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Opened 14 months ago
Closed 14 months ago
#15829 closed defect (limitation)
color radial: ArrayMemoryError
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:\\\e1004\\\e1004-painting\\\split\\\1-DNA.mrc
Opened 1-DNA.mrc as #1, grid size 512,512,512, pixel 2.2, shown at level 4.73,
step 2, values float32
> open D:\\\e1004\\\e1004-painting\\\split\\\2-capsid.mrc
Opened 2-capsid.mrc as #2, grid size 800,800,800, pixel 1.1, shown at step 1,
values float32
> open D:\\\e1004\\\e1004-painting\\\split\\\adaptor-resample.mrc
Opened adaptor-resample.mrc as #3, grid size 720,720,720, pixel 1.1, shown at
step 1, values float32
> open D:\\\e1004\\\e1004-painting\\\split\\\core-resample.mrc
Opened core-resample.mrc as #4, grid size 720,720,720, pixel 1.1, shown at
step 1, values float32
> open D:\\\e1004\\\e1004-painting\\\split\\\nozzle-resample.mrc
Opened nozzle-resample.mrc as #5, grid size 720,720,720, pixel 1.1, shown at
step 1, values float32
> open D:\\\e1004\\\e1004-painting\\\split\\\portal-resample.mrc
Opened portal-resample.mrc as #6, grid size 720,720,720, pixel 1.1, shown at
step 1, values float32
> open D:\\\e1004\\\e1004-painting\\\split\\\symmismatch_ort-6.mrc
Opened symmismatch_ort-6.mrc as #7, grid size 512,512,512, pixel 2.2, shown at
level 6.61, step 2, values float32
> volume #1 step 1
> lighting simple
[Repeated 2 time(s)]
> volume #1 level 5.145
> select add #1
2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> select add #1
2 models selected
> select subtract #1
Nothing selected
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> select #1
2 models selected
Drag select of 1 1-DNA.mrc
> select clear
> ui mousemode right translate
[Repeated 1 time(s)]
> ui tool show "Fit in Map"
> ui mousemode right "move markers"
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view #1 clip false
> volume #4 level 0.0001,0 level 9.001e-05,0.8 level 0,1
> ui tool show "Volume Viewer"
> ui mousemode right "move planes"
> volume #7 region 0,0,0,511,511,511
> ui mousemode right "move planes"
> select #1
2 models selected
> select add #4
4 models selected
> select subtract #4
2 models selected
> select clear
> select add #5
2 models selected
> select subtract #5
Nothing selected
> select add #6
2 models selected
> select subtract #6
Nothing selected
> select add #1
2 models selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-8.0029,0,1,0,-2.4233,0,0,1,-2.1102
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> select clear
> select subtract #1
Nothing selected
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-562.03,0,1,0,-484.58,0,0,1,-605.71
> view matrix models #1,1,0,0,-570.29,0,1,0,-416.65,0,0,1,-652.4
> view matrix models #1,1,0,0,-353.31,0,1,0,-459.23,0,0,1,-679.01
> view matrix models #1,1,0,0,-365.15,0,1,0,-601.71,0,0,1,-547.58
> view matrix models #1,1,0,0,-366.71,0,1,0,-595.5,0,0,1,-570.2
> view matrix models #1,1,0,0,-416.94,0,1,0,-585.64,0,0,1,-564.04
> view matrix models #1,1,0,0,-525.42,0,1,0,-564.35,0,0,1,-550.73
> view matrix models #1,1,0,0,-527.99,0,1,0,-572.4,0,0,1,-558.78
> ui tool show "Fit in Map"
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.7242, correlation about mean = 0.0838, overlap = 2.143e+07
steps = 120, shift = 15.3, angle = 3.75 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.99942452 -0.03218073 -0.01072559 -511.10914604
0.03153000 0.99792513 -0.05613638 -548.19493782
0.01250985 0.05576589 0.99836550 -586.65819047
Axis 0.85521157 -0.17757650 0.48690837
Axis point 0.00000000 4710.07774815 -11917.86223585
Rotation angle (degrees) 3.75118326
Shift along axis -625.40869727
> ui mousemode right clip
> select add #1
3 models selected
> select add #7
6 models selected
> select clear
> ui mousemode right "clip rotate"
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99942,-0.032181,-0.010726,-537.31,0.03153,0.99793,-0.056136,-531.94,0.01251,0.055766,0.99837,-585.54
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.7225, correlation about mean = 0.09318, overlap = 2.14e+07
steps = 132, shift = 12.4, angle = 3.84 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.99852271 -0.02704277 0.04712847 -565.39713549
0.02814793 0.99934037 -0.02294608 -539.35586843
-0.04647685 0.02423875 0.99862525 -535.83490424
Axis 0.39829594 0.79013982 0.46587490
Axis point -2624.87681695 0.00000000 4300.10163779
Rotation angle (degrees) 3.39581091
Shift along axis -900.99395853
> select subtract #1
Nothing selected
> select add #1
2 models selected
> view matrix models
> #1,0.99852,-0.027043,0.047128,-569.79,0.028148,0.99934,-0.022946,-563.45,-0.046477,0.024239,0.99863,-541.42
> view matrix models
> #1,0.99852,-0.027043,0.047128,-587.29,0.028148,0.99934,-0.022946,-557.39,-0.046477,0.024239,0.99863,-553.76
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.9492, correlation about mean = 0.5316, overlap = 3.681e+07
steps = 112, shift = 16.3, angle = 3.39 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.99999998 0.00005743 0.00018712 -563.35207183
-0.00005743 1.00000000 -0.00001883 -563.14742170
-0.00018712 0.00001882 0.99999998 -563.10656225
Axis 0.09575831 0.95159641 -0.29205242
Axis point -3673564.36008043 0.00000000 2792635.04800143
Rotation angle (degrees) 0.01126635
Shift along axis -425.37807404
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.9492, correlation about mean = 0.5317, overlap = 3.68e+07
steps = 36, shift = 0.0089, angle = 0.000998 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.99999998 0.00005876 0.00020406 -563.36719616
-0.00005876 1.00000000 -0.00001500 -563.14147451
-0.00020406 0.00001499 0.99999998 -563.09346618
Axis 0.07042835 0.95856303 -0.27603761
Axis point -3333325.40551828 0.00000000 2614068.44015316
Rotation angle (degrees) 0.01219722
Shift along axis -424.04864663
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.9493, correlation about mean = 0.5317, overlap = 3.679e+07
steps = 28, shift = 0.0255, angle = 0.00162 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.99999997 0.00005843 0.00022376 -563.38132423
-0.00005843 1.00000000 0.00000529 -563.15553394
-0.00022376 -0.00000530 0.99999997 -563.04574764
Axis -0.02288627 0.96730072 -0.25259756
Axis point -2956453.58935019 0.00000000 2557319.31902114
Rotation angle (degrees) 0.01325374
Shift along axis -389.62308052
> select subtract #1
Nothing selected
> ui mousemode right clip
> volume #7 level 3
> ui mousemode right "clip rotate"
[Repeated 1 time(s)]
> select add #2
2 models selected
> volume #2 level 0.0003141,0 level 0.804,0.8 level 3.836,1
> volume #2 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #2 step 1
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,22.108,0,1,0,32.28,0,0,1,-213.55
> ui mousemode right "rotate selected models"
> select add #2
3 models selected
> select subtract #2
Nothing selected
> select add #2
3 models selected
> view matrix models
> #2,0.99999,0.00074153,-0.0049463,23.964,-0.0007919,0.99995,-0.010189,37.134,0.0049384,0.010193,0.99994,-220.18
> view matrix models
> #2,0.99982,0.0025391,-0.018746,29.318,-0.0032597,0.99925,-0.03851,50.987,0.018634,0.038565,0.99908,-238.31
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99982,0.0025391,-0.018746,2.6708,-0.0032597,0.99925,-0.03851,-15.756,0.018634,0.038565,0.99908,-162.25
> view matrix models
> #2,0.99982,0.0025391,-0.018746,-3.2959,-0.0032597,0.99925,-0.03851,-7.498,0.018634,0.038565,0.99908,-294.79
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.93541,-0.079752,-0.34446,204.57,-0.18037,0.73031,-0.65888,461.73,0.30411,0.67845,0.66875,-556.61
> view matrix models
> #2,0.99823,-0.012677,0.058153,-29.735,0.0055378,0.9926,0.12132,-78.766,-0.059261,-0.12078,0.99091,-186.81
> view matrix models
> #2,0.78398,-0.409,-0.46701,469.99,-0.33762,0.3504,-0.87363,792.57,0.52096,0.84258,0.13662,-490.1
> view matrix models
> #2,0.80845,-0.37554,-0.45319,438.42,-0.28613,0.4221,-0.86021,732.46,0.51433,0.82511,0.2338,-522.25
> view matrix models
> #2,0.92194,0.063583,-0.38207,163.98,-0.38637,0.22018,-0.89567,881.02,0.027177,0.97338,0.22756,-370.41
> ui tool show "Show Volume Menu"
> volume sel showOutlineBox true
> close #2
> open D:/e1004/e1004-painting/split/2-capsid.mrc
Opened 2-capsid.mrc as #2, grid size 800,800,800, pixel 1.1, shown at step 1,
values float32
> volume #2 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #2 step 1
> ui mousemode right "map eraser"
> select add #8
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,391.67,0,1,0,478.84,0,0,1,405.09
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,391.09,0,1,0,478.81,0,0,1,405.59
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,330.1,0,1,0,593.92,0,0,1,665.94
> view matrix models #8,1,0,0,307.18,0,1,0,594.13,0,0,1,681.31
> view matrix models #8,1,0,0,240.03,0,1,0,459.84,0,0,1,583.02
> view matrix models #8,1,0,0,234.15,0,1,0,447.68,0,0,1,574.41
> view matrix models #8,1,0,0,201.67,0,1,0,447.98,0,0,1,596.2
> view matrix models #8,1,0,0,196.86,0,1,0,440.02,0,0,1,589.12
Can only have one displayed volume when erasing
[Repeated 6 time(s)]Drag select of 2 2-capsid.mrc
> select clear
> select subtract #8
Nothing selected
> select add #8
1 model selected
Drag select of eraser sphere, 6 of 1000 triangles, 2 2-capsid.mrc
> select subtract #8
2 models selected
> select add #8
3 models selected
> select subtract #8
2 models selected
> view matrix models #2,1,0,0,-1.3084,0,1,0,0.085124,0,0,1,0.79566
> view matrix models #2,1,0,0,-3.9251,0,1,0,0.25537,0,0,1,2.387
> select add #8
3 models selected
> view matrix models
> #2,1,0,0,-30.746,0,1,0,2.0004,0,0,1,18.698,#8,1,0,0,170.03,0,1,0,441.77,0,0,1,605.43
> select clear
> select subtract #8
Nothing selected
> select add #8
1 model selected
> view matrix models #8,1,0,0,148.45,0,1,0,443.17,0,0,1,618.56
Can only have one displayed volume when erasing
[Repeated 3 time(s)]
> select clear
Can only have one displayed volume when erasing
[Repeated 8 time(s)]
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
[Repeated 15 time(s)]
> ui mousemode right "map eraser"
> ui mousemode right "play map series"
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
[Repeated 3 time(s)]
> select add #8
1 model selected
Can only have one displayed volume when erasing
[Repeated 2 time(s)]
> help help:user
> select clear
Can only have one displayed volume when erasing
[Repeated 6 time(s)]
> ui mousemode right "map eraser"
[Repeated 1 time(s)]
> ui mousemode right select
[Repeated 1 time(s)]
> select add #8
1 model selected
> select #8
1 model selected
> select clear
> select #8
1 model selected
Drag select of eraser sphere, 5 of 1000 triangles, 2 2-capsid.mrc
> select clear
> select subtract #8
Nothing selected
> select add #8
1 model selected
Drag select of eraser sphere, 6 of 1000 triangles
> select subtract #8
Nothing selected
> select add #8
1 model selected
Drag select of eraser sphere, 7 of 1000 triangles
> select subtract #8
Nothing selected
> select add #8
1 model selected
> select #8
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,405.91,0,1,0,440.66,0,0,1,455.53
> view matrix models
> #8,-0.82039,-0.5175,-0.2432,406.42,0.094486,0.29679,-0.95026,440.67,0.56394,-0.80256,-0.19459,455.42
> view matrix models
> #8,0.21274,0.32161,0.92266,406.1,-0.6052,0.78472,-0.13398,440.84,-0.76712,-0.52989,0.36158,455.76
> view matrix models
> #8,-0.76386,-0.47353,-0.4385,406.4,0.21982,0.44793,-0.86663,440.63,0.60679,-0.75837,-0.23807,455.4
> view matrix models
> #8,0.3252,0.2681,0.90685,406.07,-0.53258,0.84434,-0.058633,440.81,-0.78141,-0.4639,0.41736,455.76
> view matrix models
> #8,-0.9502,-0.26232,-0.16827,406.44,0.067931,0.3526,-0.9333,440.68,0.30416,-0.89825,-0.31722,455.49
> view matrix models
> #8,0.64668,-0.48636,-0.58759,406.03,0.62208,0.78207,0.037305,440.51,0.44139,-0.38965,0.8083,455.43
> view matrix models
> #8,0.64668,-0.48636,-0.58759,119.73,0.62208,0.78207,0.037305,471.53,0.44139,-0.38965,0.8083,485.96
> view matrix models
> #8,0.64668,-0.48636,-0.58759,218.85,0.62208,0.78207,0.037305,462.8,0.44139,-0.38965,0.8083,318.26
> view matrix models
> #8,0.64668,-0.48636,-0.58759,207.21,0.62208,0.78207,0.037305,445.97,0.44139,-0.38965,0.8083,338.83
> view matrix models
> #8,0.64668,-0.48636,-0.58759,196.25,0.62208,0.78207,0.037305,445.66,0.44139,-0.38965,0.8083,332.37
> view matrix models
> #8,0.64668,-0.48636,-0.58759,199.74,0.62208,0.78207,0.037305,450.97,0.44139,-0.38965,0.8083,326.2
> view matrix models
> #8,0.64668,-0.48636,-0.58759,197.95,0.62208,0.78207,0.037305,444.15,0.44139,-0.38965,0.8083,329.57
> view matrix models
> #8,0.64668,-0.48636,-0.58759,169.46,0.62208,0.78207,0.037305,443.32,0.44139,-0.38965,0.8083,312.78
> view matrix models
> #8,0.64668,-0.48636,-0.58759,171.24,0.62208,0.78207,0.037305,446.48,0.44139,-0.38965,0.8083,311.68
Can only have one displayed volume when erasing
[Repeated 14 time(s)]
> select clear
Can only have one displayed volume when erasing
[Repeated 4 time(s)]
> select #2
3 models selected
Can only have one displayed volume when erasing
[Repeated 5 time(s)]
> select clear
> select add #2
3 models selected
> view matrix models #2,1,0,0,-310.67,0,1,0,-540.68,0,0,1,-432.77
> view matrix models #2,1,0,0,-296.4,0,1,0,-523.03,0,0,1,-446.36
> view matrix models #2,1,0,0,-494.27,0,1,0,-390.89,0,0,1,-482.51
> view matrix models #2,1,0,0,-492.36,0,1,0,-388.82,0,0,1,-485.46
Drag select of 1 1-DNA.mrc , 7 symmismatch_ort-6.mrc , 2 2-capsid.mrc
> view matrix models
> #1,1,5.8431e-05,0.00022376,-589.35,-5.8432e-05,1,5.2875e-06,-595.04,-0.00022376,-5.3006e-06,1,-537.43,#7,1,0,0,-25.97,0,1,0,-31.882,0,0,1,25.613,#2,1,0,0,-518.33,0,1,0,-420.7,0,0,1,-459.85
> select subtract #2
4 models selected
> select add #2
7 models selected
> select add #7
7 models selected
> select subtract #7
5 models selected
> view matrix models
> #1,0.64914,-0.55132,-0.52408,215.99,0.55723,0.81365,-0.16574,-704.91,0.5178,-0.18445,0.83538,-621.94,#2,0.64899,-0.55136,-0.52423,125.29,0.55724,0.81362,-0.16587,-536.36,0.51797,-0.18447,0.83527,-552.51
> view matrix models
> #1,0.98702,0.14925,-0.059372,-635.69,-0.14411,0.98606,0.083141,-554.16,0.070954,-0.073505,0.99477,-529.74,#2,0.98701,0.14919,-0.059594,-544.2,-0.14403,0.98607,0.083168,-386.03,0.071172,-0.073504,0.99475,-460.32
> select subtract #2
2 models selected
> select add #1
2 models selected
> select subtract #1
Nothing selected
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.8567, correlation about mean = 0.1614, overlap = 2.655e+07
steps = 204, shift = 4.92, angle = 8.57 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.99932569 0.00245242 -0.03663532 -543.63853477
0.00077754 0.99612974 0.08789160 -610.78633398
0.03670908 -0.08786082 0.99545614 -531.81402356
Axis -0.92282815 -0.38511151 -0.00879435
Axis point 0.00000000 -6156.01564672 3428.87027586
Rotation angle (degrees) 5.46426409
Shift along axis 741.58274475
> volume #7 level 5.081
> ui mousemode right select
[Repeated 1 time(s)]
> select add #2
3 models selected
> select #2
3 models selected
Drag select of 2 2-capsid.mrc
> select #2
3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98701,0.14919,-0.059594,-521.17,-0.14403,0.98607,0.083168,-502.65,0.071172,-0.073504,0.99475,-449.02
> view matrix models
> #2,0.98701,0.14919,-0.059594,-444.04,-0.14403,0.98607,0.083168,-1027.3,0.071172,-0.073504,0.99475,-253.56
> view matrix models
> #2,0.98701,0.14919,-0.059594,-458.52,-0.14403,0.98607,0.083168,-976.69,0.071172,-0.073504,0.99475,-234.05
> view matrix models
> #2,0.98701,0.14919,-0.059594,-483.48,-0.14403,0.98607,0.083168,-889.31,0.071172,-0.073504,0.99475,-200.46
> view matrix models
> #2,0.98701,0.14919,-0.059594,-449.29,-0.14403,0.98607,0.083168,-976.66,0.071172,-0.073504,0.99475,-284.47
> view matrix models
> #2,0.98701,0.14919,-0.059594,-522.74,-0.14403,0.98607,0.083168,-524.41,0.071172,-0.073504,0.99475,-414.89
> view matrix models
> #2,0.98701,0.14919,-0.059594,-531.4,-0.14403,0.98607,0.083168,-483.04,0.071172,-0.073504,0.99475,-416.22
> view matrix models
> #2,0.98701,0.14919,-0.059594,-531.89,-0.14403,0.98607,0.083168,-465.89,0.071172,-0.073504,0.99475,-433.68
> view matrix models
> #2,0.98701,0.14919,-0.059594,-488.75,-0.14403,0.98607,0.083168,-456.61,0.071172,-0.073504,0.99475,-425.77
> view matrix models
> #2,0.98701,0.14919,-0.059594,-488.54,-0.14403,0.98607,0.083168,-471.28,0.071172,-0.073504,0.99475,-409.73
> view matrix models
> #2,0.98701,0.14919,-0.059594,-476.68,-0.14403,0.98607,0.083168,-504.52,0.071172,-0.073504,0.99475,-435.37
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.65171,-0.74546,-0.13988,99.821,0.7399,0.66541,-0.098867,-672.26,0.16678,-0.039065,0.98522,-488.4
> view matrix models
> #2,-0.65316,-0.55743,-0.51251,755.18,0.73001,-0.64336,-0.2306,-34.087,-0.20118,-0.52475,0.82714,-43.24
> view matrix models
> #2,-0.677,-0.44201,-0.58847,748.32,0.67874,-0.68413,-0.26699,22.421,-0.28457,-0.58017,0.76317,45.983
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.677,-0.44201,-0.58847,729.06,0.67874,-0.68413,-0.26699,91.991,-0.28457,-0.58017,0.76317,69.349
> view matrix models
> #2,-0.677,-0.44201,-0.58847,733.28,0.67874,-0.68413,-0.26699,79.25,-0.28457,-0.58017,0.76317,61.326
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.064719,-0.72216,-0.68869,631.23,0.99325,-0.11319,0.02535,-438.98,-0.09626,-0.68241,0.72461,40.418
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.064719,-0.72216,-0.68869,628.16,0.99325,-0.11319,0.02535,-418.53,-0.09626,-0.68241,0.72461,59.644
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.028707,-0.71837,-0.69507,613.46,0.99528,-0.084996,0.046739,-441.24,-0.092654,-0.69045,0.71742,64.763
> view matrix models
> #2,0.057052,0.95496,-0.2912,-338.24,-0.49663,-0.22588,-0.83806,666.5,-0.86609,0.19243,0.46137,129.26
> view matrix models
> #2,0.085282,0.96236,-0.25806,-368.5,-0.49823,-0.18311,-0.84749,652.53,-0.86284,0.20085,0.46386,123.03
> fitmap #2 inMap #7
Fit map 2-capsid.mrc in map symmismatch_ort-6.mrc using 5101298 points
correlation = 0.8541, correlation about mean = 0.1846, overlap = 5.04e+07
steps = 220, shift = 16.3, angle = 14.3 degrees
Position of 2-capsid.mrc (#2) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
-0.16240021 0.95107588 -0.26283236 -231.36711930
-0.49997311 -0.30895741 -0.80905637 711.93533332
-0.85067800 0.00001819 0.52568711 142.98182433
Axis 0.45910105 0.33356697 -0.82338284
Axis point 181.18428453 471.24178270 0.00000000
Rotation angle (degrees) 118.21849669
Shift along axis 13.52844210
> view matrix models
> #2,-0.30758,0.87251,-0.37964,-107.49,-0.43227,-0.48356,-0.76113,706,-0.84767,-0.070002,0.52589,197.99
> ui mousemode right "translate selected models"
> select clear
> select subtract #2
Nothing selected
> select add #2
3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.30758,0.87251,-0.37964,-107.07,-0.43227,-0.48356,-0.76113,702.1,-0.84767,-0.070002,0.52589,193.93
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.16212,0.94831,-0.27281,-251.44,-0.47334,-0.31732,-0.82174,673.7,-0.86583,-0.0040896,0.50032,184.17
> fitmap #2 inMap #7
Fit map 2-capsid.mrc in map symmismatch_ort-6.mrc using 5101298 points
correlation = 0.8541, correlation about mean = 0.1846, overlap = 5.04e+07
steps = 80, shift = 5.63, angle = 1.79 degrees
Position of 2-capsid.mrc (#2) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
-0.16243866 0.95106883 -0.26283412 -231.35439173
-0.50000330 -0.30897912 -0.80902943 711.91973020
-0.85065292 0.00000028 0.52572770 142.95799009
Axis 0.45907833 0.33355372 -0.82340088
Axis point 181.16505013 471.22190977 0.00000000
Rotation angle (degrees) 118.21913295
Shift along axis 13.54195558
> fitmap #2 inMap #7
Fit map 2-capsid.mrc in map symmismatch_ort-6.mrc using 5101298 points
correlation = 0.8541, correlation about mean = 0.1846, overlap = 5.04e+07
steps = 24, shift = 0.0241, angle = 0.00361 degrees
Position of 2-capsid.mrc (#2) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
-0.16240094 0.95107570 -0.26283256 -231.38675965
-0.49996441 -0.30895796 -0.80906153 711.88778188
-0.85068297 0.00001457 0.52567907 142.99328222
Axis 0.45910323 0.33357062 -0.82338014
Axis point 181.16383912 471.22234130 0.00000000
Rotation angle (degrees) 118.21880030
Shift along axis 13.49661341
> fitmap #2 inMap #7
Fit map 2-capsid.mrc in map symmismatch_ort-6.mrc using 5101298 points
correlation = 0.8541, correlation about mean = 0.1846, overlap = 5.04e+07
steps = 24, shift = 0.00509, angle = 0.000944 degrees
Position of 2-capsid.mrc (#2) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
-0.16240601 0.95107098 -0.26284650 -231.37745603
-0.49995731 -0.30897248 -0.80906038 711.88850618
-0.85068618 0.00001576 0.52567388 142.99192578
Axis 0.45910671 0.33356705 -0.82337965
Axis point 181.16448750 471.21784008 0.00000000
Rotation angle (degrees) 118.21960603
Shift along axis 13.49896670
> select subtract #2
Nothing selected
> fitmap #2 inMap #7
Fit map 2-capsid.mrc in map symmismatch_ort-6.mrc using 5101298 points
correlation = 0.8541, correlation about mean = 0.1846, overlap = 5.04e+07
steps = 24, shift = 0.012, angle = 0.000995 degrees
Position of 2-capsid.mrc (#2) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
-0.16241425 0.95106563 -0.26286078 -231.37059485
-0.49995358 -0.30898896 -0.80905639 711.89549949
-0.85068680 0.00001590 0.52567287 143.00282729
Axis 0.45910813 0.33356191 -0.82338094
Axis point 181.16985110 471.21772383 0.00000000
Rotation angle (degrees) 118.22044232
Shift along axis 13.49130252
> hide #!2 models
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99933,0.0024524,-0.036635,-558.24,0.00077754,0.99613,0.087892,-670.5,0.036709,-0.087861,0.99546,-509.33
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.6842, correlation about mean = 0.07801, overlap = 1.943e+07
steps = 104, shift = 18.9, angle = 1.6 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.99963992 0.01531225 -0.02203545 -551.16198627
-0.01284267 0.99405167 0.10814962 -639.27043186
0.02356039 -0.10782768 0.99389039 -496.86327874
Axis -0.97057055 -0.20490109 -0.12652412
Axis point 0.00000000 -3997.00621847 4310.36412023
Rotation angle (degrees) 6.38813074
Shift along axis 728.79398810
> view matrix models
> #1,0.99964,0.015312,-0.022035,-577.58,-0.012843,0.99405,0.10815,-680.04,0.02356,-0.10783,0.99389,-470.86
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.6842, correlation about mean = 0.07784, overlap = 1.943e+07
steps = 60, shift = 8.88, angle = 0.0253 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.99964330 0.01558096 -0.02169108 -551.50553982
-0.01314528 0.99403963 0.10822392 -639.16063721
0.02324803 -0.10790018 0.99388987 -496.62387112
Axis -0.97087276 -0.20187551 -0.12904402
Axis point 0.00000000 -3976.37613106 4327.89518798
Rotation angle (degrees) 6.39049233
Shift along axis 728.55892398
> view matrix models
> #1,0.99964,0.015581,-0.021691,-577.91,-0.013145,0.99404,0.10822,-681.03,0.023248,-0.1079,0.99389,-472.44
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.6842, correlation about mean = 0.07751, overlap = 1.944e+07
steps = 200, shift = 10.2, angle = 0.768 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.99967750 0.00274674 -0.02524579 -542.11844335
-0.00004651 0.99432966 0.10634157 -645.54768239
0.02539473 -0.10630610 0.99400912 -499.00581913
Axis -0.97271636 -0.23164547 -0.01277719
Axis point 0.00000000 -4855.56544322 4323.28721074
Rotation angle (degrees) 6.27531703
Shift along axis 683.24156938
> ui mousemode right clip
[Repeated 1 time(s)]
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99968,0.0027467,-0.025246,-561.71,-4.6506e-05,0.99433,0.10634,-670.7,0.025395,-0.10631,0.99401,-476.6
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99857,0.050895,0.016544,-612.39,-0.051922,0.99626,0.069107,-622.45,-0.012965,-0.069867,0.99747,-478.56
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.7314, correlation about mean = 0.104, overlap = 2.184e+07
steps = 88, shift = 9.11, angle = 3.32 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.99788885 0.03728857 0.05317334 -604.51089786
-0.03875520 0.99888867 0.02682280 -582.29636935
-0.05211406 -0.02882691 0.99822499 -502.77785529
Axis -0.39384783 0.74514700 -0.53818198
Axis point -9231.31272092 0.00000000 10448.32397907
Rotation angle (degrees) 4.05124999
Shift along axis 74.77489259
> view matrix models
> #1,0.98512,0.16619,-0.043746,-645.47,-0.15827,0.97657,0.14585,-600.37,0.066959,-0.13675,0.98834,-474.6
> view matrix models
> #1,0.98081,-0.10205,0.16613,-601.64,0.099996,0.99477,0.020705,-685.49,-0.16737,-0.0036953,0.98589,-421.04
> view matrix models
> #1,0.99768,-0.034873,0.058411,-590.95,0.029188,0.995,0.095489,-687.55,-0.061449,-0.093563,0.99372,-431.54
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99768,-0.034873,0.058411,-585.66,0.029188,0.995,0.095489,-681.07,-0.061449,-0.093563,0.99372,-430.62
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.76921,0.6367,-0.054197,-790.26,-0.6322,0.77062,0.08049,-173.71,0.093013,-0.02765,0.99528,-555.96
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.76921,0.6367,-0.054197,-779.67,-0.6322,0.77062,0.08049,-162.81,0.093013,-0.02765,0.99528,-562.41
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.72837,0.68241,-0.061637,-779.67,-0.67772,0.73075,0.081806,-114.87,0.10087,-0.017812,0.99474,-572.24
> fitmap #1 inMap #7
Fit map 1-DNA.mrc in map symmismatch_ort-6.mrc using 1058275 points
correlation = 0.7018, correlation about mean = 0.1151, overlap = 1.99e+07
steps = 196, shift = 12.8, angle = 5.97 degrees
Position of 1-DNA.mrc (#1) relative to symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.71831823 0.69571468 -0.00003890 -796.31726472
-0.69571467 0.71831823 0.00016308 -12.77716493
0.00014139 -0.00009008 0.99999999 -563.05951661
Axis -0.00018194 -0.00012957 -0.99999998
Axis point -413.79619820 976.91764327 0.00000000
Rotation angle (degrees) 44.08419644
Shift along axis 563.20604123
> ui mousemode right "translate selected models"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> select clear
> volume #3 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #3 step 1
> volume #3 change image level 1.375e-05,0 level 0.08171,0.8 level 0.817,1
> volume #3 level 0.1408
> select add #3
3 models selected
> select add #4
5 models selected
> select add #5
7 models selected
> select add #6
9 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,1,0,0,-138.14,0,1,0,-274.09,0,0,1,147.25,#4,1,0,0,-138.14,0,1,0,-274.09,0,0,1,147.25,#5,1,0,0,-138.14,0,1,0,-274.09,0,0,1,147.25,#6,1,0,0,-138.14,0,1,0,-274.09,0,0,1,147.25
> volume #7 level 2
> view matrix models
> #3,1,0,0,-136.73,0,1,0,-271.43,0,0,1,134.2,#4,1,0,0,-136.73,0,1,0,-271.43,0,0,1,134.2,#5,1,0,0,-136.73,0,1,0,-271.43,0,0,1,134.2,#6,1,0,0,-136.73,0,1,0,-271.43,0,0,1,134.2
> view matrix models
> #3,1,0,0,-156.69,0,1,0,-261.44,0,0,1,134.07,#4,1,0,0,-156.69,0,1,0,-261.44,0,0,1,134.07,#5,1,0,0,-156.69,0,1,0,-261.44,0,0,1,134.07,#6,1,0,0,-156.69,0,1,0,-261.44,0,0,1,134.07
> volume #7 level 3
> volume #7 level 2.5
> volume #6 level 3.796e-05,0 level 0.07197,0.8 level 0.7193,1
> volume #6 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #6 step 1
> volume #6 level 0.1115
> volume #5 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #5 step 1
> volume #5 change image level 0.0001,0 level 9.001e-05,0.8 level 0,1
> volume #5 level 0.2383
> volume #4 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #4 step 1
> volume #4 level 0.07098
> volume #4 level 0.08787
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models
> #3,1,0,0,-157.9,0,1,0,-264.03,0,0,1,121.25,#4,1,0,0,-157.9,0,1,0,-264.03,0,0,1,121.25,#5,1,0,0,-157.9,0,1,0,-264.03,0,0,1,121.25,#6,1,0,0,-157.9,0,1,0,-264.03,0,0,1,121.25
> view matrix models
> #3,1,0,0,-210.42,0,1,0,-237.74,0,0,1,120.91,#4,1,0,0,-210.42,0,1,0,-237.74,0,0,1,120.91,#5,1,0,0,-210.42,0,1,0,-237.74,0,0,1,120.91,#6,1,0,0,-210.42,0,1,0,-237.74,0,0,1,120.91
> view matrix models
> #3,1,0,0,-210.86,0,1,0,-238.52,0,0,1,128,#4,1,0,0,-210.86,0,1,0,-238.52,0,0,1,128,#5,1,0,0,-210.86,0,1,0,-238.52,0,0,1,128,#6,1,0,0,-210.86,0,1,0,-238.52,0,0,1,128
> view matrix models
> #3,1,0,0,-220.31,0,1,0,-233.79,0,0,1,127.94,#4,1,0,0,-220.31,0,1,0,-233.79,0,0,1,127.94,#5,1,0,0,-220.31,0,1,0,-233.79,0,0,1,127.94,#6,1,0,0,-220.31,0,1,0,-233.79,0,0,1,127.94
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.98742,-0.1572,-0.017176,-183.78,0.15739,0.98748,0.010354,-264.13,0.015333,-0.012927,0.9998,127.57,#4,0.98742,-0.1572,-0.017176,-183.78,0.15739,0.98748,0.010354,-264.13,0.015333,-0.012927,0.9998,127.57,#5,0.98742,-0.1572,-0.017176,-183.78,0.15739,0.98748,0.010354,-264.13,0.015333,-0.012927,0.9998,127.57,#6,0.98742,-0.1572,-0.017176,-183.78,0.15739,0.98748,0.010354,-264.13,0.015333,-0.012927,0.9998,127.57
> fitmap #5 inMap #7
Fit map nozzle-resample.mrc in map symmismatch_ort-6.mrc using 157429 points
correlation = 0.886, correlation about mean = 0.1854, overlap = 2.341e+05
steps = 68, shift = 2.72, angle = 2.36 degrees
Position of nozzle-resample.mrc (#5) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.98125667 -0.19270467 0.00051641 -156.49905982
0.19270407 0.98125639 0.00101957 -233.17617246
-0.00070320 -0.00090095 0.99999935 104.06046591
Axis -0.00498298 0.00316441 0.99998258
Axis point 1122.38313051 -918.59493375 0.00000000
Rotation angle (degrees) 11.11084643
Shift along axis 104.10062084
> fitmap #3 inMap #7
Fit map adaptor-resample.mrc in map symmismatch_ort-6.mrc using 98827 points
correlation = 0.8348, correlation about mean = 0.1816, overlap = 1.545e+05
steps = 72, shift = 4.7, angle = 2.84 degrees
Position of adaptor-resample.mrc (#3) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.97942494 -0.20180492 -0.00124682 -155.05558596
0.20180191 0.97942390 -0.00219620 -234.49308100
0.00166437 0.00189940 0.99999681 103.09531904
Axis 0.01014672 -0.00721239 0.99992251
Axis point 1068.33101148 -882.45495289 0.00000000
Rotation angle (degrees) 11.64335257
Shift along axis 103.20528116
> select add #3
9 models selected
> select add #4
10 models selected
> select add #5
11 models selected
> select add #6
12 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98742,-0.1572,-0.017176,-185.01,0.15739,0.98748,0.010354,-264.58,0.015333,-0.012927,0.9998,127.66,#4,0.98742,-0.1572,-0.017176,-185.01,0.15739,0.98748,0.010354,-264.58,0.015333,-0.012927,0.9998,127.66,#5,0.98742,-0.1572,-0.017176,-185.01,0.15739,0.98748,0.010354,-264.58,0.015333,-0.012927,0.9998,127.66,#6,0.98742,-0.1572,-0.017176,-185.01,0.15739,0.98748,0.010354,-264.58,0.015333,-0.012927,0.9998,127.66
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.89621,-0.44209,0.036832,-118.32,0.44239,0.89682,0.00016205,-300.61,-0.033104,0.016149,0.99932,131.61,#4,0.89621,-0.44209,0.036832,-118.32,0.44239,0.89682,0.00016205,-300.61,-0.033104,0.016149,0.99932,131.61,#5,0.89621,-0.44209,0.036832,-118.32,0.44239,0.89682,0.00016205,-300.61,-0.033104,0.016149,0.99932,131.61,#6,0.89621,-0.44209,0.036832,-118.32,0.44239,0.89682,0.00016205,-300.61,-0.033104,0.016149,0.99932,131.61
> view matrix models
> #3,0.449,-0.89328,-0.021462,68.123,0.89353,0.44887,0.010733,-302.69,4.5648e-05,-0.023996,0.99971,133.22,#4,0.449,-0.89328,-0.021462,68.123,0.89353,0.44887,0.010733,-302.69,4.5648e-05,-0.023996,0.99971,133.22,#5,0.449,-0.89328,-0.021462,68.123,0.89353,0.44887,0.010733,-302.69,4.5648e-05,-0.023996,0.99971,133.22,#6,0.449,-0.89328,-0.021462,68.123,0.89353,0.44887,0.010733,-302.69,4.5648e-05,-0.023996,0.99971,133.22
> view matrix models
> #3,0.37888,-0.92484,-0.03356,90.245,0.92545,0.37862,0.013839,-295.6,-9.2013e-05,-0.036301,0.99934,135.84,#4,0.37888,-0.92484,-0.03356,90.245,0.92545,0.37862,0.013839,-295.6,-9.2013e-05,-0.036301,0.99934,135.84,#5,0.37888,-0.92484,-0.03356,90.245,0.92545,0.37862,0.013839,-295.6,-9.2013e-05,-0.036301,0.99934,135.84,#6,0.37888,-0.92484,-0.03356,90.245,0.92545,0.37862,0.013839,-295.6,-9.2013e-05,-0.036301,0.99934,135.84
> fitmap #5 inMap #7
Fit map nozzle-resample.mrc in map symmismatch_ort-6.mrc using 157429 points
correlation = 0.8857, correlation about mean = 0.1832, overlap = 2.342e+05
steps = 72, shift = 2.56, angle = 4.02 degrees
Position of nozzle-resample.mrc (#5) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.32264503 -0.94652003 0.00011092 123.32380557
0.94652003 0.32264504 0.00011795 -251.75610935
-0.00014743 0.00006694 0.99999999 103.78510816
Axis -0.00002695 0.00013648 0.99999999
Axis point 237.57225363 -39.71827762 0.00000000
Rotation angle (degrees) 71.17703931
Shift along axis 103.74742514
> fitmap #3 inMap #7
Fit map adaptor-resample.mrc in map symmismatch_ort-6.mrc using 98827 points
correlation = 0.8349, correlation about mean = 0.1801, overlap = 1.545e+05
steps = 76, shift = 2.33, angle = 4.44 degrees
Position of adaptor-resample.mrc (#3) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.31475499 -0.94917221 -0.00119189 124.50568597
0.94916820 0.31475714 -0.00276892 -250.73600642
0.00300334 -0.00025977 0.99999546 103.30258972
Axis 0.00132176 -0.00220994 0.99999668
Axis point 235.68026322 -39.11885366 0.00000000
Rotation angle (degrees) 71.65404883
Shift along axis 104.02092390
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.28252,-0.95913,-0.015797,112.84,0.95902,0.28203,0.027308,-285.72,-0.021736,-0.022865,0.9995,137.47,#4,0.28252,-0.95913,-0.015797,112.84,0.95902,0.28203,0.027308,-285.72,-0.021736,-0.022865,0.9995,137.47,#5,0.28252,-0.95913,-0.015797,112.84,0.95902,0.28203,0.027308,-285.72,-0.021736,-0.022865,0.9995,137.47,#6,0.28252,-0.95913,-0.015797,112.84,0.95902,0.28203,0.027308,-285.72,-0.021736,-0.022865,0.9995,137.47
> fitmap #5 inMap #7
Fit map nozzle-resample.mrc in map symmismatch_ort-6.mrc using 157429 points
correlation = 0.8857, correlation about mean = 0.1833, overlap = 2.342e+05
steps = 56, shift = 1.3, angle = 3.02 degrees
Position of nozzle-resample.mrc (#5) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.32278451 -0.94647248 -0.00000548 123.33085027
0.94647241 0.32278448 0.00039855 -251.87720568
-0.00037545 -0.00013383 0.99999992 103.88018122
Axis -0.00028124 0.00019545 0.99999994
Axis point 237.70527679 -39.74511109 0.00000000
Rotation angle (degrees) 71.16859938
Shift along axis 103.79626075
> fitmap #3 inMap #7
Fit map adaptor-resample.mrc in map symmismatch_ort-6.mrc using 98827 points
correlation = 0.8349, correlation about mean = 0.1801, overlap = 1.545e+05
steps = 68, shift = 2.82, angle = 2.71 degrees
Position of adaptor-resample.mrc (#3) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.31476171 -0.94916946 -0.00154825 124.58621234
0.94916665 0.31476472 -0.00241560 -250.81961680
0.00278015 -0.00070921 0.99999588 103.42770935
Axis 0.00089888 -0.00228010 0.99999700
Axis point 235.79638634 -39.07003468 0.00000000
Rotation angle (degrees) 71.65360427
Shift along axis 104.11128032
> view matrix models
> #3,0.26589,-0.9639,-0.013749,116.6,0.96371,0.26543,0.028482,-283.59,-0.023805,-0.020823,0.9995,137.59,#4,0.26589,-0.9639,-0.013749,116.6,0.96371,0.26543,0.028482,-283.59,-0.023805,-0.020823,0.9995,137.59,#5,0.26589,-0.9639,-0.013749,116.6,0.96371,0.26543,0.028482,-283.59,-0.023805,-0.020823,0.9995,137.59,#6,0.26589,-0.9639,-0.013749,116.6,0.96371,0.26543,0.028482,-283.59,-0.023805,-0.020823,0.9995,137.59
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.26589,-0.9639,-0.013749,116.6,0.96371,0.26543,0.028482,-283.59,-0.023805,-0.020823,0.9995,137.59,#4,0.26589,-0.9639,-0.013749,116.6,0.96371,0.26543,0.028482,-283.59,-0.023805,-0.020823,0.9995,137.59,#5,0.26589,-0.9639,-0.013749,116.6,0.96371,0.26543,0.028482,-283.59,-0.023805,-0.020823,0.9995,137.59,#6,0.26589,-0.9639,-0.013749,116.6,0.96371,0.26543,0.028482,-283.59,-0.023805,-0.020823,0.9995,137.59
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.24088,-0.9705,-0.01019,122.16,0.97019,0.24049,0.030101,-280.25,-0.026763,-0.017137,0.99949,137.47,#4,0.24088,-0.9705,-0.01019,122.16,0.97019,0.24049,0.030101,-280.25,-0.026763,-0.017137,0.99949,137.47,#5,0.24088,-0.9705,-0.01019,122.16,0.97019,0.24049,0.030101,-280.25,-0.026763,-0.017137,0.99949,137.47,#6,0.24088,-0.9705,-0.01019,122.16,0.97019,0.24049,0.030101,-280.25,-0.026763,-0.017137,0.99949,137.47
> fitmap #5 inMap #7
Fit map nozzle-resample.mrc in map symmismatch_ort-6.mrc using 157429 points
correlation = 0.8856, correlation about mean = 0.1829, overlap = 2.342e+05
steps = 76, shift = 1.56, angle = 5.2 degrees
Position of nozzle-resample.mrc (#5) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.32244022 -0.94658979 0.00026165 123.32877782
0.94658975 0.32244030 0.00032527 -251.79660618
-0.00039226 0.00014280 0.99999991 103.77618690
Axis -0.00009638 0.00034541 0.99999994
Axis point 237.58155730 -39.76055626 0.00000000
Rotation angle (degrees) 71.18943684
Shift along axis 103.67732149
> fitmap #3 inMap #7
Fit map adaptor-resample.mrc in map symmismatch_ort-6.mrc using 98827 points
correlation = 0.8349, correlation about mean = 0.18, overlap = 1.545e+05
steps = 60, shift = 2.87, angle = 4.82 degrees
Position of adaptor-resample.mrc (#3) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.31475742 -0.94917085 -0.00156884 124.59345302
0.94916763 0.31476060 -0.00256581 -250.78440149
0.00292920 -0.00068148 0.99999548 103.40303454
Axis 0.00099262 -0.00236945 0.99999670
Axis point 235.76352594 -39.04998211 0.00000000
Rotation angle (degrees) 71.65387048
Shift along axis 104.12058777
> fitmap #3 inMap #7
Fit map adaptor-resample.mrc in map symmismatch_ort-6.mrc using 98827 points
correlation = 0.8349, correlation about mean = 0.18, overlap = 1.545e+05
steps = 60, shift = 2.87, angle = 4.82 degrees
Position of adaptor-resample.mrc (#3) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.31475742 -0.94917085 -0.00156884 124.59345302
0.94916763 0.31476060 -0.00256581 -250.78440149
0.00292920 -0.00068148 0.99999548 103.40303454
Axis 0.00099262 -0.00236945 0.99999670
Axis point 235.76352594 -39.04998211 0.00000000
Rotation angle (degrees) 71.65387048
Shift along axis 104.12058777
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.33011,-0.94387,0.012068,96.02,0.94263,0.33029,0.048615,-295.67,-0.049872,-0.0046729,0.99874,139.65,#4,0.33011,-0.94387,0.012068,96.02,0.94263,0.33029,0.048615,-295.67,-0.049872,-0.0046729,0.99874,139.65,#5,0.33011,-0.94387,0.012068,96.02,0.94263,0.33029,0.048615,-295.67,-0.049872,-0.0046729,0.99874,139.65,#6,0.33011,-0.94387,0.012068,96.02,0.94263,0.33029,0.048615,-295.67,-0.049872,-0.0046729,0.99874,139.65
> view matrix models
> #3,0.24949,-0.96706,-0.050447,126.92,0.96837,0.24939,0.0083423,-278.95,0.0045136,-0.050932,0.99869,138.22,#4,0.24949,-0.96706,-0.050447,126.92,0.96837,0.24939,0.0083423,-278.95,0.0045136,-0.050932,0.99869,138.22,#5,0.24949,-0.96706,-0.050447,126.92,0.96837,0.24939,0.0083423,-278.95,0.0045136,-0.050932,0.99869,138.22,#6,0.24949,-0.96706,-0.050447,126.92,0.96837,0.24939,0.0083423,-278.95,0.0045136,-0.050932,0.99869,138.22
> view matrix models
> #3,0.4766,-0.86936,-0.13063,75.03,0.87802,0.47816,0.021167,-307.4,0.04406,-0.12478,0.99121,145.44,#4,0.4766,-0.86936,-0.13063,75.03,0.87802,0.47816,0.021167,-307.4,0.04406,-0.12478,0.99121,145.44,#5,0.4766,-0.86936,-0.13063,75.03,0.87802,0.47816,0.021167,-307.4,0.04406,-0.12478,0.99121,145.44,#6,0.4766,-0.86936,-0.13063,75.03,0.87802,0.47816,0.021167,-307.4,0.04406,-0.12478,0.99121,145.44
> view matrix models
> #3,0.92345,-0.35204,-0.15268,-108.87,0.36275,0.93064,0.048241,-290.58,0.1251,-0.099932,0.9871,125.1,#4,0.92345,-0.35204,-0.15268,-108.87,0.36275,0.93064,0.048241,-290.58,0.1251,-0.099932,0.9871,125.1,#5,0.92345,-0.35204,-0.15268,-108.87,0.36275,0.93064,0.048241,-290.58,0.1251,-0.099932,0.9871,125.1,#6,0.92345,-0.35204,-0.15268,-108.87,0.36275,0.93064,0.048241,-290.58,0.1251,-0.099932,0.9871,125.1
> view matrix models
> #3,0.92566,-0.35095,-0.14137,-111.43,0.36294,0.9292,0.069719,-293.81,0.10689,-0.11585,0.9875,132.41,#4,0.92566,-0.35095,-0.14137,-111.43,0.36294,0.9292,0.069719,-293.81,0.10689,-0.11585,0.9875,132.41,#5,0.92566,-0.35095,-0.14137,-111.43,0.36294,0.9292,0.069719,-293.81,0.10689,-0.11585,0.9875,132.41,#6,0.92566,-0.35095,-0.14137,-111.43,0.36294,0.9292,0.069719,-293.81,0.10689,-0.11585,0.9875,132.41
> view matrix models
> #3,0.92975,-0.36454,-0.051725,-124.4,0.36602,0.93033,0.022548,-286.93,0.039902,-0.039897,0.99841,130.3,#4,0.92975,-0.36454,-0.051725,-124.4,0.36602,0.93033,0.022548,-286.93,0.039902,-0.039897,0.99841,130.3,#5,0.92975,-0.36454,-0.051725,-124.4,0.36602,0.93033,0.022548,-286.93,0.039902,-0.039897,0.99841,130.3,#6,0.92975,-0.36454,-0.051725,-124.4,0.36602,0.93033,0.022548,-286.93,0.039902,-0.039897,0.99841,130.3
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.92975,-0.36454,-0.051725,-119.57,0.36602,0.93033,0.022548,-293.06,0.039902,-0.039897,0.99841,129.3,#4,0.92975,-0.36454,-0.051725,-119.57,0.36602,0.93033,0.022548,-293.06,0.039902,-0.039897,0.99841,129.3,#5,0.92975,-0.36454,-0.051725,-119.57,0.36602,0.93033,0.022548,-293.06,0.039902,-0.039897,0.99841,129.3,#6,0.92975,-0.36454,-0.051725,-119.57,0.36602,0.93033,0.022548,-293.06,0.039902,-0.039897,0.99841,129.3
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99162,-0.11569,-0.057545,-179.24,0.11481,0.99322,-0.018392,-247.15,0.059282,0.01163,0.99817,115.36,#4,0.99162,-0.11569,-0.057545,-179.24,0.11481,0.99322,-0.018392,-247.15,0.059282,0.01163,0.99817,115.36,#5,0.99162,-0.11569,-0.057545,-179.24,0.11481,0.99322,-0.018392,-247.15,0.059282,0.01163,0.99817,115.36,#6,0.99162,-0.11569,-0.057545,-179.24,0.11481,0.99322,-0.018392,-247.15,0.059282,0.01163,0.99817,115.36
> view matrix models
> #3,0.99441,-0.090493,-0.054438,-185.37,0.089372,0.99574,-0.022688,-241.69,0.056259,0.017696,0.99826,114.76,#4,0.99441,-0.090493,-0.054438,-185.37,0.089372,0.99574,-0.022688,-241.69,0.056259,0.017696,0.99826,114.76,#5,0.99441,-0.090493,-0.054438,-185.37,0.089372,0.99574,-0.022688,-241.69,0.056259,0.017696,0.99826,114.76,#6,0.99441,-0.090493,-0.054438,-185.37,0.089372,0.99574,-0.022688,-241.69,0.056259,0.017696,0.99826,114.76
> fitmap #3 inMap #7
Fit map adaptor-resample.mrc in map symmismatch_ort-6.mrc using 98827 points
correlation = 0.8349, correlation about mean = 0.1812, overlap = 1.545e+05
steps = 88, shift = 8.44, angle = 7.24 degrees
Position of adaptor-resample.mrc (#3) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.97943038 -0.20177761 -0.00139128 -155.02669521
0.20177311 0.97942816 -0.00284417 -234.33870253
0.00193655 0.00250494 0.99999499 102.97202435
Axis 0.01325349 -0.00824538 0.99987817
Axis point 1067.08251046 -883.84005561 0.00000000
Rotation angle (degrees) 11.64223457
Shift along axis 102.83704656
> fitmap #5 inMap #7
Fit map nozzle-resample.mrc in map symmismatch_ort-6.mrc using 157429 points
correlation = 0.886, correlation about mean = 0.1852, overlap = 2.341e+05
steps = 68, shift = 3.21, angle = 6.87 degrees
Position of nozzle-resample.mrc (#5) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.98124630 -0.19275748 0.00050517 -156.47957339
0.19275690 0.98124603 0.00100572 -233.18475441
-0.00068955 -0.00088949 0.99999937 104.04165018
Axis -0.00491597 0.00309898 0.99998311
Axis point 1122.06300961 -918.30793732 0.00000000
Rotation angle (degrees) 11.11392467
Shift along axis 104.08650890
> hide #!7 models
> fitmap #6 inMap #7
Fit map portal-resample.mrc in map symmismatch_ort-6.mrc using 250008 points
correlation = 0.8066, correlation about mean = 0.1536, overlap = 2.469e+05
steps = 96, shift = 12.2, angle = 6.58 degrees
Position of portal-resample.mrc (#6) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.98182660 -0.18973525 -0.00413112 -156.93560625
0.18973430 0.98183527 -0.00062479 -232.70914291
0.00417463 -0.00017038 0.99999127 102.41496677
Axis 0.00119717 -0.02188253 0.99975983
Axis point 1124.56098918 -935.52016550 0.00000000
Rotation angle (degrees) 10.93996639
Shift along axis 107.29475503
> hide #!1 models
> fitmap #4 inMap #7
Fit map core-resample.mrc in map symmismatch_ort-6.mrc using 565764 points
correlation = 0.7303, correlation about mean = 0.142, overlap = 3.627e+05
steps = 116, shift = 18.3, angle = 5.92 degrees
Position of core-resample.mrc (#4) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
0.98463401 -0.17462979 0.00055952 -160.72387524
0.17463066 0.98462724 -0.00365148 -229.45946480
0.00008673 0.00369308 0.99999318 102.57239796
Axis 0.02102422 0.00135339 0.99977805
Axis point 1223.19351129 -1039.90228765 0.00000000
Rotation angle (degrees) 10.05939601
Shift along axis 98.85999045
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select clear
> volume #4 level 0.2027
> show #!1 models
> show #!2 models
> volume #1 level 6.042
> volume #1 level 6.759
> hide #!2 models
> volume #1 level 6.281
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> color #2 #ffaaffff models
> color #2 #ffbcfeff models
> color #1 #ff55ffff models
> color #1 #ffaaffff models
> color #1 #ffc7feff models
> color #1 #ffe0ffff models
> color #1 #fbbdffff models
> color #1 #ff557fff models
> color #1 #ff9b9dff models
> color #1 #ffb9c4ff models
> color #1 #ffa6bbff models
> color #1 #ffabbaff models
> show #!2 models
> color #2 #ff557fff models
> color #2 #ff638dff models
> color #2 #ff6e95ff models
> color #2 #ff97b6ff models
> color #2 #ff86a6ff models
> color #2 #e77997ff models
> color #2 #d9728dff models
> color #2 #d9a3a9ff models
> color #1 #ffcdd9ff models
> color #1 #ffd7ddff models
> color #1 #ffc2c5ff models
> color #1 #b88c8eff models
> color #1 #d5a2a5ff models
> color #2 #b1858aff models
> color #2 #ce9ba1ff models
> color #2 #ca989eff models
> color #3 springgreen models
> color #3 #e2ffb7ff models
> color #3 #27ff35ff models
> color #3 #aaff7fff models
> color #3 #8aff42ff models
> color #3 #71ff18ff models
> color #3 #afff8cff models
> color #3 #97dc79ff models
> color #3 #90d374ff models
> color #3 #8aca6fff models
> color #3 #85c26bff models
> color #5 cyan models
> color #5 #5599ffff models
> color #5 #5dd4ffff models
> color #5 #4fb3d8ff models
> color #5 #4dafd3ff models
> color #3 cyan models
> color #3 #25ff80ff models
> color #3 #25ff99ff models
> color #3 #35ffd3ff models
> color #3 #2effd5ff models
> color #3 #aa5500ff models
> color #3 #ff5500ff models
> color #3 #ffaa00ff models
> color #3 #bcf8ffff models
> color #3 #98f5ffff models
> color #1 white models
> color #2 white models
> color #2 #bdbdbdff models
> color #2 #abababff models
> ui tool show "Surface Color"
> open D:/e1004/e1004-painting/overall/capsid/t=7-capsid.pdb
Chain information for t=7-capsid.pdb #8
---
Chain | Description
A B C D E F | No description available
V | No description available
> select add #8
17237 atoms, 17494 bonds, 7 pseudobonds, 2357 residues, 2 models selected
> color sel bychain
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide #!2 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!6 models
> hide #!5 models
> show #!2 models
> view matrix models
> #8,0.99514,0.098492,-0.0010748,8.5116,-0.098393,0.99453,0.035172,-5.7827,0.0045331,-0.034895,0.99938,-2.8644
> view matrix models
> #8,0.99427,0.096412,0.046113,-4.6866,-0.10049,0.99026,0.09637,-22.983,-0.036373,-0.10045,0.99428,-4.9432
> view matrix models
> #8,0.99427,0.096412,0.046113,-38.676,-0.10049,0.99026,0.09637,-8.5761,-0.036373,-0.10045,0.99428,6.7425
> view matrix models
> #8,0.93662,0.3354,0.10127,-31.969,-0.33625,0.94173,-0.0090363,27.222,-0.098402,-0.02559,0.99482,15.446
> view matrix models
> #8,0.90761,0.4088,0.095491,-23.111,-0.40379,0.91233,-0.067854,44.146,-0.11486,0.023027,0.99311,20.601
> view matrix models
> #8,0.90761,0.4088,0.095491,-61.613,-0.40379,0.91233,-0.067854,58.589,-0.11486,0.023027,0.99311,81.079
> view matrix models
> #8,0.92197,0.38654,-0.023469,-31.118,-0.38024,0.9151,0.1342,1.8039,0.073351,-0.11481,0.99068,62.143
> view matrix models
> #8,0.92197,0.38654,-0.023469,28.595,-0.38024,0.9151,0.1342,70.771,0.073351,-0.11481,0.99068,43.548
> view matrix models
> #8,0.92197,0.38654,-0.023469,39.088,-0.38024,0.9151,0.1342,71.555,0.073351,-0.11481,0.99068,42.288
> view matrix models
> #8,0.92197,0.38654,-0.023469,41.535,-0.38024,0.9151,0.1342,31.417,0.073351,-0.11481,0.99068,63.473
> view matrix models
> #8,0.77039,0.30655,-0.55904,190.14,-0.20598,0.94947,0.2368,-2.0019,0.60338,-0.067278,0.79461,97.915
> view matrix models
> #8,0.85738,0.4634,0.22397,-17.861,-0.48527,0.87283,0.051752,55.517,-0.17151,-0.15306,0.97322,76.157
> view matrix models
> #8,0.80706,0.43022,0.40444,-68.279,-0.52658,0.83429,0.16332,23.339,-0.26715,-0.34478,0.89987,85.185
> view matrix models
> #8,0.87814,0.23407,0.41723,-90.927,-0.47734,0.48689,0.7315,-164.42,-0.031919,-0.84152,0.53929,134.19
> view matrix models
> #8,0.6897,0.7033,-0.17231,118.86,0.23887,0.003651,0.97104,-302.03,0.68356,-0.71089,-0.16548,307.96
> view matrix models
> #8,0.25666,0.94022,0.22386,47.761,-0.92484,0.17165,0.33941,-61.407,0.2807,-0.29415,0.91361,60.978
> view matrix models
> #8,0.32206,0.84655,0.42384,-18.152,-0.86279,0.078173,0.49948,-116.1,0.3897,-0.52655,0.75557,81
> view matrix models
> #8,0.18948,0.94402,0.27005,38.282,-0.92039,0.074963,0.38375,-81.733,0.34202,-0.32127,0.88307,64.491
> view matrix models
> #8,0.29214,0.8194,0.49319,-38.222,-0.79676,-0.076711,0.59941,-159.3,0.52899,-0.56806,0.63046,106.05
> view matrix models
> #8,0.54881,0.8106,0.20429,29.586,-0.53284,0.52751,-0.66168,227.18,-0.64412,0.25428,0.72142,200.1
> view matrix models
> #8,0.80914,0.50221,0.3051,-35.018,-0.58234,0.61589,0.53062,-93.617,0.078576,-0.60702,0.79079,78.632
> view matrix models
> #8,0.80914,0.50221,0.3051,4.3532,-0.58234,0.61589,0.53062,-75.469,0.078576,-0.60702,0.79079,63.86
> view matrix models
> #8,0.59459,0.72011,0.35763,17.095,-0.76992,0.63812,-0.0048421,83.018,-0.2317,-0.27247,0.93385,65.286
> view matrix models
> #8,0.68833,0.64148,0.33868,11.767,-0.72142,0.65419,0.22714,17.908,-0.075852,-0.40067,0.91308,53.658
> view matrix models
> #8,0.68833,0.64148,0.33868,0.20829,-0.72142,0.65419,0.22714,24.973,-0.075852,-0.40067,0.91308,59.625
> view matrix models
> #8,0.68833,0.64148,0.33868,3.0675,-0.72142,0.65419,0.22714,29.89,-0.075852,-0.40067,0.91308,57.232
> view matrix models
> #8,0.68833,0.64148,0.33868,1.6332,-0.72142,0.65419,0.22714,31.401,-0.075852,-0.40067,0.91308,57.474
> view matrix models
> #8,0.68833,0.64148,0.33868,-2.7613,-0.72142,0.65419,0.22714,30.17,-0.075852,-0.40067,0.91308,58.566
> view matrix models
> #8,0.68833,0.64148,0.33868,-2.7868,-0.72142,0.65419,0.22714,30.526,-0.075852,-0.40067,0.91308,58.557
> view matrix models
> #8,0.68833,0.64148,0.33868,-8.7419,-0.72142,0.65419,0.22714,21.585,-0.075852,-0.40067,0.91308,31.773
> ui tool show "Fit in Map"
> fitmap #8 inMap #2
Fit molecule t=7-capsid.pdb (#8) to map 2-capsid.mrc (#2) using 17237 atoms
average map value = 0.1273, steps = 204
shifted from previous position = 10.9
rotated from previous position = 9.48 degrees
atoms outside contour = 13996, contour level = 0.56165
Position of t=7-capsid.pdb (#8) relative to 2-capsid.mrc (#2) coordinates:
Matrix rotation and translation
0.18803349 0.00939501 -0.98211768 436.42841888
0.90405057 0.38914130 0.17680953 453.04122451
0.38384368 -0.92113016 0.06467803 432.64726196
Axis -0.55798937 -0.69420198 0.45467733
Axis point -322.60544607 0.00000000 505.81138572
Rotation angle (degrees) 100.31580374
Shift along axis -361.30963007
> view matrix models
> #8,0.72837,0.6107,0.31067,-15.053,-0.6839,0.62031,0.38405,-26.099,0.041833,-0.4922,0.86948,26.407
> view matrix models
> #8,0.73551,0.61594,0.2822,-7.0634,-0.67399,0.6228,0.39731,-30.011,0.068967,-0.48243,0.87322,24.951
> view matrix models
> #8,0.90866,0.35089,0.22631,-20.85,-0.41747,0.77389,0.47626,-51.084,-0.0080208,-0.52723,0.84969,31.275
> view matrix models
> #8,0.90866,0.35089,0.22631,-32.325,-0.41747,0.77389,0.47626,-30.129,-0.0080208,-0.52723,0.84969,25.023
> fitmap #8 inMap #2
Fit molecule t=7-capsid.pdb (#8) to map 2-capsid.mrc (#2) using 17237 atoms
average map value = 1.242, steps = 112
shifted from previous position = 8.4
rotated from previous position = 6.7 degrees
atoms outside contour = 3443, contour level = 0.56165
Position of t=7-capsid.pdb (#8) relative to 2-capsid.mrc (#2) coordinates:
Matrix rotation and translation
-0.00002505 -0.00003631 -1.00000000 440.00003857
0.99999999 -0.00013546 -0.00002504 440.00061505
-0.00013546 -0.99999999 0.00003631 440.00876700
Axis -0.57735971 -0.57729596 0.57739513
Axis point 293.32782672 586.62160112 0.00000000
Rotation angle (degrees) 120.00410836
Shift along axis -253.98995280
> select subtract #8
Nothing selected
> select /A
2471 atoms, 2508 bonds, 1 pseudobond, 338 residues, 2 models selected
> select /B
2471 atoms, 2508 bonds, 1 pseudobond, 338 residues, 2 models selected
> select /V
2411 atoms, 2446 bonds, 1 pseudobond, 329 residues, 2 models selected
> help help:user
> select /V
2411 atoms, 2446 bonds, 1 pseudobond, 329 residues, 2 models selected
> select /V
2411 atoms, 2446 bonds, 1 pseudobond, 329 residues, 2 models selected
> sym chain v group i,222 center 440,440,440
Missing or invalid "structures" argument: invalid atomic structures specifier
> split
Split t=7-capsid.pdb (#8) into 7 models
Chain information for t=7-capsid.pdb A #8.1
---
Chain | Description
A | No description available
Chain information for t=7-capsid.pdb B #8.2
---
Chain | Description
B | No description available
Chain information for t=7-capsid.pdb C #8.3
---
Chain | Description
C | No description available
Chain information for t=7-capsid.pdb D #8.4
---
Chain | Description
D | No description available
Chain information for t=7-capsid.pdb E #8.5
---
Chain | Description
E | No description available
Chain information for t=7-capsid.pdb F #8.6
---
Chain | Description
F | No description available
Chain information for t=7-capsid.pdb V #8.7
---
Chain | Description
V | No description available
> hide #!8.1-7 target m
> close #8.1-7
> hide #8 models
> show #8 models
> open "D:/e1004/e1004-painting/atom model/capsid/wujuti.pdb"
Chain information for wujuti.pdb #9
---
Chain | Description
V | No description available
> hide #8 models
> hide #!2 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> color bychain
> hide atoms
> show cartoons
> hide #!9 models
> show #!9 models
> close #9
> show #!2 models
> open "D:/e1004/e1004-painting/atom model/capsid/wujuti.pdb"
Chain information for wujuti.pdb #9
---
Chain | Description
V | No description available
> color bychain
> hide atoms
> show cartoons
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> select add #9
2411 atoms, 2446 bonds, 1 pseudobond, 329 residues, 2 models selected
> view matrix models
> #9,0.99448,-0.077647,-0.070632,36.863,0.076143,0.99681,-0.023739,-8.2196,0.07225,0.01823,0.99722,-17.696
> view matrix models
> #9,0.99314,-0.086602,-0.078586,41.203,0.084734,0.99604,-0.0268,-8.9552,0.080596,0.019957,0.99655,-19.564
> view matrix models
> #9,0.99314,-0.086602,-0.078586,-211.34,0.084734,0.99604,-0.0268,-165.14,0.080596,0.019957,0.99655,-95.751
> view matrix models
> #9,0.99314,-0.086602,-0.078586,-219.53,0.084734,0.99604,-0.0268,-92.785,0.080596,0.019957,0.99655,28.532
> view matrix models
> #9,0.99314,-0.086602,-0.078586,-169.88,0.084734,0.99604,-0.0268,-277.18,0.080596,0.019957,0.99655,40.439
> view matrix models
> #9,0.99314,-0.086602,-0.078586,-175.88,0.084734,0.99604,-0.0268,-219.57,0.080596,0.019957,0.99655,75.206
> view matrix models
> #9,0.9411,0.21005,-0.26498,-197.91,-0.27701,0.029503,-0.96041,307.51,-0.19392,0.97724,0.085952,95.453
> view matrix models
> #9,0.44581,-0.62609,0.63973,-100.95,-0.53176,-0.76015,-0.37337,420.05,0.72006,-0.17373,-0.67181,385.99
> view matrix models
> #9,0.4543,-0.35238,0.81819,-212.59,0.58883,-0.57043,-0.57262,204.93,0.6685,0.74192,-0.051658,22.401
> view matrix models
> #9,0.4543,-0.35238,0.81819,-169.37,0.58883,-0.57043,-0.57262,150.25,0.6685,0.74192,-0.051658,25.677
> view matrix models
> #9,0.42819,-0.38807,0.81612,-154.93,0.5544,-0.60038,-0.57635,165.21,0.71365,0.69925,-0.041932,25.611
> view matrix models
> #9,0.2738,-0.49263,0.82604,-101.49,0.4998,-0.66091,-0.55981,187.05,0.82172,0.56614,0.065264,13.967
> view matrix models
> #9,0.67676,-0.35007,0.64764,-173.05,0.37181,-0.59675,-0.71109,229.99,0.63542,0.72204,-0.2737,88.029
> view matrix models
> #9,0.74545,-0.27336,0.60793,-196.32,0.41245,-0.5273,-0.74285,212.06,0.52363,0.8045,-0.28033,90.024
> view matrix models
> #9,0.74545,-0.27336,0.60793,-210.34,0.41245,-0.5273,-0.74285,209.23,0.52363,0.8045,-0.28033,98.299
> view matrix models
> #9,0.74545,-0.27336,0.60793,-211.96,0.41245,-0.5273,-0.74285,206.43,0.52363,0.8045,-0.28033,99.357
> view matrix models
> #9,0.74545,-0.27336,0.60793,-209.13,0.41245,-0.5273,-0.74285,208.2,0.52363,0.8045,-0.28033,98.153
> view matrix models
> #9,0.55262,-0.46016,0.69488,-145.36,0.44455,-0.5425,-0.71279,199.02,0.70497,0.70281,-0.095235,46.746
> view matrix models
> #9,0.55262,-0.46016,0.69488,-144.67,0.44455,-0.5425,-0.71279,200.64,0.70497,0.70281,-0.095235,46.272
> view matrix models
> #9,0.49495,-0.49134,0.71667,-130.85,0.48386,-0.52922,-0.697,186.19,0.72174,0.69174,-0.02419,29.54
> fitmap #9 inMap #2
Fit molecule wujuti.pdb (#9) to map 2-capsid.mrc (#2) using 2411 atoms
average map value = 1.358, steps = 208
shifted from previous position = 6.53
rotated from previous position = 17.4 degrees
atoms outside contour = 319, contour level = 0.56165
Position of wujuti.pdb (#9) relative to 2-capsid.mrc (#2) coordinates:
Matrix rotation and translation
-0.80916891 -0.49985891 0.30884743 373.17300997
0.49972613 -0.30897217 0.80920330 260.91865585
-0.30906222 0.80912129 0.49980324 328.91514127
Axis -0.00006979 0.52581246 0.85060052
Axis point 178.64199773 100.04534718 0.00000000
Rotation angle (degrees) 144.01481235
Shift along axis 416.94362900
> select subtract #9
Nothing selected
> select add #9
2411 atoms, 2446 bonds, 1 pseudobond, 329 residues, 2 models selected
> select subtract #9
Nothing selected
> select add #9
2411 atoms, 2446 bonds, 1 pseudobond, 329 residues, 2 models selected
> select subtract #9
Nothing selected
> select add #9
2411 atoms, 2446 bonds, 1 pseudobond, 329 residues, 2 models selected
> sym #9 group i,222 center 440,440,440
Expected a keyword
> sym #9 group i,222 center 440,440,440
Expected a keyword
> sym #9 group i,222 center440,440,440
Expected a keyword
> sym #9 center 440,440,440 group i,222
Expected a keyword
> sym #9 center 440,440,440 group i,n25r
Expected a keyword
> help help:user
> sym #9 center 440,440,440 group i,n25r
Expected a keyword
> sym #9 center 440,440,440 group i,n25r
Expected a keyword
> symmertry #9 center 440,440,440 group i,n25r
Unknown command: symmertry #9 center 440,440,440 group i,n25r
> help help:user
> sym #9 group i,222 center 440,440,440
Expected a keyword
> sym #8 group i,222 center 440,440,440
Expected a keyword
> select subtract #9
Nothing selected
> select add #9
2411 atoms, 2446 bonds, 1 pseudobond, 329 residues, 2 models selected
> sym #9 group i,222 center 440,440,440
Expected a keyword
> sym #9 group i,222 center 440,440,440
Expected a keyword
> sym #9 group i,222 center 440,440,440
Expected a keyword
> help help:user
> sym /9 group i,222 center 440,440,440
Expected a keyword
> sym #7 group i,222 center 440,440,440
Expected a keyword
> close #9
> open D:/e1004/e1004-painting/overall/capsid/pentamer-sym.pdb
Chain information for pentamer-sym.pdb #9
---
Chain | Description
V | No description available
> sym
Missing or invalid "structures" argument: empty atom specifier
> sym #9
pentamer-sym.pdb mmCIF Assemblies
---
> sym #9
pentamer-sym.pdb mmCIF Assemblies
---
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> Sym #9
Unknown command: Sym #9
> sym
Missing or invalid "structures" argument: empty atom specifier
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 target m
> show #!6 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> open D:/e1004/e1004-painting/overall/capsid/vertex.pdb
Chain information for vertex.pdb #10
---
Chain | Description
0 1 2 3 4 5 6 7 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e
f g h i j k l m n o p q r s t u v w x y z | No description available
> style #!10 sphere
Changed 144660 atom styles
> color #!10 bychain
> hide #!10 atoms
> show #!10 cartoons
> show #!9 models
> hide #!9 models
> close #9
> select add #10
144660 atoms, 146760 bonds, 60 pseudobonds, 19740 residues, 2 models selected
> view matrix models
> #10,0.99936,-0.032555,-0.014816,21.125,0.032612,0.99946,0.0036437,-15.716,0.01469,-0.0041246,0.99988,-4.5974
> view matrix models
> #10,0.99936,-0.032555,-0.014816,-597.29,0.032612,0.99946,0.0036437,-93.955,0.01469,-0.0041246,0.99988,-323.73
> view matrix models
> #10,0.98583,-0.096061,0.1375,-630.41,0.088864,0.99438,0.057569,-140.2,-0.14226,-0.044534,0.98883,-232.02
> view matrix models
> #10,0.98583,-0.096061,0.1375,-629.16,0.088864,0.99438,0.057569,-139.78,-0.14226,-0.044534,0.98883,-232.03
> view matrix models
> #10,0.99402,-0.072031,0.0821,-618.95,0.069206,0.99693,0.036757,-123.1,-0.084495,-0.030855,0.99595,-266.6
> view matrix models
> #10,0.99402,-0.072031,0.0821,-310.87,0.069206,0.99693,0.036757,-299.01,-0.084495,-0.030855,0.99595,-296.82
> view matrix models
> #10,0.99402,-0.072031,0.0821,-425.43,0.069206,0.99693,0.036757,-607.95,-0.084495,-0.030855,0.99595,-384.41
> view matrix models
> #10,0.96038,0.02115,-0.27789,-293.23,0.083546,0.92941,0.35947,-726.54,0.26588,-0.36844,0.89082,-343.78
> view matrix models
> #10,0.80725,0.58232,0.096171,-637.36,-0.55723,0.69826,0.44936,-382.45,0.19452,-0.41633,0.88816,-290.14
> view matrix models
> #10,0.74374,0.42257,0.51797,-724.71,-0.53833,0.83799,0.08932,-293.83,-0.39631,-0.34527,0.85072,-44.974
> view matrix models
> #10,0.95068,0.30931,0.023283,-548.27,-0.29054,0.86166,0.41608,-557.05,0.10863,-0.40232,0.90903,-267.7
> view matrix models
> #10,0.95735,0.14476,-0.25006,-358.53,0.01374,0.84166,0.53984,-736.58,0.28861,-0.52025,0.80377,-248.69
> view matrix models
> #10,0.96175,0.20912,-0.17692,-420.97,-0.10729,0.88186,0.45914,-665.51,0.25203,-0.4226,0.87057,-304.95
> view matrix models
> #10,0.96175,0.20912,-0.17692,-507.5,-0.10729,0.88186,0.45914,-614.44,0.25203,-0.4226,0.87057,-313.68
> view matrix models
> #10,0.95798,0.15572,-0.24086,-454.21,-0.025311,0.8824,0.46982,-655.45,0.2857,-0.44399,0.84926,-309.71
> view matrix models
> #10,0.95798,0.15572,-0.24086,-437.7,-0.025311,0.8824,0.46982,-654.81,0.2857,-0.44399,0.84926,-278.94
> view matrix models
> #10,0.99516,0.063348,-0.075091,-486.35,-0.05733,0.99516,0.079765,-518.71,0.079781,-0.075074,0.99398,-414.34
> view matrix models
> #10,0.90334,-0.42892,0.0022249,-263.38,0.42686,0.89847,-0.10267,-608.94,0.042036,0.093693,0.99471,-472.31
> view matrix models
> #10,0.90334,-0.42892,0.0022249,-222.23,0.42686,0.89847,-0.10267,-588.61,0.042036,0.093693,0.99471,-473.71
> view matrix models
> #10,0.81872,-0.54936,-0.16706,-57.51,0.57017,0.81221,0.12338,-713.17,0.06791,-0.19626,0.9782,-350.25
> view matrix models
> #10,0.49078,-0.73591,-0.46645,300.59,0.78931,0.60223,-0.11964,-610.28,0.36895,-0.30946,0.87642,-388.12
> view matrix models
> #10,0.49078,-0.73591,-0.46645,289.06,0.78931,0.60223,-0.11964,-572.75,0.36895,-0.30946,0.87642,-393.95
> view matrix models
> #10,-0.94351,-0.26342,-0.20101,595.47,0.30373,-0.44507,-0.84241,419.73,0.13245,-0.85587,0.49994,116.19
> view matrix models
> #10,-0.85615,0.51411,0.051944,103.62,-0.18079,-0.20387,-0.96216,579.48,-0.48406,-0.83315,0.26749,479.73
> view matrix models
> #10,-0.69008,0.40301,-0.60115,366.79,0.47218,-0.37879,-0.79597,296.02,-0.54849,-0.83313,0.071102,594.48
> fitmap #10 inMap #2
Fit molecule vertex.pdb (#10) to map 2-capsid.mrc (#2) using 144660 atoms
average map value = 1.357, steps = 208
shifted from previous position = 20.4
rotated from previous position = 4.51 degrees
atoms outside contour = 19129, contour level = 0.56165
Position of vertex.pdb (#10) relative to 2-capsid.mrc (#2) coordinates:
Matrix rotation and translation
0.30900599 0.80901073 0.50001693 -271.93468651
-0.80901715 0.49999956 -0.30901728 711.93526941
-0.50000654 -0.30903408 0.80900642 440.02012606
Axis -0.00000883 0.52574148 -0.85064440
Axis point 439.99728324 711.94379710 0.00000000
Rotation angle (degrees) 72.00066330
Shift along axis -0.00435681
> color (#!10 & sel) forest green
> hide #!2 models
> ui tool show "Color Actions"
> color #10 #ffaaffff
> color #10 #ffb8f8ff
> color #10 #ffcaffff
> color #10 #f894ffff
> color #10 #f569ffff
> color #10 #ff98fdff
> show #!2 models
> ui tool show "Color Zone"
> color zone #2 near #10 distance 4.39
> color zone #2 near #10 distance 3.82
> color zone #2 near #10 distance 3
[Repeated 1 time(s)]
> color #10 #ffaaffff
> color #10 #ff7ef4ff
> color #10 #ff80f4ff
> color #10 #ff557fff
> color zone #2 near #10 distance 3
> color #10 #ff6b86ff
> color #10 #ff7998ff
> color #10 #ff6b92ff
> color #10 #ff73a9ff
> color #10 #ea6a9bff
> color zone #2 near #10 distance 3
> color #10 #da6290ff
> color #10 #da4f7bff
> color #10 #fa5a8dff
> color zone #2 near #10 distance 3
> color #2 #ffaaffff models
> color #2 #ff557fff models
> color #2 #ff97b6ff models
> color #2 #ffafceff models
> color #2 #ff9dd5ff models
> color #2 #ffb2deff models
> color #2 #da98bdff models
> color #2 #eca5cdff models
> color #2 #ec94b7ff models
> color #2 #eca3c0ff models
> color #2 #ec85a6ff models
> color #2 #ec92afff models
> color #2 #eca6c1ff models
> color #2 #ecb4c7ff models
> color zone #2 near #10 distance 3
> color #2 #ecd4dfff models
> color #2 #ecc1d3ff models
> color #2 #ecbfd2ff models
> color #2 #ecc4d5ff models
> color #2 #ddb8c8ff models
> color zone #2 near #10 distance 3
> color #10 #fa72a8ff
> color #10 #fa7bb2ff
> color zone #2 near #10 distance 3
> color #10 #ff557fff
> color #10 #ff5500ff
> color #10 #ff7e14ff
> color #10 #ffaa7fff
> color #10 #f3a279ff
> color #10 #cb8765ff
> color zone #2 near #10 distance 3
> show #!3 models
> show #!5 models
> show #!6 models
> color #3 #63ffffff models
> color #3 #ffaa00ff models
> color #3 #ffb41eff models
> color #3 #ff7e42ff models
> color #2 #ddccdcff models
> color #2 #ffaa00ff models
> color #2 #ffe0ddff models
> color #2 #ffc8beff models
> color zone #2 near #10 distance 3
> color #3 #ffa274ff models
> color #3 #ff8349ff models
> color #3 #ff854cff models
> color #3 #ff8750ff models
> color #3 #aaaa7fff models
> color #3 #9daa63ff models
> color #3 #9eaa61ff models
> color #3 #aaa15dff models
> color #5 #555500ff models
> color #5 white models
> graphics silhouettes true
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting full
> color #3 #00aa7fff models
> color #3 #aaa129ff models
> color #3 #9faa2bff models
> color #3 #5baa49ff models
> color #3 #65aa7bff models
> color #3 #6baa7fff models
> color #5 #55aaffff models
> color #5 #ffaa7fff models
> color #5 #ffaa00ff models
> color #5 #ffd454ff models
> color #5 cyan models
> color #3 #ff5500ff models
> color #3 #ff973cff models
> color #3 #ff7070ff models
> color #3 #ff7373ff models
> color #3 #ff9a86ff models
> color #3 #bbffb3ff models
> color #3 #ff5454ff models
> color #3 #ffa16bff models
> color #3 #d8ff98ff models
> color #3 #55557fff models
> color #3 #55007fff models
> color #3 #5500ffff models
> color #3 #00007fff models
> color #3 #aa557fff models
> color #3 #ffaa00ff models
> color #3 #aaffffff models
> color #3 #aaaa7fff models
> color #5 #00aa7fff models
> color #5 #00aa00ff models
> color #5 #00aaffff models
> color #5 #55aa7fff models
> color #5 #44aa55ff models
> color #5 #78aa8aff models
> color #5 #68aa80ff models
> color #5 #66aa82ff models
> color #3 #55aaffff models
> color #3 #60daffff models
> color #3 #60d5ffff models
> color #3 yellow models
> color #3 #a5ff14ff models
> color #3 #b9ff6eff models
> color #3 #aaaa00ff models
> color #3 #99aa28ff models
> color #3 #94aa28ff models
> color #3 #ffaa7fff models
> color #3 #ffb08cff models
> color #3 #ff9966ff models
> color #3 #ffdb58ff models
> color #3 #ffe358ff models
> color #3 #aa5500ff models
> color #3 #ea7500ff models
> color #3 #ea8f1fff models
> color #3 #ea9a3fff models
> color #3 #eaab17ff models
> color #3 #ea2acaff models
> color #3 #d1ea31ff models
> color #3 #ffaaffff models
> color #3 white models
> color #5 white models
> color #3 yellow models
> color #3 #ffaa7fff models
> color #3 #bf7f5fff models
> color #3 #bf994dff models
> color #3 #8dbf4cff models
> color #3 #76bf32ff models
> color #3 #69aa2dff models
> color #3 #5f9928ff models
> color #3 #538623ff models
> color #3 #629f2aff models
> color #3 #72b830ff models
> color #3 #67a72cff models
> color #3 #54a736ff models
> color #3 #3ea71eff models
> color #3 #6aa741ff models
> color #3 white models
> color #2 #ffd3caff models
> color #2 #ffd4c7ff models
> color #2 #ffd7cbff models
> color #2 #ffd0c4ff models
> color #2 #ffcdc4ff models
> color #10 #ffcdc4ff
> color #10 #ffc5b2ff
> color #10 #ffb9a1ff
> color zone #2 near #10 distance 3
> color #6 #ffc6beff models
> color #6 #ffd4c9ff models
> color #6 #ffd5cfff models
> color #6 #ffdbdbff models
> color #6 #ffdcdcff models
> color #2 #ffe0deff models
> color #2 #ffd2d0ff models
> color zone #2 near #10 distance 3
> color #10 #ffb69dff
> color #10 #ffbaa5ff
> color #10 #ffd5c4ff
> color zone #2 near #10 distance 3
> color #10 #ffd4c6ff
> color #10 #ffd9caff
> color #10 #ffd3c2ff
> color #10 #ffd5c5ff
> color zone #2 near #10 distance 3
[Repeated 1 time(s)]
> color #10 #ffc6b8ff
> color zone #2 near #10 distance 3
[Repeated 1 time(s)]
> color #2 #ffe2ddff models
> color zone #2 near #10 distance 3
[Repeated 1 time(s)]
> set bgColor white
> set bgColor #ffffff00
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> open C:/Users/SBN/Desktop/capsid-resample-lp5.5.mrc
Opened capsid-resample-lp5.5.mrc as #9, grid size 800,800,800, pixel 1.1,
shown at step 1, values float32
> volume #9 level 7.786e-06,0 level 0.3828,0.8 level 1.099,1
> volume #9 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #9 step 1
> select subtract #10
Nothing selected
> select add #9
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,7.9704,0,1,0,-31.537,0,0,1,6.3325
> view matrix models #9,1,0,0,27.578,0,1,0,-109.16,0,0,1,22.114
> lighting simple
> view matrix models #9,1,0,0,15.977,0,1,0,-60.929,0,0,1,1.2504
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.45969,-0.30375,-0.83452,15.977,0.42557,0.90011,-0.0932,-60.929,0.77947,-0.3123,0.54304,1.2504
> view matrix models
> #9,0.94874,-0.25816,-0.18235,15.977,0.2936,0.93348,0.20596,-60.929,0.11704,-0.24894,0.96142,1.2504
> view matrix models
> #9,0.98131,0.18536,0.051595,15.977,-0.1924,0.94752,0.2553,-60.929,-0.0015645,-0.26046,0.96548,1.2504
> view matrix models
> #9,-0.75483,-0.36315,-0.54622,15.977,0.64227,-0.5782,-0.50316,-60.929,-0.13311,-0.73062,0.66968,1.2504
> view matrix models
> #9,-0.81912,-0.21516,-0.53174,15.977,0.53745,-0.61185,-0.58034,-60.929,-0.20048,-0.76115,0.61681,1.2504
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.81912,-0.21516,-0.53174,7.0353,0.53745,-0.61185,-0.58034,-15.099,-0.20048,-0.76115,0.61681,33.396
> view matrix models
> #9,-0.81912,-0.21516,-0.53174,10.296,0.53745,-0.61185,-0.58034,-35.024,-0.20048,-0.76115,0.61681,32.941
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.64934,-0.55839,-0.51629,10.296,0.75786,-0.53161,-0.37821,-35.024,-0.063276,-0.63686,0.76837,32.941
> fitmap #9 inMap #2
Fit map capsid-resample-lp5.5.mrc in map 2-capsid.mrc using 5110266 points
correlation = 0.1523, correlation about mean = 0.01079, overlap = 2.863e+05
steps = 284, shift = 37.5, angle = 3 degrees
Position of capsid-resample-lp5.5.mrc (#9) relative to 2-capsid.mrc (#2)
coordinates:
Matrix rotation and translation
-0.24136566 0.87772315 -0.41393802 439.26987754
-0.85560440 -0.39374775 -0.33601164 439.47326048
-0.45791236 0.27306552 0.84602097 439.97311380
Axis 0.33142508 0.02392833 -0.94317806
Axis point 452.60876041 41.91116330 0.00000000
Rotation angle (degrees) 113.23767578
Shift along axis -258.87207563
> fitmap #9 inMap #7
Fit map capsid-resample-lp5.5.mrc in map symmismatch_ort-6.mrc using 5110266
points
correlation = 0.9116, correlation about mean = 0.1882, overlap = 2.146e+07
steps = 148, shift = 0.905, angle = 7.62 degrees
Position of capsid-resample-lp5.5.mrc (#9) relative to symmismatch_ort-6.mrc
(#7) coordinates:
Matrix rotation and translation
-0.58779876 -0.68818366 -0.42531854 -0.00499104
0.80900718 -0.49998999 -0.30905888 -0.02060855
0.00003426 -0.52575018 0.85063902 0.00518397
Axis -0.13789243 -0.27067507 0.95274377
Axis point 0.00235717 -0.01044577 0.00000000
Rotation angle (degrees) 128.21213797
Shift along axis 0.01120544
> hide #!9 models
> show #!9 models
> hide #!2 models
> lighting shadows true
> lighting shadows false
> lighting full
[Repeated 3 time(s)]
> lighting simple
> lighting full
> show #!2 models
> hide #!9 models
> show #!9 models
> hide #!2 models
> volume #9 level 0.2984
> volume #2 level 0.2
> volume #2 change image level 0.0003141,0 level 0.804,0.8 level 3.836,1
> show #!2 models
> hide #!9 models
> show #!9 models
> hide #!2 models
> close #9
> show #!2 models
> lighting simple
[Repeated 1 time(s)]
> volume #2 level 0.5
> hide #!2 models
> hide #!3 models
> hide #!6 models
> hide #!5 models
> show #!7 models
> hide #!10 models
> set bgColor black
> set bgColor transparent
> open D:/e1004/e1004-painting/split/7-fiber.mrc
> D:/e1004/e1004-painting/split/adaptor-resample-lp5.mrc
> D:/e1004/e1004-painting/split/capsid-resample-lp7-eraser.mrc
> D:/e1004/e1004-painting/split/core-resample-lp5.mrc
> D:/e1004/e1004-painting/split/nozzle-resample-lp5.mrc
> D:/e1004/e1004-painting/split/portal-resample-lp5.mrc
Opened 7-fiber.mrc as #9.1, grid size 512,512,512, pixel 2.2, shown at level
0.886, step 2, values float32
Opened adaptor-resample-lp5.mrc as #9.2, grid size 720,720,720, pixel 1.1,
shown at step 1, values float32
Opened capsid-resample-lp7-eraser.mrc as #9.3, grid size 800,800,800, pixel
1.1, shown at step 1, values float32
Opened core-resample-lp5.mrc as #9.4, grid size 720,720,720, pixel 1.1, shown
at step 1, values float32
Opened nozzle-resample-lp5.mrc as #9.5, grid size 720,720,720, pixel 1.1,
shown at step 1, values float32
Opened portal-resample-lp5.mrc as #9.6, grid size 720,720,720, pixel 1.1,
shown at step 1, values float32
> ui tool show "Side View"
> ui tool show "Hide Dust"
> surface dust #9.1 size 13.2
> surface dust #9.1 size 38.25
> surface dust #9.1 size 194.73
> surface dust #9.1 size 50.18
> volume #9.6 level -2.165e-05,0 level 0.02745,0.8 level 0.2747,1
> volume #9.6 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #9.6 level 0.02729
> volume #9.6 step 1
> select add #9.1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #9.1,1,0,0,-25.063,0,1,0,-29.351,0,0,1,31.864
> view matrix models #9.1,1,0,0,-9.7869,0,1,0,-42.646,0,0,1,31.633
> fitmap #9.1 inMap #7
Fit map 7-fiber.mrc in map symmismatch_ort-6.mrc using 167753 points
correlation = 0.9989, correlation about mean = 0.9937, overlap = 2.769e+05
steps = 120, shift = 20.4, angle = 0.000491 degrees
Position of 7-fiber.mrc (#9.1) relative to symmismatch_ort-6.mrc (#7)
coordinates:
Matrix rotation and translation
1.00000000 0.00000372 0.00000747 0.01502157
-0.00000372 1.00000000 0.00000198 0.04890833
-0.00000747 -0.00000198 1.00000000 -0.22430304
Axis -0.23107506 0.87096380 -0.43362008
Axis point -22112.77513952 0.00000000 -6230.79554166
Rotation angle (degrees) 0.00049135
Shift along axis 0.13638858
> volume #9.1 level 1
> volume #9.1 level 1.2
> select clear
> select add #9.6
3 models selected
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models #9.6,1,0,0,-28.428,0,1,0,-261.92,0,0,1,170.2
> view matrix models #9.6,1,0,0,-28.014,0,1,0,-257.52,0,0,1,143.94
> view matrix models #9.6,1,0,0,-84.849,0,1,0,-251.25,0,0,1,144.09
> view matrix models #9.6,1,0,0,-216.28,0,1,0,-236.75,0,0,1,144.46
> fitmap #9.6 inMap #6
Fit map portal-resample-lp5.mrc in map portal-resample.mrc using 429457 points
correlation = 0.9209, correlation about mean = 0.8607, overlap = 1.404e+04
steps = 164, shift = 18.8, angle = 10.9 degrees
Position of portal-resample-lp5.mrc (#9.6) relative to portal-resample.mrc
(#6) coordinates:
Matrix rotation and translation
1.00000000 0.00002927 -0.00006291 0.00319543
-0.00002928 0.99999998 -0.00019815 0.03124073
0.00006291 0.00019815 0.99999998 -0.04488030
Axis 0.94380563 -0.29964753 -0.13943559
Axis point 0.00000000 226.57174851 157.50587632
Rotation angle (degrees) 0.01202926
Shift along axis -0.00008743
> hide #!7 models
> select add #6
6 models selected
> select subtract #6
3 models selected
> show #!6 models
> hide #!9.6 models
> show #!9.6 models
> hide #!9.6 models
> show #!9.6 models
> volume #9.6 level 0.06348
> volume #9.6 level 0.05599
> volume #9.5 level -1.189e-09,0 level 2.893e-09,0.8 level 1.256e-07,1
> volume #9.5 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #9.5 step 1
> show #!5 models
> select subtract #9.6
Nothing selected
> select add #9.5
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #9.5,1,0,0,-27.911,0,1,0,-255.55,0,0,1,102.81
> view matrix models #9.5,1,0,0,-107.46,0,1,0,-246.78,0,0,1,103.03
> view matrix models #9.5,1,0,0,-223.37,0,1,0,-233.99,0,0,1,103.35
> view matrix models #9.5,1,0,0,-224.06,0,1,0,-230.22,0,0,1,121.6
> view matrix models #9.5,1,0,0,-233.15,0,1,0,-229.22,0,0,1,121.62
> fitmap #9.5 inMap #5
Fit map nozzle-resample-lp5.mrc in map nozzle-resample.mrc using 654550 points
correlation = 0.2208, correlation about mean = 0.06129, overlap = 4211
steps = 160, shift = 6.85, angle = 13.3 degrees
Position of nozzle-resample-lp5.mrc (#9.5) relative to nozzle-resample.mrc
(#5) coordinates:
Matrix rotation and translation
0.99915973 -0.03751852 0.01649852 -2.18064696
0.03756695 0.99929064 -0.00263499 -8.85326189
-0.01638796 0.00325258 0.99986042 -7.10632230
Axis 0.07163988 0.40016259 0.91363977
Axis point 126.32219747 -41.49066164 0.00000000
Rotation angle (degrees) 2.35502667
Shift along axis -10.19158417
> volume #9.5 level 0.07456
> hide #!5 models
> hide #!6 models
> view matrix models
> #9.5,0.97317,-0.22943,0.017202,-183.39,0.22944,0.97332,0.0016002,-276.9,-0.01711,0.0023896,0.99985,48.319
> show #!5 models
> view matrix models
> #9.5,0.97317,-0.22943,0.017202,-182.42,0.22944,0.97332,0.0016002,-270.22,-0.01711,0.0023896,0.99985,134.81
> fitmap #9.5 inMap #5
Fit map nozzle-resample-lp5.mrc in map nozzle-resample.mrc using 301931 points
correlation = 0.9367, correlation about mean = 0.8944, overlap = 2.327e+04
steps = 92, shift = 4.39, angle = 2.36 degrees
Position of nozzle-resample-lp5.mrc (#9.5) relative to nozzle-resample.mrc
(#5) coordinates:
Matrix rotation and translation
0.99999999 0.00013753 0.00007667 -0.05460103
-0.00013753 0.99999999 -0.00003153 0.03798285
-0.00007667 0.00003152 1.00000000 -0.00140621
Axis 0.19629765 0.47745161 -0.85645034
Axis point 246.21499349 409.32489380 0.00000000
Rotation angle (degrees) 0.00920088
Shift along axis 0.00862127
> hide #!5 models
> select clear
> select add #9.2
2 models selected
> volume #9.4 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #9.4 step 1
> volume #9.4 change image level -1.368e-09,0 level 8.284e-09,0.8 level
> 1.319e-07,1
> volume #9.4 level 0.08331
> show #!4 models
> select add #9.4
5 models selected
> select add #9.2
5 models selected
> select add #9.2
5 models selected
> select add #9.4
5 models selected
> select add #9.4
5 models selected
> select add #9.2
5 models selected
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models
> #9.2,1,0,0,45.791,0,1,0,-126.54,0,0,1,126.83,#9.4,1,0,0,45.791,0,1,0,-126.54,0,0,1,126.83
> view matrix models
> #9.2,1,0,0,-29.653,0,1,0,-154.48,0,0,1,126.19,#9.4,1,0,0,-29.653,0,1,0,-154.48,0,0,1,126.19
> view matrix models
> #9.2,1,0,0,-214.07,0,1,0,-222.79,0,0,1,124.63,#9.4,1,0,0,-214.07,0,1,0,-222.79,0,0,1,124.63
> view matrix models
> #9.2,1,0,0,-293.71,0,1,0,-252.28,0,0,1,123.95,#9.4,1,0,0,-293.71,0,1,0,-252.28,0,0,1,123.95
> view matrix models
> #9.2,1,0,0,-291.77,0,1,0,-257.53,0,0,1,125,#9.4,1,0,0,-291.77,0,1,0,-257.53,0,0,1,125
[Repeated 1 time(s)]
> view matrix models
> #9.2,1,0,0,-264.53,0,1,0,-247.44,0,0,1,125.23,#9.4,1,0,0,-264.53,0,1,0,-247.44,0,0,1,125.23
> fitmap #9.4 inMap #4
Fit map core-resample-lp5.mrc in map core-resample.mrc using 473149 points
correlation = 0.1015, correlation about mean = 0.01648, overlap = 1109
steps = 100, shift = 3.89, angle = 2.11 degrees
Position of core-resample-lp5.mrc (#9.4) relative to core-resample.mrc (#4)
coordinates:
Matrix rotation and translation
0.98474737 0.17200614 -0.02620109 -70.60392087
-0.17259149 0.98474785 -0.02199678 30.32708192
0.02201789 0.02618336 0.99941465 -11.10570798
Axis 0.13715800 -0.13726857 -0.98099186
Axis point 136.23430601 420.19970165 0.00000000
Rotation angle (degrees) 10.11575031
Shift along axis -2.95223860
> select clear
> select add #9.4
3 models selected
> view matrix models
> #9.4,0.99977,-0.0025886,-0.021398,-249.33,0.0019484,0.99955,-0.029883,-219.98,0.021466,0.029835,0.99932,118.19
> view matrix models
> #9.4,0.99977,-0.0025886,-0.021398,-232.58,0.0019484,0.99955,-0.029883,-228.59,0.021466,0.029835,0.99932,118.81
> view matrix models
> #9.4,0.99977,-0.0025886,-0.021398,-229.23,0.0019484,0.99955,-0.029883,-222.19,0.021466,0.029835,0.99932,117.28
> view matrix models
> #9.4,0.99977,-0.0025886,-0.021398,-230.01,0.0019484,0.99955,-0.029883,-221.93,0.021466,0.029835,0.99932,117.22
> view matrix models
> #9.4,0.99977,-0.0025886,-0.021398,-232.17,0.0019484,0.99955,-0.029883,-228.55,0.021466,0.029835,0.99932,116.8
> fitmap #9.4 inMap #4
Fit map core-resample-lp5.mrc in map core-resample.mrc using 473149 points
correlation = 0.9475, correlation about mean = 0.8109, overlap = 2.554e+04
steps = 124, shift = 9.47, angle = 10.1 degrees
Position of core-resample-lp5.mrc (#9.4) relative to core-resample.mrc (#4)
coordinates:
Matrix rotation and translation
0.99999999 -0.00011193 -0.00007752 0.01671824
0.00011194 0.99999998 0.00014367 -0.01319370
0.00007750 -0.00014368 0.99999999 0.03038175
Axis -0.72586281 -0.39157647 0.56550072
Axis point 0.00000000 171.25087705 64.01762486
Rotation angle (degrees) 0.01134129
Shift along axis 0.01021209
> select clear
> hide #!4 models
> show #!4 models
> hide #!9.4 models
> show #!9.4 models
> hide #!9.4 models
> show #!9.4 models
> hide #!9.4 models
> show #!9.4 models
> hide #!4 models
> volume #9.4 level 0.09177
> volume #9.4 level 0.08472
> volume #9.2 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #9.2 change image level -8.32e-06,0 level 0.02602,0.8 level 0.2603,1
> volume #9.2 step 1
> volume #9.2 level 0.04335
> volume #9.2 level 0.04475
> volume #9.2 level 0.05453
> select add #9.5
3 models selected
> select add #9.5
3 models selected
> select add #9.5
3 models selected
> select add #9.5
3 models selected
> select clear
> select add #9.2
3 models selected
> show #!3 models
> view matrix models #9.2,1,0,0,-232.75,0,1,0,-258.36,0,0,1,136.87
> view matrix models #9.2,1,0,0,-218.96,0,1,0,-220,0,0,1,135.21
> view matrix models #9.2,1,0,0,-215.71,0,1,0,-221.31,0,0,1,132.03
> view matrix models #9.2,1,0,0,-220.23,0,1,0,-233.88,0,0,1,132.57
> fitmap #9.2 inMap #3
Fit map adaptor-resample-lp5.mrc in map adaptor-resample.mrc using 133525
points
correlation = 0.9279, correlation about mean = 0.8608, overlap = 1.074e+04
steps = 124, shift = 6.63, angle = 11.6 degrees
Position of adaptor-resample-lp5.mrc (#9.2) relative to adaptor-resample.mrc
(#3) coordinates:
Matrix rotation and translation
1.00000000 -0.00002901 0.00000171 0.00501547
0.00002901 1.00000000 -0.00000015 -0.00597167
-0.00000171 0.00000015 1.00000000 0.02638708
Axis 0.00500982 0.05888369 0.99825228
Axis point 258.62591181 168.37271599 0.00000000
Rotation angle (degrees) 0.00166525
Shift along axis 0.02601445
> view matrix models
> #9.2,0.97942,-0.20181,-0.0013896,-182.12,0.2018,0.97942,-0.002844,-269.37,0.0019349,0.002505,0.99999,128.75
> view matrix models
> #9.2,0.97942,-0.20181,-0.0013896,-187.11,0.2018,0.97942,-0.002844,-267.64,0.0019349,0.002505,0.99999,127.16
> ui mousemode right "rotate selected models"
> view matrix models
> #9.2,0.98572,-0.16813,-0.0089302,-193.36,0.16804,0.98572,-0.010702,-260.47,0.010602,0.0090483,0.9999,124.17
> view matrix models
> #9.2,0.99094,-0.13376,-0.012101,-200.5,0.13363,0.99097,-0.011196,-254.59,0.013489,0.0094772,0.99986,123.52
> ui mousemode right "translate selected models"
> view matrix models
> #9.2,0.99094,-0.13376,-0.012101,-198.72,0.13363,0.99097,-0.011196,-255.08,0.013489,0.0094772,0.99986,126.95
> view matrix models
> #9.2,0.99094,-0.13376,-0.012101,-198.49,0.13363,0.99097,-0.011196,-254.45,0.013489,0.0094772,0.99986,126.92
> fitmap #9.2 inMap #3
Fit map adaptor-resample-lp5.mrc in map adaptor-resample.mrc using 133525
points
correlation = 0.9275, correlation about mean = 0.8603, overlap = 1.076e+04
steps = 84, shift = 4.85, angle = 4.02 degrees
Position of adaptor-resample-lp5.mrc (#9.2) relative to adaptor-resample.mrc
(#3) coordinates:
Matrix rotation and translation
0.99999998 0.00018447 -0.00000126 -0.03218046
-0.00018447 0.99999998 -0.00000785 0.04096629
0.00000126 0.00000785 1.00000000 0.00502448
Axis 0.04249504 -0.00680776 -0.99907348
Axis point 221.81593358 172.93482043 0.00000000
Rotation angle (degrees) 0.01057905
Shift along axis -0.00666622
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9.2 models
> show #!9.2 models
> hide #!9.2 models
> show #!9.2 models
> hide #!3 models
> volume #9.3 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #9.3 step 1
> volume #9.3 level 0.1
> volume #9.3 change image level -1.84e-05,0 level 0.3033,0.8 level 0.6783,1
> show #!7 models
> select add #9.3
6 models selected
> select clear
> select add #9.3
3 models selected
> ui mousemode right "translate selected models"
[Repeated 3 time(s)]
> view matrix models #9.3,1,0,0,-42.323,0,1,0,506.19,0,0,1,146.77
> ui mousemode right "rotate selected models"
> view matrix models
> #9.3,0.99609,0.027201,-0.084092,-42.323,0.057546,0.52255,0.85066,506.19,0.067081,-0.85217,0.51894,146.77
> view matrix models
> #9.3,0.94976,0.23518,0.20652,-42.323,-0.30337,0.85398,0.4227,506.19,-0.076951,-0.46412,0.88242,146.77
> ui mousemode right "translate selected models"
> view matrix models
> #9.3,0.94976,0.23518,0.20652,3.9049,-0.30337,0.85398,0.4227,-37.577,-0.076951,-0.46412,0.88242,31.922
> ui mousemode right "rotate selected models"
> view matrix models
> #9.3,0.96943,0.10676,0.22094,3.9049,-0.19852,0.87044,0.45047,-37.577,-0.14422,-0.48056,0.86502,31.922
> view matrix models
> #9.3,0.841,0.53999,-0.033584,3.9049,-0.48517,0.78018,0.39487,-37.577,0.23943,-0.3158,0.91812,31.922
> ui mousemode right "translate selected models"
> view matrix models
> #9.3,0.841,0.53999,-0.033584,3.4115,-0.48517,0.78018,0.39487,-33.445,0.23943,-0.3158,0.91812,24.821
> ui mousemode right "rotate selected models"
> view matrix models
> #9.3,0.85576,0.49414,-0.15331,3.4115,-0.4122,0.83025,0.3752,-33.445,0.31268,-0.25788,0.91418,24.821
> view matrix models
> #9.3,0.85334,0.4954,-0.16243,3.4115,-0.37506,0.79975,0.46876,-33.445,0.36213,-0.3391,0.86826,24.821
> view matrix models
> #9.3,0.93915,0.33941,0.052964,3.4115,-0.321,0.8122,0.48713,-33.445,0.12232,-0.47449,0.87172,24.821
> fitmap #9.3 inMap #7
Fit map capsid-resample-lp7-eraser.mrc in map symmismatch_ort-6.mrc using
10726236 points
correlation = 0.8979, correlation about mean = 0.3601, overlap = 2.316e+07
steps = 140, shift = 29.9, angle = 7.73 degrees
Position of capsid-resample-lp7-eraser.mrc (#9.3) relative to
symmismatch_ort-6.mrc (#7) coordinates:
Matrix rotation and translation
0.95108530 0.26280018 0.16239710 -0.00319231
-0.30892839 0.80906240 0.49998128 -0.00529530
0.00000578 -0.52569392 0.85067379 -0.00097435
Axis -0.86523170 0.13698889 -0.48229467
Axis point 0.00000000 -0.00248746 0.01032785
Rotation angle (degrees) 36.35005783
Shift along axis 0.00250662
> select clear
> hide #!7 models
> lighting full
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> lighting simple
> color #9.3 #ff557fff models
> color #9.3 #ffd3d7ff models
> color #9.3 #ffd4daff models
> color #9.3 #ffd4dcff models
> color #9.3 #c3a2a8ff models
> color #9.3 #ecc4cbff models
> color #9.3 #dab5bcff models
> color #9.3 #e7c0c7ff models
> color #9.3 #e7cbcfff models
> color #9.3 #e7d0d3ff models
> color #9.3 #e7c4c8ff models
> color #9.3 #e3c0c5ff models
> color #9.3 #aa557fff models
> color #9.3 #aa9596ff models
> color #9.3 #aa9a9aff models
> color zone #2 near #10 distance 3
> color zone #9.3 near #10 distance 6.6
> color #10 #b48b82ff
> color zone #9.3 near #10 distance 6.6
> lighting full
> color #10 #ff557fff
> color #10 #ff97a1ff
> color #10 #ffafc0ff
> color #10 #ff8ca5ff
> color #10 #d37488ff
> color zone #9.3 near #10 distance 6.6
> color #10 #ffaa7fff
> color #10 #aa557fff
> color #10 #aa7783ff
> color #10 #aa6977ff
> color #10 #aa717fff
> color zone #9.3 near #10 distance 6.6
[Repeated 1 time(s)]
> color #10 #ffaa7fff
> color #10 #aa5500ff
> color #10 #aa8487ff
> color #10 #aa5500ff
> color #10 #aa641fff
> color #10 #aa8456ff
> color zone #9.3 near #10 distance 6.6
> color #10 #aa8d5fff
> color zone #9.3 near #10 distance 6.6
> color #10 #aa947aff
> color #10 #aa9c90ff
> color #10 #aa9a79ff
> color zone #9.3 near #10 distance 6.6
[Repeated 1 time(s)]
> color #10 #ffaaffff
> color #10 #ffc1ffff
> color #10 #ffaefeff
> color #10 #ffb5f3ff
> color #10 #c88ebeff
> color #10 #d698ccff
> color zone #9.3 near #10 distance 6.6
> color #10 #d6a9d0ff
> color #10 #d6b9d1ff
> color zone #9.3 near #10 distance 6.6
> color #10 #d6c5d3ff
> color zone #9.3 near #10 distance 6.6
> color #10 #d6afd2ff
> color #10 #be9bbaff
> color zone #9.3 near #10 distance 6.6
[Repeated 1 time(s)]
> color #10 white
> color #9.3 white models
> color #9.3 #d1d1d1ff models
> color #9.3 #bebebeff models
> color #9.3 #b6b6b6ff models
> color #9.3 #cacacaff models
> color #9.3 #bababaff models
> color #9.3 #a6a6a6ff models
> color #9.3 #c1c1c1ff models
> color #9.3 #abababff models
> color #9.3 #aaaa7fff models
> color #9.3 #aaaa93ff models
> color #9.3 #a8aa9bff models
> color #9.3 #cdcfbdff models
> color #9.3 #c6c8b7ff models
> color #9.3 #c3c5b4ff models
> color #9.3 #b7b9a9ff models
> color #9.3 #c6c8b7ff models
> color #10 #9966ccff
> color #10 #96c3d8ff
> color zone #9.3 near #10 distance 6.6
> color #10 #aaddf5ff
> color #10 #a2d3eaff
> color zone #9.3 near #10 distance 6.6
> color #9.3 #ffaaddff models
> color #9.3 #fadcb4ff models
> color #9.3 #fae7c1ff models
> color #9.3 #faecccff models
> color #9.3 #faf1d7ff models
> color #9.3 #faf1cbff models
> color #10 #ee33bbff
> color #10 #e3b87fff
> color zone #9.3 near #10 distance 6.6
> color #10 #d4ac77ff
> color #10 #c7a170ff
> color #10 #ba9768ff
> color zone #9.3 near #10 distance 6.6
> color #10 #f1c387ff
> color #10 #f1c794ff
> color zone #9.3 near #10 distance 6.6
> view orient
> lighting simple
> lighting full
> color #9.2 cyan models
> color #9.2 #aaaaffff models
> color #9.2 #aaaa7fff models
> color #9.2 #aaaa6fff models
> color #9.2 #aaa86dff models
> color #9.2 #8baa63ff models
> color #9.2 #8baa69ff models
> color #9.2 #738d57ff models
> color #9.5 #00aaffff models
> color #9.5 #17a6ffff models
> color #9.5 #11fff7ff models
> color #9.5 #557766ff models
> color #9.5 #576fa0ff models
> color #9.2 #bb5577ff models
> color #9.2 #b57979ff models
> color #9.1 #117799ff models
> color #9.1 #179454ff models
> color #9.1 #55aa00ff models
> color #9.1 #00aa7fff models
> color #9.1 #aa557fff models
> color #9.1 #00557fff models
> color #9.1 #55007fff models
> color #9.1 #55557fff models
> color #9.1 #aa55ffff models
> color #9.1 #aaaaffff models
> color #9.1 #996666ff models
> color #9.1 #9667b9ff models
> color #9.1 #996666ff models
> color #9.1 #44ffaaff models
> color #9.1 #4fa772ff models
> color #9.1 #44ffaaff models
> color #9.1 #aaccddff models
> color #9.1 #acd59fff models
> color #9.3 #aaffffff models
> color #9.3 #bbffffff models
> color #9.3 #d0fffdff models
> color #9.3 #ddffffff models
> color #9.3 #d0fffcff models
> color #10 #aaffffff
> color #10 #5afff1ff
> color #10 #93ffffff
> color #10 #68b4b4ff
> color zone #9.3 near #10 distance 6.6
> color #10 #7292b4ff
> color #10 #7c97b4ff
> color zone #9.3 near #10 distance 6.6
> color #10 #859db4ff
> color #10 #91a4b4ff
> color zone #9.3 near #10 distance 6.6
> color #10 #9ea6b4ff
> color #10 #95a1b4ff
> color #10 #9ca6b4ff
> color #10 #8694b4ff
> color #10 #8fa2b4ff
> color zone #9.3 near #10 distance 6.6
> color #10 #aaaa7fff
> color #10 #9c9c74ff
> color #10 #9c9b81ff
> color zone #9.3 near #10 distance 6.6
> color #10 #55aa7fff
> color #10 #69aa89ff
> color #10 #8baa9cff
> color zone #9.3 near #10 distance 6.6
> color #10 #8caa9cff
> color #10 #91aa9cff
> color #10 #92aa9cff
> color zone #9.3 near #10 distance 6.6
> color #9.3 #aaaa7fff models
> color #9.3 #a9aa8dff models
> color #9.3 #a8aa97ff models
> color #9.3 #a8aa9dff models
> color #9.3 #aaa79cff models
> color #9.3 #aaa999ff models
> color #9.3 #b8b6a5ff models
> color zone #9.3 near #10 distance 6.6
> color #10 #aaaa7fff
> color zone #9.3 near #10 distance 6.6
> color #10 #c7c794ff
> color #10 #ffaa7fff
> color #10 #c88564ff
> color zone #9.3 near #10 distance 6.6
> color #10 #c89973ff
> color #10 #c8a283ff
> color #10 #e8bc98ff
> color zone #9.3 near #10 distance 6.6
> color #9.5 #0055ffff models
> color #9.5 #55557fff models
> color #9.5 #ff5500ff models
> color #9.5 #ff5622ff models
> color #9.5 #d0461cff models
> color #9.5 #d07039ff models
> color #9.5 #d08840ff models
> color #9.5 #d09c53ff models
> color #9.2 #00aa7fff models
> color #9.2 #11aa6aff models
> color #9.2 #46aa73ff models
> color #9.2 #56d08dff models
> color #9.2 #5bdd96ff models
> color #9.2 #54cb89ff models
> color #9.1 #aaaaffff models
> color #9.1 #aa5500ff models
> color #9.1 #aa5f1dff models
> color #9.1 #aa853cff models
> color #9.3 #ffaaffff models
> color #9.3 #ffc7feff models
> color #9.3 #ffe1fbff models
> color #9.3 #fde6ffff models
> color #9.3 #fad3ffff models
> color #9.3 #e4b9ffff models
> color #9.3 #ff557fff models
> color #9.3 #ffabb6ff models
> color #9.3 #ffc1caff models
> color #9.3 #ffd3daff models
> color #9.3 #ffd9dfff models
> color #9.3 #ffdee3ff models
> color #10 #ff5500ff
> color #10 #aaaaffff
> color #10 #bdbdffff
> color #10 #a4a4ceff
> color zone #9.3 near #10 distance 6.6
> color #10 #ff557fff
> color #10 #ff8198ff
> color #10 #c56476ff
> color #10 #c58186ff
> color zone #9.3 near #10 distance 6.6
> color #10 #c58f96ff
> color zone #9.3 near #10 distance 6.6
[Repeated 1 time(s)]
> color #9.3 #ffddddff models
> color #9.3 #fdd7cdff models
> color #9.3 #ffddddff models
> color #9.3 #ffffccff models
> color #9.3 #ffcfd2ff models
> color #9.3 #ffffccff models
> color #9.3 #ee77ffff models
> color #9.3 #e7fff2ff models
> color #9.3 #ee77ffff models
> color #9.3 #dd99ddff models
> color #9.3 #d9d0bfff models
> color #10 #cc5588ff
> color #10 #dd44aaff
> color #10 #d4ab88ff
> color zone #9.3 near #10 distance 6.6
> color #9.1 #550011ff models
> color #9.1 #501d8aff models
> color #9.1 #550011ff models
> color #9.1 #555500ff models
> color #9.1 #aaaaffff models
> color #9.1 #8787cbff models
> color #9.1 #7878b4ff models
> color #9.1 #ffaa00ff models
> color #9.1 #ff5500ff models
> color #9.1 #ff557fff models
> color #9.1 #aa5500ff models
> color #9.1 #55aaffff models
> color #9.1 #ffaaffff models
> color #9.1 #55ffffff models
> color #9.1 #55ff7fff models
> color #9.1 #55ff00ff models
> color #9.1 red models
> color #9.1 #ff5500ff models
> color #9.1 #555500ff models
> color #9.1 #0055ffff models
> color #9.1 #aa00ffff models
> color #9.1 #33ffaaff models
> color #9.1 #3fab47ff models
> color #9.2 #cc9944ff models
> color #9.2 #c94733ff models
> color #9.5 #22eeffff models
> color #9.5 #22ee55ff models
> color #9.5 #2e5fa1ff models
> color #9.5 #3d7ed4ff models
> color #9.5 #438beaff models
> lighting simple
> color #9.1 #ffaa00ff models
> color #9.1 #003366ff models
> color #9.1 #036f73ff models
> color #9.3 #beb6a7ff models
> color #9.3 #a8a194ff models
> color #9.3 #bcb4a5ff models
> color #9.3 white models
> color #9.3 #c2c2c2ff models
> color #9.3 #969696ff models
> color #9.3 #b5b5b5ff models
> color #9.3 #c7c7c7ff models
> color #9.3 #b9b9b9ff models
> color #9.3 #a5a5a5ff models
> lighting shadows true
> lighting simple
> lighting full
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> lighting simple
> color #9.3 cyan models
> color #9.3 #aaffffff models
> color #9.3 #55ffffff models
> color #9.3 #aaffffff models
> color #9.3 #7dbcbcff models
> color #9.3 #92bbbcff models
> color #9.3 #9cb8bcff models
> color #9.3 #a6babcff models
> color #9.3 #9db9bcff models
> color #9.1 white models
> color #10 cyan
> color zone #9.3 near #10 distance 6.6
> color #10 #5efff2ff
> color #10 #94fff6ff
> color #10 #64aca6ff
> color zone #9.3 near #10 distance 6.6
> lighting full
> set bgColor white
> set bgColor #ffffff00
> lighting simple
> set bgColor black
> set bgColor transparent
> color #10 #aaaa7fff
> color #10 red
> color #10 #ff5500ff
> color #10 #ffaa7fff
> color #10 #ffc9aeff
> color zone #9.3 near #10 distance 6.6
> color #10 white
> color #9.3 #ffaa7fff models
> color #9.3 #ffdcabff models
> color #9.3 #ffe7c0ff models
> color #9.3 #ffd19dff models
> color #9.3 #ffc57dff models
> color #9.3 #ffe39cff models
> color #9.3 #ffdcaaff models
> color #9.3 #caae87ff models
> color #9.3 #e1c296ff models
> color #9.3 #dfc095ff models
> color #9.3 #ccb088ff models
> color #9.3 #d9bb91ff models
> color #9.3 #ccb088ff models
> set bgColor white
> set bgColor #ffffff00
> ui tool show "Color Actions"
> select add #9.3
3 models selected
> color sel moccasin
> color sel bisque
[Repeated 1 time(s)]
> color sel light steel blue
> color sel light blue
> color sel tan
> color sel lavender
> color sel light cyan
> color sel gainsboro
> color sel alice blue
> color sel honeydew
> color sel lavender
> color sel violet
> color sel light cyan
> color sel lavender
> select add #10
144660 atoms, 146760 bonds, 60 pseudobonds, 19740 residues, 5 models selected
> select clear
> select add #10
144660 atoms, 146760 bonds, 60 pseudobonds, 19740 residues, 2 models selected
> color sel plum
> color zone #9.3 near #10 distance 6.6
> color sel pink
> color zone #9.3 near #10 distance 6.6
> color sel saddle brown
> color zone #9.3 near #10 distance 6.6
> color sel sandy brown
> color zone #9.3 near #10 distance 6.6
> color sel rosy brown
> color zone #9.3 near #10 distance 6.6
> select add #9.3
144660 atoms, 146760 bonds, 60 pseudobonds, 19740 residues, 5 models selected
> select subtract #10
3 models selected
> color sel silver
> select add #9.3
3 models selected
> select add #10
144660 atoms, 146760 bonds, 60 pseudobonds, 19740 residues, 5 models selected
> color sel tan
> select clear
> select add #9.3
3 models selected
> color sel wheat
> color sel silver
> color sel dark gray
> color sel gainsboro
> color sel silver
> select clear
> select add #10
144660 atoms, 146760 bonds, 60 pseudobonds, 19740 residues, 2 models selected
> color sel wheat
> color zone #9.3 near #10 distance 6.6
> ui tool show "Surface Color"
> color radial #9.3.2 palette 320,#eab578:350,#c28161
> color radial #9.3.2 palette 320,#c6c6c6:350,#c28161
> color radial #9.3.2 palette 310,#c6c6c6:350,#c28161
> set bgColor white
> lighting full
> lighting simple
> select add #9.2
144660 atoms, 146760 bonds, 60 pseudobonds, 19740 residues, 5 models selected
> ui tool show "Color Actions"
> color sel rosy brown
> color sel burly wood
> color sel rosy brown
> color sel pale violet red
> color sel salmon
> color sel peru
> color sel light salmon
> color sel dark goldenrod
> color sel dark salmon
> color sel salmon
> color sel tomato
> color sel chocolate
> color sel indian red
> color sel fire brick
> color sel dark orange
> color sel coral
> color sel sienna
> color sel indian red
> color sel light pink
> color sel light coral
> lighting shadows true
> lighting shadows false
> lighting full
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting simple
> select clear
> select add #9.5
3 models selected
> color sel dark olive green
> color sel dark slate gray
> color sel turquoise
> color sel medium turquoise
> color sel light sea green
> color sel cornflower blue
> color sel dark cyan
> color sel cornflower blue
> color sel steel blue
> color sel light sea green
> color sel cornflower blue
> color sel slate gray
> color sel light slate gray
> color sel deep sky blue
> color sel cyan
> color sel steel blue
[Repeated 1 time(s)]
> color sel fire brick
> color sel tomato
> color sel forest green
> color sel lime green
> color sel olive drab
> color sel steel blue
> color sel cadet blue
> color sel steel blue
> color sel cadet blue
> color sel light slate gray
> color sel steel blue
> color sel cadet blue
> color sel teal
> color sel dark cyan
> color sel medium aquamarine
> color sel cornflower blue
> color sel light sea green
> color sel medium turquoise
> color sel light steel blue
> color sel medium purple
> color sel pale turquoise
> color sel light steel blue
> color sel powder blue
> color sel dark gray
> color sel pale green
> color sel dark sea green
> color sel light cyan
> color sel light blue
> color sel light sky blue
> color sel sky blue
> select clear
> select add #9.1
2 models selected
> color sel pale green
> color sel light green
> color sel dark sea green
> color sel medium aquamarine
> color sel dark cyan
> color sel yellow green
> color sel lime
> color sel olive
> color sel indian red
> color sel brown
> color sel cyan
> color sel medium purple
> color sel dark olive green
> color sel dark slate gray
> color sel dark sea green
> color sel aquamarine
> color sel dark green
> color sel teal
> color sel medium aquamarine
> color sel lime
> color sel chocolate
> color sel saddle brown
> color sel coral
> color sel sienna
> color sel indian red
> color sel sienna
> lighting soft
> lighting full
> set bgColor white
> lighting simple
> color sel crimson
> color sel maroon
> color sel fire brick
> color sel saddle brown
> color sel sienna
> color sel saddle brown
> color radial #9.3.2 palette 310,#ffc898:350,#c2826d
> color radial #9.3.2 palette 310,#ffe5dc:350,#c2826d
> color radial #9.3.2 palette 310,#b5b5b5:350,#c2826d
> color sel sienna
> color sel coral
> color sel goldenrod
> color sel sandy brown
> color sel dark orange
> color sel olive drab
> color sel burly wood
> color sel tan
> color sel wheat
> color sel peru
> color sel light salmon
> color #9.1 #ffc783ff models
> color #9.1 #ffcf95ff models
> color #9.1 #ffc198ff models
> color #9.1 #c9ffe0ff models
> color #9.1 #87ff62ff models
> color #9.1 #a7ffa6ff models
> color #9.1 #c0ff9eff models
> color #9.1 #deffacff models
> color #9.1 #dfffb0ff models
> color #9.1 #6fca37ff models
> color #9.1 #3bca2cff models
> color #9.1 #4eca5cff models
> color #9.1 #ca8889ff models
> color #9.1 #ca8e8fff models
> color #9.1 #ca8e97ff models
> color #9.1 #ca8fa4ff models
> color #9.1 #ca8087ff models
> color #9.1 #ca8085ff models
> color #9.1 #ca5b6fff models
> color #9.1 #ca8384ff models
> color #9.2 #aa0000ff models
> color #9.2 #d60000ff models
> color #9.2 #e80000ff models
> color #9.2 #670000ff models
> color #9.2 #910000ff models
> color #9.2 darkred models
> color #9.2 #9e0000ff models
> color #9.2 #9d0000ff models
> color #9.2 #a60000ff models
> color #9.2 #a10000ff models
> color #9.5 #5555ffff models
> color #9.5 #55aaffff models
> color #9.5 #00aaffff models
> color #9.5 #0099e5ff models
> color #9.5 #008bd1ff models
> color #9.5 #0090d8ff models
> color #9.1 #555500ff models
> color #9.1 #aa557fff models
> color #9.1 #00aa7fff models
> color #9.1 #aaaa7fff models
> color #9.1 #55aa7fff models
> color #9.1 #55ff7fff models
> color #9.1 #55aa7fff models
> color #9.1 #55ff7fff models
> color #9.1 yellow models
> color #9.1 #55ff00ff models
> color #9.1 #3bb100ff models
> color #9.1 #3fbe00ff models
> color #9.1 #67be57ff models
> color #9.1 #76be6eff models
> color #9.1 #95be7fff models
> color #9.1 #99be7bff models
> color #9.1 #6bbe67ff models
> color #9.1 #aaaa7fff models
> color #9.1 #97aa7bff models
> color #9.2 #97aa7bff models
> color #9.5 #ff557fff models
> color #9.5 #ff007fff models
> color #9.5 magenta models
> color #9.5 red models
> color #9.5 #aa00ffff models
> color #9.5 #aa55ffff models
> color #9.5 #aaaaffff models
> color #9.5 #9f9fefff models
> color #9.5 #9696e1ff models
> color #9.5 #9393ddff models
> color #9.1 #aa55ffff models
> color #9.1 #aaaaffff models
> color #9.1 #00aaffff models
> color #9.1 #aa5500ff models
> color #9.1 #aa4d41ff models
> color #9.1 white models
> lighting soft
> set bgColor white
> lighting simple
> color #9.2 #555500ff models
> color #9.2 #55aa00ff models
> color #9.2 #55aa7fff models
> color #9.2 #4e9d74ff models
> color #9.2 #4d9a72ff models
> color #9.2 #555500ff models
> color #9.2 #55aa00ff models
> color #9.2 #4baa3aff models
> color #9.2 #aa5500ff models
> color #9.2 #aa8b3eff models
> color #9.2 #aa783eff models
> color #9.2 #aa703eff models
> color #9.2 #aa6a4bff models
> color #9.2 #aa614bff models
> color #9.2 #aa5e4bff models
> color #9.2 #aa564bff models
> color #9.2 #aa5957ff models
> color #9.2 #aa7256ff models
> color #9.2 #8462aaff models
> color #9.2 #9063aaff models
> color #9.2 #9b63aaff models
> color #9.2 #9e63aaff models
> color #9.5 cyan models
> color #9.5 #0055ffff models
> color #9.5 blue models
> color #9.5 #55007fff models
> color #9.5 #7f00bfff models
> color #9.5 #7300adff models
> color #9.5 #7c00baff models
> color #9.5 #8300c5ff models
> color #9.2 blue models
> color #9.2 #0055ffff models
> color #9.2 #00aaffff models
> color #9.2 #008bd1ff models
> color #9.2 #0082c3ff models
> color #9.1 #00aa7fff models
> color #9.1 #aa5500ff models
> color #9.1 #aaa74eff models
> color #9.1 #aa7b5cff models
> color #9.1 #aa6b5fff models
> color #9.1 #aa665fff models
> color #9.1 #aa928eff models
> color #9.1 #aa928fff models
> color #9.1 #aa9090ff models
> lighting soft
> lighting simple
> ui tool show "Color Actions"
> color #9.2 #88eebbff models
> color #9.2 #8eb4d0ff models
> color #9.5 #bb7799ff models
> color #9.5 #b793bdff models
> color #9.5 #a786adff models
> color #9.5 #987a9dff models
> color #9.5 #8c7191ff models
> color #9.5 #826987ff models
> color #9.4 #9adcdcff models
> color #9.2 #82a5beff models
> color #9.2 #7798afff models
> color #9.2 #6e8ca1ff models
> lighting full
> lighting soft
> color #9.2 #90b7d3ff models
> color #9.2 #9ac3e1ff models
> color #9.2 #9ec9e8ff models
> color #9.2 #a9d7f8ff models
> color #9.5 #c09bc7ff models
> color #9.5 #d2a9daff models
> color #9.5 #daafe2ff models
> color #9.5 #e29fdfff models
> color #9.5 #d7a0e2ff models
> color #9.5 #d8a7e2ff models
> color #9.5 #c39ee2ff models
> color #9.5 #c29ce2ff models
> color #9.1 #cc44eeff models
> color #9.1 #c4e3ccff models
> color #9.1 #cc44eeff models
> color #9.1 #8844bbff models
> color #9.1 #84b967ff models
> color #9.1 #77cc77ff models
> color #9.1 #7c7ab7ff models
> color #9.1 #7cab7cff models
> color #9.1 #c7ab7cff models
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting shadows false
> lighting soft
> lighting simple
> lighting soft
> color #9.1 #8844ccff models
> color #9.1 #84c3b7ff models
> ui tool show "Color Actions"
> color sel tan
> color sel burly wood
> color sel tan
> color sel wheat
> color sel tan
> color sel sandy brown
> color sel goldenrod
> color sel peru
> color sel tan
> color sel burly wood
> color sel tan
> color sel peach puff
> color sel navajo white
> color sel tan
> select clear
> select add #9.5
3 models selected
> ui tool show "Color Actions"
> color sel light coral
> color sel pale violet red
> color sel medium orchid
> color sel medium violet red
> color sel fire brick
> color sel maroon
> color sel crimson
> color sel dark goldenrod
> color sel light salmon
> color sel dark khaki
> color sel peru
> color sel goldenrod
> color sel sandy brown
> color sel dark orange
> color sel indian red
> color sel sienna
> color sel coral
> color sel sienna
> color sel indian red
> color sel sienna
> color sel saddle brown
> color sel chocolate
> color sel brown
> color sel tomato
> color sel fire brick
> color sel saddle brown
> color sel chocolate
> color sel coral
> color sel sienna
[Repeated 1 time(s)]
> color sel indian red
> color sel dark goldenrod
> color sel peru
> color sel yellow green
> color sel olive
> color sel goldenrod
> color sel dark orange
> color sel orange
> color sel olive drab
> color sel tan
> color sel burly wood
> color sel light coral
> color sel burly wood
> color sel wheat
> color sel khaki
> color sel pale goldenrod
> color sel wheat
> color sel linen
> color sel antique white
> color sel light pink
> color sel bisque
> color sel navajo white
> color sel lemon chiffon
> color sel tan
> color sel gray
> color sel slate gray
> select clear
> select add #9.2
3 models selected
> color sel teal
> color sel dark cyan
> color sel rosy brown
> color sel dark olive green
> color sel coral
> color sel saddle brown
> color sel indian red
> color sel coral
> color sel dark red
> color sel sandy brown
> color sel goldenrod
> color sel olive drab
> color sel dark sea green
> color sel burly wood
> color sel orchid
> color sel wheat
> color sel pink
> set bgColor white
> set bgColor black
> set bgColor transparent
> lighting simple
> lighting soft
> set bgColor white
> set bgColor #ffffff00
> color sel medium turquoise
> color sel turquoise
> color sel light sea green
> color sel medium turquoise
> color sel turquoise
> color sel dodger blue
> color sel dark turquoise
> color sel sky blue
> color sel light sky blue
> color sel light blue
> color sel pale turquoise
> color sel sky blue
> select clear
> select add #9.2
3 models selected
> color sel steel blue
> color sel thistle
> select clear
> ui mousemode right clip
> ui tool show "Side View"
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
Drag select of 9.1 7-fiber.mrc , 9.2 adaptor-resample-lp5.mrc , 9.3 capsid-
resample-lp7-eraser.mrc , 9.4 core-resample-lp5.mrc , 9.5 nozzle-resample-
lp5.mrc , 9.6 portal-resample-lp5.mrc
> graphics silhouettes false
> select clear
> ui tool show "Color Actions"
> color sky blue
> select add #9.3
3 models selected
> color radial #9.3.2 palette 310,#e0ffff:350,#afeeee
> color radial #9.3.2 palette 310,#b0e0e6:350,#87ceeb
> color radial #9.3.2 palette 310,#fdf5e6:350,#87ceeb
> color radial #9.3.2 palette 310,#fdf5e6:350,#a9a9a9
> color radial #9.3.2 palette 310,#b0e0e6:350,#00bfff
> color radial #9.3.2 palette 310,#708090:350,#00bfff
[Repeated 2 time(s)]
> color radial #9.3.2 palette 310,#708090:350,#fdfdfd
> color radial #9.3.2 palette 310,#708090:350,#0000ff
> color radial #9.3.2 palette 310,#708090:350,#4682b4
> color radial #9.3.2 palette 310,#778899:350,#4682b4
> color radial #9.3.2 palette 310,#8da2b6:350,#4682b4
> color radial #9.3.2 palette 310,#8699ac:350,#4682b4
> ui tool show "Color Actions"
> color sel saddle brown
> color radial #9.3.2 palette 310,#8699ac:350,#4682b4
> select clear
> select add #9.2
3 models selected
> color sel sienna
> color sel coral
> color sel olive drab
> color sel dark salmon
> color sel sandy brown
> color sel cornflower blue
> color sel medium purple
> color sel blue violet
> color sel tan
> color sel dark slate blue
> color sel dark turquoise
> color sel cornflower blue
> color sel dark turquoise
> select clear
> select add #9.1
2 models selected
> select clear
> select add #9.1
2 models selected
> color sel dark turquoise
> color sel medium spring green
> color sel medium slate blue
> color sel light sea green
> color sel olive
> color sel light slate gray
> color sel teal
> color sel steel blue
> color sel dark cyan
> color sel cornflower blue
> color sel gray
> color sel light steel blue
> color sel light blue
> color sel pale turquoise
> color sel sky blue
> select clear
> select add #9.2
3 models selected
> color sel medium aquamarine
> select clear
> select add #9.5
3 models selected
> color sel orchid
> color sel medium purple
> color sel gainsboro
> select clear
> color radial #9.3.2 palette 310,#dcdcdc:350,#4682b4
> color radial #9.3.2 palette 310,#c0c0c0:350,#4682b4
> color radial #9.3.2 palette 310,#c0c0c0:350,#bc8f8f
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting soft
> select clear
> select add #9.1
2 models selected
> color sel burly wood
> color sel tan
> color sel rosy brown
> color sel antique white
> color sel wheat
> color sel navajo white
> color sel peach puff
> color sel sandy brown
> color sel dark salmon
> color sel light salmon
> color sel dark salmon
> color sel salmon
> color sel dark salmon
> color sel blanched almond
> color radial #9.3.2 palette 310,#f5deb3:350,#bc8f8f
> color radial #9.3.2 palette 310,#fff5ee:350,#bc8f8f
> color radial #9.3.2 palette 310,#d1d1d1:350,#bc8f8f
> graphics silhouettes false
> color radial #9.3.2 palette 300,#d1d1d1:350,#bc8f8f
> select clear
> select add #9.2
3 models selected
> color sel burly wood
> color sel tan
> color sel rosy brown
> color sel orchid
> color sel pale violet red
> color sel coral
> color sel saddle brown
> color sel sienna
> color sel salmon
> color sel light salmon
> color sel dark goldenrod
> color sel tomato
> color sel saddle brown
> color sel sandy brown
> color sel fire brick
> color sel maroon
> color sel orange red
> color sel crimson
> color sel rosy brown
> color sel deep pink
> color sel hot pink
> color sel dark violet
> color sel deep pink
> color sel medium violet red
> color sel deep pink
> color sel magenta
> color sel deep pink
> color sel pale violet red
> select clear
> select add #9.5
3 models selected
> color sel salmon
> color sel red
> color sel dark red
> color sel sienna
> color sel indigo
> color sel medium violet red
> color sel light coral
> color sel slate blue
> color sel medium slate blue
> color sel indigo
> color sel steel blue
> color sel teal
> color sel steel blue
> color sel sienna
> color sel saddle brown
> color sel fire brick
> color sel crimson
> color sel dark red
> color sel sienna
> color sel salmon
> color sel dark salmon
> select clear
> select add #9.1
2 models selected
> color sel coral
> color sel sienna
> color sel salmon
> color sel dark salmon
> color sel peru
> color sel dark goldenrod
> color sel olive
> color sel indian red
> color sel sienna
> color sel dark orange
> color sel goldenrod
> color sel sandy brown
> select clear
> select add #9.5
3 models selected
> color sel indian red
> color sel purple
> color sel dark olive green
> color sel light coral
> color sel pink
> color sel light pink
> color sel deep pink
> color sel magenta
> color sel hot pink
> color sel pale violet red
> color sel cadet blue
> color sel light slate gray
> color sel slate gray
> color sel light slate gray
> hide #!9.3 models
> select clear
> select add #9.2
3 models selected
> select add #9.2
3 models selected
> select add #9.6
6 models selected
> select add #9.2
6 models selected
> select clear
> select add #9.6
3 models selected
> color sel teal
> color sel light sea green
> color sel medium turquoise
> color sel turquoise
> color sel dark turquoise
> color sel pale turquoise
> hide #!9.1 models
> color sel royal blue
> color sel slate gray
> color sel cadet blue
> color sel cornflower blue
> color sel blue violet
> color sel dark violet
> color sel rebecca purple
> color sel medium purple
> color sel sky blue
> hide #!9.2 models
> show #!9.2 models
> select add #9
18 models selected
> select clear
> select add #9.4
3 models selected
> color sel deep pink
> color sel blue violet
> color sel medium orchid
> color sel medium purple
> color sel thistle
> color sel light pink
> color sel medium purple
> color sel plum
> color sel violet
> color sel hot pink
> color sel rosy brown
> color sel violet
> color sel plum
> color sel pale violet red
> color sel salmon
> color sel coral
> color sel light salmon
> color sel plum
> color sel violet
> color sel medium violet red
> color sel dark orchid
> color sel dark magenta
> color sel purple
> color sel medium purple
> color sel brown
> color sel chocolate
> color sel indian red
> color sel light salmon
> color sel light coral
> color sel blue violet
> color sel orchid
> color sel medium orchid
> color sel medium purple
> show #!9.3 models
> select clear
> select add #9.2
3 models selected
> color sel peach puff
> color sel navajo white
> show #!9.1 models
> select clear
> select add #9.1
2 models selected
> color sel peach puff
> color sel navajo white
> color sel moccasin
> color sel burly wood
> color sel wheat
> color sel antique white
> color sel tan
> color sel rosy brown
> color sel tan
> color sel burly wood
> color sel tan
> select subtract #9.1
Nothing selected
> select add #9.2
3 models selected
> color sel thistle
> hide #!9.1 models
> show #!9.1 models
> hide #!9.1 models
> color sel burly wood
> color sel light coral
> color sel pale violet red
> color sel rosy brown
> color sel light coral
> color sel light pink
> color sel light salmon
> color sel dark salmon
> color sel orchid
> color sel hot pink
> color sel pale violet red
> color sel thistle
> color sel plum
> color sel lavender
> color sel violet
> color sel pink
> color sel peach puff
> color sel misty rose
> color sel lavender blush
> color sel alice blue
> color sel burly wood
> color sel light pink
> color sel plum
> color sel salmon
> color sel light salmon
> color sel hot pink
> color sel pale violet red
> show #!9.1 models
> select clear
> select add #9.1
2 models selected
> color sel burly wood
> color sel tan
> color sel rosy brown
> color sel thistle
> color sel silver
> color sel antique white
> color sel wheat
> color sel peach puff
> color sel tan
> color sel peach puff
> color sel burly wood
> color sel tan
> color sel wheat
> color sel antique white
> color sel linen
> color sel burly wood
> color #9.1 #c6a984ff models
> color #9.1 #b09775ff models
> color #9.1 #bca17dff models
> color #9.1 #b49a78ff models
> color #9.1 #ba9f7cff models
> color #9.1 #b89d7bff models
> color #9.1 #ad9473ff models
> color #9.1 #a78f6fff models
> color #9.1 #af9675ff models
> color #9.1 #b49a78ff models
> color #9.1 #ad9473ff models
> color #9.1 #988265ff models
> color #9.1 #87745aff models
> color #9.1 #aa9171ff models
> color #9.1 #b99e7bff models
> color #9.1 #a38b6dff models
> color #9.1 #b89d7bff models
> color #9.1 #a58d6eff models
> color #9.1 #ccaf88ff models
> color #9.1 #b69c79ff models
> select clear
> hide #!9.1 models
> select add #9.2
3 models selected
> color #9.2 #be6180ff models
> color #9.2 #b65d7bff models
> color #9.2 #954c64ff models
> color #9.2 #d96f92ff models
> color #9.2 #e8769cff models
> color #9.2 #fa7fa8ff models
> color #9.2 #ff82acff models
> color sel light coral
[Repeated 1 time(s)]
> color sel rosy brown
> color sel pink
> color sel wheat
> color sel orchid
> color sel thistle
> color sel burly wood
> color sel pink
> color sel light salmon
> color sel plum
> color sel violet
> color sel light pink
> color sel light coral
> color sel pale violet red
> select clear
> select add #9.2
3 models selected
> color #9.2 #ec789fff models
> color #9.2 #f17ba2ff models
> color #9.2 #fd81aaff models
> color #9.2 #eb789eff models
> color #9.2 #f07aa2ff models
> color #9.2 #f17ba2ff models
> color #9.2 #ff82acff models
> color #9.2 #f07aa2ff models
> color #9.2 #f97fa8ff models
> color #9.2 #ef7aa1ff models
> show #!9.1 models
> hide #!9.1 models
> show #!9.1 models
> hide #!9.1 models
> select add #9.2
3 models selected
> select add #9.5
6 models selected
> select clear
> select add #9.5
3 models selected
> color #9.2 #55557fff models
> color sel pale violet red
> select clear
> select add #9.2
3 models selected
> color sel pale violet red
> select clear
> color #9.2 #ef7aa1ff models
> color #9.2 #f97fa8ff models
> color #9.2 #a65570ff models
> color #9.2 #e5759aff models
[Repeated 1 time(s)]
> color #9.2 #de7195ff models
> select add #9.5
3 models selected
> color sel slate blue
> color sel cornflower blue
> color sel light blue
[Repeated 1 time(s)]
> color sel slate gray
> color sel light slate gray
> select clear
> color #9.5 #a0b7ceff models
> color #9.5 #8b9fb3ff models
> color #9.5 #9bb2c8ff models
> color #9.5 #94aabfff models
> show #!9.1 models
> hide #!9.1 models
> show #!9.1 models
> hide #!9.1 models
> show #!9.1 models
> hide #!9.1 models
> color #9.2 #aaaaffff models
> select add #9.2
3 models selected
> color sel dark turquoise
> color sel cadet blue
> color sel sandy brown
> color sel old lace
> color sel silver
> color sel light gray
> color sel pale turquoise
> color sel sky blue
> color sel hot pink
> color sel orchid
> color sel steel blue
> color sel light steel blue
> color sel pale turquoise
> color sel azure
> color sel turquoise
> color sel tan
> color sel rosy brown
> color sel tan
> color sel pink
> color sel plum
> select clear
> color #9.2 #f1aff1ff models
> color #9.2 #f5b2f5ff models
> color #9.2 #c891c8ff models
> show #!9.1 models
> hide #!9.1 models
> color #9.2 #e5a6e5ff models
> color #9.2 #f4b1f4ff models
> color #9.2 #b382b3ff models
> color #9.2 #8c668cff models
> hide #!9.3 models
> color #9.2 #ecabecff models
> color #9.2 #f4b1f4ff models
> color #9.2 #feb8feff models
> color #9.2 #876287ff models
> color #9.2 #fdb8fdff models
> color #9.2 #e1a3e1ff models
> color #9.2 #eeadeeff models
> color #9.6 #aaaaffff models
> color #9.6 #aa557fff models
> color #9.6 #aaaaffff models
> color #9.4 #aa557fff models
> color #9.4 #aa00ffff models
> color #9.4 #aa55ffff models
> color #9.4 #aaaaffff models
> color #9.4 #00aaffff models
> color #9.4 #aaaaffff models
> color #9.4 #00aaffff models
> color #9.4 #aaaaffff models
> color #9.6 cyan models
> color #9.6 #00aaffff models
> color #9.6 #55aaffff models
> color #9.6 #5ee4ffff models
> color #9.6 #61c8ffff models
> color #9.6 #5da6ffff models
> color #9.6 #61b3ffff models
> show #!9.3 models
> show #!9.1 models
> lighting soft
> lighting simple
> lighting soft
> color radial #9.3.2 palette 300,#d1d1d1:350,#a77f7f
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\surfcolorgui.py", line 439, in _color
run(self.session, cmd, log = log_command)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 55, in color_radial
_color_geometry(session, surfaces, geometry = 'radial',
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 126, in _color_geometry
cs.set_vertex_colors()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 194, in set_vertex_colors
s.vertex_colors = self.vertex_colors()
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 180, in vertex_colors
va = vertices if sp.is_identity() else sp * vertices
~~~^~~~~~~~~~
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 130, in __mul__
return m34.apply_matrix(self._matrix, p)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color radial #9.3.2 palette 300,#d1d1d1:350,#a77f7f
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\surfcolorgui.py", line 439, in _color
run(self.session, cmd, log = log_command)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 55, in color_radial
_color_geometry(session, surfaces, geometry = 'radial',
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 126, in _color_geometry
cs.set_vertex_colors()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 194, in set_vertex_colors
s.vertex_colors = self.vertex_colors()
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 180, in vertex_colors
va = vertices if sp.is_identity() else sp * vertices
~~~^~~~~~~~~~
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 130, in __mul__
return m34.apply_matrix(self._matrix, p)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color radial #9.3.2 palette 300,#d1d1d1:350,#a77d6a
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\surfcolorgui.py", line 439, in _color
run(self.session, cmd, log = log_command)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 55, in color_radial
_color_geometry(session, surfaces, geometry = 'radial',
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 126, in _color_geometry
cs.set_vertex_colors()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 194, in set_vertex_colors
s.vertex_colors = self.vertex_colors()
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 180, in vertex_colors
va = vertices if sp.is_identity() else sp * vertices
~~~^~~~~~~~~~
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 130, in __mul__
return m34.apply_matrix(self._matrix, p)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color radial #9.3.2 palette 300,#d1d1d1:350,#a77d6a
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\surfcolorgui.py", line 439, in _color
run(self.session, cmd, log = log_command)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 55, in color_radial
_color_geometry(session, surfaces, geometry = 'radial',
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 126, in _color_geometry
cs.set_vertex_colors()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 194, in set_vertex_colors
s.vertex_colors = self.vertex_colors()
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 180, in vertex_colors
va = vertices if sp.is_identity() else sp * vertices
~~~^~~~~~~~~~
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 130, in __mul__
return m34.apply_matrix(self._matrix, p)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color radial #9.3.2 palette 300,#d1d1d1:350,#a77d6a
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\surfcolorgui.py", line 439, in _color
run(self.session, cmd, log = log_command)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 55, in color_radial
_color_geometry(session, surfaces, geometry = 'radial',
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 126, in _color_geometry
cs.set_vertex_colors()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 194, in set_vertex_colors
s.vertex_colors = self.vertex_colors()
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 180, in vertex_colors
va = vertices if sp.is_identity() else sp * vertices
~~~^~~~~~~~~~
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 130, in __mul__
return m34.apply_matrix(self._matrix, p)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color radial #9.3.2 palette 300,#d1d1d1:350,#a77d6a
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\surfcolorgui.py", line 439, in _color
run(self.session, cmd, log = log_command)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 55, in color_radial
_color_geometry(session, surfaces, geometry = 'radial',
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 126, in _color_geometry
cs.set_vertex_colors()
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 194, in set_vertex_colors
s.vertex_colors = self.vertex_colors()
^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\surface\colorgeom.py", line 180, in vertex_colors
va = vertices if sp.is_identity() else sp * vertices
~~~^~~~~~~~~~
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\place.py", line 130, in __mul__
return m34.apply_matrix(self._matrix, p)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 233. MiB for an
array with shape (10170704, 3) and data type float64
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\geometry\matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 552.41
OpenGL renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Inspiron 3020
OS: Microsoft Windows 11 家庭中文版 (Build 22631)
Memory: 16,924,782,592
MaxProcessMemory: 137,438,953,344
CPU: 24 13th Gen Intel(R) Core(TM) i7-13700F
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
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: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
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: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
comtypes: 1.1.14
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pywin32: 305
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
Change History (2)
comment:1 by , 14 months ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → color radial: ArrayMemoryError |
comment:2 by , 14 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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Trying to allocate 233 Mbyte numpy array of 10 million vertex positions for computing radial coloring. User had many large maps open up to 800 cubed. Computer had 16 Gbytes of memory. Still would not expect it to run out of memory. But somehow Windows is prone to running out of memory.