,-0.55077,217.58,-0.20099,0.51556,-0.83295,170.18

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.95655,0.28662,-0.053415,-19.45,0.2112,-0.8075,-0.55077,230.35,-0.20099,0.51556,-0.83295,157.59

> view matrix models
> #9,0.95655,0.28662,-0.053415,-22.831,0.2112,-0.8075,-0.55077,229.6,-0.20099,0.51556,-0.83295,156.28

> view matrix models
> #9,0.95655,0.28662,-0.053415,-23.573,0.2112,-0.8075,-0.55077,226.21,-0.20099,0.51556,-0.83295,159.72

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.99281,0.069089,-0.097758,-0.91961,0.04298,-0.96792,-0.24756,226.6,-0.11173,0.24158,-0.96393,191.9

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.04029, steps = 176  
shifted from previous position = 3.39  
rotated from previous position = 4.02 degrees  
atoms outside contour = 13166, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
-0.50855375 -0.41490719 -0.75447008 131.86431009  
-0.56832064 0.82000348 -0.06786717 108.53668816  
0.64682667 0.39426682 -0.65281616 134.99332340  
Axis 0.31151856 -0.94459607 -0.10341403  
Axis point 53.93732376 0.00000000 98.06502096  
Rotation angle (degrees) 132.11981789  
Shift along axis -75.40535209  
  

> transparency sel 50

> select subtract #9

Nothing selected  

> select add #2

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 3 models selected  

> view matrix models
> #2,-0.16597,0.85306,0.49471,75.91,-0.94431,-0.28204,0.16952,88.679,0.28414,-0.43902,0.85236,71.315

> view matrix models
> #2,0.18974,0.71839,0.66927,71.355,-0.88853,-0.16438,0.42836,79.135,0.41774,-0.67594,0.60712,81.461

> view matrix models
> #2,0.32251,0.52668,0.78651,68.871,-0.78437,-0.31641,0.53352,76.75,0.52985,-0.78898,0.31106,92.443

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.32251,0.52668,0.78651,69.839,-0.78437,-0.31641,0.53352,87.686,0.52985,-0.78898,0.31106,85.278

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.61814,-0.18852,-0.76313,126.31,0.23101,-0.97151,0.052879,109.82,-0.75136,-0.1436,0.64408,67.896

> view matrix models
> #2,-0.38114,-0.16715,-0.90928,131.42,0.25436,-0.96452,0.07069,109.2,-0.88884,-0.20435,0.41013,76.098

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.38114,-0.16715,-0.90928,130.42,0.25436,-0.96452,0.07069,99.988,-0.88884,-0.20435,0.41013,87.51

> view matrix models
> #2,-0.38114,-0.16715,-0.90928,131.05,0.25436,-0.96452,0.07069,102.17,-0.88884,-0.20435,0.41013,87.777

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.52432,-0.30165,-0.7963,127.97,0.47408,-0.88023,0.021289,103.53,-0.70734,-0.36634,0.60453,82.525

> view matrix models
> #2,0.29118,-0.55512,-0.77914,130.16,0.44363,-0.64321,0.62407,81.366,-0.84759,-0.52737,0.05898,102.01

> view matrix models
> #2,0.26435,0.46817,0.84317,67.883,-0.93171,-0.10181,0.34864,85.262,0.24906,-0.87775,0.40929,93.894

> view matrix models
> #2,0.156,0.054917,0.98623,65.77,-0.8465,-0.5071,0.16214,94.526,0.50902,-0.86014,-0.032623,109.1

> view matrix models
> #2,-0.49294,0.39741,0.774,69.796,-0.39722,-0.89426,0.20618,96.279,0.77409,-0.20582,0.59868,83.423

> view matrix models
> #2,-0.23962,0.23546,0.94188,65.532,-0.66637,-0.74543,0.016827,101.34,0.70607,-0.62361,0.33552,95.19

> view matrix models
> #2,0.34759,-0.05086,0.93626,68.439,-0.74993,-0.61445,0.24504,92.577,0.56283,-0.78731,-0.25172,116.1

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.34759,-0.05086,0.93626,69.947,-0.74993,-0.61445,0.24504,96.3,0.56283,-0.78731,-0.25172,101.34

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.29768,0.2556,0.91981,68.309,-0.5866,-0.71117,0.38747,92.336,0.75318,-0.65491,-0.061769,94.201

> view matrix models
> #2,-0.05521,0.25737,0.96473,66.338,-0.58329,-0.79251,0.17804,100.02,0.81039,-0.55289,0.19387,84.876

> view matrix models
> #2,0.32166,0.14048,0.93638,68.578,-0.60289,-0.73216,0.31695,94.858,0.73011,-0.66648,-0.15081,97.278

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.32166,0.14048,0.93638,73.945,-0.60289,-0.73216,0.31695,81.622,0.73011,-0.66648,-0.15081,118.53

> view matrix models
> #2,0.32166,0.14048,0.93638,73.111,-0.60289,-0.73216,0.31695,78.646,0.73011,-0.66648,-0.15081,115.85

> view matrix models
> #2,0.32166,0.14048,0.93638,73.945,-0.60289,-0.73216,0.31695,83.709,0.73011,-0.66648,-0.15081,116.84

> view matrix models
> #2,0.32166,0.14048,0.93638,74.102,-0.60289,-0.73216,0.31695,82.742,0.73011,-0.66648,-0.15081,118.47

> view matrix models
> #2,0.32166,0.14048,0.93638,75.385,-0.60289,-0.73216,0.31695,74.844,0.73011,-0.66648,-0.15081,130.99

> ui mousemode right pivot

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.25251,0.33659,0.90716,74.926,-0.65072,-0.63479,0.41666,70.72,0.7161,-0.69552,0.058736,124.05

> view matrix models
> #2,0.84534,-0.36817,-0.38711,124.53,0.013637,-0.7095,0.70457,62.276,-0.53406,-0.60088,-0.59475,144.06

> view matrix models
> #2,0.16189,-0.36529,-0.91671,141.66,0.24785,-0.88413,0.39608,74.259,-0.95518,-0.29133,-0.052596,122.97

> view matrix models
> #2,0.42869,0.32898,-0.84143,134.59,0.21948,-0.94137,-0.25624,96.783,-0.87639,-0.074828,-0.47576,135.93

> view matrix models
> #2,0.1966,0.95872,-0.20544,108.32,-0.95872,0.14406,-0.24516,87.397,-0.20545,0.24516,0.94746,86.177

> view matrix models
> #2,0.59434,0.42727,0.68132,82.385,-0.76715,0.046998,0.63975,58.248,0.24133,-0.9029,0.35572,114.83

> view matrix models
> #2,0.21088,0.42133,0.88205,75.137,-0.88522,-0.30043,0.35515,70.192,0.41463,-0.8557,0.30961,116.28

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.03076, steps = 244  
shifted from previous position = 4.69  
rotated from previous position = 7.6 degrees  
atoms outside contour = 13877, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
0.08067453 0.60672398 0.79080821 82.56475246  
0.97111108 0.13091637 -0.19950985 140.84243386  
-0.22457716 0.78405798 -0.57863476 108.41042459  
Axis 0.67374122 0.69553615 0.24960414  
Axis point -7.19643000 0.00000000 41.13433793  
Rotation angle (degrees) 133.11947604  
Shift along axis 180.64797266  
  

> view matrix models
> #2,0.13169,0.5881,0.79799,80.783,-0.73111,-0.48601,0.47883,64.822,0.66943,-0.64647,0.36596,113.34

> view matrix models
> #2,-0.23824,0.66614,0.70675,82.884,-0.75361,-0.58582,0.29812,71.629,0.61263,-0.46159,0.64158,102.62

> view matrix models
> #2,-0.20247,-0.073715,-0.97651,145.26,0.00085827,-0.99718,0.075097,82.997,-0.97929,0.014367,0.20197,112.28

> view matrix models
> #2,-0.16389,0.376,-0.91201,139.99,-0.078576,-0.92655,-0.36788,97.456,-0.98334,0.011372,0.18139,113

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.16389,0.376,-0.91201,138.64,-0.078576,-0.92655,-0.36788,111.03,-0.98334,0.011372,0.18139,93.345

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.49302,0.14585,-0.85771,138,-0.022998,-0.98769,-0.15473,104.28,-0.86971,-0.056562,0.4903,83.464

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.03376, steps = 276  
shifted from previous position = 3  
rotated from previous position = 1.91 degrees  
atoms outside contour = 13599, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
-0.39031110 0.08969360 -0.91630361 145.17085790  
-0.20526537 0.96171562 0.18157420 105.69133104  
0.89750954 0.25895583 -0.35695729 122.30811448  
Axis 0.04207197 -0.98616032 -0.16036759  
Axis point 40.21486517 0.00000000 102.81858187  
Rotation angle (degrees) 113.12736494  
Shift along axis -117.73523073  
  

> ui tool show "Fit in Map"

Average map value = 0.03376 for 15954 atoms, 13599 outside contour  

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.03377, steps = 80  
shifted from previous position = 0.00932  
rotated from previous position = 0.0135 degrees  
atoms outside contour = 13602, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
-0.39051105 0.08960016 -0.91622755 145.17319659  
-0.20530326 0.96171177 0.18155176 105.69200336  
0.89741389 0.25900248 -0.35716387 122.31366156  
Axis 0.04211355 -0.98616098 -0.16035267  
Axis point 40.22391410 0.00000000 102.81221126  
Rotation angle (degrees) 113.14014929  
Shift along axis -117.72889330  
  

> select add #9

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 5 models selected  

> view matrix models
> #2,-0.28897,0.30967,-0.90587,140.1,-0.16658,-0.94807,-0.27096,104.93,-0.94274,0.072598,0.32554,88.681,#9,0.97058,0.19267,0.14443,-38.833,0.22836,-0.92676,-0.29826,206.21,0.076381,0.32247,-0.94349,158.91

> view matrix models
> #2,-0.43343,0.53592,-0.72452,133.17,0.11954,-0.76267,-0.63565,115.57,-0.89323,-0.36212,0.2665,92.511,#9,0.8811,0.47285,0.0086149,-45.774,0.46738,-0.87341,0.13678,123.31,0.072199,-0.11649,-0.99056,215.5

> view matrix models
> #2,-0.76105,0.45279,-0.46452,123.03,-0.53294,-0.84469,0.049785,90.929,-0.36983,0.28545,0.88416,71.573,#9,0.76337,0.50737,-0.39979,7.4867,0.086821,-0.69389,-0.71483,239.1,-0.64009,0.51097,-0.57375,180.67

> view matrix models
> #2,-0.65326,0.50362,-0.56535,127.16,-0.62243,-0.78236,0.02228,91.583,-0.43109,0.36644,0.82455,73.518,#9,0.81822,0.51581,-0.25388,-15.084,0.15255,-0.62057,-0.76917,229.11,-0.5543,0.59062,-0.58645,163.29

> select subtract #2

2 models selected  

> view matrix models
> #9,0.63616,0.45587,-0.62248,50.212,-0.001392,-0.80611,-0.59176,244.25,-0.77156,0.37732,-0.51218,199.1

> view matrix models
> #9,-0.2384,0.67282,0.70035,-24.378,-0.87233,0.16862,-0.45893,224.1,-0.42686,-0.72034,0.54672,156.28

> view matrix models
> #9,0.15313,-0.0072091,0.98818,-29.289,-0.58371,-0.80755,0.08456,231.42,0.79739,-0.58976,-0.12787,88.909

> view matrix models
> #9,-0.26623,0.1102,0.95759,6.2872,-0.91243,-0.34912,-0.21349,252.88,0.31079,-0.93057,0.1935,138.56

> view matrix models
> #9,0.070647,0.31727,0.9457,-48.234,-0.78467,-0.56768,0.24906,210.66,0.61587,-0.75966,0.20885,87.978

> view matrix models
> #9,0.092074,0.23734,0.96705,-44.874,-0.66769,-0.70577,0.23679,213.47,0.73872,-0.6675,0.093486,78.576

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.092074,0.23734,0.96705,-35.281,-0.66769,-0.70577,0.23679,210.41,0.73872,-0.6675,0.093486,87.036

> view matrix models
> #9,0.092074,0.23734,0.96705,-28.384,-0.66769,-0.70577,0.23679,220.72,0.73872,-0.6675,0.093486,92.991

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.03922, steps = 140  
shifted from previous position = 3.21  
rotated from previous position = 5.44 degrees  
atoms outside contour = 13243, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
0.07788551 0.79434945 0.60244734 86.09917803  
0.54023279 0.47424633 -0.69515390 138.53322005  
-0.83790356 0.37960423 -0.39219670 114.91250908  
Axis 0.59214731 0.79357381 -0.14000777  
Axis point 45.79958275 0.00000000 69.54071466  
Rotation angle (degrees) 114.83663503  
Shift along axis 144.83108689  
  

> view matrix models
> #9,0.092074,0.23734,0.96705,-24.946,-0.66769,-0.70577,0.23679,218.75,0.73872,-0.6675,0.093486,90.784

> ui mousemode right "rotate selected models"

> view matrix models
> #9,-0.035795,0.34121,0.9393,-18.845,-0.8545,-0.49784,0.14828,227.33,0.51822,-0.79732,0.30939,103.16

> view matrix models
> #9,-0.45831,0.16317,0.87369,50.23,-0.57432,-0.80458,-0.15101,261.17,0.67831,-0.57099,0.46246,47.196

> view matrix models
> #9,0.26652,0.90043,0.34379,-40.929,0.25158,0.27934,-0.92665,151.87,-0.93042,0.33346,-0.15208,192.93

> view matrix models
> #9,0.42577,0.84781,0.31613,-49.349,0.24045,0.23081,-0.94282,159.62,-0.8723,0.47743,-0.10558,167.47

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.42577,0.84781,0.31613,-51.343,0.24045,0.23081,-0.94282,153.12,-0.8723,0.47743,-0.10558,162.85

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.35011,0.89579,0.27382,-43.565,0.35917,0.1416,-0.92247,147.33,-0.86511,0.42131,-0.27216,185.87

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.03619, steps = 332  
shifted from previous position = 5.39  
rotated from previous position = 16.6 degrees  
atoms outside contour = 13358, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
0.04963898 -0.52103932 -0.85208802 132.22245808  
-0.79851668 0.49174578 -0.34721348 108.26461033  
0.59992256 0.69764182 -0.39164883 129.38577911  
Axis 0.57718435 -0.80209938 -0.15328016  
Axis point 55.68113988 0.00000000 113.63312561  
Rotation angle (degrees) 115.15902094  
Shift along axis -30.35451624  
  

> view matrix models
> #9,0.3609,0.87549,0.32136,-47.874,0.45916,0.13312,-0.87832,132.88,-0.81174,0.46455,-0.35394,184.93

> select add #2

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 5 models selected  

> select subtract #9

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 3 models selected  

> view matrix models
> #2,-0.56802,0.017555,-0.82283,141.71,-0.51023,-0.79197,0.33533,79.995,-0.64577,0.61031,0.45881,88.876

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.04062, steps = 104  
shifted from previous position = 3.49  
rotated from previous position = 6.12 degrees  
atoms outside contour = 13099, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
0.08157705 -0.89276635 -0.44307272 116.72020119  
-0.82628226 0.18800582 -0.53095333 117.77993776  
0.55731752 0.40941673 -0.72234003 139.65942016  
Axis 0.68410968 -0.72777375 0.04836650  
Axis point 75.52969575 0.00000000 105.50212663  
Rotation angle (degrees) 136.58365070  
Shift along axis 0.88711010  
  

> view matrix models
> #2,-0.52764,0.24071,-0.81465,138.94,-0.68926,-0.68186,0.24495,82.812,-0.49651,0.69075,0.52568,90.157

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.52764,0.24071,-0.81465,150.24,-0.68926,-0.68186,0.24495,90.353,-0.49651,0.69075,0.52568,91.609

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.41205,0.86408,-0.28911,128.19,-0.90674,-0.35766,0.22338,88.559,0.089614,0.35419,0.93087,80.91

> view matrix models
> #2,-0.56927,0.70869,-0.41676,133.42,-0.79694,-0.60023,0.067901,95.666,-0.20203,0.37079,0.90648,81.265

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.03406, steps = 108  
shifted from previous position = 2.05  
rotated from previous position = 4.14 degrees  
atoms outside contour = 13509, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
-0.35363647 -0.34506289 -0.86940948 134.11803982  
-0.74242496 0.66893477 0.03648912 106.48975962  
0.56898719 0.65837518 -0.49274303 125.91450985  
Axis 0.38467085 -0.88972773 -0.24579037  
Axis point 59.28472183 0.00000000 94.74682766  
Rotation angle (degrees) 126.06639598  
Shift along axis -74.10416522  
  

> view matrix models
> #2,-0.40733,0.7819,-0.47193,134.77,-0.82449,-0.53708,-0.17822,104.56,-0.39281,0.31651,0.86344,82.235

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.0338, steps = 140  
shifted from previous position = 1.79  
rotated from previous position = 4.82 degrees  
atoms outside contour = 13412, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
-0.24855260 -0.17372087 -0.95291273 135.66967198  
-0.59298610 0.80517410 0.00788393 107.59304164  
0.76589104 0.56702358 -0.30314217 118.80462009  
Axis 0.30134936 -0.92635249 -0.22596378  
Axis point 49.07018857 0.00000000 105.15937122  
Rotation angle (degrees) 111.91683175  
Shift along axis -85.63065496  
  

> view matrix models
> #2,-0.38276,0.72642,-0.5708,138.76,-0.80381,-0.56642,-0.18183,106.28,-0.45539,0.38922,0.8007,84.926

> view matrix models
> #2,-0.1756,0.95966,-0.2196,125.45,-0.97179,-0.1333,0.19457,90.275,0.15745,0.24757,0.95599,81.39

> view matrix models
> #2,-0.33293,0.66309,-0.67043,142.64,-0.9191,-0.3871,0.073562,96.218,-0.21074,0.64068,0.73832,85.593

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.03913, steps = 228  
shifted from previous position = 3.71  
rotated from previous position = 8.99 degrees  
atoms outside contour = 13238, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
-0.38366832 -0.46758984 -0.79634060 133.33700140  
-0.62599212 0.76566054 -0.14797907 112.16063573  
0.67892009 0.44172806 -0.58646725 132.73945679  
Axis 0.36934398 -0.92398180 -0.09921014  
Axis point 55.10315350 0.00000000 103.02628534  
Rotation angle (degrees) 127.03031674  
Shift along axis -67.55626736  
  

> view matrix models
> #2,-0.5036,0.37468,-0.77846,148.81,-0.75152,-0.63445,0.18081,91.771,-0.42615,0.67609,0.60109,87.146

> fitmap #2 inMap #9

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1214_map_sharp.mrc (#9)
using 15954 atoms  
average map value = 0.04067, steps = 68  
shifted from previous position = 1.32  
rotated from previous position = 1.53 degrees  
atoms outside contour = 13120, contour level = 0.0091134  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1214_map_sharp.mrc
(#9) coordinates:  
Matrix rotation and translation  
-0.16514693 -0.69447667 -0.70030610 132.02741350  
-0.74690496 0.55177618 -0.37104721 120.04107495  
0.64409585 0.46178480 -0.60983221 132.85143081  
Axis 0.52633203 -0.84963331 -0.03313356  
Axis point 65.16769838 0.00000000 107.83916696  
Rotation angle (degrees) 127.70539084  
Shift along axis -36.90247973  
  

> show #!8 models

> hide #!9 models

> view matrix models
> #2,0.89697,0.14092,0.41904,110.44,-0.422,0.55542,0.71653,66.033,-0.13177,-0.81954,0.55766,99.014

> view matrix models
> #2,-0.37496,-0.63424,-0.67612,151.49,0.54955,-0.73944,0.38888,87.379,-0.74659,-0.22575,0.62581,91.807

> view matrix models
> #2,-0.55534,-0.52303,-0.64656,149.49,0.45701,-0.84148,0.28818,91.397,-0.6948,-0.13545,0.70633,88.506

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.55534,-0.52303,-0.64656,125.07,0.45701,-0.84148,0.28818,91.318,-0.6948,-0.13545,0.70633,77.057

> view matrix models
> #2,-0.55534,-0.52303,-0.64656,125,0.45701,-0.84148,0.28818,93.138,-0.6948,-0.13545,0.70633,75.196

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.57651,-0.51938,-0.63078,124.42,0.63669,-0.76939,0.051602,100.89,-0.51212,-0.37186,0.77424,74.76

> transparency #8.1 50

> fitmap #2 inMap #8

Fit molecule 5n69 (1).pdb (#2) to map
cryosparc_P20_J1196_005_volume_map_sharp.mrc (#8) using 15954 atoms  
average map value = 0.03036, steps = 104  
shifted from previous position = 1.82  
rotated from previous position = 3.92 degrees  
atoms outside contour = 12567, contour level = 0.05108  
  
Position of 5n69 (1).pdb (#2) relative to
cryosparc_P20_J1196_005_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.60351854 -0.47650278 -0.63930468 126.21560051  
0.58285421 -0.81077517 0.05407953 98.25883449  
-0.54410140 -0.33998343 0.76704950 74.50771148  
Axis -0.34741304 -0.08393293 0.93394831  
Axis point 60.36156257 74.50335977 0.00000000  
Rotation angle (degrees) 145.44904163  
Shift along axis 17.49025395  
  

> view matrix models
> #2,-0.77506,-0.4625,-0.43055,118.82,0.51327,-0.85822,-0.0020573,100.41,-0.36856,-0.22259,0.90256,69.302

Average map value = 0.02229 for 15954 atoms, 13086 outside contour  

> fitmap #2 inMap #8

Fit molecule 5n69 (1).pdb (#2) to map
cryosparc_P20_J1196_005_volume_map_sharp.mrc (#8) using 15954 atoms  
average map value = 0.08478, steps = 208  
shifted from previous position = 4.41  
rotated from previous position = 15.2 degrees  
atoms outside contour = 10156, contour level = 0.05108  
  
Position of 5n69 (1).pdb (#2) relative to
cryosparc_P20_J1196_005_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.61791917 -0.45266295 -0.64286247 124.75852513  
0.55737655 -0.82887736 0.04789270 101.77930274  
-0.55453339 -0.32872265 0.76448292 71.38358156  
Axis -0.34820766 -0.08166651 0.93385331  
Axis point 59.49000687 74.44737503 0.00000000  
Rotation angle (degrees) 147.26247742  
Shift along axis 14.90796009  
  

> volume #8 level 0.06488

> ui mousemode right translate

> ui mousemode right "translate selected models"

> open /Users/ruchigautamsharma/Downloads/cryosparc_P20_J1219_map.mrc

Opened cryosparc_P20_J1219_map.mrc as #10, grid size 256,256,256, pixel 0.82,
shown at level 0.00164, step 1, values float32  

> volume #10 level 0.02323

> surface dust #8 size 8.2

> surface dust #10 size 8.2

> hide #!8 models

> select add #10

15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 5 models selected  

> view matrix models
> #2,-0.61792,-0.45266,-0.64286,120.93,0.55738,-0.82888,0.047893,103.22,-0.55453,-0.32872,0.76448,62.617,#10,1,0,0,-3.8259,0,1,0,1.4397,0,0,1,-8.767

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.8156,-0.50986,-0.27359,100.68,0.5779,-0.69421,-0.42908,121.39,0.028844,-0.50806,0.86084,61.826,#10,0.91064,-0.04509,0.41072,-37.664,0.23298,0.87697,-0.42029,33.065,-0.34124,0.47843,0.80911,-2.0521

> view matrix models
> #2,-0.80899,-0.5146,0.28413,78.102,0.38195,-0.82758,-0.41137,120.43,0.44683,-0.22426,0.86605,61.731,#10,0.55017,-0.010763,0.83498,-49.045,0.40306,0.87915,-0.25424,-1.1862,-0.73134,0.47642,0.48802,69.646

> select subtract #2

2 models selected  

> view matrix models
> #10,-0.56409,-0.81254,0.14691,222.97,-0.53065,0.22042,-0.81843,224.1,0.63263,-0.53962,-0.55551,140.49

> view matrix models
> #10,0.24493,0.35012,-0.90411,137.09,0.66523,-0.73908,-0.10599,115.46,-0.70532,-0.57548,-0.41394,269.62

> view matrix models
> #10,0.27534,0.16264,-0.94749,157.21,0.59127,-0.80578,0.033511,114.65,-0.75802,-0.56945,-0.31803,264.11

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.27534,0.16264,-0.94749,150.34,0.59127,-0.80578,0.033511,125.62,-0.75802,-0.56945,-0.31803,266.07

> view matrix models
> #10,0.27534,0.16264,-0.94749,149.8,0.59127,-0.80578,0.033511,124.79,-0.75802,-0.56945,-0.31803,265.07

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.27209,0.22353,-0.93595,142.85,0.70634,-0.70693,0.036499,102.54,-0.6535,-0.67103,-0.35024,267.64

> view matrix models
> #10,0.17362,0.19121,-0.96607,159.72,0.5527,-0.83083,-0.06511,142.1,-0.8151,-0.52264,-0.24993,259.02

> fitmap #2 inMap #10

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1219_map.mrc (#10) using
15954 atoms  
average map value = 0.03688, steps = 156  
shifted from previous position = 1.12  
rotated from previous position = 8.23 degrees  
atoms outside contour = 13707, contour level = 0.023229  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1219_map.mrc (#10)
coordinates:  
Matrix rotation and translation  
-0.29695226 -0.33170285 -0.89542871 134.97225726  
-0.60051642 0.79395353 -0.09496226 109.71083642  
0.74242803 0.50952038 -0.43495930 128.10248350  
Axis 0.34220804 -0.92721891 -0.15217999  
Axis point 49.90060759 0.00000000 107.13315950  
Rotation angle (degrees) 117.96804272  
Shift along axis -75.03200605  
  

> view matrix models
> #10,0.41528,0.53684,-0.7344,74.701,0.74465,-0.66433,-0.064551,105.3,-0.52254,-0.52006,-0.67564,274.37

> undo

Average map value = 0.03688 for 15954 atoms, 13707 outside contour  

> fitmap #2 inMap #10

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1219_map.mrc (#10) using
15954 atoms  
average map value = 0.03688, steps = 48  
shifted from previous position = 0.00752  
rotated from previous position = 0.0346 degrees  
atoms outside contour = 13704, contour level = 0.023229  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1219_map.mrc (#10)
coordinates:  
Matrix rotation and translation  
-0.29714943 -0.33117482 -0.89555874 134.98015746  
-0.60048399 0.79404592 -0.09439307 109.69026987  
0.74237537 0.50971984 -0.43481547 128.09749729  
Axis 0.34199471 -0.92725182 -0.15245877  
Axis point 49.89847342 0.00000000 107.11806556  
Rotation angle (degrees) 117.96677605  
Shift along axis -75.07759011  
  

> view matrix models
> #10,0.33651,0.027111,-0.94129,156.12,0.15016,-0.98834,0.025216,190.29,-0.92963,-0.14983,-0.33665,243.58

> fitmap #2 inMap #10

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1219_map.mrc (#10) using
15954 atoms  
average map value = 0.03872, steps = 124  
shifted from previous position = 2.56  
rotated from previous position = 3.81 degrees  
atoms outside contour = 13620, contour level = 0.023229  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1219_map.mrc (#10)
coordinates:  
Matrix rotation and translation  
-0.57874977 0.03814726 -0.81461248 136.56726657  
-0.31533488 0.91073862 0.26668162 96.42601664  
0.75207222 0.41121765 -0.51506060 129.51292341  
Axis 0.08963156 -0.97155285 -0.21920593  
Axis point 45.24215359 -0.00000000 92.05071574  
Rotation angle (degrees) 126.26607439  
Shift along axis -109.83223528  
  

> open /Users/ruchigautamsharma/Downloads/cryosparc_P20_J1220_map.mrc

Opened cryosparc_P20_J1220_map.mrc as #11, grid size 256,256,256, pixel 0.82,
shown at level 0.00164, step 1, values float32  

> volume #11 level 0.01659

> surface dust #10 size 8.2

[Repeated 1 time(s)]

> select subtract #10

Nothing selected  

> hide #!10 models

> select add #11

2 models selected  
Average map value = 0.02484 for 15954 atoms, 14314 outside contour  

> fitmap #2 inMap #11

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1220_map.mrc (#11) using
15954 atoms  
average map value = 0.03491, steps = 240  
shifted from previous position = 11.1  
rotated from previous position = 4.59 degrees  
atoms outside contour = 13821, contour level = 0.01659  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1220_map.mrc (#11)
coordinates:  
Matrix rotation and translation  
-0.89118802 -0.41480578 0.18363027 84.14565273  
0.32030067 -0.86203944 -0.39280463 121.76824677  
0.32123417 -0.29124588 0.90110179 69.36052950  
Axis 0.13456147 -0.18231992 0.97398802  
Axis point 23.99473824 75.07218107 0.00000000  
Rotation angle (degrees) 157.82917117  
Shift along axis 56.67831087  
  

> view matrix models
> #11,0.83629,0.19378,0.51291,-56,-0.12284,0.9779,-0.16916,32.343,-0.53435,0.078461,0.84161,63.181

> transparency sel 50

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.83629,0.19378,0.51291,-65.867,-0.12284,0.9779,-0.16916,34.439,-0.53435,0.078461,0.84161,65.043

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.83284,0.053495,0.55092,-53.809,0.090314,0.96885,-0.23061,19.33,-0.5461,0.24181,0.80206,52.176

> fitmap #2 inMap #11

Fit molecule 5n69 (1).pdb (#2) to map cryosparc_P20_J1220_map.mrc (#11) using
15954 atoms  
average map value = 0.1327, steps = 336  
shifted from previous position = 10.9  
rotated from previous position = 24.7 degrees  
atoms outside contour = 10321, contour level = 0.01659  
  
Position of 5n69 (1).pdb (#2) relative to cryosparc_P20_J1220_map.mrc (#11)
coordinates:  
Matrix rotation and translation  
-0.61804436 -0.45153970 -0.64353171 124.74897555  
0.55721287 -0.82906249 0.04657479 101.77800378  
-0.55455837 -0.32979887 0.76400113 71.33913667  
Axis -0.34838137 -0.08235607 0.93372796  
Axis point 59.50552773 74.43790191 0.00000000  
Rotation angle (degrees) 147.30446290  
Shift along axis 14.76909033  
  

> select subtract #11

Nothing selected  

> save "/Users/ruchigautamsharma/Desktop/S1 with Mava120523.cxs"

——— End of log from Wed Dec 6 12:06:25 2023 ———

opened ChimeraX session  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 119, in restore_snapshot  
ti.set_state_from_snapshot(session, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/log/tool.py", line 505, in set_state_from_snapshot  
if self.settings.session_restore_clears and session.restore_options['clear
log']:  
KeyError: 'clear log'  
  
opened ChimeraX session  




OpenGL version: 4.1 INTEL-20.6.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

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: MacBookPro15,4
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 1.7 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
      OS Loader Version: 577.140.2~15

Software:

    System Software Overview:

      System Version: macOS 13.6.1 (22G313)
      Kernel Version: Darwin 22.6.0
      Time since boot: 6 days, 10 hours, 10 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          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: 0.21.0
    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: 1.6.1
    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: 1.6.0
    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-NIHPresets: 1.1.15
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-OpenCommands: 1.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.2
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.1
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 0.2
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.0
    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-StarMap: 1.2.15
    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-TugLigands: 1.1
    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-XMAS: 1.1.3
    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
    et-xmlfile: 1.1.0
    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
    MolecularDynamicsViewer: 1.4
    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
    openpyxl: 3.1.2
    openvr: 1.23.701
    packaging: 21.3
    pandas: 2.1.1
    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
    pyqtgraph: 0.13.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    seaborn: 0.12.2
    Send2Trash: 1.8.2
    SEQCROW: 1.8.3
    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]

Hi Ruchi,

Thanks for reporting this problem. Looking at the code, I'm having difficulty imagining how it could occur. Is there any chance you could provide the S1 with Mava120523.cxs session file?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab