"clear log" missing from session-restore options

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-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/haotiandu/Desktop/EBV_TRACeR_fitting.cxs

[Repeated 1 time(s)]

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "VolumeImage" returned None  

Opened EBV_TRACeR_complex.mrc copy as #12, grid size 450,450,450, pixel 0.684,
shown at level 0.0125, step 1, values float32  
Log from Fri Dec 22 17:41:50 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/haotiandu/Desktop/fitting.cxs

Opened EBV_TRACeR_complex.mrc as #1, grid size 450,450,450, pixel 0.684, shown
at level 0.0125, step 4, values float32  
Log from Sun Nov 26 02:10:31 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/haotiandu/Desktop/EBV_TRACeR_complex.mrc

Opened EBV_TRACeR_complex.mrc as #1, grid size 450,450,450, pixel 0.684, shown
at level 0.0158, step 2, values float32  

> volume #1 style mesh

> volume #1 level 0.0114

> volume #1 level 0.01527

> open "/Users/haotiandu/Desktop/chimera model/MHC_1.pdb"

Chain information for MHC_1.pdb #2  
---  
Chain | Description  
F | No description available  
G | No description available  
H | No description available  
  

> open "/Users/haotiandu/Desktop/chimera model/MHC_2.pdb"

Chain information for MHC_2.pdb #3  
---  
Chain | Description  
F | No description available  
G | No description available  
H | No description available  
  

> style stick

Changed 6284 atom styles  

> style stick

Changed 6284 atom styles  

> style sphere

Changed 6284 atom styles  

> style sphere

Changed 6284 atom styles  

> style stick

Changed 6284 atom styles  

> hide atoms

> show atoms

> hide atoms

> select add #3

3142 atoms, 3231 bonds, 382 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #3

3142 atoms, 3231 bonds, 382 residues, 1 model selected  

> select add #2

6284 atoms, 6462 bonds, 764 residues, 2 models selected  

> select subtract #3

3142 atoms, 3231 bonds, 382 residues, 1 model selected  

> hide #!1 models

> ui mousemode right translate

> ui mousemode right select

[Repeated 1 time(s)]Drag select of 50 residues  
Drag select of 305 residues  
Drag select of 373 residues  
Drag select of 58 residues  
Drag select of 370 residues  

> select clear

Drag select of 373 residues  
Drag select of 41 residues  
Drag select of 373 residues  

> ui mousemode right translate

> select add #1

3066 atoms, 373 residues, 3 models selected  

> select subtract #1

3066 atoms, 373 residues, 1 model selected  

> show #!1 models

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-3.3248,0,1,0,6.7729,0,0,1,2.7367

> view matrix models #2,1,0,0,-7.7111,0,1,0,5.6893,0,0,1,7.515

> view matrix models #2,1,0,0,-11.747,0,1,0,5.0179,0,0,1,5.0543

> view matrix models #2,1,0,0,-13.129,0,1,0,2.8989,0,0,1,3.7472

> view matrix models #2,1,0,0,-12.71,0,1,0,2.779,0,0,1,4.8568

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.9993,-0.036383,-0.0088167,-7.0321,0.036235,0.99921,-0.016326,-0.96874,0.0094037,0.015995,0.99983,1.3892

> view matrix models
> #2,0.99351,-0.11362,0.0054251,0.27386,0.11298,0.99121,0.068857,-28.285,-0.013201,-0.067798,0.99761,15.241

> select add #3

6208 atoms, 3231 bonds, 755 residues, 2 models selected  

> select add #2

6284 atoms, 6462 bonds, 764 residues, 2 models selected  

> view matrix models
> #2,0.99573,-0.078808,-0.048082,3.8641,0.082014,0.99425,0.068814,-23.482,0.042383,-0.072463,0.99647,6.7686,#3,0.99796,0.031068,-0.055769,5.3195,-0.031108,0.99952,0.00015867,4.7952,0.055747,0.0015765,0.99844,-8.4191

> select subtract #3

3142 atoms, 3231 bonds, 382 residues, 1 model selected  

> undo

[Repeated 4 time(s)]

> view matrix models
> #2,0.99677,-0.07761,0.020408,-6.8615,0.076541,0.99587,0.048785,-18.829,-0.02411,-0.047066,0.9986,14.734

> view matrix models
> #2,0.98723,-0.059134,-0.14789,21.031,0.10422,0.942,0.31903,-63.148,0.12045,-0.33037,0.93614,30.691

> undo

[Repeated 1 time(s)]

> view matrix models
> #2,0.98604,0.1156,-0.11985,-3.0131,-0.091152,0.97706,0.19249,-10.401,0.13936,-0.17888,0.97395,3.9627

> undo

> view matrix models
> #2,0.99957,-0.01882,0.022458,-14.293,0.018023,0.99922,0.035162,-6.3014,-0.023102,-0.034743,0.99913,13.083

> view matrix models
> #2,0.99961,-0.023001,0.015619,-12.686,0.022357,0.99894,0.040181,-7.8986,-0.016527,-0.039816,0.99907,12.468

> select add #2

3142 atoms, 3231 bonds, 382 residues, 1 model selected  

> select add #3

6284 atoms, 6462 bonds, 764 residues, 2 models selected  

> select subtract #2

3142 atoms, 3231 bonds, 382 residues, 1 model selected  

> view matrix models
> #3,0.99836,-0.036146,-0.044476,14.454,0.040018,0.99518,0.089483,-19.71,0.041028,-0.091115,0.99499,12.147

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.99836,-0.036146,-0.044476,18.686,0.040018,0.99518,0.089483,-10.625,0.041028,-0.091115,0.99499,12.843

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.9939,-0.088269,-0.0661,32.565,0.087984,0.9961,-0.0072173,-0.72906,0.066479,0.0013575,0.99779,-8.0647

> view matrix models
> #3,0.99437,-0.083193,-0.065601,31.482,0.082732,0.99652,-0.0097291,0.32225,0.066182,0.0042471,0.9978,-8.5591

> select subtract #3

Nothing selected  

> hide #3 models

> open "/Users/haotiandu/Desktop/chimera model/helical_1.pdb"

Chain information for helical_1.pdb #4  
---  
Chain | Description  
A | No description available  
D | No description available  
  

> select add #4

758 atoms, 772 bonds, 88 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,-5.7695,0,1,0,-2.0396,0,0,1,-5.1535

> view matrix models #4,1,0,0,-4.3789,0,1,0,-2.5076,0,0,1,-5.6919

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.99923,0.03911,0.0034444,-10.535,-0.038787,0.99695,-0.067758,14.167,-0.0060838,0.067572,0.9977,-14.347

> view matrix models
> #4,0.99904,0.03381,-0.027777,-5.3151,-0.036311,0.9948,-0.095124,17.917,0.024416,0.096041,0.99508,-23.447

> view matrix models
> #4,0.99897,0.038465,0.024043,-13.298,-0.03716,0.99793,-0.052528,11.595,-0.026013,0.051581,0.99833,-8.6365

> view matrix models
> #4,0.99585,0.075883,0.050191,-22,-0.070963,0.99309,-0.093448,23.893,-0.056935,0.089499,0.99436,-8.3853

> view matrix models
> #4,0.91469,0.33125,0.23153,-71.497,-0.37116,0.91522,0.1569,51.777,-0.15993,-0.22945,0.96009,61.48

> view matrix models
> #4,0.9591,0.25251,0.12794,-52.847,-0.27152,0.94844,0.16354,28.779,-0.080047,-0.19159,0.9782,39.572

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.9591,0.25251,0.12794,-55.327,-0.27152,0.94844,0.16354,32.807,-0.080047,-0.19159,0.9782,35.525

> view matrix models
> #4,0.9591,0.25251,0.12794,-53.303,-0.27152,0.94844,0.16354,34.306,-0.080047,-0.19159,0.9782,39.566

> view matrix models
> #4,0.9591,0.25251,0.12794,-50.953,-0.27152,0.94844,0.16354,33.389,-0.080047,-0.19159,0.9782,38.029

> view matrix models
> #4,0.9591,0.25251,0.12794,-52.941,-0.27152,0.94844,0.16354,33.499,-0.080047,-0.19159,0.9782,35.485

> view matrix models
> #4,0.9591,0.25251,0.12794,-53.589,-0.27152,0.94844,0.16354,30.219,-0.080047,-0.19159,0.9782,38.124

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.95539,0.27751,-0.10111,-24.371,-0.28276,0.95829,-0.041609,59.609,0.085348,0.068343,0.994,-31.112

> view matrix models
> #4,0.95602,0.23515,-0.1753,-7.7364,-0.25703,0.95959,-0.11455,65.275,0.14128,0.15457,0.97783,-51.244

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.95602,0.23515,-0.1753,-7.611,-0.25703,0.95959,-0.11455,67.152,0.14128,0.15457,0.97783,-52.833

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.92569,0.36658,0.093359,-59.769,-0.36634,0.80723,0.46279,27.17,0.094288,-0.4626,0.88154,60.392

> open "/Users/haotiandu/Desktop/chimera model/Fab_1.pdb"

Chain information for Fab_1.pdb #5  
---  
Chain | Description  
H | No description available  
L | No description available  
P | No description available  
  

> hide #5 models

> open "/Users/haotiandu/Desktop/chimera model/Fab_2.pdb"

Chain information for Fab_2.pdb #6  
---  
Chain | Description  
H | No description available  
L | No description available  
P | No description available  
  

> hide #6 models

> show #6 models

> color #6 #db6668ff

> select add #6

4149 atoms, 4242 bonds, 535 residues, 2 models selected  

> select subtract #4

3391 atoms, 3470 bonds, 447 residues, 1 model selected  

> view matrix models
> #6,0.61799,0.7244,-0.30549,50.76,-0.7071,0.3423,-0.61874,311.75,-0.34365,0.59839,0.72376,51.467

> view matrix models
> #6,-0.086385,0.4711,-0.87784,312.9,-0.41491,-0.81809,-0.39821,338.58,-0.90575,0.32982,0.26614,267.78

> view matrix models
> #6,-0.18367,-0.13111,-0.97421,411.23,0.18413,-0.97811,0.096925,154.01,-0.96559,-0.16158,0.20379,341.42

> view matrix models
> #6,-0.083463,-0.41471,-0.90612,409.44,0.46679,-0.81963,0.33213,42.062,-0.88042,-0.39524,0.26199,339.08

> view matrix models
> #6,0.20927,-0.23091,-0.9502,331.3,0.49116,-0.81543,0.30633,39.793,-0.84556,-0.53081,-0.057236,389.86

> view matrix models
> #6,0.38448,-0.29623,-0.87431,288.82,0.58349,-0.65595,0.47883,-21.374,-0.71535,-0.69425,-0.079352,381.27

> view matrix models
> #6,0.39826,-0.3464,-0.84935,287.58,0.45421,-0.72999,0.5107,10.664,-0.79692,-0.58917,-0.13339,395.78

> view matrix models
> #6,0.74944,-0.031955,-0.6613,150.56,0.35561,-0.8231,0.44278,51.739,-0.55846,-0.567,-0.6055,406.01

> undo

[Repeated 7 time(s)]

> hide sel atoms

> view matrix models
> #4,0.7822,0.53689,0.3161,-83.198,-0.60755,0.76971,0.19606,120.51,-0.13804,-0.34541,0.92825,87.449,#6,0.9504,0.29312,0.10404,-40.641,-0.26193,0.93464,-0.24051,93.988,-0.16774,0.20133,0.96505,13.672

> undo

> select subtract #4

3391 atoms, 3470 bonds, 447 residues, 1 model selected  

> view matrix models
> #6,0.71288,0.67928,-0.17432,16.296,-0.66789,0.58183,-0.46411,256.41,-0.21383,0.44728,0.86846,18.544

> view matrix models
> #6,-0.30148,0.13155,-0.94435,405.55,-0.25969,-0.96432,-0.051428,271.51,-0.91743,0.22974,0.32488,272.76

> view matrix models
> #6,-0.14215,-0.23079,-0.96256,410.9,0.0069622,-0.97265,0.23218,173.96,-0.98982,0.026302,0.13987,335.87

> view matrix models
> #6,0.27513,-0.73512,-0.6196,323.96,0.31967,-0.53785,0.78008,-17.075,-0.9067,-0.41269,0.087017,370.99

> undo

[Repeated 3 time(s)]

> ui mousemode right "translate selected models"

> view matrix models #6,1,0,0,1.9456,0,1,0,1.4312,0,0,1,3.6241

> view matrix models #6,1,0,0,1.765,0,1,0,-0.15664,0,0,1,3.4785

> view matrix models #6,1,0,0,2.0162,0,1,0,-1.1503,0,0,1,3.3518

> undo

[Repeated 1 time(s)]

> view matrix models #6,1,0,0,-3.7581,0,1,0,-14.485,0,0,1,11.15

> undo

> select add #4

4149 atoms, 4242 bonds, 535 residues, 2 models selected  

> select subtract #6

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #4,0.92569,0.36658,0.093359,-57.508,-0.36634,0.80723,0.46279,24.748,0.094288,-0.4626,0.88154,60.11

> view matrix models
> #4,0.92569,0.36658,0.093359,-59.577,-0.36634,0.80723,0.46279,25.425,0.094288,-0.4626,0.88154,60.232

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.94307,0.32622,-0.064834,-34.277,-0.26747,0.8597,0.43517,4.5303,0.1977,-0.39305,0.89801,29.808

> view matrix models
> #4,0.93532,0.333,-0.11957,-26.234,-0.26516,0.88346,0.38624,7.5046,0.23425,-0.32955,0.91462,11.761

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.93532,0.333,-0.11957,-27.284,-0.26516,0.88346,0.38624,6.977,0.23425,-0.32955,0.91462,13.133

> view matrix models
> #4,0.93532,0.333,-0.11957,-26.314,-0.26516,0.88346,0.38624,8.6885,0.23425,-0.32955,0.91462,14.615

> view matrix models
> #4,0.93532,0.333,-0.11957,-26.537,-0.26516,0.88346,0.38624,7.8709,0.23425,-0.32955,0.91462,15.348

> view matrix models
> #4,0.93532,0.333,-0.11957,-26.783,-0.26516,0.88346,0.38624,7.0017,0.23425,-0.32955,0.91462,16.116

> open "/Users/haotiandu/Desktop/chimera model/ARE.pdb"

Chain information for ARE.pdb #7  
---  
Chain | Description  
D | No description available  
  

> hide #7 models

> show #7 models

> select subtract #4

Nothing selected  

> ui mousemode right select

Drag select of 23 residues  
Drag select of 8 residues  

> select clear

Drag select of 23 residues  

> ui mousemode right "translate selected models"

> view matrix models #7,1,0,0,130.99,0,1,0,31.513,0,0,1,-27.955

> view matrix models #7,1,0,0,182.87,0,1,0,42.12,0,0,1,-22.645

> view matrix models #7,1,0,0,223.07,0,1,0,54.276,0,0,1,-18.88

> view matrix models #7,1,0,0,132.89,0,1,0,132.95,0,0,1,87.04

> view matrix models #7,1,0,0,160.7,0,1,0,163.93,0,0,1,78.309

> view matrix models #7,1,0,0,161.03,0,1,0,159.55,0,0,1,81.235

> view matrix models #7,1,0,0,164.7,0,1,0,163.56,0,0,1,93.693

> view matrix models #7,1,0,0,163.48,0,1,0,163.33,0,0,1,94.969

> color #7 #7ed17eff

> view matrix models #7,1,0,0,158.69,0,1,0,162.16,0,0,1,92.366

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.76413,-0.32505,-0.55718,169.65,0.56815,0.74817,0.3427,138.95,0.30547,-0.57843,0.75638,81.242

> view matrix models
> #7,-0.39805,0.27876,-0.87398,203.64,0.88961,-0.11525,-0.44193,140.51,-0.22392,-0.95342,-0.20211,106.97

> view matrix models
> #7,-0.44443,0.25082,-0.85998,201.76,0.87562,-0.081063,-0.47615,143.34,-0.18914,-0.96463,-0.1836,105.82

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.44443,0.25082,-0.85998,202.02,0.87562,-0.081063,-0.47615,144.14,-0.18914,-0.96463,-0.1836,105.03

> view matrix models
> #7,-0.44443,0.25082,-0.85998,201.83,0.87562,-0.081063,-0.47615,144.07,-0.18914,-0.96463,-0.1836,105.6

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.49766,0.25256,-0.82979,200.38,0.84183,-0.089805,-0.53222,146.09,-0.20894,-0.9634,-0.16792,104.89

> view matrix models
> #7,-0.52574,0.18762,-0.82969,197.7,0.76748,-0.316,-0.55778,137.99,-0.36683,-0.93002,0.022139,97.263

> view matrix models
> #7,-0.57959,0.058311,-0.81282,191.64,0.59271,-0.65437,-0.46958,120.06,-0.55926,-0.75393,0.3447,89.317

> view matrix models
> #7,-0.63064,-0.11275,-0.76784,182.69,0.44826,-0.86058,-0.2418,101.31,-0.63353,-0.49668,0.59326,88.271

> view matrix models
> #7,-0.76399,-0.22536,-0.60459,170.54,0.12729,-0.97125,0.20117,76.216,-0.63254,0.076732,0.77071,103.17

> view matrix models
> #7,-0.81838,-0.16458,-0.5506,170.38,-0.13798,-0.87381,0.46627,67.443,-0.55786,0.45756,0.6924,122

> view matrix models
> #7,-0.84438,-0.15906,-0.51159,168.78,-0.1776,-0.81781,0.5474,65.939,-0.50545,0.55307,0.66229,127.3

> view matrix models
> #7,-0.8508,-0.23894,-0.46803,163.66,-0.091779,-0.80939,0.58006,65.122,-0.51742,0.53646,0.6667,126.41

> view matrix models
> #7,-0.84845,-0.22213,-0.48041,164.88,-0.11474,-0.8089,0.57665,65.214,-0.51669,0.54438,0.66082,126.99

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.84845,-0.22213,-0.48041,165.84,-0.11474,-0.8089,0.57665,66.971,-0.51669,0.54438,0.66082,126.27

> view matrix models
> #7,-0.84845,-0.22213,-0.48041,165.4,-0.11474,-0.8089,0.57665,67.983,-0.51669,0.54438,0.66082,126.15

> view matrix models
> #7,-0.84845,-0.22213,-0.48041,166.08,-0.11474,-0.8089,0.57665,69.321,-0.51669,0.54438,0.66082,126.28

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.93337,-0.098508,-0.34512,164.71,-0.08981,-0.8669,0.49033,70.925,-0.34749,0.48865,0.80029,118.48

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.93337,-0.098508,-0.34512,165.81,-0.08981,-0.8669,0.49033,73.178,-0.34749,0.48865,0.80029,124.17

> view matrix models
> #7,-0.93337,-0.098508,-0.34512,166.35,-0.08981,-0.8669,0.49033,73.584,-0.34749,0.48865,0.80029,121.37

> view matrix models
> #7,-0.93337,-0.098508,-0.34512,166.35,-0.08981,-0.8669,0.49033,73.574,-0.34749,0.48865,0.80029,121.39

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.95316,-0.027009,-0.30124,167.17,-0.12108,-0.87864,0.46188,74.26,-0.27716,0.47672,0.83422,119.66

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.95316,-0.027009,-0.30124,164.3,-0.12108,-0.87864,0.46188,75.996,-0.27716,0.47672,0.83422,120.82

> view matrix models
> #7,-0.95316,-0.027009,-0.30124,163.9,-0.12108,-0.87864,0.46188,74.731,-0.27716,0.47672,0.83422,122.68

> ui mousemode right select

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.98827,-0.056761,-0.14178,155.54,0.0025974,-0.93448,0.35601,77.623,-0.1527,0.35147,0.92366,114.18

> view matrix models
> #7,-0.99023,0.12522,-0.06142,159.2,-0.13878,-0.92857,0.34424,77.895,-0.013926,0.3494,0.93687,113.99

> select add #7

193 atoms, 197 bonds, 23 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select add #4

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #4,0.92988,0.33984,-0.14084,-23.864,-0.27061,0.89126,0.3639,9.9311,0.2492,-0.30027,0.92073,8.3393

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.92988,0.33984,-0.14084,-21.549,-0.27061,0.89126,0.3639,10.367,0.2492,-0.30027,0.92073,5.9483

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.90065,0.36214,-0.2402,-5.8257,-0.31466,0.9247,0.21431,34.068,0.29972,-0.11744,0.94677,-33.538

> view matrix models
> #4,0.80923,0.47674,-0.34331,7.4252,-0.5188,0.8541,-0.03683,115.05,0.27566,0.20791,0.9385,-76.508

> undo

> view matrix models
> #4,0.93874,0.25268,-0.23436,3.0428,-0.24268,0.9675,0.071036,35.537,0.24469,-0.009809,0.96955,-43.256

> view matrix models
> #4,0.92918,0.25305,-0.26944,9.577,-0.26062,0.96541,0.0078896,47.835,0.26212,0.062892,0.96299,-56.113

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.92918,0.25305,-0.26944,9.9482,-0.26062,0.96541,0.0078896,46.085,0.26212,0.062892,0.96299,-55.613

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.9244,0.30581,-0.22796,-2.9058,-0.32985,0.94104,-0.075138,73.309,0.19154,0.14465,0.97077,-56.706

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.9244,0.30581,-0.22796,-2.9241,-0.32985,0.94104,-0.075138,75.365,0.19154,0.14465,0.97077,-58.007

> view matrix models
> #4,0.9244,0.30581,-0.22796,-3.2199,-0.32985,0.94104,-0.075138,74.079,0.19154,0.14465,0.97077,-57.411

> view matrix models
> #4,0.9244,0.30581,-0.22796,-7.1184,-0.32985,0.94104,-0.075138,79.632,0.19154,0.14465,0.97077,-56.852

> view matrix models
> #4,0.9244,0.30581,-0.22796,-2.3106,-0.32985,0.94104,-0.075138,74.182,0.19154,0.14465,0.97077,-55.767

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.93622,0.31604,-0.15369,-16.331,-0.31792,0.94803,0.012793,58.699,0.14974,0.036884,0.98804,-35.023

> view matrix models
> #4,0.94507,0.3065,-0.11357,-22.093,-0.3023,0.95174,0.052956,49.799,0.12432,-0.015715,0.99212,-23.423

> view matrix models
> #4,0.94343,0.31816,-0.093339,-26.394,-0.31436,0.9478,0.05338,52.398,0.10545,-0.021019,0.9942,-19.685

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.94343,0.31816,-0.093339,-27.829,-0.31436,0.9478,0.05338,53.045,0.10545,-0.021019,0.9942,-18.847

> save /Users/haotiandu/Desktop/complex1.pdb models #2,4-5,7 relModel #1

> open /Users/haotiandu/Desktop/complex1.pdb

Summary of feedback from opening /Users/haotiandu/Desktop/complex1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO F 50
ILE F 52 1 3  
Start residue of secondary structure not found: HELIX 2 2 PRO F 57 TYR F 84 1
28  
Start residue of secondary structure not found: HELIX 3 3 MET F 138 ALA F 149
1 12  
Start residue of secondary structure not found: HELIX 4 4 VAL F 152 GLY F 162
1 11  
Start residue of secondary structure not found: HELIX 5 5 THR F 163 ASN F 174
1 12  
76 messages similar to the above omitted  
  
Chain information for complex1.pdb  
---  
Chain | Description  
8.2/A | No description available  
8.2/D | No description available  
8.4/D | No description available  
8.1/F | No description available  
8.1/G | No description available  
8.1/H | No description available  
8.3/H | No description available  
8.3/L | No description available  
8.3/P | No description available  
  

> hide #6 models

> show #6 models

> hide #8.4 models

> show #8.4 models

> hide #8.3 models

> hide #8.2 models

> show #8.2 models

> select add #8.1

3900 atoms, 4003 bonds, 470 residues, 2 models selected  

> view matrix models
> #4,0.94343,0.31816,-0.093339,-41.081,-0.31436,0.9478,0.05338,163.73,0.10545,-0.021019,0.9942,-29.49,#8.1,1,0,0,-13.252,0,1,0,110.68,0,0,1,-10.643

> view matrix models
> #4,0.94343,0.31816,-0.093339,-55.696,-0.31436,0.9478,0.05338,176.81,0.10545,-0.021019,0.9942,-41.498,#8.1,1,0,0,-27.867,0,1,0,123.76,0,0,1,-22.651

> close #8

> view matrix models
> #4,0.94343,0.31816,-0.093339,-5.3931,-0.31436,0.9478,0.05338,198.02,0.10545,-0.021019,0.9942,-51.941

> undo

[Repeated 2 time(s)]

> hide #7 models

> show #7 models

> select subtract #4

Nothing selected  

> show #5 models

> hide #5 models

> hide #6 models

> show #6 models

> save /Users/haotiandu/Desktop/complex1.pdb models #2,4,6-7

> open /Users/haotiandu/Desktop/complex1.pdb

Summary of feedback from opening /Users/haotiandu/Desktop/complex1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO F 50
ILE F 52 1 3  
Start residue of secondary structure not found: HELIX 2 2 PRO F 57 TYR F 84 1
28  
Start residue of secondary structure not found: HELIX 3 3 MET F 138 ALA F 149
1 12  
Start residue of secondary structure not found: HELIX 4 4 VAL F 152 GLY F 162
1 11  
Start residue of secondary structure not found: HELIX 5 5 THR F 163 ASN F 174
1 12  
76 messages similar to the above omitted  
  
Chain information for complex1.pdb  
---  
Chain | Description  
8.2/A | No description available  
8.2/D | No description available  
8.4/D | No description available  
8.1/F | No description available  
8.1/G | No description available  
8.1/H | No description available  
8.3/H | No description available  
8.3/L | No description available  
8.3/P | No description available  
  

> select add #8

7484 atoms, 7670 bonds, 940 residues, 5 models selected  

> view matrix models #8,1,0,0,-28.475,0,1,0,79.197,0,0,1,-13.691

> view matrix models #8,1,0,0,-41.3,0,1,0,81.327,0,0,1,-6.5616

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.17303,0.15711,0.97231,21.424,0.94064,0.31903,0.11584,-43.27,-0.29199,0.93463,-0.20299,128.95

> view matrix models
> #8,-0.56527,0.48737,0.66554,105.8,0.82343,0.28504,0.49063,-73.132,0.049413,0.82537,-0.56243,129.47

> view matrix models
> #8,0.025514,0.89671,-0.44188,114.89,0.64854,0.32153,0.68994,-73.485,0.76075,-0.30418,-0.57335,122.74

> view matrix models
> #8,-0.88612,0.024572,0.46281,255.39,0.14261,0.9646,0.22184,23.871,-0.44097,0.26258,-0.85825,337.47

> view matrix models
> #8,-0.92218,0.079603,0.37848,268.7,0.31162,0.73255,0.60519,-42.819,-0.22909,0.67604,-0.70035,224.73

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,-4.4386,0,1,0,-2.4907,0,0,1,2.5545

> undo

> view matrix models
> #8.1,1,-8.3267e-17,-3.3307e-16,14.874,-6.1062e-16,1,1.3878e-15,4.0731,5.5511e-17,-1.1102e-16,1,-7.8314

> undo

> view matrix models
> #8.3,1,2.7756e-17,-3.6082e-16,7.5786,-6.6613e-16,1,1.6098e-15,0.54803,-1.1102e-16,5.5511e-17,1,-2.5068

> undo

> view matrix models
> #8.1,1,-1.1102e-16,-2.7756e-16,7.5613,-5.2736e-16,1,1.2768e-15,1.2378,5.5511e-17,-1.1102e-16,1,-1.1802

> undo

[Repeated 1 time(s)]

> view matrix models
> #8.1,1,8.3267e-17,5.5511e-17,11.812,-5.2736e-16,1,-1.3878e-16,2.2444,1.1102e-16,2.498e-16,1,-5.9816

> undo

[Repeated 6 time(s)]

> view matrix models #1,1,0,0,-18.164,0,1,0,8.8262,0,0,1,-0.9442

> undo

> view matrix models #1,1,0,0,-49.959,0,1,0,-10.513,0,0,1,-1.8904

> undo

> view matrix models
> #4,0.94343,0.31816,-0.093339,-30.978,-0.31436,0.9478,0.05338,43.48,0.10545,-0.021019,0.9942,-16.644

> undo

> ui mousemode right select

> ui mousemode right "translate selected models"

> view matrix models #8,1,0,0,-89.879,0,1,0,-45.027,0,0,1,3.5011

> view matrix models #8,1,0,0,-124.78,0,1,0,22.817,0,0,1,14.217

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.48771,0.86012,-0.14941,94.371,-0.77586,-0.34859,0.52586,253.16,0.40022,0.37239,0.83734,-83.998

> view matrix models
> #8,-0.73084,-0.57312,0.37068,229.65,0.67986,-0.56311,0.46979,-4.1129,-0.060517,0.59535,0.80119,-12.22

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.73084,-0.57312,0.37068,265.9,0.67986,-0.56311,0.46979,36.168,-0.060517,0.59535,0.80119,-38.791

> view matrix models
> #8,-0.73084,-0.57312,0.37068,262.91,0.67986,-0.56311,0.46979,53.23,-0.060517,0.59535,0.80119,-33.726

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.89941,-0.3817,0.21302,297.22,0.43407,-0.83731,0.33242,154.84,0.05148,0.39144,0.91876,-49.391

> view matrix models
> #8,-0.9435,-0.33133,-0.0055071,334.06,0.33123,-0.94345,0.01356,237.78,-0.0096886,0.01097,0.99989,-4.4125

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,0.1938,0,1,0,-2.8861,0,0,1,-3.1544

> undo

> ui mousemode right select

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.9435,-0.33133,-0.0055071,338.16,0.33123,-0.94345,0.01356,234.81,-0.0096886,0.01097,0.99989,-7.5946

> view matrix models
> #8,-0.9435,-0.33133,-0.0055071,333.7,0.33123,-0.94345,0.01356,233.98,-0.0096886,0.01097,0.99989,-0.50973

> view matrix models
> #8,-0.9435,-0.33133,-0.0055071,332.79,0.33123,-0.94345,0.01356,234.28,-0.0096886,0.01097,0.99989,-0.47867

> view matrix models
> #8,-0.9435,-0.33133,-0.0055071,332.33,0.33123,-0.94345,0.01356,233.03,-0.0096886,0.01097,0.99989,1.222

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.95829,-0.28563,0.0096444,327.45,0.28483,-0.95729,-0.049778,253.9,0.02345,-0.044954,0.99871,1.4439

> view matrix models
> #8,-0.96818,-0.23406,0.088551,311.07,0.22454,-0.96874,-0.1055,275.98,0.11047,-0.082256,0.99047,-10.225

> view matrix models
> #8,-0.97894,-0.20407,0.0064474,322.43,0.20398,-0.97615,0.074304,252.75,-0.0088694,0.074054,0.99721,-6.1162

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.97894,-0.20407,0.0064474,321.89,0.20398,-0.97615,0.074304,251.83,-0.0088694,0.074054,0.99721,-4.6736

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.98986,-0.14168,-0.010266,319.18,0.14171,-0.98991,-0.0022395,278.01,-0.0098453,-0.0036716,0.99994,4.4707

> view matrix models
> #8,-0.99704,-0.044694,-0.062587,317.39,0.052272,-0.99075,-0.12521,315.6,-0.056413,-0.12811,0.99015,30.216

> select subtract #8.2

6726 atoms, 6898 bonds, 852 residues, 4 models selected  

> select add #8.2

7484 atoms, 7670 bonds, 940 residues, 5 models selected  

> select subtract #8.3

4093 atoms, 4200 bonds, 493 residues, 4 models selected  

> select subtract #8.4

3900 atoms, 4003 bonds, 470 residues, 3 models selected  

> select subtract #8.1

758 atoms, 772 bonds, 88 residues, 2 models selected  

> view matrix models
> #8,-0.98406,-0.088427,-0.15428,334.57,0.10118,-0.99189,-0.076877,298.22,-0.14623,-0.091262,0.98503,44.693

> undo

> view matrix models
> #8,-0.98511,-0.1656,-0.046116,326.76,0.16783,-0.98456,-0.049785,279.71,-0.037159,-0.056784,0.99769,16.64

> undo

> ui mousemode right select

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.99704,-0.044694,-0.062587,318.38,0.052272,-0.99075,-0.12521,314.5,-0.056413,-0.12811,0.99015,31.195

> undo

> view matrix models
> #8,-0.99704,-0.044694,-0.062587,321.34,0.052272,-0.99075,-0.12521,326.27,-0.056413,-0.12811,0.99015,23.232

> undo

> select subtract #8.2

1 model selected  

> select add #7

193 atoms, 197 bonds, 23 residues, 2 models selected  

> select subtract #7

1 model selected  

> select add #4

758 atoms, 772 bonds, 88 residues, 2 models selected  

> view matrix models
> #4,0.94343,0.31816,-0.093339,-29.861,-0.31436,0.9478,0.05338,53.397,0.10545,-0.021019,0.9942,-18.771,#8,-0.99704,-0.044694,-0.062587,315.35,0.052272,-0.99075,-0.12521,315.95,-0.056413,-0.12811,0.99015,30.292

> undo

> select add #8

8242 atoms, 8442 bonds, 1028 residues, 6 models selected  

> select subtract #8

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #4,0.94343,0.31816,-0.093339,-32.348,-0.31436,0.9478,0.05338,54.485,0.10545,-0.021019,0.9942,-19.063

> view matrix models
> #4,0.94343,0.31816,-0.093339,-30.701,-0.31436,0.9478,0.05338,52.33,0.10545,-0.021019,0.9942,-18.549

> undo

> select subtract #4

Nothing selected  

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #8.2,1,5.2042e-18,0,-7.5547,7.9797e-17,1,0,6.1028,1.4572e-16,2.498e-16,1,-0.28007

> view matrix models
> #8.2,1,2.6021e-18,0,-9.2034,8.0665e-17,1,0,4.8039,1.4572e-16,2.498e-16,1,-0.20533

> view matrix models
> #8.2,1,6.0715e-18,0,-8.2388,7.7195e-17,1,0,1.6058,1.4572e-16,2.498e-16,1,0.61447

> view matrix models
> #8.2,1,6.0715e-18,0,-8.8188,7.7195e-17,1,0,1.3663,1.4572e-16,2.498e-16,1,1.0043

> ui mousemode right "rotate selected models"

> view matrix models
> #8.2,0.99853,-0.012809,-0.052734,0.49982,0.012084,0.99983,-0.014033,1.2938,0.052904,0.013375,0.99851,-9.5634

> select subtract #8.2

Nothing selected  

> select add #4

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #4,0.93724,0.29507,-0.18578,-14.825,-0.29806,0.95447,0.012259,56.491,0.18094,0.043884,0.98251,-40.026

> select subtract #4

Nothing selected  

> select add #8.1

3142 atoms, 3231 bonds, 382 residues, 1 model selected  

> select subtract #8.1

Nothing selected  

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #8.2,0.99966,0.011287,-0.023303,-7.2404,-0.012515,0.9985,-0.053251,10.934,0.022667,0.053525,0.99831,-10.394

> view matrix models
> #8.2,0.99937,0.017588,-0.030934,-7.0745,-0.019893,0.99692,-0.075843,15.476,0.029505,0.07641,0.99664,-14.663

> ui mousemode right "translate selected models"

> view matrix models
> #8.2,0.99937,0.017588,-0.030934,-7.5866,-0.019893,0.99692,-0.075843,15.972,0.029505,0.07641,0.99664,-14.554

> color #8.2 #a5ffa5ff

> select subtract #8.2

Nothing selected  

> select add #8.1

3142 atoms, 3231 bonds, 382 residues, 1 model selected  

> color #8.1 #88ceecff

> select subtract #8.1

Nothing selected  

> select add #8.3

3391 atoms, 3470 bonds, 447 residues, 1 model selected  

> color #8.3 #c0595bff

> select subtract #8.3

Nothing selected  

> select add #8.4

193 atoms, 197 bonds, 23 residues, 1 model selected  

> color #8.4 #9fff9fff

> select subtract #8.4

Nothing selected  

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #8.2,0.99861,0.046541,-0.024569,-12.578,-0.048832,0.9935,-0.10282,24.972,0.019624,0.10387,0.9944,-16.634

> view matrix models
> #8.2,0.99815,0.041269,0.044639,-21.168,-0.038537,0.99743,-0.060407,16.896,-0.047017,0.058575,0.99718,0.7304

> view matrix models
> #8.2,0.99537,0.024394,0.092936,-24.818,-0.022142,0.99944,-0.025192,9.0679,-0.093498,0.023017,0.99535,13.936

> view matrix models
> #8.2,0.99058,-0.0006073,0.13694,-26.354,-0.0042506,0.99937,0.035179,-2.1368,-0.13687,-0.03543,0.98995,30.471

> ui mousemode right "translate selected models"

> view matrix models
> #8.2,0.99058,-0.0006073,0.13694,-24.562,-0.0042506,0.99937,0.035179,-1.7695,-0.13687,-0.03543,0.98995,28.757

> undo

[Repeated 5 time(s)]

> style #2,4,6-7#8.1-4 stick

Changed 14968 atom styles  

> style #2,4,6-7#8.1-4 stick

Changed 14968 atom styles  

> hide #2,4,6-7#8.1-4 atoms

> select add #8.1

3142 atoms, 3231 bonds, 382 residues, 1 model selected  

> select subtract #8.1

Nothing selected  

> select add #8

7484 atoms, 7670 bonds, 940 residues, 5 models selected  

> select subtract #8

Nothing selected  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/haotiandu/Desktop/movie1.mp4

Movie saved to /Users/haotiandu/Desktop/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/haotiandu/Desktop/movie2.mp4

Movie saved to /Users/haotiandu/Desktop/movie2.mp4  
  

> hide #!1 models

> show #!1 models

> volume #1 style image

> volume #1 level -0.001661,0 level 0.01581,0.8 level 0.2468,1

> volume #1 level -0.001661,0 level 0.004747,0.7706 level 0.2468,1

> volume #1 style mesh

> volume #1 level 0.01251

> volume #1 step 1

Error processing trigger "graphics update":  
  
You deleted or moved a volume file that is still open in ChimeraX.  
  
/Users/haotiandu/Desktop/EBV_TRACeR_complex.mrc  
  
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.  

> volume #1 step 4

> volume #1 style surface

> volume #1 style mesh

> volume #1 style image maximumIntensityProjection true

  
You deleted or moved a volume file that is still open in ChimeraX.  
  
/Users/haotiandu/Desktop/EBV_TRACeR_complex.mrc  
  
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.  

> volume #1 region 0,0,0,449,449,449 step 4

> volume #1 region 0,0,0,449,449,449 step 1 colorMode opaque8 orthoplanes xyz
> positionPlanes 224,224,224 imageMode orthoplanes

> volume #1 region 0,0,0,449,449,449 step 4 colorMode auto8 imageMode "full
> region"

> volume #1 style mesh

> hide #!1 models

> color #2 #d7d7ecff

> color #2 #dbdaecff

> color #8.1 #d8d7e9ff

> select add #1

3 models selected  

> select add #1

3 models selected  

> show #!1 models

> select add #1

3 models selected  

> select add #1

3 models selected  

> select add #1

3 models selected  

> hide #!1 models

> select add #1

3 models selected  

> hide #2 models

> show #2 models

> select add #2

3142 atoms, 3231 bonds, 382 residues, 4 models selected  

> select subtract #2

3 models selected  

> select add #1

3 models selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #1

3 models selected  

> select add #1

3 models selected  

> select add #1

3 models selected  

> ui mousemode right select

[Repeated 1 time(s)]

> select add #1

3 models selected  

> select add #1

3 models selected  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/haotiandu/Desktop/movie3.mp4

Movie saved to /Users/haotiandu/Desktop/movie3.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/haotiandu/Desktop/movie4.mp4

Movie saved to /Users/haotiandu/Desktop/movie4.mp4  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #1 style surface

> show #!1 models

> select add #1

3 models selected  

> select add #1

3 models selected  

> select add #2

3142 atoms, 3231 bonds, 382 residues, 4 models selected  

> select subtract #2

3 models selected  

> select add #1

3 models selected  

> select add #1

3 models selected  

> save /Users/haotiandu/Desktop/fitting.cxs

——— End of log from Sun Nov 26 02:10:31 2023 ———

opened ChimeraX session  

> volume showOutlineBox false

> transparency 50

> hide #!1 models

> hide #2 models

> show #2 models

> show #!1 models

> hide #!1 models

> hide #4 models

> hide #6 models

> hide #7 models

> hide #!8 models

> hide #8.1 models

> hide #8.2 models

> hide #8.3 models

> hide #8.4 models

> show #!1 models

> fitmap #2 inMap #1

Fit molecule MHC_1.pdb (#2) to map EBV_TRACeR_complex.mrc (#1) using 3142
atoms  
average map value = 0.04832, steps = 128  
shifted from previous position = 6.7  
rotated from previous position = 15 degrees  
atoms outside contour = 250, contour level = 0.012507  
  
Position of MHC_1.pdb (#2) relative to EBV_TRACeR_complex.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.96248122 -0.04452161 0.26767093 -41.00377313  
0.01907789 0.99510964 0.09691666 -13.36037534  
-0.27067681 -0.08817387 0.95862372 65.28992481  
Axis -0.32312215 0.93982160 0.11102896  
Axis point 211.47012619 0.00000000 173.24130169  
Rotation angle (degrees) 16.64312193  
Shift along axis 7.94193026  
  

> hide #2 models

> show #5 models

> fitmap #5 inMap #1

Fit molecule Fab_1.pdb (#5) to map EBV_TRACeR_complex.mrc (#1) using 3391
atoms  
average map value = 0.02454, steps = 228  
shifted from previous position = 14.3  
rotated from previous position = 35.2 degrees  
atoms outside contour = 635, contour level = 0.012507  
  
Position of Fab_1.pdb (#5) relative to EBV_TRACeR_complex.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.92542891 -0.28214809 -0.25293040 96.78519312  
0.13388014 0.86791528 -0.47832957 90.68131807  
0.35448193 0.40879766 0.84096791 -100.45569538  
Axis 0.76951928 -0.52688666 0.36087467  
Axis point 0.00000000 277.18300094 102.51619969  
Rotation angle (degrees) 35.19889153  
Shift along axis -9.55261998  
  

> hide #5 models

> show #6 models

> fitmap #6 inMap #1

Fit molecule Fab_2.pdb (#6) to map EBV_TRACeR_complex.mrc (#1) using 3391
atoms  
average map value = 0.02583, steps = 196  
shifted from previous position = 3.9  
rotated from previous position = 16.6 degrees  
atoms outside contour = 500, contour level = 0.012507  
  
Position of Fab_2.pdb (#6) relative to EBV_TRACeR_complex.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.98883011 0.07224585 0.13036702 -21.87908440  
-0.10211689 0.96551302 0.23949271 -6.17555202  
-0.10856870 -0.25013027 0.96210586 55.71289427  
Axis -0.85593282 0.41769471 -0.30481165  
Axis point 0.00000000 213.37767165 55.05711071  
Rotation angle (degrees) 16.61965974  
Shift along axis -0.83440815  
  

> hide #6 models

> show #2 models

> hide #2 models

> show #3 models

> fitmap #3 inMap #1

Fit molecule MHC_2.pdb (#3) to map EBV_TRACeR_complex.mrc (#1) using 3142
atoms  
average map value = 0.04833, steps = 128  
shifted from previous position = 5.95  
rotated from previous position = 16.3 degrees  
atoms outside contour = 266, contour level = 0.012507  
  
Position of MHC_2.pdb (#3) relative to EBV_TRACeR_complex.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.95684702 0.00050160 -0.29059168 55.19362620  
-0.04149054 0.98998889 -0.13490932 35.48903352  
0.28761486 0.14114439 0.94728874 -59.39296926  
Axis 0.42992356 -0.90049365 -0.06539818  
Axis point 237.02620875 0.00000000 161.16430929  
Rotation angle (degrees) 18.72642183  
Shift along axis -4.34441681  
  

> hide #3 models

> show #3 models

> hide #3 models

> show #8.1 models

> fitmap #8.1 inMap #1

Fit molecule complex1.pdb (#8.1) to map EBV_TRACeR_complex.mrc (#1) using 3142
atoms  
average map value = 0.04833, steps = 112  
shifted from previous position = 9.95  
rotated from previous position = 12.4 degrees  
atoms outside contour = 265, contour level = 0.012507  
  
Position of complex1.pdb (#8.1) relative to EBV_TRACeR_complex.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.97880590 -0.06131963 0.19539424 -23.35264100  
0.07354534 0.99572205 -0.05593464 -1.75709823  
-0.19112846 0.06911949 0.97912839 18.08691491  
Axis 0.29214833 0.90298471 0.31506819  
Axis point 85.47905488 -0.00000000 124.73467590  
Rotation angle (degrees) 12.35833558  
Shift along axis -2.71045643  
  

> hide #8.1 models

> show #8.1 models

> hide #8.1 models

> hide #!8 models

> show #!8 models

> show #8.2 models

> show #8.1 models

> hide #!8 models

> show #!8 models

> hide #8.1 models

> show #8.1 models

> hide #8.2 models

> show #8.2 models

> hide #8.2 models

> show #8.2 models

> hide #8.2 models

> show #8.2 models

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #8.2,0.99937,0.017588,-0.030934,-9.9104,-0.019893,0.99692,-0.075843,18.667,0.029505,0.07641,0.99664,-16.706

> view matrix models
> #8.2,0.99937,0.017588,-0.030934,-5.3622,-0.019893,0.99692,-0.075843,18.998,0.029505,0.07641,0.99664,-19.622

> view matrix models
> #8.2,0.99937,0.017588,-0.030934,-4.2856,-0.019893,0.99692,-0.075843,20.921,0.029505,0.07641,0.99664,-20.776

> view matrix models
> #8.2,0.99937,0.017588,-0.030934,-3.8919,-0.019893,0.99692,-0.075843,17.503,0.029505,0.07641,0.99664,-20.228

> view matrix models
> #8.2,0.99937,0.017588,-0.030934,-5.4747,-0.019893,0.99692,-0.075843,19.799,0.029505,0.07641,0.99664,-21.842

> ui mousemode right "rotate selected models"

> view matrix models
> #8.2,0.99576,-0.058739,-0.070864,11.775,0.060253,0.99799,0.019414,-6.6968,0.069582,-0.023601,0.9973,-13.927

> ui mousemode right "translate selected models"

> view matrix models
> #8.2,0.99576,-0.058739,-0.070864,11.813,0.060253,0.99799,0.019414,-7.7167,0.069582,-0.023601,0.9973,-13.409

> view matrix models
> #8.2,0.99576,-0.058739,-0.070864,13.472,0.060253,0.99799,0.019414,-9.9933,0.069582,-0.023601,0.9973,-13.266

> ui mousemode right "rotate selected models"

> view matrix models
> #8.2,0.98524,-0.081296,-0.15064,29.416,0.07571,0.99623,-0.042465,-3.8661,0.15353,0.030433,0.98768,-33.859

> view matrix models
> #8.2,0.87953,-0.24953,-0.40517,106.42,0.29007,0.95614,0.040815,-45.032,0.37721,-0.15342,0.91333,-33.978

> view matrix models
> #8.2,0.91853,-0.205,-0.33805,84.241,0.1246,0.96159,-0.24458,20.647,0.3752,0.18253,0.90879,-82.326

> select add #8

7484 atoms, 7670 bonds, 940 residues, 5 models selected  

> select subtract #8

Nothing selected  

> hide #8.2 models

> show #2 models

> show #6 models

> show #5 models

> show #4 models

> hide #8.1 models

> hide #!8 models

> show #7 models

> hide #6 models

> hide #5 models

> hide #4 models

> hide #2 models

> hide #7 models

> show #8.2 models

> fitmap #8.2 inMap #1

Fit molecule complex1.pdb (#8.2) to map EBV_TRACeR_complex.mrc (#1) using 758
atoms  
average map value = 0.04508, steps = 112  
shifted from previous position = 7.26  
rotated from previous position = 17.9 degrees  
atoms outside contour = 79, contour level = 0.012507  
  
Position of complex1.pdb (#8.2) relative to EBV_TRACeR_complex.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.84714224 0.00030207 -0.53136610 92.17268472  
-0.14499337 0.96218245 -0.23061193 58.74676109  
0.51120147 0.27240567 0.81514919 -99.83159545  
Axis 0.43116214 -0.89363805 -0.12454016  
Axis point 233.86020658 0.00000000 106.45203481  
Rotation angle (degrees) 35.68493404  
Shift along axis -0.32392584  
  

> show #2 models

> show #8.1 models

> hide #2 models

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.  

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #8.2,0.72979,-0.21468,-0.64909,159.32,-0.080453,0.91585,-0.39337,77.003,0.67892,0.3393,0.65111,-115.19

> select subtract #8.2

Nothing selected  

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> select subtract #8.2

Nothing selected  

> hide #8.2 models

> open /Users/haotiandu/Desktop/MAM_02_06_refine_4-coot-Fixed.pdb

Chain information for MAM_02_06_refine_4-coot-Fixed.pdb #9  
---  
Chain | Description  
A | No description available  
B F | No description available  
C | No description available  
D | No description available  
E H | No description available  
G | No description available  
  

> open "/Users/haotiandu/Desktop/domain_swapped dimer.pdb"

Chain information for domain_swapped dimer.pdb #10  
---  
Chain | Description  
A | No description available  
D | No description available  
  

> hide #!9 models

> hide #8.1 models

> hide #!8 models

> hide #!10 models

> show #!10 models

> fitmap #10 inMap #1

Fit molecule domain_swapped dimer.pdb (#10) to map EBV_TRACeR_complex.mrc (#1)
using 2070 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 2070, contour level = 0.012507  
  
Position of domain_swapped dimer.pdb (#10) relative to EBV_TRACeR_complex.mrc
(#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> fitmap #10 inMap #1

Fit molecule domain_swapped dimer.pdb (#10) to map EBV_TRACeR_complex.mrc (#1)
using 2070 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 2070, contour level = 0.012507  
  
Position of domain_swapped dimer.pdb (#10) relative to EBV_TRACeR_complex.mrc
(#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> fitmap #10 inMap #1

Fit molecule domain_swapped dimer.pdb (#10) to map EBV_TRACeR_complex.mrc (#1)
using 2070 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 2070, contour level = 0.012507  
  
Position of domain_swapped dimer.pdb (#10) relative to EBV_TRACeR_complex.mrc
(#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> fitmap #10 inMap #1

Fit molecule domain_swapped dimer.pdb (#10) to map EBV_TRACeR_complex.mrc (#1)
using 2070 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 2070, contour level = 0.012507  
  
Position of domain_swapped dimer.pdb (#10) relative to EBV_TRACeR_complex.mrc
(#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> fitmap #10 inMap #1

Fit molecule domain_swapped dimer.pdb (#10) to map EBV_TRACeR_complex.mrc (#1)
using 2070 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 2070, contour level = 0.012507  
  
Position of domain_swapped dimer.pdb (#10) relative to EBV_TRACeR_complex.mrc
(#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> select add #10

2070 atoms, 2113 bonds, 1 pseudobond, 242 residues, 2 models selected  

> view matrix models
> #10,0.93239,-0.10815,-0.34489,15.736,-0.080501,0.86808,-0.48985,23.201,0.35237,0.48449,0.80069,30.555

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.93239,-0.10815,-0.34489,67.69,-0.080501,0.86808,-0.48985,31.597,0.35237,0.48449,0.80069,-5.9028

> view matrix models
> #10,0.93239,-0.10815,-0.34489,44.914,-0.080501,0.86808,-0.48985,46.975,0.35237,0.48449,0.80069,38.014

> view matrix models
> #10,0.93239,-0.10815,-0.34489,103.71,-0.080501,0.86808,-0.48985,162.79,0.35237,0.48449,0.80069,183.12

> view matrix models
> #10,0.93239,-0.10815,-0.34489,180.6,-0.080501,0.86808,-0.48985,230.01,0.35237,0.48449,0.80069,173.72

> view matrix models
> #10,0.93239,-0.10815,-0.34489,184.33,-0.080501,0.86808,-0.48985,206.03,0.35237,0.48449,0.80069,116.16

> fitmap #10 inMap #1

Fit molecule domain_swapped dimer.pdb (#10) to map EBV_TRACeR_complex.mrc (#1)
using 2070 atoms  
average map value = 0.03389, steps = 140  
shifted from previous position = 1.67  
rotated from previous position = 23.2 degrees  
atoms outside contour = 458, contour level = 0.012507  
  
Position of domain_swapped dimer.pdb (#10) relative to EBV_TRACeR_complex.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.93287533 -0.08807863 -0.34926462 183.90698892  
0.04531629 0.99063680 -0.12878339 190.78070652  
0.35733745 0.10431147 0.92813203 94.40014119  
Axis 0.30835947 -0.93475868 0.17646715  
Axis point -184.34763801 0.00000000 654.65692407  
Rotation angle (degrees) 22.20735417  
Shift along axis -104.96593629  
  

> show #2 models

> show #8.1 models

> select subtract #10

Nothing selected  

> hide #!10 models

> show #8.2 models

> show #4 models

> select add #4

758 atoms, 772 bonds, 88 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #4

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #4,0.93724,0.29507,-0.18578,-16.218,-0.29806,0.95447,0.012259,60.814,0.18094,0.043884,0.98251,-42.088

> view matrix models
> #4,0.93724,0.29507,-0.18578,-16.345,-0.29806,0.95447,0.012259,60.735,0.18094,0.043884,0.98251,-41.993

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.93767,0.28225,-0.20273,-12.129,-0.28386,0.95862,0.021726,56.343,0.20047,0.037176,0.97899,-43.861

> select subtract #4

Nothing selected  

> select add #4

758 atoms, 772 bonds, 88 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #7

193 atoms, 197 bonds, 23 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select add #7

193 atoms, 197 bonds, 23 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select add #7

193 atoms, 197 bonds, 23 residues, 1 model selected  

> hide #!1 models

> hide #2 models

> hide #4 models

> select subtract #7

Nothing selected  

> show #7 models

> show #!1 models

> show #4 models

> show #2 models

> select add #7

193 atoms, 197 bonds, 23 residues, 1 model selected  

> view matrix models
> #7,-0.96355,0.17814,-0.19958,167.51,-0.23575,-0.91805,0.31874,79.108,-0.12644,0.35418,0.92659,114.25

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.96355,0.17814,-0.19958,164.16,-0.23575,-0.91805,0.31874,87.197,-0.12644,0.35418,0.92659,107.81

> view matrix models
> #7,-0.96355,0.17814,-0.19958,163.45,-0.23575,-0.91805,0.31874,85.877,-0.12644,0.35418,0.92659,104.5

> view matrix models
> #7,-0.96355,0.17814,-0.19958,170.06,-0.23575,-0.91805,0.31874,85.326,-0.12644,0.35418,0.92659,103.46

> view matrix models
> #7,-0.96355,0.17814,-0.19958,170.93,-0.23575,-0.91805,0.31874,85.199,-0.12644,0.35418,0.92659,104.17

> view matrix models
> #7,-0.96355,0.17814,-0.19958,171.04,-0.23575,-0.91805,0.31874,85.752,-0.12644,0.35418,0.92659,104.35

> view matrix models
> #7,-0.96355,0.17814,-0.19958,171.3,-0.23575,-0.91805,0.31874,78.281,-0.12644,0.35418,0.92659,106.69

> select subtract #7

Nothing selected  

> select add #8.3

3391 atoms, 3470 bonds, 447 residues, 1 model selected  

> select subtract #8.3

Nothing selected  

> select add #8.4

193 atoms, 197 bonds, 23 residues, 1 model selected  

> select subtract #8.4

Nothing selected  

> select add #8.4

193 atoms, 197 bonds, 23 residues, 1 model selected  

> select subtract #8.4

Nothing selected  

> hide #2 models

> hide #4 models

> hide #7 models

> hide #!8 models

> show #!8 models

> hide #8.1 models

> show #8.1 models

> hide #8.2 models

> show #8.2 models

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #8.2,0.72979,-0.21468,-0.64909,154.1,-0.080453,0.91585,-0.39337,84.645,0.67892,0.3393,0.65111,-116.03

> view matrix models
> #8.2,0.72979,-0.21468,-0.64909,156.64,-0.080453,0.91585,-0.39337,88.361,0.67892,0.3393,0.65111,-115.01

> ui mousemode right "rotate selected models"

> view matrix models
> #8.2,0.67417,-0.16049,-0.72093,167.74,-0.015438,0.97283,-0.23101,47.026,0.73841,0.16687,0.65338,-99.923

> view matrix models
> #8.2,0.88293,-0.28891,-0.37009,103.97,0.12714,0.90593,-0.40389,56.689,0.45197,0.30955,0.8366,-98.165

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,0.67465,0,1,0,-0.091455,0,0,1,0.058434

> view matrix models #1,1,0,0,2.3019,0,1,0,0.73445,0,0,1,0.43359

> view matrix models
> #8.2,0.88293,-0.28891,-0.37009,100.42,0.12714,0.90593,-0.40389,52.855,0.45197,0.30955,0.8366,-104.45

> view matrix models #1,1,0,0,-0.59186,0,1,0,5.3438,0,0,1,1.004

> undo

> view matrix models #1,1,0,0,3.0495,0,1,0,-0.90927,0,0,1,0.32207

> undo

> view matrix models #1,1,0,0,2.3043,0,1,0,0.10623,0,0,1,0.52707

> undo

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #8.2,0.88293,-0.28891,-0.37009,99.223,0.12714,0.90593,-0.40389,55.068,0.45197,0.30955,0.8366,-104.42

> view matrix models
> #8.2,0.88293,-0.28891,-0.37009,99.348,0.12714,0.90593,-0.40389,54.446,0.45197,0.30955,0.8366,-104.55

> view matrix models
> #8.2,0.88293,-0.28891,-0.37009,97.1,0.12714,0.90593,-0.40389,55.038,0.45197,0.30955,0.8366,-104.26

> select add #2

3900 atoms, 4003 bonds, 470 residues, 2 models selected  

> select add #4

4658 atoms, 4775 bonds, 558 residues, 3 models selected  

> select subtract #4

3900 atoms, 4003 bonds, 470 residues, 2 models selected  

> select add #4

4658 atoms, 4775 bonds, 558 residues, 3 models selected  

> select subtract #2

1516 atoms, 1544 bonds, 176 residues, 2 models selected  

> select add #2

4658 atoms, 4775 bonds, 558 residues, 3 models selected  

> select subtract #4

3900 atoms, 4003 bonds, 470 residues, 2 models selected  

> select subtract #2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> show #2 models

> show #4 models

> select add #8

7484 atoms, 7670 bonds, 940 residues, 5 models selected  

> select subtract #8

Nothing selected  

> select add #4

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #4,0.93767,0.28225,-0.20273,-9.7159,-0.28386,0.95862,0.021726,51.818,0.20047,0.037176,0.97899,-43.398

> view matrix models
> #4,0.93767,0.28225,-0.20273,-10.82,-0.28386,0.95862,0.021726,52.619,0.20047,0.037176,0.97899,-42.963

> view matrix models
> #4,0.93767,0.28225,-0.20273,-8.21,-0.28386,0.95862,0.021726,53.31,0.20047,0.037176,0.97899,-42.297

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.82806,0.45422,-0.32863,2.8708,-0.38098,0.88593,0.26453,46.567,0.4113,-0.093851,0.90666,-48.912

> view matrix models
> #4,0.72286,0.59631,-0.34911,2.766,-0.422,0.78105,0.46031,41.585,0.54716,-0.18542,0.81623,-45.943

> view matrix models
> #4,0.77797,0.51696,-0.35709,6.1874,-0.22161,0.75759,0.61397,-11.054,0.58792,-0.39852,0.70394,-5.5038

> view matrix models
> #4,0.74686,0.56367,-0.35282,4.0066,-0.29278,0.75511,0.58659,5.4117,0.59706,-0.3348,0.72899,-20.06

> view matrix models
> #4,0.82328,0.54763,-0.14938,-35.435,-0.28275,0.62381,0.72864,3.1431,0.49221,-0.55764,0.66841,39.573

> select subtract #4

Nothing selected  

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #8.2,0.88853,-0.21839,-0.40352,90.377,0.075863,0.93728,-0.34022,50.29,0.45251,0.27168,0.84937,-100.53

> view matrix models
> #8.2,0.88298,-0.33434,-0.32949,98.219,0.24901,0.92864,-0.27499,13.833,0.39792,0.16077,0.90322,-82.511

> hide #!8 models

> hide #8.1 models

> select subtract #8.2

Nothing selected  

> hide #8.2 models

> show #8.2 models

> hide #8.2 models

> hide #!8 models

> hide #4 models

> show #4 models

> select add #4

758 atoms, 772 bonds, 88 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.82328,0.54763,-0.14938,-40.823,-0.28275,0.62381,0.72864,1.0727,0.49221,-0.55764,0.66841,39.346

> view matrix models
> #4,0.82328,0.54763,-0.14938,-41.91,-0.28275,0.62381,0.72864,0.59249,0.49221,-0.55764,0.66841,39.368

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.737,0.3964,-0.54745,51.481,-0.093633,0.86203,0.49814,-34.779,0.66938,-0.31587,0.67243,-27.537

> view matrix models
> #4,0.7035,0.31423,-0.63746,82.123,-0.075433,0.92489,0.37267,-29.549,0.70669,-0.21409,0.67436,-49.326

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.7035,0.31423,-0.63746,88.613,-0.075433,0.92489,0.37267,-26.397,0.70669,-0.21409,0.67436,-49.763

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.64187,0.37352,-0.66969,94.957,0.094925,0.82792,0.55275,-66.689,0.76092,-0.41837,0.49596,-3.63

> view matrix models
> #4,0.82858,0.27647,-0.48684,51.474,-0.21371,0.95991,0.18139,19.15,0.51747,-0.046253,0.85445,-67.515

> view matrix models
> #4,0.90229,-0.026066,-0.43034,75.723,0.12393,0.97172,0.20099,-43.427,0.41293,-0.23469,0.88,-25.183

> view matrix models
> #4,0.97845,0.16487,0.12432,-43.892,-0.18862,0.95862,0.21324,10.537,-0.08402,-0.23209,0.96906,47.334

> view matrix models
> #4,0.70672,-0.19729,0.67943,-21.683,-0.55178,0.44735,0.70385,79.684,-0.44281,-0.87232,0.20729,311.41

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.70672,-0.19729,0.67943,-32.022,-0.55178,0.44735,0.70385,80.634,-0.44281,-0.87232,0.20729,313.06

> view matrix models
> #4,0.70672,-0.19729,0.67943,-24.638,-0.55178,0.44735,0.70385,73.207,-0.44281,-0.87232,0.20729,303.42

> view matrix models
> #4,0.70672,-0.19729,0.67943,-23.95,-0.55178,0.44735,0.70385,65.32,-0.44281,-0.87232,0.20729,313.03

> view matrix models
> #4,0.70672,-0.19729,0.67943,-35.251,-0.55178,0.44735,0.70385,70.428,-0.44281,-0.87232,0.20729,307.36

> view matrix models
> #4,0.70672,-0.19729,0.67943,-40.868,-0.55178,0.44735,0.70385,70.394,-0.44281,-0.87232,0.20729,306.38

> view matrix models
> #4,0.70672,-0.19729,0.67943,-39.298,-0.55178,0.44735,0.70385,67.029,-0.44281,-0.87232,0.20729,305.91

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.81821,-0.29145,0.49557,-18.58,-0.43116,0.25913,0.86426,51.6,-0.38031,-0.92082,0.086362,319.41

> view matrix models
> #4,0.95573,0.27367,0.10812,-71.459,-0.26035,0.61523,0.74412,-13.67,0.13712,-0.73932,0.65924,122.74

> view matrix models
> #4,0.94895,0.15816,-0.2729,0.55642,0.14909,0.53755,0.82995,-84.65,0.27796,-0.82827,0.48653,136.07

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.94895,0.15816,-0.2729,11.945,0.14909,0.53755,0.82995,-90.318,0.27796,-0.82827,0.48653,131.49

> view matrix models
> #4,0.94895,0.15816,-0.2729,10.556,0.14909,0.53755,0.82995,-84.775,0.27796,-0.82827,0.48653,135.34

> view matrix models
> #4,0.94895,0.15816,-0.2729,14.728,0.14909,0.53755,0.82995,-77.084,0.27796,-0.82827,0.48653,136.25

> view matrix models
> #4,0.94895,0.15816,-0.2729,14.923,0.14909,0.53755,0.82995,-76.803,0.27796,-0.82827,0.48653,135.23

> view matrix models
> #4,0.94895,0.15816,-0.2729,15.908,0.14909,0.53755,0.82995,-77.57,0.27796,-0.82827,0.48653,136.49

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.95009,0.20103,-0.23855,4.509,-0.004254,0.77296,0.63444,-58.57,0.31194,-0.60176,0.73524,61.979

> view matrix models
> #4,0.94229,0.12092,-0.31221,28.122,0.069415,0.84169,0.53548,-67.486,0.32753,-0.52625,0.78472,41.119

> view matrix models
> #4,0.99118,0.0574,-0.11949,1.9715,-0.0019908,0.90773,0.41954,-48.662,0.13254,-0.4156,0.89984,42.003

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.99118,0.0574,-0.11949,4.113,-0.0019908,0.90773,0.41954,-47.573,0.13254,-0.4156,0.89984,44.371

> view matrix models
> #4,0.99118,0.0574,-0.11949,4.2099,-0.0019908,0.90773,0.41954,-46.568,0.13254,-0.4156,0.89984,42.787

> view matrix models
> #4,0.99118,0.0574,-0.11949,4.2192,-0.0019908,0.90773,0.41954,-46.55,0.13254,-0.4156,0.89984,42.796

> hide #!1 models

> show #!1 models

> show #8.1 models

> show #8.2 models

> hide #8.2 models

> show #8.2 models

> select subtract #4

Nothing selected  

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> select subtract #8.2

Nothing selected  

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #8.2,0.88298,-0.33434,-0.32949,99.542,0.24901,0.92864,-0.27499,13.502,0.39792,0.16077,0.90322,-81.993

> view matrix models
> #8.2,0.88298,-0.33434,-0.32949,101.04,0.24901,0.92864,-0.27499,10.271,0.39792,0.16077,0.90322,-81.7

> select add #7

951 atoms, 969 bonds, 111 residues, 2 models selected  

> select add #8.4

1144 atoms, 1166 bonds, 134 residues, 3 models selected  

> select subtract #8.4

951 atoms, 969 bonds, 111 residues, 2 models selected  

> select subtract #7

758 atoms, 772 bonds, 88 residues, 1 model selected  

> show #7 models

> show #8.4 models

> hide #7 models

> show #7 models

> select subtract #8.2

Nothing selected  

> select add #7

193 atoms, 197 bonds, 23 residues, 1 model selected  

> view matrix models
> #7,-0.96355,0.17814,-0.19958,172.02,-0.23575,-0.91805,0.31874,77.671,-0.12644,0.35418,0.92659,108.9

> view matrix models
> #7,-0.96355,0.17814,-0.19958,171.85,-0.23575,-0.91805,0.31874,79.676,-0.12644,0.35418,0.92659,108.68

> view matrix models
> #7,-0.96355,0.17814,-0.19958,167.87,-0.23575,-0.91805,0.31874,81.918,-0.12644,0.35418,0.92659,109.96

> select subtract #7

Nothing selected  

> hide #8.1 models

> show #8.1 models

> hide #7 models

> hide #8.4 models

> show #8.4 models

> select add #8.4

193 atoms, 197 bonds, 23 residues, 1 model selected  

> view matrix models
> #8.4,1,5.2042e-18,0,-4.8962,7.9797e-17,1,0,1.1157,1.4572e-16,2.498e-16,1,-3.9054

> view matrix models
> #8.4,1,5.2042e-18,0,-8.1184,7.9797e-17,1,0,4.356,1.4572e-16,2.498e-16,1,-4.3523

> view matrix models
> #8.4,1,1.7347e-18,0,-6.2332,7.6328e-17,1,0,5.3778,1.4572e-16,2.498e-16,1,-3.0998

> view matrix models
> #8.4,1,7.8063e-18,0,-7.4014,7.893e-17,1,0,6.2995,1.4572e-16,2.498e-16,1,-5.0384

> view matrix models
> #8.4,1,1.7347e-18,0,-7.8661,7.6328e-17,1,0,5.3159,1.4572e-16,2.498e-16,1,-5.2355

> select add #7

386 atoms, 394 bonds, 46 residues, 2 models selected  

> show #7 models

> select subtract #7

193 atoms, 197 bonds, 23 residues, 1 model selected  

> select subtract #8.4

Nothing selected  

> select add #5

3391 atoms, 3470 bonds, 447 residues, 1 model selected  

> select subtract #5

Nothing selected  

> show #5 models

> show #6 models

> select add #7

193 atoms, 197 bonds, 23 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select add #8.4

193 atoms, 197 bonds, 23 residues, 1 model selected  

> view matrix models
> #8.4,1,6.0715e-18,0,-11.052,7.7195e-17,1,0,2.0733,1.4572e-16,2.498e-16,1,-6.68

> view matrix models
> #8.4,1,4.3368e-18,0,-11.239,7.546e-17,1,0,2.7163,1.4572e-16,2.498e-16,1,-6.6873

> view matrix models
> #8.4,1,6.0715e-18,0,-10.801,7.7195e-17,1,0,0.9052,1.4572e-16,2.498e-16,1,-7.4373

> ui mousemode right "rotate selected models"

> view matrix models
> #8.4,0.99817,-0.056637,0.021072,-6.0756,0.054174,0.99318,0.10327,-21.081,-0.026777,-0.10194,0.99443,10.806

> view matrix models
> #8.4,0.92843,-0.29761,-0.22235,70.387,0.32655,0.93916,0.10649,-56.573,0.17713,-0.17148,0.96913,-8.068

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,2.1026,0,1,0,0.41904,0,0,1,0.80236

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #8.4,0.92843,-0.29761,-0.22235,70.482,0.32655,0.93916,0.10649,-56.332,0.17713,-0.17148,0.96913,-7.8697

> select subtract #8.4

Nothing selected  

> select add #8.4

193 atoms, 197 bonds, 23 residues, 1 model selected  

> select subtract #8.4

Nothing selected  

> select add #4

758 atoms, 772 bonds, 88 residues, 1 model selected  

> view matrix models
> #4,0.99118,0.0574,-0.11949,3.7942,-0.0019908,0.90773,0.41954,-47.003,0.13254,-0.4156,0.89984,42.863

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.99548,0.060697,-0.073059,-3.9802,-0.052773,0.99298,0.1059,-6.7047,0.078974,-0.10156,0.99169,-7.468

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.99548,0.060697,-0.073059,-7.506,-0.052773,0.99298,0.1059,-5.476,0.078974,-0.10156,0.99169,-7.3279

> view matrix models
> #4,0.99548,0.060697,-0.073059,-6.6574,-0.052773,0.99298,0.1059,-2.7904,0.078974,-0.10156,0.99169,-3.517

> hide #8.4 models

> show #8.4 models

> select subtract #4

Nothing selected  

> save /Users/haotiandu/Desktop/EBV_TRACeR_fitting.cxs

> show #2,4-7#8.1-2,4 surfaces

> show #!2,4-7#!8.1-2,4 surfaces

> hide #!2,4-7#!8.1-2,4 surfaces

> show #!2,4-7#!8.1-2,4 atoms

> hide #!2,4-7#!8.1-2,4 atoms

> show #!2,4-7#!8.1-2,4 cartoons

> hide #!2,4-7#!8.1-2,4 cartoons

[Repeated 1 time(s)]

> show #!2,4-7#!8.1-2,4 cartoons

> ui mousemode right "map eraser"

> volume erase #1 center 115.87,134.77,170.79 radius 30.875

Opened EBV_TRACeR_complex.mrc copy as #12, grid size 450,450,450, pixel 0.684,
shown at step 1, values float32  

> hide #11 models

> hide #!12 models

> show #!12 models

> volume #!12 style mesh

> select add #4

758 atoms, 772 bonds, 88 residues, 1 model selected  

> select subtract #4

2 models selected  

> select add #8.2

758 atoms, 772 bonds, 88 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #8.2,0.9461,-0.31791,-0.061824,51.605,0.29761,0.92871,-0.22119,-5.1717,0.12773,0.19086,0.97327,-50.688

> select add #8

7484 atoms, 7670 bonds, 940 residues, 7 models selected  

> select subtract #8

6 models selected  

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!8.1 models

> hide #!8.2 models

> show #!8.2 models

> hide #!8.4 models

> show #!8.4 models

> show #!7 models

> show #!4 models

> color #4 #dd00ecff

> color #7 #dd00ecff

> color #8.2 #dd00ecff

> color #8.4 #dd00ecff

> show #!8.1 models

> show #!5 models

> show #!6 models

> save /Users/haotiandu/Desktop/EBV_TRACeR_fitting.cxs

> volume #!12 style mesh

> volume #!12 style surface

[Repeated 1 time(s)]

> transparency #2.1-3#4.1-2#5.1-3#6.1-3#7.1#12.1#8.1.1-3#8.2.1-2#8.4.1 0

> transparency #2.1-3#4.1-2#5.1-3#6.1-3#7.1#12.1#8.1.1-3#8.2.1-2#8.4.1 50

> transparency #2.1-3#4.1-2#5.1-3#6.1-3#7.1#12.1#8.1.1-3#8.2.1-2#8.4.1 0

> transparency #2.1-3#4.1-2#5.1-3#6.1-3#7.1#12.1#8.1.1-3#8.2.1-2#8.4.1 50

> ui tool show "Selection Inspector"

> save "/Users/haotiandu/Desktop/EBV .jpg" width 792 height 637 supersample 3

> set bgColor white

> color #8.1 #0800ecff

> color #8.1 #0011ecff

> color #8.1 #2f61ecff

> color #8.1 #144becff

> color #8.1 #0d49ecff

> color #7 #1842ecff

> color #7 #dd00ecff

> color #2 #1842ecff

> save "/Users/haotiandu/Desktop/EBV .jpg" width 792 height 637 supersample 3

> save /Users/haotiandu/Desktop/EBV_TRACeR_fitting.cxs

——— End of log from Fri Dec 22 17:41:50 2023 ———

opened ChimeraX session  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "VolumeImage" 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  

> open /Users/haotiandu/Desktop/EBV_TRACeR_complex.mrc

Opened EBV_TRACeR_complex.mrc as #1, grid size 450,450,450, pixel 0.684, shown
at level 0.0158, step 2, values float32  

> open /Users/haotiandu/Desktop/EBV_TRACeR_complex.mrc

Opened EBV_TRACeR_complex.mrc as #2, grid size 450,450,450, pixel 0.684, shown
at level 0.0158, step 2, values float32  




OpenGL version: 4.1 INTEL-14.7.18
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 i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1323)
      Kernel Version: Darwin 19.6.0
      Time since boot: 25 days 11:16

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: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2415:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: CFV9N93Q1WAL
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Automatically Adjust Brightness: No


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-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-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]

I think this has been reported once before, but looking at the code I really can't see how it can happen, so would need a reproducible case.