The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Volumes/groups/haselbach/Sascha/210421_26s_d1_3s_ist/relion_j273_beta_split_600_to_480px_bin/Class3D/19s_wo_rpn1_T=10/run_it025_class001.mrc
Opened run_it025_class001.mrc as #1, grid size 480,480,480, pixel 1.34, shown
at level 2.61e-06, step 2, values float32
> open
> /Volumes/groups/haselbach/Sascha/210421_26s_d1_3s_ist/relion_j273_beta_split_600_to_480px_bin/Class3D/19s_wo_rpn1_T=10/run_it025_class002.mrc
Opened run_it025_class002.mrc as #2, grid size 480,480,480, pixel 1.34, shown
at level 8.99e-07, step 2, values float32
> open
> /Volumes/groups/haselbach/Sascha/210421_26s_d1_3s_ist/relion_j273_beta_split_600_to_480px_bin/Class3D/19s_wo_rpn1_T=10/run_it025_class003.mrc
Opened run_it025_class003.mrc as #3, grid size 480,480,480, pixel 1.34, shown
at level 0.000636, step 2, values float32
> open
> /Volumes/groups/haselbach/Sascha/210421_26s_d1_3s_ist/relion_j273_beta_split_600_to_480px_bin/Class3D/19s_wo_rpn1_T=10/run_it025_class004.mrc
Opened run_it025_class004.mrc as #4, grid size 480,480,480, pixel 1.34, shown
at level 2.36e-06, step 2, values float32
> open
> /Volumes/groups/haselbach/Sascha/210421_26s_d1_3s_ist/relion_j273_beta_split_600_to_480px_bin/Class3D/19s_wo_rpn1_T=10/run_it025_class005.mrc
Opened run_it025_class005.mrc as #5, grid size 480,480,480, pixel 1.34, shown
at level 0.000107, step 2, values float32
> open
> /Volumes/groups/haselbach/Sascha/210421_26s_d1_3s_ist/relion_j273_beta_split_600_to_480px_bin/Class3D/19s_wo_rpn1_T=10/run_it025_class006.mrc
Opened run_it025_class006.mrc as #6, grid size 480,480,480, pixel 1.34, shown
at level 2e-06, step 2, values float32
> open
> /Volumes/groups/haselbach/Sascha/210421_26s_d1_3s_ist/relion_j273_beta_split_600_to_480px_bin/Class3D/19s_wo_rpn1_T=10/run_it025_class007.mrc
Opened run_it025_class007.mrc as #7, grid size 480,480,480, pixel 1.34, shown
at level 5.14e-06, step 2, values float32
> open
> /Volumes/groups/haselbach/Sascha/210421_26s_d1_3s_ist/relion_j273_beta_split_600_to_480px_bin/Class3D/19s_wo_rpn1_T=10/run_it025_class008.mrc
Opened run_it025_class008.mrc as #8, grid size 480,480,480, pixel 1.34, shown
at level 3.06e-06, step 2, values float32
> open
> /Volumes/groups/haselbach/Sascha/210421_26s_d1_3s_ist/relion_j273_beta_split_600_to_480px_bin/Class3D/19s_wo_rpn1_T=10/run_it025_class009.mrc
Opened run_it025_class009.mrc as #9, grid size 480,480,480, pixel 1.34, shown
at level 9.17e-08, step 2, values float32
> volume #1 level 0.003681
> volume #1 level 0.001894
> volume #1 level 0.00284
> volume #2 level 0.003445
> volume #3 level 0.002994
> volume #3 level 0.002936
> volume #4 level 0.002013
> volume #4 level 0.001956
> open /Users/sascha.amann/Downloads/AF-O43396-F1-model_v1.pdb
AF-O43396-F1-model_v1.pdb title:
Alphafold V2.0 prediction for thioredoxin-like protein 1 (O43396) [more
info...]
Chain information for AF-O43396-F1-model_v1.pdb #10
---
Chain | Description
A | thioredoxin-like protein 1
> ui mousemode right "translate selected models"
> select #10
2263 atoms, 2309 bonds, 289 residues, 1 model selected
> view matrix models #10,1,0,0,195.54,0,1,0,291.31,0,0,1,116.7
> view matrix models #10,1,0,0,225.51,0,1,0,363.62,0,0,1,119.53
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.016192,0.78061,0.6248,215.55,0.49775,0.53566,-0.68214,372.29,-0.86717,0.32204,-0.37988,129.92
> view matrix models
> #10,-0.082717,0.83257,0.54771,215.94,0.57432,0.48898,-0.65655,372.33,-0.81444,0.26025,-0.51861,131.5
> view matrix models
> #10,0.32959,0.92883,-0.16928,223.06,0.46997,-0.31691,-0.82383,376.18,-0.81884,0.19197,-0.54097,131.91
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.32959,0.92883,-0.16928,257.21,0.46997,-0.31691,-0.82383,301.75,-0.81884,0.19197,-0.54097,124.31
> view matrix models
> #10,0.32959,0.92883,-0.16928,273.47,0.46997,-0.31691,-0.82383,292.52,-0.81884,0.19197,-0.54097,157.18
> open /Users/sascha.amann/PhD/p242_26s+4-7-[k48]-ub-
> gfp-35_3s/p242_relion145_3d_class_j141_T=40/refined_classes_19s_w_o_rpn1_mask/class3/p242_relion145_j149_extra_density_only.mrc
Opened p242_relion145_j149_extra_density_only.mrc as #11, grid size
480,480,480, pixel 1.34, shown at level 1.39e-05, step 2, values float32
> view matrix models
> #10,0.32959,0.92883,-0.16928,255.71,0.46997,-0.31691,-0.82383,302.93,-0.81884,0.19197,-0.54097,96.153
> volume #11 step 1
> volume #11 level 0.2809
> volume #11 level 0.2
> ~select #10
Nothing selected
> select #11
2 models selected
> view matrix models #11,1,0,0,105.86,0,1,0,18.423,0,0,1,-33.144
> view matrix models #11,1,0,0,100.91,0,1,0,17.059,0,0,1,-79.061
> view matrix models #11,1,0,0,102.04,0,1,0,16.584,0,0,1,-84.488
> volume #11 color darkgrey
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.2527,-0.25623,0.933,213.37,0.35345,-0.9221,-0.15751,543.17,0.90068,0.28997,0.32358,-194.11
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.2527,-0.25623,0.933,206.47,0.35345,-0.9221,-0.15751,537.81,0.90068,0.28997,0.32358,-159.15
> volume #4 step 1
> view matrix models
> #11,-0.2527,-0.25623,0.933,206.81,0.35345,-0.9221,-0.15751,539.87,0.90068,0.28997,0.32358,-159.88
> sequence chain #10/A
Alignment identifier is 10/A
> select /A:289
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:108-289
1450 atoms, 1478 bonds, 182 residues, 1 model selected
> select /A:26-77
386 atoms, 394 bonds, 52 residues, 1 model selected
> select /A:26-77
386 atoms, 394 bonds, 52 residues, 1 model selected
> select /A:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:127-289
1304 atoms, 1329 bonds, 163 residues, 1 model selected
> select /A:27-28
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:27-28
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:107-108
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-107
813 atoms, 830 bonds, 107 residues, 1 model selected
> select /A:289
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:108-289
1450 atoms, 1478 bonds, 182 residues, 1 model selected
> hide sel cartoons
> select #10
2263 atoms, 2309 bonds, 289 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.32959,0.92883,-0.16928,266.05,0.46997,-0.31691,-0.82383,296.19,-0.81884,0.19197,-0.54097,124.47
> view matrix models
> #10,0.32959,0.92883,-0.16928,281.91,0.46997,-0.31691,-0.82383,283.46,-0.81884,0.19197,-0.54097,165.62
> view matrix models
> #10,0.32959,0.92883,-0.16928,291.66,0.46997,-0.31691,-0.82383,280.53,-0.81884,0.19197,-0.54097,182.26
> view matrix models
> #10,0.32959,0.92883,-0.16928,255.97,0.46997,-0.31691,-0.82383,274.82,-0.81884,0.19197,-0.54097,157.71
> view matrix models
> #10,0.32959,0.92883,-0.16928,256.91,0.46997,-0.31691,-0.82383,284.38,-0.81884,0.19197,-0.54097,125.15
> select /A:241-289
387 atoms, 393 bonds, 49 residues, 1 model selected
> select /A:241-287
370 atoms, 375 bonds, 47 residues, 1 model selected
> select /A:288-289
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:174-289
933 atoms, 952 bonds, 116 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-107
813 atoms, 830 bonds, 107 residues, 1 model selected
> select /A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:107-108
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:107
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:107
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:107
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:96-107
95 atoms, 95 bonds, 12 residues, 1 model selected
> show sel atoms
> show sel surfaces
> hide sel surfaces
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.30848,-0.88611,-0.3459,239.5,-0.52491,0.14469,-0.83877,276.06,0.79329,0.44031,-0.4205,148.15
> view matrix models
> #10,0.32978,-0.87723,-0.34889,239.93,-0.5142,0.14303,-0.84566,276.29,0.79174,0.45828,-0.4039,148.07
> view matrix models
> #10,0.84799,-0.46694,-0.25077,250.04,-0.17068,0.20735,-0.96326,283.44,0.50178,0.85964,0.096133,141.05
> view matrix models
> #10,0.047709,-0.73475,-0.67666,242.48,0.72046,0.49453,-0.48618,291.69,0.69185,-0.46432,0.55295,122.49
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.047709,-0.73475,-0.67666,265.25,0.72046,0.49453,-0.48618,306.35,0.69185,-0.46432,0.55295,170.14
> view matrix models
> #10,0.047709,-0.73475,-0.67666,271.39,0.72046,0.49453,-0.48618,314.23,0.69185,-0.46432,0.55295,186.27
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.43519,-0.8481,-0.30222,269.91,0.6878,0.52978,-0.49626,314.31,0.58099,0.0081004,0.81387,186.02
> view matrix models
> #10,-0.37296,-0.92784,-0.0018693,253.54,0.91809,-0.36933,0.14388,298.36,-0.13419,0.051948,0.98959,174.1
> view matrix models
> #10,-0.2156,0.0749,-0.9736,280.89,-0.5623,-0.82468,0.061077,274.36,-0.79833,0.56062,0.21992,181.85
> volume #4 level 0.002656
> view matrix models
> #10,0.67816,0.062538,-0.73225,289.42,0.72815,0.077703,0.681,292.52,0.099486,-0.99501,0.0071577,180.27
> view matrix models
> #10,0.60304,0.77492,0.18932,282.62,-0.68477,0.6246,-0.37545,294.73,-0.40919,0.096774,0.9073,171.83
> view matrix models
> #10,0.49065,-0.85258,-0.17991,268.85,0.81689,0.37822,0.43548,300.64,-0.30324,-0.36063,0.88204,168.68
> hide #!10 models
> hide #!11 models
> select #10
2263 atoms, 2309 bonds, 289 residues, 1 model selected
> ~select #10
1 model selected
> hide #!4 models
> show #!5 models
> volume #5 level 0.002483
> volume #5 level 0.003002
> volume #5 level 0.003193
> volume #6 level 0.00287
> volume #7 level 0.001644
> volume #7 level 0.002309
> volume #8 level 0.003501
> volume #9 level 0.001174
> open 1wwy
1wwy title:
Solution structure of the DUF1000 domain of a thioredoxin-like protein 1 [more
info...]
Chain information for 1wwy
---
Chain | Description
12.1/A 12.2/A 12.3/A 12.4/A 12.5/A 12.6/A 12.7/A 12.8/A 12.9/A 12.10/A 12.11/A
12.12/A 12.13/A 12.14/A 12.15/A 12.16/A 12.17/A 12.18/A 12.19/A 12.20/A |
Thioredoxin-like protein 1
> select #12
52040 atoms, 52560 bonds, 3420 residues, 21 models selected
> ~select #12
Nothing selected
> select #12
52040 atoms, 52560 bonds, 3420 residues, 21 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.076095,0.24307,-0.96702,6.3369,-0.79477,0.60044,0.088386,8.508,0.60213,0.76183,0.23887,-8.7516
> view matrix models
> #12,-0.48991,-0.064425,-0.86939,13.122,-0.82526,0.35567,0.43869,9.6674,0.28095,0.93239,-0.22741,-6.1018
> view matrix models
> #12,0.41949,0.31415,-0.85167,2.7873,-0.6608,0.74895,-0.049213,6.9283,0.6224,0.58342,0.52177,-8.6666
> view matrix models
> #12,-0.59054,-0.77027,-0.24071,18.908,-0.79371,0.6083,0.00066834,12.503,0.14591,0.19145,-0.9706,-4.7435
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.59054,-0.77027,-0.24071,320.11,-0.79371,0.6083,0.00066834,118.55,0.14591,0.19145,-0.9706,30.371
> view matrix models
> #12,-0.59054,-0.77027,-0.24071,295.58,-0.79371,0.6083,0.00066834,310.94,0.14591,0.19145,-0.9706,143.63
> view matrix models
> #12,-0.59054,-0.77027,-0.24071,278.6,-0.79371,0.6083,0.00066834,290.68,0.14591,0.19145,-0.9706,128.74
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.60986,-0.73465,0.29724,266.1,-0.78135,-0.49469,0.38049,294.59,-0.13249,-0.46429,-0.87571,134
> view matrix models
> #12,0.63883,-0.59271,0.49051,265.82,-0.76863,-0.51928,0.37357,294.51,0.033291,-0.61567,-0.7873,132.84
> view matrix models
> #12,0.70571,0.57928,-0.40794,262.26,0.43461,0.10078,0.89496,280.07,0.55955,-0.80888,-0.18064,127.72
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.70571,0.57928,-0.40794,284.81,0.43461,0.10078,0.89496,279.98,0.55955,-0.80888,-0.18064,139.68
> view matrix models
> #12,0.70571,0.57928,-0.40794,279.56,0.43461,0.10078,0.89496,303.92,0.55955,-0.80888,-0.18064,155.59
> ui tool show "Fit in Map"
> view matrix models
> #12,0.70571,0.57928,-0.40794,310.31,0.43461,0.10078,0.89496,322.54,0.55955,-0.80888,-0.18064,151.45
> view matrix models
> #12,0.70571,0.57928,-0.40794,308.87,0.43461,0.10078,0.89496,321.64,0.55955,-0.80888,-0.18064,150.5
> view matrix models
> #12,0.70571,0.57928,-0.40794,312.13,0.43461,0.10078,0.89496,325.25,0.55955,-0.80888,-0.18064,149.44
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.88517,-5.6546e-05,0.46526,311.73,0.36033,0.6327,-0.68546,322.72,-0.29433,0.7744,0.56007,155.64
> view matrix models
> #12,0.68512,0.64401,0.34039,312.4,-0.20135,0.61651,-0.76117,328.54,-0.70005,0.45295,0.55205,160.41
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.68512,0.64401,0.34039,273.92,-0.20135,0.61651,-0.76117,315.98,-0.70005,0.45295,0.55205,163.81
> view matrix models
> #12,0.68512,0.64401,0.34039,268.25,-0.20135,0.61651,-0.76117,305.62,-0.70005,0.45295,0.55205,156.15
> view matrix models
> #12,0.68512,0.64401,0.34039,271.91,-0.20135,0.61651,-0.76117,307.46,-0.70005,0.45295,0.55205,157.92
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.26225,0.76919,-0.58272,280.71,-0.86364,-0.45649,-0.21389,318.48,-0.43052,0.44717,0.78402,155.59
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.26225,0.76919,-0.58272,273.72,-0.86364,-0.45649,-0.21389,309.7,-0.43052,0.44717,0.78402,158.3
> view matrix models
> #12,-0.26225,0.76919,-0.58272,277.2,-0.86364,-0.45649,-0.21389,308.45,-0.43052,0.44717,0.78402,156.55
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.13206,0.89258,-0.43112,275.6,-0.97492,-0.19555,-0.10624,308.94,-0.17913,0.40627,0.89602,154.13
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.13206,0.89258,-0.43112,276.83,-0.97492,-0.19555,-0.10624,305.19,-0.17913,0.40627,0.89602,153.8
Fit molecule 1wwy (#12.1) to map p242_relion145_j149_extra_density_only.mrc
(#11) using 2602 atoms
average map value = 0.1458, steps = 84
shifted from previous position = 2.56
rotated from previous position = 25.6 degrees
atoms outside contour = 1878, contour level = 0.2
Position of 1wwy (#12.1) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.54348169 0.48479765 0.68527286 77.13666594
-0.46880235 -0.85248416 0.23129009 645.41174398
0.69631315 -0.19555560 0.69058381 -34.76255285
Axis -0.40853079 -0.01056658 -0.91268337
Axis point 146.03874637 311.40813635 0.00000000
Rotation angle (degrees) 148.50557733
Shift along axis -6.60529555
> close #12
> open 1wwy
1wwy title:
Solution structure of the DUF1000 domain of a thioredoxin-like protein 1 [more
info...]
Chain information for 1wwy
---
Chain | Description
12.1/A 12.2/A 12.3/A 12.4/A 12.5/A 12.6/A 12.7/A 12.8/A 12.9/A 12.10/A 12.11/A
12.12/A 12.13/A 12.14/A 12.15/A 12.16/A 12.17/A 12.18/A 12.19/A 12.20/A |
Thioredoxin-like protein 1
> hide #12.2 models
> hide #12.3 models
> hide #12.4 models
> hide #12.6 models
> hide #12.5 models
> hide #12.7 models
> hide #12.8 models
> hide #12.9 models
> hide #12.11 models
> hide #12.10 models
> hide #12.12 models
> hide #12.13 models
> hide #12.14 models
> hide #12.15 models
> hide #12.16 models
> hide #12.17 models
> hide #12.18 models
> hide #12.19 models
> hide #12.20 models
> select #12
52040 atoms, 52560 bonds, 3420 residues, 21 models selected
> view matrix models #12,1,0,0,286.32,0,1,0,217.48,0,0,1,66.461
> view matrix models #12,1,0,0,272.08,0,1,0,301.15,0,0,1,149.86
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.77346,0.35387,-0.52587,272.94,-0.61209,0.20152,-0.76468,300.51,-0.16463,0.91333,0.37247,151.58
> view matrix models
> #12,0.33534,0.69585,-0.63509,275.39,-0.91372,0.076034,-0.39916,302.13,-0.22947,0.71415,0.66132,151.9
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.33534,0.69585,-0.63509,290.76,-0.91372,0.076034,-0.39916,327.59,-0.22947,0.71415,0.66132,169.07
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.19108,0.96126,-0.19868,294.37,-0.96357,-0.22229,-0.14874,327.55,-0.18714,0.16302,0.96871,168.15
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.19108,0.96126,-0.19868,273.58,-0.96357,-0.22229,-0.14874,307.71,-0.18714,0.16302,0.96871,159.27
> view matrix models
> #12,-0.19108,0.96126,-0.19868,272.68,-0.96357,-0.22229,-0.14874,306.62,-0.18714,0.16302,0.96871,159.03
> view matrix models
> #12,-0.19108,0.96126,-0.19868,276.18,-0.96357,-0.22229,-0.14874,306.47,-0.18714,0.16302,0.96871,156.71
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.061746,0.37716,-0.92409,272.98,0.91219,-0.35444,-0.20561,298.16,-0.40508,-0.85564,-0.32216,152.96
> view matrix models
> #12,0.46159,-0.84526,-0.26919,269.07,0.0034163,-0.30175,0.95338,304.16,-0.88709,-0.44099,-0.1364,156.29
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.46159,-0.84526,-0.26919,275.63,0.0034163,-0.30175,0.95338,306.46,-0.88709,-0.44099,-0.1364,156.27
> view matrix models
> #12,0.46159,-0.84526,-0.26919,277.08,0.0034163,-0.30175,0.95338,302.82,-0.88709,-0.44099,-0.1364,154.14
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.30991,-0.93867,-0.15116,277.71,-0.029358,-0.16836,0.98529,303.32,-0.95031,-0.30091,-0.079734,154.83
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.30991,-0.93867,-0.15116,276.08,-0.029358,-0.16836,0.98529,302.84,-0.95031,-0.30091,-0.079734,153.16
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.19719,-0.97998,0.02731,276.78,-0.14747,-0.0021098,0.98906,303.74,-0.96921,-0.19906,-0.14493,153.37
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.19719,-0.97998,0.02731,278.16,-0.14747,-0.0021098,0.98906,304.12,-0.96921,-0.19906,-0.14493,154.01
> view matrix models
> #12,0.19719,-0.97998,0.02731,275.19,-0.14747,-0.0021098,0.98906,300.99,-0.96921,-0.19906,-0.14493,153.51
> view matrix models
> #12,0.19719,-0.97998,0.02731,275.77,-0.14747,-0.0021098,0.98906,301.36,-0.96921,-0.19906,-0.14493,153.93
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.1182,0.98345,0.1373,281.89,-0.61017,0.037154,-0.7914,300.25,-0.7834,-0.17732,0.59568,154.51
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.1182,0.98345,0.1373,264.19,-0.61017,0.037154,-0.7914,316.54,-0.7834,-0.17732,0.59568,170.53
> view matrix models
> #12,-0.1182,0.98345,0.1373,259.89,-0.61017,0.037154,-0.7914,309.83,-0.7834,-0.17732,0.59568,166.9
> view matrix models
> #12,-0.1182,0.98345,0.1373,272.6,-0.61017,0.037154,-0.7914,303.27,-0.7834,-0.17732,0.59568,152.69
> view matrix models
> #12,-0.1182,0.98345,0.1373,273.84,-0.61017,0.037154,-0.7914,299.83,-0.7834,-0.17732,0.59568,151.35
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.0036273,0.91385,0.40602,273.67,-0.84376,0.21512,-0.49172,301.76,-0.5367,-0.34437,0.7703,150.23
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.0036273,0.91385,0.40602,275.86,-0.84376,0.21512,-0.49172,303.55,-0.5367,-0.34437,0.7703,151.96
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.080917,0.98259,0.16723,275.92,-0.81957,0.029889,-0.57219,302.87,-0.56723,-0.18335,0.80289,152.53
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.080917,0.98259,0.16723,276.62,-0.81957,0.029889,-0.57219,306.29,-0.56723,-0.18335,0.80289,149.83
> view matrix models
> #12,-0.080917,0.98259,0.16723,276.31,-0.81957,0.029889,-0.57219,306.08,-0.56723,-0.18335,0.80289,149.57
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.023206,0.99215,0.12285,276.01,-0.87057,0.040359,-0.49039,306.47,-0.4915,-0.11833,0.8628,149.51
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.023206,0.99215,0.12285,276.82,-0.87057,0.040359,-0.49039,305.79,-0.4915,-0.11833,0.8628,150.66
> volume #11 level 0.1409
> volume #11 level 0.15
> view matrix models
> #12,-0.023206,0.99215,0.12285,277.32,-0.87057,0.040359,-0.49039,305.48,-0.4915,-0.11833,0.8628,151.78
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.020494,0.98732,0.15739,277.36,-0.88749,0.054524,-0.45759,305.64,-0.46037,-0.14906,0.87512,151.6
> view matrix models
> #12,-0.024749,0.99606,0.085109,277.27,-0.85094,0.023693,-0.52473,305.3,-0.52468,-0.085409,0.847,151.97
> view matrix models
> #12,-0.069963,0.99754,0.0035673,277.32,-0.88579,-0.06048,-0.46013,305.36,-0.45878,-0.035352,0.88785,151.88
> view matrix models
> #12,-0.17518,0.96611,-0.18958,277.35,-0.93763,-0.22244,-0.26715,305.54,-0.30027,0.13096,0.94482,151.71
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.17518,0.96611,-0.18958,277.23,-0.93763,-0.22244,-0.26715,304.29,-0.30027,0.13096,0.94482,152.25
> view matrix models
> #12,-0.17518,0.96611,-0.18958,277.85,-0.93763,-0.22244,-0.26715,304.5,-0.30027,0.13096,0.94482,152.3
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.092421,0.98496,-0.146,277.62,-0.95441,-0.12942,-0.26896,304.78,-0.28381,0.11449,0.95202,152.2
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.092421,0.98496,-0.146,277.69,-0.95441,-0.12942,-0.26896,304.65,-0.28381,0.11449,0.95202,152.31
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.10544,0.98432,-0.14143,277.75,-0.94385,-0.14384,-0.29742,304.52,-0.31309,0.10213,0.94422,152.39
> ~select #12
Nothing selected
> show #12.2 models
> show #12.3 models
> show #12.4 models
> show #12.5 models
> show #12.6 models
> show #12.7 models
> show #12.8 models
> show #12.9 models
> show #12.10 models
> show #12.11 models
> show #12.12 models
> show #12.13 models
> show #12.14 models
> show #12.15 models
> show #12.16 models
> show #12.17 models
> show #12.18 models
> show #12.19 models
> show #12.20 models
> select #12
52040 atoms, 52560 bonds, 3420 residues, 21 models selected
> ui tool show "Fit in Map"
Fit molecules 1wwy (#12.1), 1wwy (#12.2), 1wwy (#12.3), 1wwy (#12.4), 1wwy
(#12.5), 1wwy (#12.6), 1wwy (#12.7), 1wwy (#12.8), 1wwy (#12.9), 1wwy
(#12.10), 1wwy (#12.11), 1wwy (#12.12), 1wwy (#12.13), 1wwy (#12.14), 1wwy
(#12.15), 1wwy (#12.16), 1wwy (#12.17), 1wwy (#12.18), 1wwy (#12.19), 1wwy
(#12.20) to map p242_relion145_j149_extra_density_only.mrc (#11) using 52040
atoms
average map value = 0.1457, steps = 76
shifted from previous position = 1.69
rotated from previous position = 8.42 degrees
atoms outside contour = 34038, contour level = 0.15
Position of 1wwy (#12.1) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.2) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.3) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.4) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.5) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.6) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.7) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.8) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.9) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.10) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.11) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.12) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.13) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.14) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.15) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.16) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.17) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.18) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.19) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
Position of 1wwy (#12.20) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
-0.35664471 0.30048405 0.88459815 52.77106463
-0.31311729 -0.93054498 0.18985151 632.47564745
0.88020572 -0.20927344 0.42596070 -41.16014233
Axis -0.54525133 0.00600057 -0.83825114
Axis point 111.28543573 309.53596402 0.00000000
Rotation angle (degrees) 158.53080760
Shift along axis 9.52425757
> close #11
> open /Users/sascha.amann/PhD/p242_26s+4-7-[k48]-ub-
> gfp-35_3s/p242_relion145_3d_class_j141_T=40/refined_classes_19s_w_o_rpn1_mask/class3/p242_relion145_j149_extra_density_only.mrc
Opened p242_relion145_j149_extra_density_only.mrc as #11, grid size
480,480,480, pixel 1.34, shown at level 1.39e-05, step 2, values float32
> volume #11 step 1
> volume #11 level 0.05669
> volume #11 level 0.15
Fit molecules 1wwy (#12.1), 1wwy (#12.2), 1wwy (#12.3), 1wwy (#12.4), 1wwy
(#12.5), 1wwy (#12.6), 1wwy (#12.7), 1wwy (#12.8), 1wwy (#12.9), 1wwy
(#12.10), 1wwy (#12.11), 1wwy (#12.12), 1wwy (#12.13), 1wwy (#12.14), 1wwy
(#12.15), 1wwy (#12.16), 1wwy (#12.17), 1wwy (#12.18), 1wwy (#12.19), 1wwy
(#12.20) to map p242_relion145_j149_extra_density_only.mrc (#11) using 52040
atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 52040, contour level = 0.15
Position of 1wwy (#12.1) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.2) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.3) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.4) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.5) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.6) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.7) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.8) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.9) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.10) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.11) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.12) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.13) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.14) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.15) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.16) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.17) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.18) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.19) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
Position of 1wwy (#12.20) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.99158570 -0.03274706 0.12524150 -6.99005969
0.02402779 0.99722182 0.07050751 -18.20086437
-0.12720247 -0.06690496 0.98961773 57.73005414
Axis -0.46902681 0.86166116 0.19378830
Axis point 448.31213945 0.00000000 90.49012876
Rotation angle (degrees) 8.42338575
Shift along axis -1.21704346
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.10544,0.98432,-0.14143,209.35,-0.94385,-0.14384,-0.29742,299.42,-0.31309,0.10213,0.94422,140.98
Fit molecules 1wwy (#12.1), 1wwy (#12.2), 1wwy (#12.3), 1wwy (#12.4), 1wwy
(#12.5), 1wwy (#12.6), 1wwy (#12.7), 1wwy (#12.8), 1wwy (#12.9), 1wwy
(#12.10), 1wwy (#12.11), 1wwy (#12.12), 1wwy (#12.13), 1wwy (#12.14), 1wwy
(#12.15), 1wwy (#12.16), 1wwy (#12.17), 1wwy (#12.18), 1wwy (#12.19), 1wwy
(#12.20) to map p242_relion145_j149_extra_density_only.mrc (#11) using 52040
atoms
average map value = 0.1125, steps = 92
shifted from previous position = 7.83
rotated from previous position = 13.6 degrees
atoms outside contour = 38062, contour level = 0.15
Position of 1wwy (#12.1) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.2) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.3) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.4) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.5) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.6) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.7) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.8) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.9) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.10) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.11) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.12) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.13) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.14) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.15) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.16) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.17) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.18) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.19) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
Position of 1wwy (#12.20) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.94979577 -0.25579052 0.18016441 55.09580877
0.23183779 0.96207966 0.14371486 -62.64145084
-0.21009342 -0.09473085 0.97308110 90.41492367
Axis -0.35666906 0.58375088 0.72939844
Axis point 321.81478527 165.79943753 0.00000000
Rotation angle (degrees) 19.52799763
Shift along axis 9.73053189
> view matrix models
> #12,-0.10544,0.98432,-0.14143,260.99,-0.94385,-0.14384,-0.29742,350.13,-0.31309,0.10213,0.94422,162.55
> view matrix models
> #12,-0.10544,0.98432,-0.14143,260.51,-0.94385,-0.14384,-0.29742,363.07,-0.31309,0.10213,0.94422,143.82
Fit molecules 1wwy (#12.1), 1wwy (#12.2), 1wwy (#12.3), 1wwy (#12.4), 1wwy
(#12.5), 1wwy (#12.6), 1wwy (#12.7), 1wwy (#12.8), 1wwy (#12.9), 1wwy
(#12.10), 1wwy (#12.11), 1wwy (#12.12), 1wwy (#12.13), 1wwy (#12.14), 1wwy
(#12.15), 1wwy (#12.16), 1wwy (#12.17), 1wwy (#12.18), 1wwy (#12.19), 1wwy
(#12.20) to map p242_relion145_j149_extra_density_only.mrc (#11) using 52040
atoms
average map value = 0.1125, steps = 96
shifted from previous position = 7.25
rotated from previous position = 8.59 degrees
atoms outside contour = 38052, contour level = 0.15
Position of 1wwy (#12.1) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.2) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.3) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.4) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.5) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.6) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.7) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.8) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.9) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.10) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.11) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.12) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.13) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.14) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.15) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.16) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.17) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.18) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.19) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
Position of 1wwy (#12.20) relative to
p242_relion145_j149_extra_density_only.mrc (#11) coordinates:
Matrix rotation and translation
0.92201341 -0.26314068 0.28398637 45.87755531
0.19688637 0.95027096 0.24129000 -76.89266299
-0.33335722 -0.16655957 0.92797138 139.06679125
Axis -0.46811919 0.70857101 0.52800715
Axis point 429.68874953 0.00000000 -39.37654396
Rotation angle (degrees) 25.82511969
Shift along axis -2.53181594
> close #11
> close #12
> show #!1 models
> volume #1 level 0.002052
> volume #1 level 0.001526
> volume #2 level 0.001328
> volume #3 level 0.002936
> volume #4 level 0.00221
> volume #4 level 0.001829
> volume #4 level 0.002401
> show #!10 models
> ui mousemode right "rotate selected models"
> select #10
2263 atoms, 2309 bonds, 289 residues, 1 model selected
> view matrix models
> #10,0.92745,-0.076088,0.36611,275.17,0.16399,0.96267,-0.21536,307.71,-0.33606,0.25977,0.90531,174.63
> view matrix models
> #10,0.26571,0.2351,-0.93495,288.79,-0.60915,-0.71074,-0.35184,280.95,-0.74722,0.66301,-0.045641,187.49
> view matrix models
> #10,0.5283,-0.34382,-0.77633,283.74,0.61187,-0.47974,0.62885,285.79,-0.58865,-0.80724,-0.043077,173.73
> view matrix models
> #10,-0.38762,-0.70296,0.59633,246.97,-0.90176,0.42336,-0.087093,285.5,-0.19124,-0.5715,-0.798,192.88
> view matrix models
> #10,-0.23635,0.91257,0.3337,270.5,0.78051,-0.026246,0.62459,293.13,0.57874,0.40808,-0.70607,212.72
> view matrix models
> #10,0.36725,0.92387,-0.1077,285.43,-0.90239,0.38197,0.1995,280.83,0.22545,0.023925,0.97396,178.8
> view matrix models
> #10,0.27691,0.91778,-0.28461,286.74,-0.92031,0.33849,0.19611,280.16,0.27632,0.20763,0.93837,182.03
> view matrix models
> #10,0.61176,0.72442,-0.31776,289.72,-0.79102,0.55729,-0.25242,290.96,-0.0057714,0.40577,0.91396,180.68
> view matrix models
> #10,0.8361,0.32764,-0.43998,290.29,-0.28453,0.94474,0.16282,295.95,0.46901,-0.010944,0.88312,183.11
> view matrix models
> #10,0.77172,-0.028232,-0.63533,288.43,0.34916,0.85379,0.38617,300.33,0.53154,-0.51985,0.66875,181.61
> view matrix models
> #10,0.82828,-0.56025,-0.0090331,274.13,0.52405,0.76886,0.36637,302.09,-0.19831,-0.30819,0.93042,170.04
> view matrix models
> #10,0.96787,-0.23063,0.10018,278.03,0.16295,0.87874,0.44863,297.12,-0.1915,-0.41789,0.88809,169.53
> select /A:286-289
30 atoms, 30 bonds, 4 residues, 1 model selected
> select /A:216-289
593 atoms, 602 bonds, 74 residues, 1 model selected
> select /A:215
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:1-215
1670 atoms, 1706 bonds, 215 residues, 1 model selected
> select /A:289
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:212-289
622 atoms, 632 bonds, 78 residues, 1 model selected
> select /A:286-289
30 atoms, 30 bonds, 4 residues, 1 model selected
> select /A:108-289
1450 atoms, 1478 bonds, 182 residues, 1 model selected
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.96787,-0.23063,0.10018,229.01,0.16295,0.87874,0.44863,311.79,-0.1915,-0.41789,0.88809,117.76
> view matrix models
> #10,0.96787,-0.23063,0.10018,242.54,0.16295,0.87874,0.44863,314.71,-0.1915,-0.41789,0.88809,126.73
> view matrix models
> #10,0.96787,-0.23063,0.10018,252.33,0.16295,0.87874,0.44863,281.5,-0.1915,-0.41789,0.88809,150.88
> view matrix models
> #10,0.96787,-0.23063,0.10018,254.67,0.16295,0.87874,0.44863,282.13,-0.1915,-0.41789,0.88809,147.22
> view matrix models
> #10,0.96787,-0.23063,0.10018,278.78,0.16295,0.87874,0.44863,286.95,-0.1915,-0.41789,0.88809,168.78
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.9695,-0.084795,0.22994,277.12,0.0064984,0.9468,0.32176,287.65,-0.24499,-0.31045,0.91848,168.07
> view matrix models
> #10,0.77404,-0.4033,0.48807,275.35,0.37679,0.91293,0.15682,289.94,-0.50882,0.062511,0.8586,167.02
> view matrix models
> #10,0.90007,-0.078449,0.42863,275.13,0.028266,0.9921,0.12222,289.41,-0.43483,-0.097894,0.89518,167.3
> view matrix models
> #10,0.40257,-0.91196,-0.079223,281.56,0.58586,0.19018,0.78779,286.63,-0.70336,-0.36355,0.61083,170.3
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.40257,-0.91196,-0.079223,221.36,0.58586,0.19018,0.78779,275.24,-0.70336,-0.36355,0.61083,133.32
> view matrix models
> #10,0.40257,-0.91196,-0.079223,264.41,0.58586,0.19018,0.78779,314.87,-0.70336,-0.36355,0.61083,167.16
> view matrix models
> #10,0.40257,-0.91196,-0.079223,277.35,0.58586,0.19018,0.78779,309.08,-0.70336,-0.36355,0.61083,163.87
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.20508,-0.97859,-0.01764,276.63,0.58985,0.10919,0.80009,309.22,-0.78103,-0.17449,0.59962,163.26
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.20508,-0.97859,-0.01764,278.61,0.58985,0.10919,0.80009,287.91,-0.78103,-0.17449,0.59962,169.97
> hide sel cartoons
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.20508,-0.97859,-0.01764,265.75,0.58985,0.10919,0.80009,286.98,-0.78103,-0.17449,0.59962,166.65
> volume #4 level 0.002274
> volume #4 level 0.0025
> volume #4 level 0.002
> volume #4 level 0.0022
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.33014,-0.2444,0.91174,261.66,0.51132,0.85822,0.04491,305.25,-0.79345,0.45136,0.4083,176.12
> view matrix models
> #10,0.80292,-0.41108,0.43166,273.44,0.4977,0.86085,-0.10595,307.33,-0.32804,0.2999,0.89579,173.62
> view matrix models
> #10,0.91925,-0.042258,0.39141,279.65,0.15773,0.95047,-0.26782,306.05,-0.3607,0.30793,0.88038,173.49
> view matrix models
> #10,0.99002,-0.14,-0.015877,285.59,0.072555,0.40996,0.90921,281.55,-0.12078,-0.90129,0.41603,170.51
> view matrix models
> #10,-0.32273,0.22162,0.92018,257.67,0.11915,-0.95495,0.27178,276.8,0.93896,0.19735,0.28178,198.96
> view matrix models
> #10,0.64818,0.56275,-0.51301,295.75,0.43315,-0.82656,-0.35942,291.86,-0.62629,0.010759,-0.77951,191.21
> select #10
2263 atoms, 2309 bonds, 289 residues, 1 model selected
> hide #!10 models
> ~select #10
1 model selected
> ui tool show "Map Eraser"
> volume erase #4 center 272.8,299.83,171.76 radius 41.642 outside true
Opened run_it025_class004.mrc copy as #12, grid size 480,480,480, pixel 1.34,
shown at step 1, values float32
> volume erase #12 center 333.19,284.24,169.78 radius 41.409
> volume erase #12 center 333.06,310.49,138.58 radius 41.409
> volume erase #12 center 324.87,280.82,135.47 radius 41.409
> volume erase #12 center 229.16,335.4,176.37 radius 41.409
> volume erase #12 center 219.09,271.25,210.76 radius 41.409
> volume erase #12 center 289.73,278.62,239.01 radius 41.409
> volume erase #12 center 312.57,327.43,203.7 radius 41.409
> volume #12 level 0.00121
> volume #12 level 0.001448
> volume #12 level 0.002636
> volume #12 level 0.002
> volume erase #12 center 322.99,278.87,209.48 radius 41.409
> volume erase #12 center 331.59,320.83,173.35 radius 41.409
> volume erase #12 center 283.63,362.18,207.11 radius 41.409
> volume erase #12 center 283.41,337.41,224.24 radius 41.409
> volume erase #12 center 269.63,363.69,185.13 radius 41.409
> volume erase #12 center 242.96,357.98,159.48 radius 41.409
> volume erase #12 center 312.4,358.34,182.08 radius 41.409
> volume erase #12 center 289.84,317.93,234.1 radius 41.409
> volume erase #12 center 222.32,293.82,175.81 radius 26.322
> show #!10 models
> select /A:289
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:108-289
1450 atoms, 1478 bonds, 182 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-107
813 atoms, 830 bonds, 107 residues, 1 model selected
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.004278, steps = 184
shifted from previous position = 24.7
rotated from previous position = 35.4 degrees
atoms outside contour = 296, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.27671220 0.89880993 -0.33995747 290.03968252
0.85581737 -0.39139710 -0.33820845 322.60653590
-0.43704348 -0.19735510 -0.87752150 182.54737435
Axis 0.79852995 0.55040288 -0.24373466
Axis point -0.00000000 53.83607278 138.91009254
Rotation angle (degrees) 174.94020141
Shift along axis 364.67581824
> ui tool show "Map Eraser"
> volume erase #12 center 278.81,306.79,141.39 radius 31.137
> volume erase #12 center 239.41,302.89,154.95 radius 31.137
> volume erase #12 center 259.71,335.34,166.7 radius 31.137
> volume erase #12 center 245.89,320.34,163.21 radius 31.137
> volume erase #12 center 283.84,331.67,157 radius 31.137
> volume erase #12 center 314.78,312.36,167.51 radius 31.137
> volume erase #12 center 315.55,298.99,186.23 radius 31.137
> volume erase #12 center 245.24,301.1,228.7 radius 31.137
> volume erase #12 center 269.42,291.7,189.72 radius 31.137 outside true
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.002442, steps = 132
shifted from previous position = 15.1
rotated from previous position = 15.8 degrees
atoms outside contour = 484, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.12426885 0.82568956 -0.55026721 291.43800513
0.83446174 -0.38702142 -0.39228566 310.27767306
-0.53687137 -0.41042805 -0.73710105 185.26840880
Axis -0.74974557 -0.55359165 0.36251601
Axis point 0.00000000 48.76394731 162.56190130
Rotation angle (degrees) 179.30675998
Shift along axis -323.10872050
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.12427,0.82569,-0.55027,281.75,0.83446,-0.38702,-0.39229,301.17,-0.53687,-0.41043,-0.7371,192.56
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.002496, steps = 124
shifted from previous position = 13.5
rotated from previous position = 35.8 degrees
atoms outside contour = 480, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.33054190 0.53692019 -0.77618218 293.34313736
0.40901559 -0.82265968 -0.39488900 300.57765365
-0.85055765 -0.18694325 -0.49153221 179.55684765
Axis 0.81479883 0.29142722 -0.50117167
Axis point 0.00000000 86.10808964 189.09979250
Rotation angle (degrees) 172.66875057
Shift along axis 236.62335079
> view matrix models
> #10,0.33054,0.53692,-0.77618,284.74,0.40902,-0.82266,-0.39489,292.34,-0.85056,-0.18694,-0.49153,186.19
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.075523,0.17045,-0.98247,278.25,-0.79627,-0.60337,-0.043469,273.05,-0.6002,0.77903,0.18129,190.17
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.002755, steps = 264
shifted from previous position = 17
rotated from previous position = 82.8 degrees
atoms outside contour = 447, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
-0.61625574 0.43791731 -0.65456650 279.40240212
0.16139276 -0.74328303 -0.64921702 302.33047057
-0.77083154 -0.50572600 0.38737575 165.30632141
Axis 0.43151914 0.34964270 -0.83158957
Axis point 196.24513754 173.78240248 0.00000000
Rotation angle (degrees) 170.42940857
Shift along axis 88.80811333
> view matrix models
> #10,-0.87747,-0.39391,-0.27364,261.13,-0.096242,-0.41431,0.90503,279.33,-0.46988,0.82047,0.32563,184.77
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.002334, steps = 124
shifted from previous position = 6.49
rotated from previous position = 29.9 degrees
atoms outside contour = 526, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
-0.66068812 -0.73650392 -0.14509720 263.81886955
-0.12952800 -0.07854027 0.98846039 283.51963302
-0.73940092 0.67185818 -0.04350725 182.07953477
Axis -0.34923414 0.65555813 0.66953644
Axis point 153.95417674 113.31524870 0.00000000
Rotation angle (degrees) 153.04563288
Shift along axis 215.63792970
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.66069,-0.7365,-0.1451,246.42,-0.12953,-0.07854,0.98846,272.92,-0.7394,0.67186,-0.043507,188.78
> volume #12 level 0.002445
> volume #12 level 0.002964
> ui tool show "Map Eraser"
> volume #12 level 0.00289
> volume erase #12 center 280.51,316.14,185 radius 13.325
> volume erase #12 center 273.86,312.59,194.65 radius 13.325
> volume erase #12 center 290.63,310.78,175.38 radius 13.325
> volume erase #12 center 269.62,313.98,174.75 radius 13.325
> volume #12 level 0.002184
> volume erase #12 center 291.88,296.98,203.2 radius 13.325
> volume erase #12 center 282.77,307.67,202.53 radius 13.325
> volume #12 level 0.002116
> volume erase #12 center 290.76,308.6,184.36 radius 13.325
> ui tool show "Fit in Map"
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.0018, steps = 192
shifted from previous position = 7.9
rotated from previous position = 68 degrees
atoms outside contour = 574, contour level = 0.002116
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.09220032 -0.72020676 -0.68760552 271.17285451
0.34085786 -0.62599931 0.70138491 275.80958436
-0.93558273 -0.29904365 0.18777080 172.81947228
Axis -0.67630371 0.16763607 0.71729453
Axis point 131.38077067 198.52656967 0.00000000
Rotation angle (degrees) 132.30012266
Shift along axis -13.19711085
> volume #12 level 0.001866
> volume #12 level 0.002
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.73074,-0.19953,0.65285,265.76,0.33923,-0.72376,-0.60091,293.99,0.5924,0.66057,-0.46119,213.8
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001925, steps = 164
shifted from previous position = 5.19
rotated from previous position = 88.1 degrees
atoms outside contour = 483, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.45746649 0.50234511 0.73373961 268.26937422
-0.23715630 -0.72633235 0.64513426 269.84122511
0.85701886 -0.46913827 -0.21313840 200.09991324
Axis -0.82968585 -0.09179356 -0.55063176
Axis point 0.00000000 120.83173134 -44.06294248
Rotation angle (degrees) 137.81685181
Shift along axis -357.53035802
> view matrix models
> #10,0.54267,0.14378,0.82755,264.15,-0.83534,-0.01069,0.54964,270.85,0.087875,-0.98955,0.11431,179.05
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001887, steps = 140
shifted from previous position = 3.29
rotated from previous position = 31.5 degrees
atoms outside contour = 506, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.85249461 0.10823084 0.51140888 271.83493339
-0.46966892 -0.27090970 0.84024940 267.89900602
0.22948653 -0.95650093 -0.18011640 188.39218029
Axis -0.94152546 0.14773175 -0.30282857
Axis point 0.00000000 196.45800666 -69.75355124
Rotation angle (degrees) 107.41350739
Shift along axis -273.41285605
> view matrix models
> #10,0.68288,-0.53423,-0.49828,277.5,0.70611,0.65757,0.2627,302.66,0.18731,-0.53123,0.82626,177.52
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001898, steps = 116
shifted from previous position = 5.18
rotated from previous position = 56.3 degrees
atoms outside contour = 513, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.46907772 -0.62183591 -0.62712536 279.67757958
0.29468733 0.77960451 -0.55260852 307.52344217
0.83254158 0.07441045 0.54894227 192.48839899
Axis 0.34187387 -0.79586425 0.49972227
Axis point -3.92743832 0.00000000 478.15342178
Rotation angle (degrees) 66.49605264
Shift along axis -52.94171738
> view matrix models
> #10,0.017954,0.52888,-0.8485,289.3,-0.90117,-0.35904,-0.24286,274.17,-0.43309,0.76901,0.47017,183.88
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001729, steps = 140
shifted from previous position = 5.46
rotated from previous position = 16.5 degrees
atoms outside contour = 530, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
-0.20898010 0.36608845 -0.90681121 282.64756802
-0.88656811 -0.46225948 0.01769633 274.07803350
-0.41270366 0.80764808 0.42116538 185.15764216
Axis 0.50599332 -0.31649416 -0.80237286
Axis point 273.00337283 1.93682401 0.00000000
Rotation angle (degrees) 128.68491057
Shift along axis -92.29178392
> view matrix models
> #10,-0.37113,0.59604,-0.71204,280.04,-0.56842,0.46053,0.68178,278.62,0.73428,0.65776,0.16788,202.99
> view matrix models
> #10,-0.43356,-0.81629,-0.38171,258.93,0.67549,-0.57477,0.4619,287.66,-0.59644,-0.057583,0.80059,167.61
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001952, steps = 144
shifted from previous position = 4.67
rotated from previous position = 46.9 degrees
atoms outside contour = 475, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
-0.68845756 -0.15540853 -0.70843093 269.99237254
0.32770405 -0.93803599 -0.11268782 287.94714235
-0.64702106 -0.30973646 0.69672597 167.95277402
Axis -0.37507764 -0.11689230 0.91959391
Axis point 148.15189461 174.80533047 0.00000000
Rotation angle (degrees) 164.77102717
Shift along axis 19.52144209
> view matrix models
> #10,-0.51851,-0.83023,-0.2046,257.51,0.60154,-0.52423,0.60277,285.59,-0.60769,0.18947,0.77124,172.82
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001952, steps = 152
shifted from previous position = 2.82
rotated from previous position = 55.8 degrees
atoms outside contour = 476, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
-0.68834401 -0.15553945 -0.70851254 269.99475202
0.32783909 -0.93800080 -0.11258791 287.94843585
-0.64707347 -0.30977731 0.69665913 167.95354596
Axis -0.37513080 -0.11688096 0.91957366
Axis point 148.14591546 174.81747581 0.00000000
Rotation angle (degrees) 164.76209641
Shift along axis 19.50661840
> view matrix models
> #10,0.8568,0.16594,-0.48822,291.38,0.4963,-0.52231,0.69345,282.82,-0.13993,-0.83645,-0.52987,187.36
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001851, steps = 120
shifted from previous position = 6.1
rotated from previous position = 31.4 degrees
atoms outside contour = 509, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.91776949 0.39706764 -0.00603786 281.72499229
0.24352474 -0.55073528 0.79836480 275.09390994
0.31367957 -0.73418523 -0.60214383 196.92489721
Axis -0.97425032 -0.20324610 -0.09760805
Axis point 0.00000000 148.78715318 33.43233811
Rotation angle (degrees) 128.13779260
Shift along axis -349.60388390
> view matrix models
> #10,0.57832,0.80875,0.10715,279.88,0.81264,-0.58265,0.011659,294.21,0.071857,0.080329,-0.99417,208.29
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001782, steps = 72
shifted from previous position = 2.27
rotated from previous position = 8.6 degrees
atoms outside contour = 534, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.60892746 0.77636253 0.16269163 278.28604928
0.76556046 -0.62889095 0.13569586 290.40792582
0.20766447 0.04192134 -0.97730142 207.66986939
Axis -0.89684444 -0.43011305 -0.10330926
Axis point 0.00000000 80.90506964 86.05519754
Rotation angle (degrees) 177.00319581
Shift along axis -395.94175714
> view matrix models
> #10,-0.47263,0.54506,0.69248,253.1,0.19479,-0.70173,0.68529,273.65,0.85946,0.45878,0.22549,203.29
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001899, steps = 72
shifted from previous position = 3.48
rotated from previous position = 30.5 degrees
atoms outside contour = 492, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
-0.15671690 0.57014595 0.80645733 258.40253510
-0.17018895 -0.81992201 0.54659274 271.83868091
0.97286975 -0.05158981 0.22552817 199.44567854
Axis -0.61908561 -0.17222759 -0.76620537
Axis point 83.90960580 107.49022041 0.00000000
Rotation angle (degrees) 151.11077122
Shift along axis -359.60776050
> view matrix models
> #10,-0.95264,0.30317,-0.023781,256.91,0.28212,0.91028,0.30297,300.44,0.1135,0.28192,-0.9527,208.76
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001894, steps = 148
shifted from previous position = 6.55
rotated from previous position = 52.8 degrees
atoms outside contour = 509, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
-0.54055833 0.35655637 0.76201329 253.37332027
0.64638369 0.75576738 0.10489898 300.77912749
-0.53850239 0.54925698 -0.63900857 196.92489826
Axis 0.31636762 0.92592246 0.20634709
Axis point 100.67384641 0.00000000 36.80213795
Rotation angle (degrees) 135.38969569
Shift along axis 399.29214467
> view matrix models
> #10,0.83639,-0.1961,0.51186,269.93,0.48895,0.68899,-0.535,307.39,-0.24775,0.69774,0.67215,183.08
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001791, steps = 104
shifted from previous position = 3.48
rotated from previous position = 22.8 degrees
atoms outside contour = 504, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.76278959 0.06942390 0.64290930 271.64702928
0.28985898 0.85203352 -0.43591359 306.59495970
-0.57804310 0.51886338 0.62979915 176.61757356
Axis 0.60987070 0.77989218 0.14080450
Axis point 170.23890814 0.00000000 47.85407050
Rotation angle (degrees) 51.51489773
Shift along axis 429.64912641
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.00179, steps = 48
shifted from previous position = 0.0296
rotated from previous position = 0.0875 degrees
atoms outside contour = 504, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.76336762 0.06955964 0.64220818 271.65057236
0.28870519 0.85262476 -0.43552305 306.55815665
-0.57785743 0.51787303 0.63078390 176.58325676
Axis 0.60965647 0.78018034 0.14013431
Axis point 170.91585470 0.00000000 47.74016024
Rotation angle (degrees) 51.43602157
Shift along axis 429.52954845
> view matrix models
> #10,0.75497,0.21911,0.61808,273.52,0.20663,0.81503,-0.54133,306.59,-0.62236,0.5364,0.57004,177.08
> view matrix models
> #10,0.80691,0.58127,0.10495,285.78,-0.35804,0.62266,-0.69578,299.06,-0.46978,0.52386,0.71055,176.95
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.00179, steps = 152
shifted from previous position = 1.96
rotated from previous position = 43.7 degrees
atoms outside contour = 503, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.76324841 0.06988209 0.64231485 271.65217504
0.28861049 0.85256337 -0.43570596 306.55640754
-0.57806216 0.51793069 0.63054893 176.58897911
Axis 0.60968116 0.78021422 0.13983795
Axis point 171.04175494 0.00000000 47.79131867
Rotation angle (degrees) 51.45124547
Shift along axis 429.49472230
> view matrix models
> #10,-0.65984,0.73587,0.15201,266.69,-0.6643,-0.66583,0.33967,265.66,0.35116,0.12315,0.92818,180.6
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001894, steps = 72
shifted from previous position = 5.69
rotated from previous position = 25 degrees
atoms outside contour = 511, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
-0.82397111 0.52712711 0.20786688 258.33960347
-0.54549109 -0.83719685 -0.03925465 275.51313967
0.15333330 -0.14573423 0.97736914 176.48181725
Axis -0.09865897 0.05052825 -0.99383766
Axis point 162.41227506 106.88320354 0.00000000
Rotation angle (degrees) 147.34123865
Shift along axis -186.96059990
> view matrix models
> #10,-0.47787,0.56032,-0.67652,276.49,-0.87681,-0.25746,0.40611,270.73,0.053377,0.78725,0.61432,190.64
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001729, steps = 120
shifted from previous position = 2.63
rotated from previous position = 32.2 degrees
atoms outside contour = 533, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
-0.20887104 0.36467175 -0.90740697 282.63431535
-0.88603632 -0.46327519 0.01776926 274.10117232
-0.41389920 0.80770702 0.41987718 185.15823397
Axis 0.50655541 -0.31646675 -0.80202893
Axis point 273.01425107 2.09227076 0.00000000
Rotation angle (degrees) 128.76550662
Shift along axis -92.07622537
> view matrix models
> #10,0.18648,0.7606,0.62186,269.74,0.26175,0.57163,-0.77764,312.87,-0.94695,0.30779,-0.092494,179.98
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001834, steps = 124
shifted from previous position = 6.99
rotated from previous position = 39.9 degrees
atoms outside contour = 530, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.37699240 0.20404908 0.90346041 259.87786808
0.22897931 0.92462092 -0.30437582 302.55757547
-0.89746600 0.32162112 0.30185204 176.31081581
Axis 0.32829967 0.94448313 0.01307448
Axis point 201.26594536 0.00000000 -13.17818354
Rotation angle (degrees) 72.43829857
Shift along axis 373.38351812
> view matrix models
> #10,0.2519,0.16044,0.95436,256.94,0.30214,0.92383,-0.23505,302.52,-0.91938,0.34757,0.18424,178.04
Fit molecule AF-O43396-F1-model_v1.pdb (#10) to map run_it025_class004.mrc
copy (#12) using 813 atoms
average map value = 0.001834, steps = 68
shifted from previous position = 0.237
rotated from previous position = 8.64 degrees
atoms outside contour = 529, contour level = 0.002
Position of AF-O43396-F1-model_v1.pdb (#10) relative to run_it025_class004.mrc
copy (#12) coordinates:
Matrix rotation and translation
0.37701945 0.20374774 0.90351713 259.87167430
0.22833914 0.92494822 -0.30386186 302.53924384
-0.89761773 0.32087016 0.30219988 176.29915425
Axis 0.32767451 0.94470262 0.01289829
Axis point 201.43792624 0.00000000 -13.36946928
Rotation angle (degrees) 72.41719756
Shift along axis 373.23690001
> open 1GH2
Summary of feedback from opening 1GH2 fetched from pdb
---
note | Fetching compressed mmCIF 1gh2 from
http://files.rcsb.org/download/1gh2.cif
1gh2 title:
Crystal structure of the catalytic domain of a new human thioredoxin-like
protein [more info...]
Chain information for 1gh2 #11
---
Chain | Description
A | thioredoxin-like protein
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.37702,0.20375,0.90352,258.66,0.22834,0.92495,-0.30386,302.23,-0.89762,0.32087,0.3022,175.08
> select #10
2263 atoms, 2309 bonds, 289 residues, 1 model selected
> ~select #10
1 model selected
> select #11
860 atoms, 834 bonds, 151 residues, 1 model selected
> view matrix models #11,1,0,0,170.22,0,1,0,190.57,0,0,1,191.26
> view matrix models #11,1,0,0,202.32,0,1,0,230.64,0,0,1,198.34
> hide #!12 models
> sequence chain #11/A
Alignment identifier is 11/A
> select #10/A:289
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #10/A:108-289
1450 atoms, 1478 bonds, 182 residues, 1 model selected
> select #10/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:1-107
813 atoms, 830 bonds, 107 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.0048766,0.30355,0.9528,253.78,0.33027,0.89984,-0.28499,303.08,-0.94387,0.31329,-0.10464,180.4
> view matrix models
> #10,0.67816,-0.62655,-0.3841,272.85,-0.72067,-0.66937,-0.18052,270.07,-0.144,0.39923,-0.90547,204.16
> view matrix models
> #10,0.76736,-0.12243,-0.62942,283.19,0.27037,-0.8283,0.49073,271.96,-0.58143,-0.54675,-0.60251,183.39
> view matrix models
> #10,0.90048,-0.29408,-0.32041,278.56,0.073497,-0.62324,0.77857,267.23,-0.42865,-0.72463,-0.5396,182.62
> view matrix models
> #10,0.89694,-0.17011,-0.40812,281.16,0.2827,-0.48907,0.82516,270.86,-0.33996,-0.8555,-0.39058,180.2
> view matrix models
> #10,0.64998,-0.038813,-0.75896,284.41,0.50538,-0.72378,0.46982,276.62,-0.56756,-0.68894,-0.45082,179.79
> view matrix models
> #10,0.72573,0.19381,-0.66011,286.51,0.55547,-0.73118,0.39601,278.32,-0.40591,-0.65407,-0.6383,185.16
> close #10
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 635, in _mmap_mod_cb
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 392, in disassociate
self.session.alignments.destroy_alignment(self)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment
alignment._destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy
self._notify_observers(self.NOTE_DESTROYED, None)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification
self.delete()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete
ToolInstance.delete(self)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool
tw._destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy
sbar.destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy
v.delete()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete
self.make_current()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current
qc = self._initialize_context()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
Error processing trigger "modified":
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
> ui mousemode right "translate selected models"
> select #12
2 models selected
> ~select #12
Nothing selected
> select #11
860 atoms, 834 bonds, 151 residues, 1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/rmsd.py", line 199, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> view matrix models #11,1,0,0,204.83,0,1,0,268.98,0,0,1,190.11
OpenGL version: 4.1 ATI-4.5.14
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2,6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1554.120.19.0.0 (iBridge: 18.16.14663.0.0,0)
Software:
System Software Overview:
System Version: macOS 11.4 (20F71)
Kernel Version: Darwin 20.5.0
Time since boot: 56 days 14:36
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LEN T24d-10:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: V5LR4801
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
HP Z24i:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: CN471105CW
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fixed 4 months ago cleanup of status line after a screen has been disconnected, but not in ChimeraX 1.2.5. #4643