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Opened 2 years ago
Closed 2 years ago
#9069 closed defect (fixed)
fitmap: mismatch coordinate array sizes
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/wkeliason/Downloads/cryosparc_P5_J167_005_volume_map_sharp_RNA-
> DNA-Hybrid (1).mrc" format mrc
Opened cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc as #1,
grid size 360,360,360, pixel 0.97, shown at level 0.0899, step 2, values
float32
> select add #1
2 models selected
> ui tool show "Volume Viewer"
> volume #1 style mesh
> vop gaussian #1 sdev 2.91
Opened cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian
as #2, grid size 360,360,360, pixel 0.97, shown at step 1, values float32
> volume #2 level 0.07036
> open /Users/wkeliason/Downloads/ChimeraX/PDB/GsDnaB_Xray/4esv.pdb.gz
4esv.pdb.gz title:
A new twist on the translocation mechanism of helicases from the structure of
DNAb with its substrates [more info...]
Chain information for 4esv.pdb.gz #3
---
Chain | Description | UniProt
A B C D E F G H I J K L | DNAB | Q9X4C9_GEOSE 1-445 1-454
V | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' |
W | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' |
Non-standard residues in 4esv.pdb.gz #3
---
ALF — tetrafluoroaluminate ion
CA — calcium ion
GDP — guanosine-5'-diphosphate
MES — 2-(N-morpholino)-ethanesulfonic acid
> delete /F,G,H,I,J,K,L,W
> show atoms
> hide atoms
> show cartoons
> ui tool show "Model Panel"
> select subtract #1
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-24.384,0,1,0,110.09,0,0,1,37.302
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99863,-0.05072,0.01313,-22.395,0.047412,0.98151,0.18545,89.137,-0.022293,-0.18457,0.98257,52.366
> view matrix models
> #3,0.76771,-0.090839,0.63433,-55.072,0.010973,0.99162,0.12872,97.462,-0.64071,-0.091861,0.76227,128.98
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.76771,-0.090839,0.63433,45.001,0.010973,0.99162,0.12872,107.41,-0.64071,-0.091861,0.76227,152.1
> view matrix models
> #3,0.76771,-0.090839,0.63433,47.306,0.010973,0.99162,0.12872,111.24,-0.64071,-0.091861,0.76227,160.87
> view matrix models
> #3,0.76771,-0.090839,0.63433,46.798,0.010973,0.99162,0.12872,111.37,-0.64071,-0.091861,0.76227,164.59
> ui tool show "Model Panel"
> select subtract #3
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.76771,-0.090839,0.63433,47.51,0.010973,0.99162,0.12872,111.14,-0.64071,-0.091861,0.76227,173.13
> view matrix models
> #3,0.76771,-0.090839,0.63433,42.915,0.010973,0.99162,0.12872,110.79,-0.64071,-0.091861,0.76227,172.68
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.78639,0.08113,0.61238,32.662,-0.1083,0.99409,0.0073778,133.88,-0.60816,-0.072124,0.79053,165.59
> view matrix models
> #3,0.80403,0.10572,0.58512,31.961,-0.15798,0.98668,0.038817,136.34,-0.57322,-0.12365,0.81002,163.41
> view matrix models
> #3,0.84389,0.047588,0.5344,36.265,-0.03823,0.99886,-0.028577,129.97,-0.53515,0.003686,0.84475,148.64
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.84389,0.047588,0.5344,37.25,-0.03823,0.99886,-0.028577,137.05,-0.53515,0.003686,0.84475,147.28
> fitmap #3 inMap #2
Fit molecule 4esv.pdb.gz (#3) to map
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
using 16995 atoms
average map value = 0.05238, steps = 120
shifted from previous position = 10.8
rotated from previous position = 10.5 degrees
atoms outside contour = 12015, contour level = 0.07036
Position of 4esv.pdb.gz (#3) relative to
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
coordinates:
Matrix rotation and translation
0.77401095 -0.09468342 0.62605279 34.64323104
0.07311972 0.99550712 0.06015876 109.46615004
-0.62893605 -0.00078674 0.77745664 164.38128436
Axis -0.04807855 0.99003283 0.13237617
Axis point 228.24251148 0.00000000 17.18775591
Rotation angle (degrees) 39.33190824
Shift along axis 128.46965059
> show #!1 models
> volume #1 level 0.09829
> hide #!1 models
> select subtract #3
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.77401,-0.094683,0.62605,35.003,0.07312,0.99551,0.060159,109.75,-0.62894,-0.00078674,0.77746,165.8
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.96934,0.037867,0.24279,43.349,0.19996,-0.69582,-0.68982,270.01,0.14282,0.71722,-0.68205,181.84
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.96934,0.037867,0.24279,44.636,0.19996,-0.69582,-0.68982,253.09,0.14282,0.71722,-0.68205,188.87
> view matrix models
> #3,0.96934,0.037867,0.24279,45.345,0.19996,-0.69582,-0.68982,254.81,0.14282,0.71722,-0.68205,190.7
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.75786,0.17932,0.62728,21.851,0.11659,0.90878,-0.40065,138.6,-0.64191,0.37677,0.66783,163.27
> select subtract #3
Nothing selected
> ui mousemode right "translate selected models"
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.75786,0.17932,0.62728,22.78,0.11659,0.90878,-0.40065,151.19,-0.64191,0.37677,0.66783,162.73
> view matrix models
> #3,0.75786,0.17932,0.62728,24.865,0.11659,0.90878,-0.40065,157.94,-0.64191,0.37677,0.66783,160.8
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.74396,-0.0063526,0.6682,33.7,0.24405,0.93346,-0.26285,130.85,-0.62207,0.35862,0.696,157.29
> view matrix models
> #3,0.71667,0.025423,0.69695,31.799,0.10455,0.98413,-0.14341,130.5,-0.68953,0.17564,0.70263,174.51
> view matrix models
> #3,0.7133,-0.26596,0.64843,54.373,0.70084,0.26503,-0.66225,163.3,0.0042769,0.92684,0.37544,90.35
> view matrix models
> #3,0.41297,-0.47152,0.77918,84.555,0.55479,-0.54824,-0.62581,223.84,0.72226,0.69072,0.035191,64.975
> view matrix models
> #3,0.23106,-0.37425,0.89808,85.651,0.09997,-0.90904,-0.40454,270.38,0.96779,0.18325,-0.17263,90.774
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.23106,-0.37425,0.89808,88.901,0.09997,-0.90904,-0.40454,258.51,0.96779,0.18325,-0.17263,84.301
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.23697,-0.25597,0.93719,77.468,-0.128,-0.96448,-0.23106,268.36,0.96305,-0.065208,-0.26131,108.16
> view matrix models
> #3,0.33348,-0.13034,0.9337,60.545,-0.62113,-0.77543,0.1136,273.77,0.70922,-0.61783,-0.33955,174.35
> view matrix models
> #3,0.35638,-0.12275,0.92624,58.499,-0.60564,-0.78522,0.12897,271.39,0.71147,-0.60693,-0.35418,174.83
> view matrix models
> #3,0.86523,-0.0059913,0.50134,40.455,-0.0048302,0.99978,0.020284,113.26,-0.50135,-0.019972,0.86501,145.97
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.86523,-0.0059913,0.50134,42.039,-0.0048302,0.99978,0.020284,124.31,-0.50135,-0.019972,0.86501,147.01
> color #3 #942192ff
> view matrix models
> #3,0.86523,-0.0059913,0.50134,43.213,-0.0048302,0.99978,0.020284,125.98,-0.50135,-0.019972,0.86501,148.52
> select subtract #3
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.79156,-0.040803,0.60973,42.527,0.014941,0.99876,0.04744,121.54,-0.61091,-0.028441,0.79119,166.86
> select subtract #3
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.7572,-0.021548,0.65283,40.749,0.034885,0.99936,-0.0074758,124.65,-0.65225,0.028434,0.75747,170.68
> view matrix models
> #3,0.82345,0.19715,0.53203,32.166,-0.12665,0.9779,-0.16635,156.92,-0.55307,0.069598,0.83022,151.49
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.82345,0.19715,0.53203,19.036,-0.12665,0.9779,-0.16635,153.94,-0.55307,0.069598,0.83022,149.98
> view matrix models
> #3,0.82345,0.19715,0.53203,20.671,-0.12665,0.9779,-0.16635,155.06,-0.55307,0.069598,0.83022,149.03
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.86926,0.34415,0.3549,23.753,-0.26742,0.93113,-0.24794,179.56,-0.41579,0.12062,0.90143,125.59
> view matrix models
> #3,0.93943,0.19883,0.27919,32.671,-0.092853,0.93172,-0.35111,171.78,-0.32993,0.30392,0.89374,106.62
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.93943,0.19883,0.27919,37.936,-0.092853,0.93172,-0.35111,179.83,-0.32993,0.30392,0.89374,108.03
> view matrix models
> #3,0.93943,0.19883,0.27919,37.093,-0.092853,0.93172,-0.35111,180.24,-0.32993,0.30392,0.89374,109.49
> select subtract #3
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!2 models
> ui mousemode right "rotate selected models"
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right "translate selected models"
> hide #!2 models
> show #!2 models
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.93943,0.19883,0.27919,36.776,-0.092853,0.93172,-0.35111,174.34,-0.32993,0.30392,0.89374,111.34
> select subtract #3
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.95563,0.12863,0.26501,40.752,0.029521,0.85329,-0.52061,182.76,-0.29309,0.50533,0.81163,103.12
> view matrix models
> #3,0.88804,-0.15886,0.43145,49.375,0.31808,0.88988,-0.32702,133.67,-0.33199,0.42764,0.84078,108.99
> view matrix models
> #3,0.89354,-0.14479,0.42499,48.576,0.30489,0.89053,-0.33763,135.94,-0.32958,0.43126,0.83987,108.61
> select subtract #3
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.91619,-0.018991,0.4003,40.989,-0.25484,0.74329,0.61853,111.19,-0.30928,-0.6687,0.67615,188.72
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.91619,-0.018991,0.4003,41.955,-0.25484,0.74329,0.61853,108.84,-0.30928,-0.6687,0.67615,180.77
> select subtract #3
Nothing selected
> hide #!3 models
> show #!3 models
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.91619,-0.018991,0.4003,48.757,-0.25484,0.74329,0.61853,109.5,-0.30928,-0.6687,0.67615,183.54
> select subtract #3
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.91619,-0.018991,0.4003,47.872,-0.25484,0.74329,0.61853,109.88,-0.30928,-0.6687,0.67615,184.94
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.86996,0.19172,0.45432,34.625,-0.48887,0.45605,0.74366,138.94,-0.064623,-0.86906,0.49047,190.1
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.86996,0.19172,0.45432,37.205,-0.48887,0.45605,0.74366,139.08,-0.064623,-0.86906,0.49047,185.18
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> view matrix models
> #3,0.86996,0.19172,0.45432,37.032,-0.48887,0.45605,0.74366,141.59,-0.064623,-0.86906,0.49047,184.56
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.76022,0.38928,0.52013,29.812,-0.085894,0.8538,-0.51346,194.91,-0.64397,0.34567,0.68251,150.55
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.76022,0.38928,0.52013,30.827,-0.085894,0.8538,-0.51346,194.11,-0.64397,0.34567,0.68251,156.35
> view matrix models
> #3,0.76022,0.38928,0.52013,32.158,-0.085894,0.8538,-0.51346,193.88,-0.64397,0.34567,0.68251,164.09
> hide #!2 models
> select subtract #3
Nothing selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right "rotate selected models"
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.68769,0.064897,0.7231,40.096,0.16437,0.95622,-0.24214,137.32,-0.70715,0.28538,0.64691,177.38
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.68769,0.064897,0.7231,32.288,0.16437,0.95622,-0.24214,136.56,-0.70715,0.28538,0.64691,177.98
> select subtract #3
Nothing selected
> hide #!3 models
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> cartoon #2
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.41195,0.19399,0.89032,36.28,-0.77028,0.59612,0.22652,207.73,-0.48679,-0.77911,0.395,244.25
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.41195,0.19399,0.89032,37.207,-0.77028,0.59612,0.22652,204.62,-0.48679,-0.77911,0.395,237.33
> view matrix models
> #3,0.41195,0.19399,0.89032,33.326,-0.77028,0.59612,0.22652,208.27,-0.48679,-0.77911,0.395,232.82
> hide #!3 models
> surface style #2 solid
> transparency #2.1 50
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.6246,0.39515,0.67359,20.195,-0.75732,0.51702,0.39894,195.65,-0.19062,-0.7593,0.62219,180.84
> view matrix models
> #3,0.71557,0.33835,0.61113,20.424,-0.63508,0.67947,0.36742,176.55,-0.29093,-0.65103,0.70108,176.88
> view matrix models
> #3,0.65554,0.37915,0.65307,20.003,-0.72065,0.57255,0.39097,189.37,-0.22568,-0.72693,0.64856,179.9
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.65554,0.37915,0.65307,26.247,-0.72065,0.57255,0.39097,186.78,-0.22568,-0.72693,0.64856,170.92
> view matrix models
> #3,0.65554,0.37915,0.65307,25.803,-0.72065,0.57255,0.39097,185.72,-0.22568,-0.72693,0.64856,171.31
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.73448,0.26534,0.6246,27.513,-0.62553,0.62162,0.47149,165.72,-0.26316,-0.73701,0.62255,178.09
> view matrix models
> #3,0.73988,0.34589,0.57701,26.536,-0.45749,0.88754,0.054586,171.84,-0.49324,-0.30436,0.81491,156.74
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.73988,0.34589,0.57701,26.378,-0.45749,0.88754,0.054586,164.06,-0.49324,-0.30436,0.81491,168.4
> view matrix models
> #3,0.73988,0.34589,0.57701,27.546,-0.45749,0.88754,0.054586,170.65,-0.49324,-0.30436,0.81491,169.95
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.78637,0.39963,0.47108,29.561,-0.090895,0.82912,-0.55163,194.39,-0.61103,0.39097,0.68832,151.3
> view matrix models
> #3,0.80925,0.14867,0.56834,33.422,0.086968,0.92647,-0.36618,153.4,-0.58099,0.34576,0.73681,146.52
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.80925,0.14867,0.56834,34.168,0.086968,0.92647,-0.36618,160.25,-0.58099,0.34576,0.73681,147.64
> hide #!2 models
> show #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.75383,0.36502,0.54636,28.608,0.58892,-0.7441,-0.31542,206.94,0.29141,0.55953,-0.77589,189.26
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.75383,0.36502,0.54636,30.685,0.58892,-0.7441,-0.31542,184.62,0.29141,0.55953,-0.77589,188.79
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.82104,0.31768,0.47431,33.604,0.52676,-0.74183,-0.41498,200,0.22003,0.59057,-0.77641,194.07
> view matrix models
> #3,0.79571,0.13105,0.59133,36.514,0.4743,-0.74199,-0.4738,210.74,0.37667,0.65747,-0.65257,162.81
> select /B
3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 2 models selected
> view matrix models
> #3,0.82364,0.18478,0.53616,35.629,0.52044,-0.62187,-0.58517,209.26,0.2253,0.76101,-0.60836,167.47
> view matrix models
> #3,0.64453,0.14444,0.75081,35.844,0.029097,-0.98591,0.1647,210.18,0.76403,-0.084306,-0.63965,168.05
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.64453,0.14444,0.75081,29.15,0.029097,-0.98591,0.1647,199.77,0.76403,-0.084306,-0.63965,165.35
> view matrix models
> #3,0.64453,0.14444,0.75081,30.133,0.029097,-0.98591,0.1647,199.88,0.76403,-0.084306,-0.63965,162.01
> show #!1 models
> hide #!1 models
> select add #2
3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 4 models selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 5 models selected
> select subtract #3
2 models selected
> hide #!3 models
> surface style #2 solid
> transparency #2.1 50
> transparency #2.1 100
> transparency #2.1 60
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99958,0.0023976,-0.029041,4.8268,-0.002289,0.99999,0.0037706,-0.26881,0.02905,-0.0037025,0.99957,-4.3647
> select subtract #2
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.69628,0.36934,0.61545,23.981,0.64997,0.03935,-0.75894,162.16,-0.30453,0.92846,-0.21266,167.03
> view matrix models
> #3,0.63372,0.34764,0.69105,24.461,0.7541,-0.078497,-0.65205,148.94,-0.17243,0.93434,-0.3119,162.8
> view matrix models
> #3,0.48003,0.34765,0.80542,29.074,0.86527,-0.036436,-0.49998,121.07,-0.14447,0.93692,-0.3183,160.45
> view matrix models
> #3,0.57993,0.35536,0.73307,25.419,0.79648,-0.058238,-0.60186,138.79,-0.17119,0.93291,-0.31681,163.22
> view matrix models
> #3,0.47319,0.33303,0.81558,29.693,0.84441,-0.43535,-0.31215,129.81,0.2511,0.8364,-0.48722,142.94
> view matrix models
> #3,0.49578,0.34394,0.79744,28.477,0.86313,-0.2966,-0.4087,128.55,0.095955,0.89092,-0.44391,151.04
> view matrix models
> #3,0.77527,0.24059,0.58401,26.871,0.62501,-0.42565,-0.65435,183.1,0.091152,0.87232,-0.48037,156.06
> view matrix models
> #3,0.74842,0.030337,0.66254,34.97,0.61599,-0.40206,-0.67743,184.73,0.24583,0.91511,-0.31959,123
> view matrix models
> #3,0.50945,0.35383,0.78439,27.735,-0.73968,0.64585,0.18908,175.11,-0.43969,-0.67653,0.59075,202.81
> view matrix models
> #3,0.72597,0.18254,0.66306,27.913,-0.64019,0.53159,0.55459,137.93,-0.25124,-0.8271,0.50278,201.4
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.72597,0.18254,0.66306,32.841,-0.64019,0.53159,0.55459,161.64,-0.25124,-0.8271,0.50278,195.31
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.73055,0.18368,0.65769,32.818,-0.62847,0.55753,0.54239,160.04,-0.26706,-0.80958,0.52274,193.95
> view matrix models
> #3,0.75612,0.3673,0.54164,29.976,-0.64637,0.54868,0.53025,163.5,-0.10242,-0.75103,0.65228,161.87
> view matrix models
> #3,0.91746,0.18817,0.3505,42.662,0.051554,0.81739,-0.57378,180.93,-0.39447,0.54449,0.74022,104.06
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.91746,0.18817,0.3505,44.333,0.051554,0.81739,-0.57378,199.03,-0.39447,0.54449,0.74022,111.15
> select subtract #3
Nothing selected
> ui mousemode right "rotate selected models"
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.82674,-0.088875,0.55553,51.018,0.32328,0.88319,-0.33981,146.06,-0.46043,0.46052,0.7589,121.08
> view matrix models
> #3,0.84579,-0.047728,0.53138,48.88,0.28696,0.88035,-0.37768,153.4,-0.44977,0.47192,0.75828,119.38
> view matrix models
> #3,0.77669,-0.22695,0.58758,61.393,0.62172,0.42594,-0.6573,173.8,-0.1011,0.87582,0.47192,86.893
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.77669,-0.22695,0.58758,54.699,0.62172,0.42594,-0.6573,153.5,-0.1011,0.87582,0.47192,88.831
> view matrix models
> #3,0.77669,-0.22695,0.58758,54.724,0.62172,0.42594,-0.6573,151.84,-0.1011,0.87582,0.47192,95.498
> view matrix models
> #3,0.77669,-0.22695,0.58758,48.001,0.62172,0.42594,-0.6573,149.73,-0.1011,0.87582,0.47192,94.225
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule 4esv.pdb.gz (#3) to map
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
using 16995 atoms
average map value = 0.04866, steps = 200
shifted from previous position = 5.51
rotated from previous position = 25.2 degrees
atoms outside contour = 12337, contour level = 0.07036
Position of 4esv.pdb.gz (#3) relative to
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
coordinates:
Matrix rotation and translation
0.73705548 -0.25928832 0.62411441 46.54334356
0.56774984 0.73851176 -0.36367637 110.90652387
-0.36661880 0.62239052 0.69153504 107.97414385
Axis 0.60712692 0.61000000 0.50921204
Axis point 17.84925748 0.00000000 79.73037780
Rotation angle (degrees) 54.29929976
Shift along axis 150.89243060
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #2 level 0.08867
> surface style #2 solid
> transparency #2 50
> transparency #2 40
> surface style #2 solid
> select add #2
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 5 models selected
> select subtract #3
2 models selected
> transparency #2.1 50
> transparency #2.1 40
> transparency #2.1 80
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 5 models selected
> show #!3 models
> select subtract #2
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> select subtract #3
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.74875,-0.27548,0.60289,48.224,0.56467,0.74144,-0.36249,111.1,-0.34715,0.61186,0.71072,106.87
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.6152,-0.50595,0.6046,75.373,0.72602,0.66251,-0.18434,83.147,-0.30728,0.55236,0.77491,100.5
> view matrix models
> #3,0.79581,0.096124,0.59786,21.434,0.34402,0.74074,-0.57702,153.21,-0.49833,0.66488,0.55642,133.15
> view matrix models
> #3,0.81777,0.11395,0.56415,21.318,0.12473,0.92182,-0.36699,144.41,-0.56186,0.37048,0.73963,140.22
> select subtract #3
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.77859,0.16429,0.60564,18.282,-0.030016,0.97377,-0.22556,143.45,-0.62681,0.15744,0.7631,157.44
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.77859,0.16429,0.60564,21.059,-0.030016,0.97377,-0.22556,154.18,-0.62681,0.15744,0.7631,161.56
> select subtract #3
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.77859,0.16429,0.60564,20.842,-0.030016,0.97377,-0.22556,161.95,-0.62681,0.15744,0.7631,171.65
> select subtract #3
Nothing selected
> select add #3
16995 atoms, 17204 bonds, 21 pseudobonds, 2170 residues, 3 models selected
> view matrix models
> #3,0.77859,0.16429,0.60564,22.946,-0.030016,0.97377,-0.22556,170.23,-0.62681,0.15744,0.7631,176.45
> select subtract #3
Nothing selected
> select /V
280 atoms, 307 bonds, 14 residues, 1 model selected
> color sel red
> hide #!3 models
> select /V
280 atoms, 307 bonds, 14 residues, 1 model selected
> cartoon #2
> show #!3 models
> hide #!3 models
> show #!3 models
> delete /v
> lighting simple
> lighting shadows true
> lighting soft
> hide #!2 models
> show #!2 models
> select add #3
16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected
> view matrix models
> #3,0.77859,0.16429,0.60564,24.43,-0.030016,0.97377,-0.22556,150.73,-0.62681,0.15744,0.7631,162.81
> view matrix models
> #3,0.77859,0.16429,0.60564,23.161,-0.030016,0.97377,-0.22556,157.09,-0.62681,0.15744,0.7631,161.28
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.67008,-0.090884,0.73671,37.211,0.14357,0.9896,-0.0084999,118.52,-0.72827,0.11146,0.67616,182.32
> fitmap #3 inMap #2
Fit molecule 4esv.pdb.gz (#3) to map
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
using 16715 atoms
average map value = 0.05205, steps = 116
shifted from previous position = 10.1
rotated from previous position = 11.9 degrees
atoms outside contour = 14723, contour level = 0.088672
Position of 4esv.pdb.gz (#3) relative to
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
coordinates:
Matrix rotation and translation
0.77427283 -0.09859350 0.62512472 34.91206194
0.07661590 0.99512778 0.06205406 109.12031465
-0.62819710 -0.00015228 0.77805423 164.37435490
Axis -0.04909590 0.98917515 0.13828275
Axis point 227.55345512 0.00000000 16.19159201
Rotation angle (degrees) 39.31020189
Shift along axis 128.95520228
> fitmap #3 inMap #2
Fit molecule 4esv.pdb.gz (#3) to map
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
using 16715 atoms
average map value = 0.05205, steps = 36
shifted from previous position = 0.00277
rotated from previous position = 0.0141 degrees
atoms outside contour = 14724, contour level = 0.088672
Position of 4esv.pdb.gz (#3) relative to
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
coordinates:
Matrix rotation and translation
0.77414897 -0.09876516 0.62525101 34.91852212
0.07675219 0.99511076 0.06215848 109.09729217
-0.62833310 -0.00013054 0.77794441 164.39640167
Axis -0.04914928 0.98914318 0.13849233
Axis point 227.49227834 0.00000000 16.18924699
Rotation angle (degrees) 39.32153728
Shift along axis 128.96426304
Average map value = 0.05205 for 16715 atoms, 14724 outside contour
> select subtract #3
Nothing selected
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> view matrix models
> #3,0.79065,-0.11184,0.60197,36.373,0.13083,0.99133,0.012349,108.61,-0.59813,0.068991,0.79843,154.94
> view matrix models
> #3,0.74028,-0.29228,0.60544,52.028,-0.35501,-0.9347,-0.01717,276.77,0.57093,-0.20223,-0.7957,204.07
> hide #!2 models
> view matrix models
> #3,0.77287,-0.33857,0.5367,58.024,-0.21507,0.65596,0.72351,96.906,-0.59701,-0.6746,0.43415,234.08
> show #!2 models
> select /A/B/C/D/E
16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected
> ui tool show "Basic Actions"
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 16540 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> view matrix models
> #3,0.6688,-0.31806,0.67196,54.482,-0.35738,0.65503,0.66575,116.47,-0.65191,-0.6854,0.32442,250.41
> view matrix models
> #3,0.55023,-0.51777,0.6551,80.01,-0.23541,0.65653,0.71662,99.531,-0.80114,-0.54852,0.23936,264.8
> view matrix models
> #3,0.70899,0.20915,0.67349,18.167,0.26354,-0.9644,0.022056,213.76,0.65413,0.16186,-0.73887,168.28
> view matrix models
> #3,0.53089,0.3275,0.78161,18.529,0.67755,-0.71801,-0.15936,174.56,0.50901,0.61417,-0.60307,142.4
> view matrix models
> #3,0.4429,0.30822,0.84193,22.81,0.80749,-0.54521,-0.22519,157.26,0.38961,0.77958,-0.49036,133.63
> view matrix models
> #3,0.22663,-0.39531,0.89015,82.718,0.34195,0.88805,0.30731,66.288,-0.91198,0.23474,0.33643,218.92
> view matrix models
> #3,0.7246,-0.50097,0.47326,78.643,-0.32775,0.35359,0.8761,112.31,-0.60624,-0.78994,0.092017,273.94
> view matrix models
> #3,0.96295,-0.098254,0.25116,51.124,-0.26356,-0.54037,0.79908,167.7,0.057208,-0.83567,-0.54624,270.43
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> view matrix models
> #3,0.94174,0.13247,0.30916,33.733,-0.057996,-0.84145,0.53721,190.11,0.33131,-0.52384,-0.78475,246.44
> view matrix models
> #3,0.84253,0.37453,0.38713,21.527,0.0707,-0.78938,0.60983,167.39,0.53399,-0.48643,-0.69155,215.36
> view matrix models
> #3,0.63119,0.14831,0.76132,21.409,-0.22907,-0.90212,0.36566,226.79,0.74103,-0.40519,-0.53543,175.3
> view matrix models
> #3,0.50389,0.51593,0.69275,17.99,-0.85733,0.39646,0.32833,213.32,-0.10525,-0.75936,0.6421,171.07
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.50389,0.51593,0.69275,22.627,-0.85733,0.39646,0.32833,209.26,-0.10525,-0.75936,0.6421,171.59
> view matrix models
> #3,0.50389,0.51593,0.69275,33.904,-0.85733,0.39646,0.32833,214.26,-0.10525,-0.75936,0.6421,163.38
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.50723,0.84425,0.17307,61.994,-0.81381,0.40313,0.41857,201.12,0.28361,-0.35316,0.89154,76.742
> view matrix models
> #3,0.67498,0.73168,0.095128,59.493,-0.71996,0.62492,0.30187,189.15,0.16143,-0.27225,0.94859,78.604
> view matrix models
> #3,0.73282,0.67397,0.093443,57.434,-0.66233,0.67513,0.32484,178.22,0.15585,-0.29994,0.94114,81.542
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.73282,0.67397,0.093443,60.338,-0.66233,0.67513,0.32484,181,0.15585,-0.29994,0.94114,76.709
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.78363,0.61128,0.11077,57.509,-0.5941,0.68528,0.42124,164.63,0.18159,-0.3959,0.90016,83.835
> view matrix models
> #3,0.76957,0.48443,0.41605,38.178,-0.62354,0.71057,0.32602,174.88,-0.1377,-0.51032,0.84889,127.28
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.76957,0.48443,0.41605,39.789,-0.62354,0.71057,0.32602,175.03,-0.1377,-0.51032,0.84889,133.23
> view matrix models
> #3,0.76957,0.48443,0.41605,38.931,-0.62354,0.71057,0.32602,175.39,-0.1377,-0.51032,0.84889,133.66
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.78512,-0.35494,0.50754,80.098,0.59799,0.22111,-0.7704,186.33,0.16122,0.90837,0.38585,60.574
> view matrix models
> #3,0.51984,-0.40841,0.75031,87.041,0.27816,-0.74952,-0.6007,261.49,0.80771,0.52098,-0.27603,81.811
> view matrix models
> #3,0.52409,-0.47827,0.70469,95.138,0.2356,-0.71372,-0.65962,269.03,0.81843,0.51172,-0.26138,79.946
> view matrix models
> #3,0.28753,-0.55343,0.78169,116.02,0.32522,-0.71125,-0.62319,256.59,0.90087,0.4334,-0.024518,54.459
> view matrix models
> #3,0.28386,-0.60263,0.74583,122.73,0.28165,-0.69111,-0.66561,263.64,0.91657,0.39901,-0.026449,55.182
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.28386,-0.60263,0.74583,121.41,0.28165,-0.69111,-0.66561,264.62,0.91657,0.39901,-0.026449,57.601
> view matrix models
> #3,0.28386,-0.60263,0.74583,111.88,0.28165,-0.69111,-0.66561,241.51,0.91657,0.39901,-0.026449,66.246
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.19418,-0.020926,0.98074,63.355,-0.68749,-0.71607,0.12084,265.84,0.69975,-0.69771,-0.15344,166.55
> view matrix models
> #3,0.13483,0.2596,0.95626,54.401,-0.52931,-0.79697,0.29099,239.22,0.83765,-0.54539,0.029948,126.47
> view matrix models
> #3,0.13526,0.291,0.94711,53.294,-0.50638,-0.80132,0.31853,234.64,0.85164,-0.52268,0.03897,122.85
> view matrix models
> #3,-0.074076,0.34924,0.9341,71.721,-0.5898,-0.77064,0.24135,248.24,0.80415,-0.53305,0.26307,107.3
> view matrix models
> #3,0.18255,0.60669,0.77369,45.503,-0.80206,-0.36325,0.47408,222.73,0.56866,-0.70709,0.42029,126.63
> ui mousemode right "move picked models"
> view matrix models
> #2,0.99958,0.0023976,-0.029041,2.3053,-0.002289,0.99999,0.0037706,1.5128,0.02905,-0.0037025,0.99957,-2.0813
> select subtract #3
Nothing selected
> select add #3
16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected
> view matrix models
> #3,0.18255,0.60669,0.77369,-1.364,-0.80206,-0.36325,0.47408,164.12,0.56866,-0.70709,0.42029,159.87
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.18255,0.60669,0.77369,3.4731,-0.80206,-0.36325,0.47408,158.82,0.56866,-0.70709,0.42029,80.097
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.52562,0.022188,0.85043,-2.0361,-0.84729,-0.076083,0.52566,140.96,0.076366,-0.99685,-0.021191,187.8
> view matrix models
> #3,0.70514,0.068068,0.7058,-9.1591,0.13903,0.96279,-0.23175,50.322,-0.69531,0.26155,0.66943,123.13
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.70514,0.068068,0.7058,-1.1567,0.13903,0.96279,-0.23175,140.09,-0.69531,0.26155,0.66943,173.46
> view matrix models
> #3,0.70514,0.068068,0.7058,-1.4915,0.13903,0.96279,-0.23175,137.99,-0.69531,0.26155,0.66943,174.42
> view matrix models
> #3,0.70514,0.068068,0.7058,16.888,0.13903,0.96279,-0.23175,135.45,-0.69531,0.26155,0.66943,176.94
> view matrix models
> #3,0.70514,0.068068,0.7058,17.43,0.13903,0.96279,-0.23175,141.1,-0.69531,0.26155,0.66943,175.46
> fitmap #3 inMap #2
Fit molecule 4esv.pdb.gz (#3) to map
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
using 16715 atoms
average map value = 0.05205, steps = 184
shifted from previous position = 9.64
rotated from previous position = 19.7 degrees
atoms outside contour = 14724, contour level = 0.088672
Position of 4esv.pdb.gz (#3) relative to
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
coordinates:
Matrix rotation and translation
0.77427187 -0.09860007 0.62512487 34.91407469
0.07662472 0.99512712 0.06205359 109.11924009
-0.62819719 -0.00014633 0.77805415 164.37478168
Axis -0.04909075 0.98917374 0.13829467
Axis point 227.55226949 0.00000000 16.18928083
Rotation angle (degrees) 39.31027841
Shift along axis 128.95608459
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> select clear
> sel:A
Unknown command: sel:A
> sel/A
Unknown command: sel/A
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule 4esv.pdb.gz (#3) to map
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
using 3286 atoms
average map value = 0.05931, steps = 300
shifted from previous position = 28.2
rotated from previous position = 31.8 degrees
atoms outside contour = 2828, contour level = 0.088672
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.73014,0.05375,0.68118,22.368,-0.093022,0.99544,0.021162,131.54,-0.67693,-0.078816,0.73181,180.25
> view matrix models
> #3,0.58401,0.19074,0.78902,18.446,0.74153,0.2701,-0.61415,152.27,-0.33026,0.94375,0.016303,150.16
> select /B
3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 2 models selected
> hide #!2 models
> view matrix models
> #3,0.48391,0.52076,0.70331,16.223,0.79719,-0.59385,-0.1088,152.36,0.361,0.61332,-0.70251,168.79
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> view matrix models
> #3,0.13217,0.05584,0.98965,52.798,0.99059,0.02839,-0.1339,97.53,-0.035573,0.99804,-0.051562,123.94
> show #!2 models
> hide #!2 models
> view matrix models
> #3,0.65823,-0.53979,0.52475,80.326,-0.036274,0.6735,0.7383,78.684,-0.75195,-0.505,0.42373,242.45
> view matrix models
> #3,0.89289,-0.22835,0.38807,50.778,-0.36505,0.1374,0.92079,127.01,-0.26358,-0.96383,0.039327,257.86
> show #!2 models
> hide #!2 models
> view matrix models
> #3,0.76911,-0.4217,0.48025,66.266,-0.020828,0.73449,0.6783,79.023,-0.63878,-0.53169,0.55612,220.5
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> view matrix models
> #3,0.89454,0.044908,0.44472,28.649,-0.41681,-0.27557,0.86622,162.45,0.16145,-0.96023,-0.22779,240.38
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> view matrix models
> #3,0.64793,0.30508,0.69793,13.619,0.09381,-0.94127,0.32436,202.96,0.7559,-0.14469,-0.6385,169.92
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> view matrix models
> #3,0.87946,-0.12917,0.45811,39.524,-0.15405,-0.98791,0.017179,259.05,0.45036,-0.08568,-0.88873,219.96
> hide #!2 models
> view matrix models
> #3,-0.1975,-0.65819,-0.72649,289.14,0.77154,0.35282,-0.52939,136.34,0.60476,-0.66506,0.43814,116.27
> view matrix models
> #3,0.92694,-0.1748,0.33202,49.359,-0.23281,-0.96187,0.14356,253.48,0.29426,-0.21037,-0.93229,247.12
> show #!2 models
> hide #!2 models
> show #!2 models
> view matrix models
> #3,0.93639,-0.071022,0.3437,40.996,-0.10911,-0.98969,0.09274,247.65,0.33357,-0.12434,-0.93449,238.18
> view matrix models
> #3,0.22026,0.735,0.64129,35.084,0.28332,0.58089,-0.76308,192.65,-0.93339,0.34977,-0.080299,255.27
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.22026,0.735,0.64129,40.849,0.28332,0.58089,-0.76308,191.81,-0.93339,0.34977,-0.080299,264.37
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.58166,0.72477,0.3693,30.984,-0.029172,0.4723,-0.88096,240.44,-0.81291,0.50165,0.29586,208.06
> view matrix models
> #3,0.54276,0.041705,0.83885,32.754,-0.57229,0.74939,0.33303,164.19,-0.61474,-0.66082,0.4306,246.8
> view matrix models
> #3,0.55594,-0.048294,0.82982,37.783,-0.55438,0.72231,0.41344,156.57,-0.61936,-0.68988,0.37479,254.24
> view matrix models
> #3,0.36803,-0.50803,0.77876,89.254,0.86583,-0.11807,-0.48621,150.87,0.33896,0.85321,0.39641,62.946
> view matrix models
> #3,0.36965,-0.50795,0.77804,89.155,0.86735,-0.1117,-0.485,150.22,0.33327,0.85411,0.39928,63.188
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> view matrix models
> #3,0.58881,-0.085349,0.80375,39.215,-0.38676,0.84343,0.37289,136.32,-0.70973,-0.53042,0.46361,245.19
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.58881,-0.085349,0.80375,42.016,-0.38676,0.84343,0.37289,136.55,-0.70973,-0.53042,0.46361,234.88
> view matrix models
> #3,0.58881,-0.085349,0.80375,43.968,-0.38676,0.84343,0.37289,136.83,-0.70973,-0.53042,0.46361,235.47
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.50172,-0.40411,0.76483,75.698,0.38539,-0.68715,-0.61588,245.87,0.77444,0.60376,-0.18902,79.851
> view matrix models
> #3,0.48021,-0.60975,0.63056,102.91,0.39422,-0.49216,-0.77613,248.04,0.78358,0.62128,0.0040348,59.87
> view matrix models
> #3,0.36348,0.82972,0.42361,45.911,-0.84146,0.48753,-0.23291,260.16,-0.39978,-0.27179,0.87539,150.53
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.36348,0.82972,0.42361,52.339,-0.84146,0.48753,-0.23291,268.95,-0.39978,-0.27179,0.87539,151.34
> view matrix models
> #3,0.36348,0.82972,0.42361,55.78,-0.84146,0.48753,-0.23291,266.85,-0.39978,-0.27179,0.87539,144.2
> select add #3
16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected
> select subtract #3
Nothing selected
> select add #3
16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected
> view matrix models
> #3,0.36348,0.82972,0.42361,33.124,-0.84146,0.48753,-0.23291,382.51,-0.39978,-0.27179,0.87539,122.73
> view matrix models
> #3,0.36348,0.82972,0.42361,54.294,-0.84146,0.48753,-0.23291,371.3,-0.39978,-0.27179,0.87539,127.66
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.82706,0.078404,0.55662,41.764,-0.30907,0.89054,0.33379,241.03,-0.46953,-0.44809,0.76076,156.03
> view matrix models
> #3,0.69891,-0.13556,0.70225,53.959,-0.61391,-0.61746,0.4918,348.6,0.36694,-0.77484,-0.51476,211.95
> view matrix models
> #3,0.56613,0.038898,0.8234,45.184,0.24756,-0.9608,-0.12482,341.6,0.78626,0.2745,-0.55357,109.9
> view matrix models
> #3,0.5764,-0.0081112,0.81713,47.62,0.7149,-0.47937,-0.50904,301.68,0.39584,0.87757,-0.27051,85.425
> view matrix models
> #3,0.6191,0.1162,0.77667,39.567,0.68582,0.40181,-0.6068,259.88,-0.38258,0.90832,0.16906,119.78
> view matrix models
> #3,0.79023,-0.023751,0.61235,46.457,-0.073749,0.9883,0.13351,230.4,-0.60835,-0.15066,0.77924,149.93
> view matrix models
> #3,0.61289,-0.017424,0.78997,47.1,-0.39139,0.8618,0.32267,251.99,-0.68642,-0.50695,0.52137,203.47
> view matrix models
> #3,0.56705,-0.026808,0.82325,49.118,-0.69318,0.52434,0.49454,286.51,-0.44492,-0.85109,0.27874,223.15
> view matrix models
> #3,0.60659,0.090162,0.78988,41.165,-0.77261,0.30107,0.55896,302.01,-0.18741,-0.94933,0.25229,206.06
> view matrix models
> #3,0.4977,-0.13993,0.85599,59.851,-0.76607,0.39189,0.50947,300.43,-0.40674,-0.90931,0.087849,240.72
> view matrix models
> #3,0.61655,0.14784,0.77331,38.202,-0.77972,0.2508,0.5737,304.41,-0.10914,-0.95668,0.2699,197.11
> view matrix models
> #3,0.31191,0.30931,0.89835,46.907,-0.94422,0.20607,0.25688,353,-0.10567,-0.92837,0.35633,186.97
> view matrix models
> #3,0.25419,0.16131,0.95361,56.515,-0.94326,0.25918,0.20759,354.26,-0.21367,-0.95226,0.21804,212.04
> view matrix models
> #3,0.19102,0.082624,0.9781,65.302,-0.981,-0.018474,0.19314,376.3,0.034027,-0.99641,0.077525,203.27
> view matrix models
> #3,0.36428,-0.46497,0.80691,97.507,-0.42671,-0.85348,-0.29916,418.2,0.82778,-0.23534,-0.50931,132.78
> view matrix models
> #3,0.83082,-0.35451,0.42903,79.719,0.50878,0.17133,-0.84368,313.61,0.22559,0.91922,0.32272,44.45
> view matrix models
> #3,0.64718,0.22397,0.72869,34.676,-0.42691,0.8984,0.10303,273.76,-0.63159,-0.37777,0.67704,175.63
> view matrix models
> #3,0.61698,0.22207,0.755,35.335,-0.45337,0.88446,0.11034,276.56,-0.64326,-0.41038,0.64638,181.64
> view matrix models
> #3,0.69087,-0.16572,0.70373,56.46,-0.22389,0.87649,0.4262,224.82,-0.68744,-0.452,0.56844,195.83
> view matrix models
> #3,0.39899,-0.0097501,0.91691,56.016,-0.68251,-0.67094,0.28986,377.51,0.61236,-0.74145,-0.27435,163.14
> view matrix models
> #3,0.39834,-0.06371,0.91502,59.55,-0.12187,-0.99242,-0.016046,370.04,0.9091,-0.10512,-0.40309,106.86
> view matrix models
> #3,0.65042,-0.16137,0.74224,56.616,-0.21463,-0.9764,-0.024193,379.02,0.72862,-0.14357,-0.6697,151.98
> view matrix models
> #3,0.61975,-0.18445,0.76281,59.149,-0.014761,-0.97456,-0.22366,377.68,0.78466,0.12735,-0.60671,124
> view matrix models
> #3,0.36142,0.39819,0.8431,41.721,-0.077117,-0.88836,0.45262,315.54,0.92921,-0.2286,-0.29036,101.89
> view matrix models
> #3,0.063985,-0.22245,0.97284,97.02,-0.30904,-0.93134,-0.19263,401.35,0.94889,-0.28832,-0.12834,88.473
> view matrix models
> #3,0.49313,-0.46564,0.73485,91.486,-0.45569,-0.8578,-0.23776,415.61,0.74106,-0.21762,-0.63519,152.04
> view matrix models
> #3,0.64355,-0.21994,0.73312,61.723,-0.2712,-0.96121,-0.050299,386.14,0.71575,-0.16645,-0.67823,155.45
> view matrix models
> #3,0.40812,-0.077508,0.90963,59.924,-0.32419,-0.94375,0.065039,379.58,0.85343,-0.32144,-0.4103,126.26
> view matrix models
> #3,0.35449,-0.17546,0.91845,70.403,-0.38848,-0.92109,-0.026024,393.06,0.85054,-0.34758,-0.39468,126.69
> view matrix models
> #3,0.92953,-0.19655,0.312,71.196,0.19305,0.98027,0.042399,212.91,-0.31418,0.02082,0.94914,94.429
> view matrix models
> #3,0.89398,-0.16992,0.41465,63.525,0.1318,0.98409,0.11911,211.6,-0.42829,-0.051832,0.90215,114.57
> view matrix models
> #3,0.90191,-0.1603,0.40108,63.416,0.097932,0.98029,0.17157,210.3,-0.42068,-0.11547,0.89983,117.91
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.90191,-0.1603,0.40108,45.199,0.097932,0.98029,0.17157,98.109,-0.42068,-0.11547,0.89983,130.4
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.90462,-0.15228,0.39808,44.72,0.075784,0.97658,0.20136,97.755,-0.41942,-0.15198,0.89498,132.96
> view matrix models
> #3,0.91324,0.096479,0.39584,28.888,-0.12657,0.99067,0.05056,131.03,-0.38727,-0.096276,0.91693,124.32
> view matrix models
> #3,0.91314,0.10295,0.39444,28.633,-0.13416,0.98958,0.052321,131.69,-0.38494,-0.1007,0.91743,124.31
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.91314,0.10295,0.39444,38.931,-0.13416,0.98958,0.052321,137.5,-0.38494,-0.1007,0.91743,125.84
> select subtract #3
Nothing selected
> hide #!3 models
> select /E
3290 atoms, 3325 bonds, 4 pseudobonds, 423 residues, 3 models selected
> cartoon #2
> show #2 target ab
> hide #2 target a
> cartoon #2
> show #!3 models
> cartoon (#!3 & sel)
> cartoon hide (#!3 & sel)
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> close #3
> open /Users/wkeliason/Downloads/ChimeraX/PDB/GsDnaB_Xray/4esv.pdb.gz
4esv.pdb.gz title:
A new twist on the translocation mechanism of helicases from the structure of
DNAb with its substrates [more info...]
Chain information for 4esv.pdb.gz #3
---
Chain | Description | UniProt
A B C D E F G H I J K L | DNAB | Q9X4C9_GEOSE 1-445 1-454
V | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' |
W | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' |
Non-standard residues in 4esv.pdb.gz #3
---
ALF — tetrafluoroaluminate ion
CA — calcium ion
GDP — guanosine-5'-diphosphate
MES — 2-(N-morpholino)-ethanesulfonic acid
> delete /F,G,H,I,J,K,L,W
> delete /v
[Repeated 1 time(s)]
> select add #3
16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected
> cartoon (#!3 & sel)
> hide (#!3 & sel) target a
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 16540 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> volume #1 level 0.2654
> hide #!1 models
> volume #2 level 0.08099
> view matrix models #3,1,0,0,65.58,0,1,0,7.5259,0,0,1,72.001
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.70395,-0.49414,0.51018,77.539,0.70925,0.52724,-0.46796,9.6638,-0.037747,0.69127,0.72161,59.506
> view matrix models
> #3,0.67942,-0.51298,0.52464,79.775,0.7322,0.52044,-0.43935,5.1332,-0.047661,0.68264,0.7292,60.309
> view matrix models
> #3,0.63903,-0.33515,0.69232,57.288,0.73768,0.522,-0.42819,3.4541,-0.21788,0.78434,0.58081,84.827
> view matrix models
> #3,0.84451,-0.17702,0.50544,44.676,0.19976,0.9798,0.0093847,-11.934,-0.49689,0.09304,0.86281,128.41
> view matrix models
> #3,0.5956,0.17738,0.78345,21.809,-0.65655,0.66943,0.34756,60.432,-0.46282,-0.72138,0.51517,207.17
> view matrix models
> #3,0.030322,-0.20685,0.9779,83.213,-0.93797,-0.34396,-0.043672,186.7,0.34539,-0.91592,-0.20445,205.97
> view matrix models
> #3,0.16586,-0.50242,0.84857,99.872,-0.94262,-0.33361,-0.013285,183.7,0.28977,-0.79767,-0.52892,234.53
> view matrix models
> #3,0.66924,-0.093912,0.73709,35.389,-0.52061,-0.76706,0.37495,132.09,0.53018,-0.63467,-0.56223,203.84
> view matrix models
> #3,0.70123,0.13542,0.69996,21.677,0.3901,0.7489,-0.5357,34.111,-0.59674,0.6487,0.47232,140.81
> view matrix models
> #3,-0.97484,0.15632,-0.15893,266.78,0.22095,0.5828,-0.782,84.002,-0.029612,-0.79744,-0.60268,273.08
> view matrix models
> #3,-0.45098,0.065232,-0.89015,288.56,0.82758,0.40405,-0.38968,-1.8569,0.33424,-0.91241,-0.2362,209.83
> view matrix models
> #3,-0.59029,0.011327,-0.80711,297.93,0.73803,0.41254,-0.53397,19.966,0.32692,-0.91087,-0.25188,211.92
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.59029,0.011327,-0.80711,309.31,0.73803,0.41254,-0.53397,127.63,0.32692,-0.91087,-0.25188,215.01
> view matrix models
> #3,-0.59029,0.011327,-0.80711,406.93,0.73803,0.41254,-0.53397,81.769,0.32692,-0.91087,-0.25188,237.18
> volume #2 level 0.07452
> view matrix models
> #3,-0.59029,0.011327,-0.80711,398.31,0.73803,0.41254,-0.53397,83.254,0.32692,-0.91087,-0.25188,236.2
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.47596,-0.18535,0.85971,149.08,-0.28466,-0.95739,-0.048805,223.1,0.83212,-0.2215,-0.50844,167.92
> view matrix models
> #3,0.64643,-0.37319,0.66548,161.75,0.50354,-0.44662,-0.73958,178.14,0.57322,0.81318,-0.1008,92.424
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.64643,-0.37319,0.66548,60.211,0.50354,-0.44662,-0.73958,204.52,0.57322,0.81318,-0.1008,94.66
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.78879,0.019271,0.61436,26.895,0.53693,-0.50814,-0.67343,198.79,0.29921,0.86106,-0.41116,147.87
> view matrix models
> #3,0.90842,0.28772,0.30329,27.648,0.047112,0.6504,-0.75813,184.56,-0.41539,0.70299,0.57729,136.23
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.90842,0.28772,0.30329,33.608,0.047112,0.6504,-0.75813,204.08,-0.41539,0.70299,0.57729,128.75
> view matrix models
> #3,0.90842,0.28772,0.30329,32.824,0.047112,0.6504,-0.75813,206.68,-0.41539,0.70299,0.57729,129.07
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.62608,-0.58151,0.51949,93.739,0.071494,-0.6206,-0.78086,283.97,0.77648,0.52602,-0.34697,107.83
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.62608,-0.58151,0.51949,94.457,0.071494,-0.6206,-0.78086,282.34,0.77648,0.52602,-0.34697,107.72
> view matrix models
> #3,0.62608,-0.58151,0.51949,96.634,0.071494,-0.6206,-0.78086,285.08,0.77648,0.52602,-0.34697,104.75
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.93946,0.14061,0.31248,40.764,0.031465,0.87267,-0.48729,170.51,-0.34121,0.46762,0.81542,110.79
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.93946,0.14061,0.31248,41.628,0.031465,0.87267,-0.48729,173.62,-0.34121,0.46762,0.81542,112.84
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.87648,-0.033962,0.48023,42.889,0.22412,0.91161,-0.34458,138.82,-0.42608,0.40965,0.80662,125.62
> view matrix models
> #3,0.78869,-0.29785,0.53782,62.338,0.61458,0.35876,-0.70256,167.22,0.016307,0.88463,0.466,84.496
> view matrix models
> #3,0.90549,-0.027236,0.4235,44.892,0.044557,0.99852,-0.031051,122.09,-0.42203,0.046986,0.90537,138.15
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> select /B
3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 2 models selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> select /C
3418 atoms, 3458 bonds, 2 pseudobonds, 439 residues, 2 models selected
> volume #2 level 0.0618
> view matrix models
> #3,0.13396,-0.34893,0.92753,94.07,-0.23303,-0.92081,-0.31275,293.08,0.9632,-0.17425,-0.20466,117.74
> view matrix models
> #3,0.89292,0.021068,0.44973,40.744,0.027763,0.99443,-0.10171,130.6,-0.44937,0.1033,0.88735,139.1
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> select /B
3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select /C
3418 atoms, 3458 bonds, 2 pseudobonds, 439 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select /D
3369 atoms, 3406 bonds, 5 pseudobonds, 436 residues, 3 models selected
> cartoon hide (#!3 & sel)
> select /E
3290 atoms, 3325 bonds, 4 pseudobonds, 423 residues, 3 models selected
> cartoon hide (#!3 & sel)
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> view matrix models
> #3,0.72662,0.40274,0.55662,34.599,0.1959,0.65508,-0.72972,168.88,-0.65852,0.63927,0.3971,169.9
> view matrix models
> #3,0.95188,0.17484,0.25169,38.556,0.034591,0.75474,-0.65511,178.87,-0.3045,0.6323,0.71238,105.23
> view matrix models
> #3,0.97656,0.11228,0.18363,43.236,0.023622,0.79208,-0.60996,175.3,-0.21394,0.6,0.77086,91.74
> view matrix models
> #3,0.97171,-0.049536,-0.23092,79.715,-0.066705,0.88038,-0.46956,172.68,0.22655,0.47168,0.85217,38.102
> view matrix models
> #3,0.99099,0.13201,-0.022807,54.104,-0.092826,0.55388,-0.82741,216.58,-0.096595,0.82207,0.56114,79.512
> view matrix models
> #3,0.62442,-0.48693,0.61073,89.859,0.77961,0.34054,-0.52558,98.894,0.047937,0.80432,0.59226,60.356
> view matrix models
> #3,0.62682,-0.63027,0.45811,107.11,0.76344,0.37926,-0.5228,98.719,0.15576,0.67744,0.7189,45.097
> view matrix models
> #3,0.84973,-0.44481,0.28301,81.327,0.50892,0.55186,-0.66065,130.64,0.13769,0.7054,0.6953,47.464
> view matrix models
> #3,0.67878,-0.56332,0.4711,96.303,0.30807,0.80078,0.51366,64.899,-0.6666,-0.20353,0.71709,193.37
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.67878,-0.56332,0.4711,97.779,0.30807,0.80078,0.51366,72.361,-0.6666,-0.20353,0.71709,195.13
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.6429,-0.60672,0.46751,104.74,0.71681,0.26146,-0.64639,126.29,0.26994,0.75068,0.603,36.515
> view matrix models
> #3,0.68082,-0.53968,0.49521,94.701,-0.032325,-0.69758,-0.71578,273.96,0.73174,0.47131,-0.49237,66.074
> view matrix models
> #3,0.69054,-0.52587,0.4966,92.682,-0.52843,-0.83561,-0.15006,305.44,0.49387,-0.15879,-0.85491,152.42
> view matrix models
> #3,0.71671,-0.62356,0.31225,106.71,-0.5753,-0.78174,-0.24066,314.49,0.39416,-0.0071565,-0.91901,161.23
> view matrix models
> #3,0.81611,-0.54196,0.20062,97.493,-0.4851,-0.83112,-0.27189,307.88,0.31409,0.12457,-0.94118,165.86
> view matrix models
> #3,0.87155,-0.37531,0.31549,74.328,0.12763,0.79494,0.59311,89.883,-0.4734,-0.47666,0.74074,183.64
> select /B
3352 atoms, 3390 bonds, 2 pseudobonds, 432 residues, 2 models selected
> cartoon (#!3 & sel)
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> cartoon hide (#!3 & sel)
> select add #3
16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected
> select subtract #3
Nothing selected
> select clear
> ui mousemode right "translate selected models"
> select add #3
16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected
> view matrix models
> #3,0.87155,-0.37531,0.31549,42.11,0.12763,0.79494,0.59311,134.68,-0.4734,-0.47666,0.74074,172.23
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.88341,-0.26432,0.38693,32.081,0.035206,0.86084,0.50766,150.87,-0.46727,-0.43485,0.76978,168.09
> view matrix models
> #3,0.88674,-0.29358,0.35707,34.93,0.12642,0.897,0.42356,146.82,-0.44464,-0.33045,0.83252,157.73
> view matrix models
> #3,0.81929,-0.1734,0.54652,23.644,0.024558,0.96291,0.2687,169.98,-0.57285,-0.20672,0.79316,172.69
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.81929,-0.1734,0.54652,14.935,0.024558,0.96291,0.2687,141.37,-0.57285,-0.20672,0.79316,189.52
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.80687,-0.17987,0.56268,15.122,0.031751,0.96434,0.26274,141.03,-0.58988,-0.19413,0.78381,191.95
> view matrix models
> #3,0.15747,-0.32503,0.9325,60.701,-0.97655,0.08911,0.19597,281.57,-0.14679,-0.9415,-0.30337,251.72
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.15747,-0.32503,0.9325,54.828,-0.97655,0.08911,0.19597,291.49,-0.14679,-0.9415,-0.30337,270.28
> view matrix models
> #3,0.15747,-0.32503,0.9325,72.5,-0.97655,0.08911,0.19597,279.94,-0.14679,-0.9415,-0.30337,274.97
> view matrix models
> #3,0.15747,-0.32503,0.9325,98.378,-0.97655,0.08911,0.19597,280.5,-0.14679,-0.9415,-0.30337,264.25
> view matrix models
> #3,0.15747,-0.32503,0.9325,51.247,-0.97655,0.08911,0.19597,292.25,-0.14679,-0.9415,-0.30337,249.77
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.58342,-0.27173,0.76537,15.928,-0.81138,-0.23677,0.53442,252.44,0.035998,-0.93279,-0.35861,233.55
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.58342,-0.27173,0.76537,51.723,-0.81138,-0.23677,0.53442,237.73,0.035998,-0.93279,-0.35861,247.74
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.81864,-0.39772,0.41431,57.868,0.35959,-0.20754,-0.90974,227.08,0.44781,0.89373,-0.026883,129.87
> view matrix models
> #3,0.81724,0.018472,0.57599,34.486,-0.20938,0.9407,0.26692,164.53,-0.53691,-0.33874,0.77265,202.54
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.81724,0.018472,0.57599,28.538,-0.20938,0.9407,0.26692,183.87,-0.53691,-0.33874,0.77265,209.64
> cartoon hide (#!3 & sel)
> select /C
3418 atoms, 3458 bonds, 2 pseudobonds, 439 residues, 2 models selected
> cartoon (#!3 & sel)
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.1212,-0.56143,0.8186,79.062,-0.34029,-0.79821,-0.49706,330.97,0.93248,-0.21832,-0.28779,196.17
> view matrix models
> #3,0.64865,-0.73504,-0.19741,148.27,-0.43965,-0.15014,-0.88553,359.53,0.62126,0.66119,-0.42055,207.86
> view matrix models
> #3,0.91612,-0.38479,0.11251,82.198,-0.40023,-0.89407,0.20114,265.23,0.023195,-0.22929,-0.97308,344.2
> view matrix models
> #3,0.98654,-0.054124,0.15428,61.392,-0.1556,-0.60051,0.78433,173.99,0.050196,-0.79778,-0.60085,320.8
> view matrix models
> #3,0.98485,-0.040736,0.16856,59.596,-0.15875,-0.6029,0.78186,174.59,0.069774,-0.79677,-0.60023,319.08
> view matrix models
> #3,0.869,-0.43736,0.23142,75.216,-0.48251,-0.85264,0.20046,270.79,0.10965,-0.28586,-0.95198,336.62
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.869,-0.43736,0.23142,79.462,-0.48251,-0.85264,0.20046,237.9,0.10965,-0.28586,-0.95198,315.64
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.84982,-0.47442,0.22964,82.422,-0.51728,-0.8343,0.19068,241.23,0.10113,-0.28083,-0.95442,316.45
> view matrix models
> #3,0.84938,-0.51368,0.12117,95.171,-0.4249,-0.80173,-0.42034,297.09,0.31307,0.30554,-0.89924,274.34
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.84938,-0.51368,0.12117,100.72,-0.4249,-0.80173,-0.42034,308.31,0.31307,0.30554,-0.89924,267.3
> view matrix models
> #3,0.84938,-0.51368,0.12117,83.829,-0.4249,-0.80173,-0.42034,310.35,0.31307,0.30554,-0.89924,262.25
> cartoon hide (#!3 & sel)
> select /C
3418 atoms, 3458 bonds, 2 pseudobonds, 439 residues, 2 models selected
> cartoon (#!3 & sel)
[Repeated 1 time(s)]
> select /D
3369 atoms, 3406 bonds, 5 pseudobonds, 436 residues, 3 models selected
> select /C
3418 atoms, 3458 bonds, 2 pseudobonds, 439 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select /D
3369 atoms, 3406 bonds, 5 pseudobonds, 436 residues, 3 models selected
> cartoon (#!3 & sel)
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.8296,-0.53655,-0.15452,118.58,-0.55754,-0.78103,-0.28132,304.91,0.030258,0.31954,-0.94709,291.96
> view matrix models
> #3,0.96881,-0.24466,0.039447,67.532,-0.24391,-0.91325,0.32631,214.74,-0.043809,-0.32575,-0.94444,334.53
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.96881,-0.24466,0.039447,94.457,-0.24391,-0.91325,0.32631,219.87,-0.043809,-0.32575,-0.94444,341.23
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.79164,-0.58362,0.18082,112.93,-0.60815,-0.78115,0.14128,265.9,0.058792,-0.2218,-0.97332,329.63
> view matrix models
> #3,0.69294,-0.56391,0.44926,89.657,-0.33601,-0.80389,-0.49078,315.85,0.63791,0.18913,-0.74653,229.23
> view matrix models
> #3,0.73886,-0.52971,0.41652,87.441,-0.24974,-0.78935,-0.56085,315.47,0.62587,0.31037,-0.71552,219.9
> view matrix models
> #3,0.65906,-0.67181,0.3381,111.52,-0.41179,-0.6985,-0.58525,327.48,0.62934,0.24649,-0.737,225.67
> view matrix models
> #3,0.66733,-0.73385,0.12704,138.56,-0.37076,-0.47528,-0.7979,335.75,0.64591,0.48536,-0.58925,193.75
> view matrix models
> #3,0.67235,-0.73042,0.12014,138.72,-0.37573,-0.47659,-0.79479,335.91,0.63779,0.48924,-0.59487,194.9
> view matrix models
> #3,0.68781,-0.72359,-0.057779,157.44,-0.31113,-0.22196,-0.92408,330.74,0.65583,0.65357,-0.3778,159.08
> view matrix models
> #3,0.64491,-0.76357,-0.032473,160.57,-0.28977,-0.20499,-0.93489,329.14,0.70719,0.61233,-0.35346,154.06
> view matrix models
> #3,0.7787,-0.58224,0.23372,107.91,-0.070287,-0.45114,-0.88968,318.41,0.62345,0.67637,-0.39223,162.31
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.7787,-0.58224,0.23372,103.2,-0.070287,-0.45114,-0.88968,317.95,0.62345,0.67637,-0.39223,149.5
> view matrix models
> #3,0.7787,-0.58224,0.23372,102.8,-0.070287,-0.45114,-0.88968,321.43,0.62345,0.67637,-0.39223,146.14
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.62476,-0.61605,0.47974,89.995,-0.61338,-0.76741,-0.18667,306.33,0.48316,-0.17764,-0.85732,260.13
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.62476,-0.61605,0.47974,92.192,-0.61338,-0.76741,-0.18667,316.7,0.48316,-0.17764,-0.85732,273.08
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.3024,-0.8011,-0.51652,245.72,0.64025,0.57216,-0.51256,168.01,0.70615,-0.1757,0.68592,75.712
> cartoon hide (#!3 & sel)
> select /E
3290 atoms, 3325 bonds, 4 pseudobonds, 423 residues, 3 models selected
> cartoon (#!3 & sel)
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.3024,-0.8011,-0.51652,255.76,0.64025,0.57216,-0.51256,131.81,0.70615,-0.1757,0.68592,77.029
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.17246,-0.68248,0.71027,126.93,-0.8021,0.32124,0.50343,186.83,-0.57175,-0.65653,-0.49201,370.69
> view matrix models
> #3,0.23996,-0.68921,0.68367,123.82,-0.82843,0.22176,0.51432,197.38,-0.50609,-0.68979,-0.51775,370.11
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.23996,-0.68921,0.68367,121.13,-0.82843,0.22176,0.51432,209.21,-0.50609,-0.68979,-0.51775,371.57
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.42674,-0.58321,-0.6912,322.39,0.90019,-0.3474,-0.26264,176.44,-0.086954,-0.73429,0.67325,208.25
> view matrix models
> #3,0.22001,-0.86784,0.44547,164.85,-0.84172,0.061931,0.53636,222.87,-0.49306,-0.49296,-0.71685,373.37
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.22001,-0.86784,0.44547,162.26,-0.84172,0.061931,0.53636,221.59,-0.49306,-0.49296,-0.71685,377.35
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule 4esv.pdb.gz (#3) to map
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
using 3290 atoms
average map value = 0.05965, steps = 152
shifted from previous position = 20.7
rotated from previous position = 20.2 degrees
atoms outside contour = 1691, contour level = 0.061802
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.18294,-0.92075,0.3446,216.99,0.70487,-0.36718,-0.60691,232.58,0.68535,0.13187,0.71618,52.955
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.18294,-0.92075,0.3446,232.52,0.70487,-0.36718,-0.60691,243.7,0.68535,0.13187,0.71618,42.599
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule 4esv.pdb.gz (#3) to map
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
using 3290 atoms
average map value = 0.06099, steps = 324
shifted from previous position = 30.7
rotated from previous position = 52.4 degrees
atoms outside contour = 1621, contour level = 0.061802
> cartoon hide (#!3 & sel)
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> cartoon (#!3 & sel)
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.42976,-0.1716,0.88648,188.52,-0.76437,-0.45349,-0.45835,421.43,0.48067,-0.87458,0.063726,163.53
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.42976,-0.1716,0.88648,179.52,-0.76437,-0.45349,-0.45835,373.56,0.48067,-0.87458,0.063726,195.17
> volume #2 level 0.08387
> view matrix models
> #3,-0.42976,-0.1716,0.88648,176.01,-0.76437,-0.45349,-0.45835,386.53,0.48067,-0.87458,0.063726,245.26
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.42469,0.60485,0.67364,149.25,-0.81072,-0.58526,0.014384,367.79,0.40295,-0.54002,0.73892,192.83
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.42469,0.60485,0.67364,136.46,-0.81072,-0.58526,0.014384,341.23,0.40295,-0.54002,0.73892,136.85
> cartoon hide (#!3 & sel)
> ui tool show AlphaFold
> alphafold predict
> MSELFSERIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSQRKHSGAFKNIKDILVQTYDNIEMLHNRDGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDIRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNLERRFDEAQIPPGA
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16
> open
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/best_model.pdb
Chain information for best_model.pdb #4
---
Chain | Description
A | No description available
> view matrix models
> #3,-0.42469,0.60485,0.67364,203.26,-0.81072,-0.58526,0.014384,409.53,0.40295,-0.54002,0.73892,207.6
> select add #4
6839 atoms, 6917 bonds, 8 pseudobonds, 880 residues, 4 models selected
> select add #3
20268 atoms, 20496 bonds, 21 pseudobonds, 2610 residues, 4 models selected
> select subtract #3
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models #4,1,0,0,141.3,0,1,0,149.35,0,0,1,155.44
> select subtract #4
Nothing selected
> select add #4
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.86622,0.39715,0.30319,137.08,-0.47116,0.85124,0.23106,147.93,-0.16632,-0.34301,0.92449,157.46
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.86622,0.39715,0.30319,175.97,-0.47116,0.85124,0.23106,178.41,-0.16632,-0.34301,0.92449,148.23
> select subtract #4
Nothing selected
> close #3
> ui mousemode right "rotate selected models"
> select add #4
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models
> #4,0.7569,0.59018,0.28069,174.62,-0.59868,0.7984,-0.064323,179.83,-0.26207,-0.11936,0.95764,146.46
> view matrix models
> #4,0.68329,0.6034,-0.41113,177.7,-0.59588,0.78623,0.16359,178.81,0.42195,0.13321,0.89678,146.97
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.68329,0.6034,-0.41113,176.57,-0.59588,0.78623,0.16359,179.38,0.42195,0.13321,0.89678,140.29
> select subtract #4
Nothing selected
> ui mousemode right "rotate selected models"
> select add #4
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models
> #4,0.27144,0.95624,-0.10919,171.92,-0.95029,0.28426,0.12703,181.7,0.15251,0.069281,0.98587,139.56
> select subtract #4
Nothing selected
> ui mousemode right "translate selected models"
> select add #4
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models
> #4,0.27144,0.95624,-0.10919,173.31,-0.95029,0.28426,0.12703,182.49,0.15251,0.069281,0.98587,144.88
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.36509,0.91022,-0.19548,174.24,-0.91108,0.3925,0.12603,181.94,0.19144,0.13209,0.97258,144.67
> view matrix models
> #4,0.49451,0.86802,-0.044869,174.1,-0.85284,0.49453,0.16764,181.27,0.1677,-0.044631,0.98483,145.62
> select subtract #4
Nothing selected
> fitmap #4 inMap #2 moveWholeMolecules false
Fit molecule best_model.pdb (#4) to map
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
using 3553 atoms
average map value = 0.06568, steps = 752
shifted from previous position = 18.2
rotated from previous position = 44.9 degrees
atoms outside contour = 2624, contour level = 0.083873
> select : 181-454
2138 atoms, 2162 bonds, 274 residues, 1 model selected
> view matrix models
> #4,0.56866,0.81473,-0.1133,175.51,-0.75309,0.57107,0.3267,176.57,0.33088,-0.10045,0.93831,145.99
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.56866,0.81473,-0.1133,173.91,-0.75309,0.57107,0.3267,172.57,0.33088,-0.10045,0.93831,141.71
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.24758,0.50377,-0.8276,193.81,-0.53409,0.78365,0.31723,169.26,0.80836,0.36347,0.46308,143.86
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.24758,0.50377,-0.8276,177.82,-0.53409,0.78365,0.31723,172.67,0.80836,0.36347,0.46308,135.98
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule best_model.pdb (#4) to map
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
using 2138 atoms
average map value = 0.06752, steps = 216
shifted from previous position = 2.51
rotated from previous position = 41.1 degrees
atoms outside contour = 1556, contour level = 0.083873
> close #4
> open
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
Chain information for
af454_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb #3
---
Chain | Description
A | No description available
Chain information for
af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb #4
---
Chain | Description
A | No description available
Chain information for
af454_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb #5
---
Chain | Description
A | No description available
Chain information for
af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb #6
---
Chain | Description
A | No description available
Chain information for
af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #7
---
Chain | Description
A | No description available
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #3
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models #3,1,0,0,154.8,0,1,0,136.78,0,0,1,74.917
> select subtract #3
Nothing selected
> select add #4
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models #4,1,0,0,121.71,0,1,0,112.13,0,0,1,212.54
> select subtract #4
Nothing selected
> select add #5
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models #5,1,0,0,71.136,0,1,0,66.941,0,0,1,171.15
> select subtract #5
Nothing selected
> select add #6
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models #6,1,0,0,91.563,0,1,0,80.861,0,0,1,42.954
> select subtract #6
Nothing selected
> select add #7
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models #7,1,0,0,55.655,0,1,0,56.71,0,0,1,278.98
> select subtract #7
Nothing selected
> select add #3
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #4
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #5
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #6
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models #6,1,0,0,177.24,0,1,0,98.919,0,0,1,161.92
> view matrix models #6,1,0,0,142.92,0,1,0,164.64,0,0,1,140.27
> view matrix models #6,1,0,0,175.1,0,1,0,164.55,0,0,1,150.54
> select : 181-454
10690 atoms, 10810 bonds, 1370 residues, 5 models selected
> select add #5
12105 atoms, 12247 bonds, 1550 residues, 5 models selected
> select subtract #5
8552 atoms, 8648 bonds, 1096 residues, 4 models selected
> select add #4
9967 atoms, 10085 bonds, 1276 residues, 4 models selected
> select subtract #4
6414 atoms, 6486 bonds, 822 residues, 3 models selected
> select add #3
7829 atoms, 7923 bonds, 1002 residues, 3 models selected
> select subtract #3
4276 atoms, 4324 bonds, 548 residues, 2 models selected
> select add #7
5691 atoms, 5761 bonds, 728 residues, 2 models selected
> select subtract #7
2138 atoms, 2162 bonds, 274 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.91502,0.14207,0.37756,172.81,-0.19726,0.97398,0.11155,162.71,-0.35189,-0.17655,0.91924,148.54
> view matrix models
> #6,0.98386,-0.002578,0.17891,174.34,0.0049876,0.9999,-0.01302,164.64,-0.17886,0.013702,0.98378,149.22
> view matrix models
> #6,0.81065,0.57137,-0.12802,172.96,-0.563,0.70052,-0.43853,162.49,-0.16088,0.42757,0.88955,148.85
> view matrix models
> #6,0.83929,0.53608,-0.090665,173.12,-0.52084,0.74492,-0.41692,162.64,-0.15596,0.39713,0.90441,148.9
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.83929,0.53608,-0.090665,181.69,-0.52084,0.74492,-0.41692,174.18,-0.15596,0.39713,0.90441,151.56
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.84525,0.52583,-0.09519,181.77,-0.51417,0.75175,-0.41293,174.21,-0.14557,0.39797,0.90577,151.63
> view matrix models
> #6,0.82652,0.55604,-0.087673,181.54,-0.54773,0.7585,-0.35308,173.72,-0.12983,0.33985,0.93147,151.78
> view matrix models
> #6,0.90974,-0.023251,-0.41452,184.53,-0.068681,0.97625,-0.20549,176.37,0.40945,0.21542,0.88654,156.27
> view matrix models
> #6,0.35444,-0.92362,-0.14593,181.21,-0.93037,-0.36398,0.043969,171.7,-0.093728,0.12019,-0.98832,159.41
> view matrix models
> #6,0.16354,-0.98512,-0.05295,179.56,-0.98394,-0.15898,-0.081181,171.32,0.071555,0.065375,-0.99529,160.8
> view matrix models
> #6,0.65346,-0.53695,-0.53355,184.08,-0.71214,-0.19712,-0.6738,175.59,0.25663,0.82026,-0.51119,158.91
> view matrix models
> #6,0.34096,-0.85598,-0.38863,181.85,-0.80085,-0.047977,-0.59694,174.34,0.49233,0.51477,-0.70187,162
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.34096,-0.85598,-0.38863,177.63,-0.80085,-0.047977,-0.59694,159.07,0.49233,0.51477,-0.70187,147.06
> select add #6
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #5
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #4
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #3
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models #3,1,0,0,119.56,0,1,0,9.4868,0,0,1,77.51
> select subtract #3
Nothing selected
> select add #6
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> view matrix models
> #6,0.34096,-0.85598,-0.38863,178.08,-0.80085,-0.047977,-0.59694,138.06,0.49233,0.51477,-0.70187,162.59
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.11441,-0.20695,-0.97164,177.14,-0.59668,0.76767,-0.23377,136.63,0.79428,0.60651,-0.035655,162.29
> view matrix models
> #6,-0.051355,-0.48219,-0.87456,176.1,-0.99395,0.10979,-0.0021657,134.14,0.097061,0.86916,-0.48491,158.1
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.051355,-0.48219,-0.87456,189.87,-0.99395,0.10979,-0.0021657,183.47,0.097061,0.86916,-0.48491,150.03
> view matrix models
> #6,-0.051355,-0.48219,-0.87456,178.97,-0.99395,0.10979,-0.0021657,183.9,0.097061,0.86916,-0.48491,142.53
> view matrix models
> #6,-0.051355,-0.48219,-0.87456,180.06,-0.99395,0.10979,-0.0021657,182.13,0.097061,0.86916,-0.48491,140.82
> view matrix models
> #6,-0.051355,-0.48219,-0.87456,176.75,-0.99395,0.10979,-0.0021657,179.41,0.097061,0.86916,-0.48491,139.55
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.09051,-0.21443,-0.97254,177.62,-0.96608,0.21824,-0.13803,179.88,0.24184,0.95205,-0.1874,139.41
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.09051,-0.21443,-0.97254,175.79,-0.96608,0.21824,-0.13803,179.73,0.24184,0.95205,-0.1874,139.72
> fitmap #6 inMap #2 moveWholeMolecules false
Fit molecule af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb (#6)
to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian
(#2) using 3553 atoms
average map value = 0.05906, steps = 248
shifted from previous position = 13.1
rotated from previous position = 39.5 degrees
atoms outside contour = 2867, contour level = 0.083873
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.057493,-0.31556,-0.94716,176.74,-0.95956,0.24441,-0.13967,179.55,0.27557,0.91689,-0.28875,138.72
> view matrix models
> #6,-0.27637,-0.23646,-0.93151,176.85,-0.94173,0.26003,0.21339,183.52,0.19177,0.9362,-0.29454,138.64
> hide #7 models
> select subtract #6
Nothing selected
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #!2 models
> show #!2 models
> open /Users/wkeliason/Downloads/output_raw.cif
Summary of feedback from opening /Users/wkeliason/Downloads/output_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for output_raw.cif #8
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A8 CF | No description available
AA | No description available
AB | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
AP | No description available
AQ | No description available
AR | No description available
AS | No description available
AT | No description available
AU | No description available
AV | No description available
AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
Al | No description available
Am | No description available
An | No description available
Ao | No description available
Ap | No description available
Aq | No description available
Ar | No description available
As | No description available
At | No description available
Au | No description available
Av | No description available
Aw | No description available
Ax | No description available
Ay | No description available
Az | No description available
B | No description available
B0 | No description available
B1 | No description available
B2 | No description available
B7 | No description available
BC DN | No description available
BH | No description available
BK | No description available
BO | No description available
BQ | No description available
BT | No description available
BU | No description available
BW | No description available
Ba | No description available
Bk | No description available
Bl | No description available
Bn | No description available
Br | No description available
Bs | No description available
Bw | No description available
C | No description available
C2 | No description available
CD | No description available
CG | No description available
CH | No description available
CI | No description available
CM | No description available
CN | No description available
CO | No description available
CQ | No description available
CS | No description available
CW | No description available
Ca | No description available
Ce DC | No description available
Cp | No description available
Cs | No description available
Cw | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> select add #8
14223 atoms, 14113 bonds, 1763 residues, 1 model selected
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 9993 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> hide sel atoms
> show sel cartoons
> volume #2 level 0.07633
> volume #2 level 0.06654
> select subtract #8
Nothing selected
> hide #8 models
> select #8/0
27 atoms, 27 bonds, 4 residues, 1 model selected
> cartoon #2
> show #7 models
> hide #7 models
> show #8 models
> select #8/0
27 atoms, 27 bonds, 4 residues, 1 model selected
> select #8/1
33 atoms, 32 bonds, 4 residues, 1 model selected
> select add #8
14223 atoms, 14113 bonds, 1763 residues, 1 model selected
> select subtract #8
Nothing selected
> close #8
> show #7 models
> select add #7
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> show sel cartoons
[Repeated 2 time(s)]
> delete :1-155
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,152.43,0,1,0,80.28,0,0,1,187.44
> view matrix models #7,1,0,0,159.07,0,1,0,154.68,0,0,1,214.81
> view matrix models #7,1,0,0,171.43,0,1,0,185.17,0,0,1,224.39
> view matrix models #7,1,0,0,166.15,0,1,0,190.88,0,0,1,217.73
> select subtract #7
Nothing selected
> select add #7
2343 atoms, 2370 bonds, 299 residues, 1 model selected
> view matrix models #7,1,0,0,161.85,0,1,0,191.26,0,0,1,223.25
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.99942,0.0068874,0.033254,162.16,0.030437,0.2526,-0.96709,185.41,-0.015061,0.96755,0.25224,209.69
> view matrix models
> #7,-0.53661,-0.17096,-0.82633,168.44,-0.59827,-0.6135,0.51544,211.98,-0.59508,0.77097,0.22693,215.98
> view matrix models
> #7,0.907,-0.29347,0.30204,167.65,0.30553,0.95215,0.0076701,188.81,-0.28984,0.085327,0.95326,224.92
> view matrix models
> #7,0.91992,-0.39162,-0.019694,164.76,0.38703,0.89877,0.20596,190.45,-0.062958,-0.19709,0.97836,224.8
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.91992,-0.39162,-0.019694,174.26,0.38703,0.89877,0.20596,210.17,-0.062958,-0.19709,0.97836,216.98
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.91592,-0.39848,-0.047943,174.04,0.21966,0.39772,0.89083,221.91,-0.33591,-0.82646,0.45181,217.82
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.91592,-0.39848,-0.047943,173.6,0.21966,0.39772,0.89083,217.47,-0.33591,-0.82646,0.45181,212.02
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.90922,-0.4163,0.0022603,174.29,0.18724,0.41379,0.89091,217.68,-0.37182,-0.80961,0.45418,212.27
> view matrix models
> #7,0.99285,-0.10223,0.061702,172.23,0.00040162,0.51961,0.8544,218.38,-0.1194,-0.84827,0.51593,210.82
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.99285,-0.10223,0.061702,173.43,0.00040162,0.51961,0.8544,221.07,-0.1194,-0.84827,0.51593,207.88
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.80697,0.24993,0.53511,177.95,-0.59048,0.3232,0.73951,226.52,0.011879,-0.91273,0.40839,205.94
> view matrix models
> #7,0.81773,0.25389,0.51658,177.64,-0.57559,0.36549,0.73152,226.04,-0.0030836,-0.89552,0.44501,206.35
> view matrix models
> #7,0.8666,0.24178,0.43651,176.42,-0.49693,0.33865,0.79898,226.18,0.045355,-0.90932,0.41363,205.66
> view matrix models
> #7,0.60088,-0.76471,-0.23273,178,0.017504,-0.2785,0.96028,226.86,-0.79915,-0.58108,-0.15396,205.54
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.60088,-0.76471,-0.23273,178.54,0.017504,-0.2785,0.96028,223.28,-0.79915,-0.58108,-0.15396,209.47
> hide #7 models
> show #7 models
Opened af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 as
#8, grid size 113,115,103, pixel 0.667, shown at level 0.187, step 1, values
float32
Opened af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 as
#9, grid size 113,115,103, pixel 0.667, shown at level 0.187, step 1, values
float32
> fitmap #7 inMap #2 resolution 2 moveWholeMolecules false
Fit map af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 in
map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian
using 42152 points
correlation = 0.7124, correlation about mean = 0.009181, overlap = 3491
steps = 264, shift = 21.1, angle = 28.8 degrees
Position of af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2
(#9) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc
gaussian (#2) coordinates:
Matrix rotation and translation
0.46276591 -0.86980490 0.17113491 189.05644106
-0.40941583 -0.03847764 0.91153616 201.96759635
-0.78627375 -0.49189320 -0.37391803 203.19240477
Axis -0.79732539 0.54392922 0.26155923
Axis point 0.00000000 240.30764452 59.52254519
Rotation angle (degrees) 118.34729718
Shift along axis 12.26342377
Average map value = 0.07022 for 2343 atoms, 973 outside contour
Opened af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 as
#8, grid size 103,121,117, pixel 0.667, shown at level 0.189, step 1, values
float32
> view matrix models
> #7,0.60088,-0.76471,-0.23273,161.53,0.017504,-0.2785,0.96028,226.51,-0.79915,-0.58108,-0.15396,201.13
> view matrix models
> #7,0.60088,-0.76471,-0.23273,168.24,0.017504,-0.2785,0.96028,222.16,-0.79915,-0.58108,-0.15396,214.41
> view matrix models
> #7,0.60088,-0.76471,-0.23273,159.81,0.017504,-0.2785,0.96028,215.29,-0.79915,-0.58108,-0.15396,210.9
> view matrix models
> #7,0.60088,-0.76471,-0.23273,165,0.017504,-0.2785,0.96028,238.4,-0.79915,-0.58108,-0.15396,205.35
> view matrix models
> #7,0.60088,-0.76471,-0.23273,169.4,0.017504,-0.2785,0.96028,238.12,-0.79915,-0.58108,-0.15396,206.92
> fitmap #7 inMap #2 resolution 2 moveWholeMolecules false
Fit map af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 in
map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian
using 42169 points
correlation = 0.7144, correlation about mean = 0.007115, overlap = 3477
steps = 224, shift = 16.8, angle = 33.8 degrees
Position of af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2
(#8) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc
gaussian (#2) coordinates:
Matrix rotation and translation
0.47279123 -0.84163271 0.26100354 194.78227338
-0.47935219 0.00288471 0.87761790 220.85853234
-0.73938484 -0.54004266 -0.40207461 201.01378164
Axis -0.79980477 0.56439138 0.20438862
Axis point -0.00000000 254.49891858 43.89231021
Rotation angle (degrees) 117.59374784
Shift along axis 9.94779082
Average map value = 0.07 for 2343 atoms, 988 outside contour
Opened af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 as
#8, grid size 101,118,129, pixel 0.667, shown at level 0.189, step 1, values
float32
> view matrix models
> #7,0.60088,-0.76471,-0.23273,175.55,0.017504,-0.2785,0.96028,248.33,-0.79915,-0.58108,-0.15396,197.34
> select subtract #7
Nothing selected
> hide #7 models
> show #6 models
> ui mousemode right "rotate selected models"
> select add #6
2343 atoms, 2370 bonds, 299 residues, 1 model selected
> view matrix models
> #6,-0.33064,-0.084353,-0.93998,178.51,-0.94332,-0.00078486,0.33189,183.17,-0.028733,0.99644,-0.079312,144.56
> view matrix models
> #6,0.71325,-0.21129,0.66831,181.91,-0.25318,0.81144,0.52675,181.34,-0.65359,-0.54491,0.52526,149.9
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.71325,-0.21129,0.66831,172.23,-0.25318,0.81144,0.52675,181.35,-0.65359,-0.54491,0.52526,152.59
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.46751,0.088384,0.87956,180.05,0.88114,0.033262,-0.47169,149.02,-0.070946,0.99553,-0.062328,148.02
> view matrix models
> #6,0.72867,-0.15612,0.66683,172.37,0.49177,0.79694,-0.35079,160.86,-0.47666,0.58353,0.65748,159.19
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.72867,-0.15612,0.66683,164.32,0.49177,0.79694,-0.35079,183.84,-0.47666,0.58353,0.65748,149.9
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.38638,0.16351,0.90773,173.94,0.02955,0.98146,-0.18937,193.29,-0.92187,0.09999,0.37438,149.53
> view matrix models
> #6,0.34491,0.30842,0.88652,175.23,-0.21603,0.9452,-0.24479,195.79,-0.91344,-0.10708,0.39264,148.25
> view matrix models
> #6,-0.21778,0.75653,0.61663,182.83,-0.40663,0.50402,-0.76198,189.49,-0.88726,-0.41668,0.19786,143.58
> view matrix models
> #6,0.60024,0.24849,0.76024,169.86,-0.18876,0.96768,-0.16725,196.46,-0.77723,-0.043108,0.62774,149.52
> view matrix models
> #6,0.60796,0.094348,0.78835,169.05,0.02922,0.98958,-0.14097,193.91,-0.79343,0.10874,0.59887,150.42
> view matrix models
> #6,0.67479,0.16734,0.71879,167.81,-0.14964,0.98475,-0.08878,196.94,-0.72268,-0.04765,0.68954,149.46
> view matrix models
> #6,0.66227,0.22921,0.71335,168.33,-0.23018,0.96826,-0.097426,197.84,-0.71304,-0.099673,0.694,149.03
> view matrix models
> #6,0.50574,-0.12517,0.85356,169.75,-0.28329,0.91045,0.30137,202.8,-0.81484,-0.39422,0.42499,145.36
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> view matrix models
> #6,0.33406,-0.40229,0.85239,170.25,-0.60937,0.59775,0.52093,207.74,-0.71908,-0.69344,-0.045459,136.61
> view matrix models
> #6,0.83581,0.10274,0.53931,163.09,0.12501,0.92091,-0.36918,189.5,-0.53459,0.37599,0.75687,150.46
> view matrix models
> #6,0.7681,-0.42208,0.48153,159.86,0.52431,0.84626,-0.094562,186.69,-0.36759,0.3251,0.87131,149.15
> view matrix models
> #6,0.67901,-0.68107,-0.27403,150.63,-0.13429,0.25174,-0.95843,181.8,0.72174,0.68759,0.079469,127.42
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.67901,-0.68107,-0.27403,164.99,-0.13429,0.25174,-0.95843,191.02,0.72174,0.68759,0.079469,157.78
> view matrix models
> #6,0.67901,-0.68107,-0.27403,158.08,-0.13429,0.25174,-0.95843,190.6,0.72174,0.68759,0.079469,151.8
> view matrix models
> #6,0.67901,-0.68107,-0.27403,156.73,-0.13429,0.25174,-0.95843,204.59,0.72174,0.68759,0.079469,149.05
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.64204,-0.66056,-0.38915,156.05,-0.076998,0.44947,-0.88997,205.91,0.76279,0.60136,0.23772,149.74
> view matrix models
> #6,0.5273,-0.67905,-0.51072,156.1,0.34032,0.71955,-0.60534,205.26,0.77855,0.14539,0.61052,150.8
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.5273,-0.67905,-0.51072,158.03,0.34032,0.71955,-0.60534,198.28,0.77855,0.14539,0.61052,150.38
> volume #2 level 0.03253
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.66289,-0.71104,-0.23452,159.15,0.55438,0.67666,-0.48455,196.45,0.50322,0.19119,0.84274,157.16
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.66289,-0.71104,-0.23452,154.59,0.55438,0.67666,-0.48455,193.66,0.50322,0.19119,0.84274,155.31
> view matrix models
> #6,0.66289,-0.71104,-0.23452,154.55,0.55438,0.67666,-0.48455,193.6,0.50322,0.19119,0.84274,154.83
> view matrix models
> #6,0.66289,-0.71104,-0.23452,154.86,0.55438,0.67666,-0.48455,194.4,0.50322,0.19119,0.84274,160.28
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.87991,-0.34689,-0.3247,153.25,0.33984,0.93706,-0.080162,203.76,0.33207,-0.039811,0.94241,162.25
> view matrix models
> #6,0.75803,-0.40097,-0.51441,152.38,0.18085,0.887,-0.42489,201.63,0.62665,0.22905,0.74488,157.7
> view matrix models
> #6,0.99081,-0.066427,-0.11786,155.99,0.030732,0.9589,-0.28208,205.82,0.13176,0.27587,0.95212,167.22
> view matrix models
> #6,0.96964,0.14912,0.19379,161.32,-0.16452,0.98417,0.065852,212.7,-0.18091,-0.095735,0.97883,169.36
> view matrix models
> #6,0.97498,0.18985,0.11566,160.61,-0.21363,0.94406,0.2512,215.25,-0.061498,-0.26963,0.961,166.35
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.97498,0.18985,0.11566,162.07,-0.21363,0.94406,0.2512,215.02,-0.061498,-0.26963,0.961,156.24
> view matrix models
> #6,0.97498,0.18985,0.11566,159.56,-0.21363,0.94406,0.2512,216.1,-0.061498,-0.26963,0.961,153.9
> view matrix models
> #6,0.97498,0.18985,0.11566,160.51,-0.21363,0.94406,0.2512,215.65,-0.061498,-0.26963,0.961,156.92
Opened af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 as
#9, grid size 122,99,112, pixel 0.667, shown at level 0.188, step 1, values
float32
Opened af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 as
#10, grid size 122,99,112, pixel 0.667, shown at level 0.188, step 1, values
float32
> fitmap #6 inMap #2 resolution 2 moveWholeMolecules false
Fit map af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 in
map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian
using 42271 points
correlation = 0.7036, correlation about mean = 0.01127, overlap = 2794
steps = 144, shift = 7.4, angle = 28.3 degrees
Position of af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2
(#10) relative to cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid
(1).mrc gaussian (#2) coordinates:
Matrix rotation and translation
0.95237226 -0.29842926 0.06266634 155.62319591
0.27551743 0.93018957 0.24256449 201.71537793
-0.13067991 -0.21374603 0.96810919 160.34007064
Axis -0.60175566 0.25497374 0.75688738
Axis point -467.42126069 755.65977572 0.00000000
Rotation angle (degrees) 22.28099987
Shift along axis 79.14436176
Average map value = 0.05619 for 2343 atoms, 401 outside contour
> hide #6 models
> show #6 models
> ui mousemode right "rotate selected models"
Opened af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 as
#9, grid size 115,102,111, pixel 0.667, shown at level 0.188, step 1, values
float32
> view matrix models
> #6,0.98601,0.13563,0.096872,159.5,-0.16086,0.92652,0.34011,215.79,-0.043625,-0.35094,0.93538,155.41
> view matrix models
> #6,0.87993,0.38691,0.27573,165.57,0.11429,0.39093,-0.9133,193.99,-0.46116,0.83515,0.29977,169.05
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.87993,0.38691,0.27573,164.23,0.11429,0.39093,-0.9133,201.71,-0.46116,0.83515,0.29977,170.95
> hide #6 models
> select subtract #6
Nothing selected
> show #5 models
> select add #5
2343 atoms, 2370 bonds, 299 residues, 1 model selected
> view matrix models #5,1,0,0,166.55,0,1,0,114.7,0,0,1,265.84
> view matrix models #5,1,0,0,165.34,0,1,0,114.85,0,0,1,262.35
> view matrix models #5,1,0,0,219.19,0,1,0,155.58,0,0,1,273.84
> view matrix models #5,1,0,0,198.96,0,1,0,157.81,0,0,1,216.14
> view matrix models #5,1,0,0,179.29,0,1,0,216.98,0,0,1,161.09
> view matrix models #5,1,0,0,167.19,0,1,0,215.34,0,0,1,158.86
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.57409,0.77382,0.26763,185.22,0.81855,-0.53448,-0.2105,182.52,-0.019845,0.33991,-0.94025,147.94
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.57409,0.77382,0.26763,182.38,0.81855,-0.53448,-0.2105,185.36,-0.019845,0.33991,-0.94025,152.94
> view matrix models
> #5,0.57409,0.77382,0.26763,183.39,0.81855,-0.53448,-0.2105,183.42,-0.019845,0.33991,-0.94025,142.8
> volume #2 level 0.07938
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.44186,0.89691,0.017905,183.81,0.23124,-0.13316,0.96374,202.98,0.86677,-0.4217,-0.26623,132.23
> view matrix models
> #5,0.60308,0.75597,-0.25457,178.31,-0.32768,0.52575,0.78499,215.2,0.72727,-0.38999,0.56479,140.62
> view matrix models
> #5,0.78362,-0.19766,0.58896,167.48,0.62107,0.27168,-0.73516,194.38,-0.014694,0.94187,0.33565,165.51
> hide #5 models
> volume #2 level 0.07344
> show #5 models
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.78362,-0.19766,0.58896,146.41,0.62107,0.27168,-0.73516,267.2,-0.014694,0.94187,0.33565,189.98
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.96992,0.06731,0.23394,147.73,-0.057054,0.9971,-0.050346,288.7,-0.23665,0.035484,0.97095,179.21
> view matrix models
> #5,0.48633,-0.82236,0.2953,132.82,0.45623,0.52722,0.71686,285.41,-0.74521,-0.21391,0.63159,172.81
> view matrix models
> #5,0.69742,-0.61006,-0.37607,130.25,0.68172,0.40289,0.61069,281.55,-0.22104,-0.68228,0.69688,163.24
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.69742,-0.61006,-0.37607,147.39,0.68172,0.40289,0.61069,196.94,-0.22104,-0.68228,0.69688,159.02
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.71446,-0.59108,-0.37439,147.71,0.64692,0.35423,0.67529,196.7,-0.26653,-0.72467,0.63546,157.79
> view matrix models
> #5,0.6798,-0.70324,-0.20817,147.18,0.61681,0.39466,0.68102,197.58,-0.39676,-0.59135,0.70206,161.23
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.6798,-0.70324,-0.20817,156.18,0.61681,0.39466,0.68102,197.22,-0.39676,-0.59135,0.70206,162.12
> view matrix models
> #5,0.6798,-0.70324,-0.20817,157.02,0.61681,0.39466,0.68102,199.73,-0.39676,-0.59135,0.70206,157.94
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.71951,-0.66469,-0.20123,157.7,0.58082,0.41708,0.69906,200.41,-0.38073,-0.61986,0.68616,157.22
> view matrix models
> #5,0.87431,0.020849,0.48492,176.32,-0.4732,-0.18564,0.86117,193.26,0.10797,-0.9824,-0.15244,141.65
> view matrix models
> #5,0.78591,0.11843,0.60689,179.47,0.14794,0.91697,-0.37052,201.35,-0.60038,0.38098,0.70314,176.74
> view matrix models
> #5,0.64111,0.33857,0.68873,184.71,-0.0003113,0.89754,-0.44093,200.74,-0.76745,0.28247,0.57553,174.18
> view matrix models
> #5,0.75666,0.16185,0.63346,180.6,0.081032,0.93819,-0.33651,202.22,-0.64877,0.30595,0.69678,175.4
> view matrix models
> #5,0.85912,0.34491,0.37808,181.49,-0.17773,0.89387,-0.41159,201.39,-0.47992,0.28641,0.82924,175.78
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.85912,0.34491,0.37808,178.95,-0.17773,0.89387,-0.41159,209.25,-0.47992,0.28641,0.82924,170.48
> view matrix models
> #5,0.85912,0.34491,0.37808,169.16,-0.17773,0.89387,-0.41159,206.67,-0.47992,0.28641,0.82924,165.79
> volume #2 level 0.06574
> view matrix models
> #5,0.85912,0.34491,0.37808,169.26,-0.17773,0.89387,-0.41159,206.83,-0.47992,0.28641,0.82924,164.8
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.74319,0.33892,0.57689,171.22,-0.66897,0.36066,0.64992,207.59,0.01221,-0.86894,0.49477,138.84
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.74319,0.33892,0.57689,173.61,-0.66897,0.36066,0.64992,205.21,0.01221,-0.86894,0.49477,146.75
> view matrix models
> #5,0.74319,0.33892,0.57689,177.19,-0.66897,0.36066,0.64992,204.65,0.01221,-0.86894,0.49477,148.27
> hide #5 models
> show #5 models
> view matrix models
> #5,0.74319,0.33892,0.57689,242.82,-0.66897,0.36066,0.64992,215.78,0.01221,-0.86894,0.49477,154.91
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.88942,-0.12031,-0.44098,229.31,0.45666,-0.19198,-0.86868,188.91,0.019857,-0.974,0.22569,150.51
> view matrix models
> #5,-0.91637,-0.071816,-0.39385,230.71,0.39797,-0.27029,-0.87668,187.51,-0.043491,-0.9601,0.27626,151.39
> view matrix models
> #5,-0.8734,0.08532,-0.47948,232.79,0.38965,-0.46819,-0.79308,184.57,-0.29215,-0.8795,0.37567,154.43
> view matrix models
> #5,-0.65617,-0.1466,-0.74024,225.54,0.71732,-0.42573,-0.55154,186.68,-0.23429,-0.8929,0.38451,154.11
> view matrix models
> #5,0.69556,0.56702,0.44123,246.02,-0.01502,0.62547,-0.78011,206.27,-0.71831,0.53599,0.44357,182.73
> view matrix models
> #5,-0.56554,-0.67758,-0.47015,217.75,0.24456,-0.68222,0.68904,194.18,-0.78763,0.2747,0.55153,178.97
> view matrix models
> #5,0.86781,-0.35365,-0.34905,221.21,0.084519,0.79728,-0.59766,210.87,0.48965,0.48916,0.72178,181.22
> view matrix models
> #5,0.97362,-0.1677,-0.1547,226.17,0.032453,0.77294,-0.63365,210.23,0.22584,0.61192,0.75799,184.53
> view matrix models
> #5,0.90662,0.096232,-0.41083,229.01,-0.32847,0.77212,-0.544,211.95,0.26486,0.62815,0.73163,184.5
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.90662,0.096232,-0.41083,160.03,-0.32847,0.77212,-0.544,216.57,0.26486,0.62815,0.73163,179.73
> view matrix models
> #5,0.90662,0.096232,-0.41083,163.98,-0.32847,0.77212,-0.544,216.47,0.26486,0.62815,0.73163,161.7
> view matrix models
> #5,0.90662,0.096232,-0.41083,163.5,-0.32847,0.77212,-0.544,215.34,0.26486,0.62815,0.73163,161.38
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.90215,0.24978,-0.35176,166.92,-0.36487,0.87682,-0.31315,219.47,0.23021,0.41086,0.88216,158.73
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.90215,0.24978,-0.35176,165.16,-0.36487,0.87682,-0.31315,215.46,0.23021,0.41086,0.88216,157.78
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.89927,0.29139,-0.3262,166.18,-0.37697,0.89455,-0.24014,216.48,0.22183,0.33892,0.91429,156.74
> view matrix models
> #5,0.99108,-0.078858,-0.10747,160.94,0.051066,0.96934,-0.24036,216.77,0.12313,0.23272,0.96472,155.45
> view matrix models
> #5,0.99917,0.040015,0.0069341,164.18,-0.040003,0.9992,-0.0018819,219.7,-0.0070039,0.001603,0.99997,151.76
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99917,0.040015,0.0069341,161.55,-0.040003,0.9992,-0.0018819,220.37,-0.0070039,0.001603,0.99997,158.49
> view matrix models
> #5,0.99917,0.040015,0.0069341,161.48,-0.040003,0.9992,-0.0018819,217.64,-0.0070039,0.001603,0.99997,157.91
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.96287,0.26576,0.047407,166.18,0.14849,-0.37475,-0.91516,183.18,-0.22544,0.88822,-0.4003,162.6
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.96287,0.26576,0.047407,164.19,0.14849,-0.37475,-0.91516,198.54,-0.22544,0.88822,-0.4003,162.37
> hide #5 models
> select subtract #5
Nothing selected
> close #3
> close #4
> close #5
> close #6
> close #7
> close #8
> close #9
> open /Users/wkeliason/Downloads/ChimeraX/PDB/GsDnaB_Xray/4esv.pdb.gz
4esv.pdb.gz title:
A new twist on the translocation mechanism of helicases from the structure of
DNAb with its substrates [more info...]
Chain information for 4esv.pdb.gz #3
---
Chain | Description | UniProt
A B C D E F G H I J K L | DNAB | Q9X4C9_GEOSE 1-445 1-454
V | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' |
W | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' |
Non-standard residues in 4esv.pdb.gz #3
---
ALF — tetrafluoroaluminate ion
CA — calcium ion
GDP — guanosine-5'-diphosphate
MES — 2-(N-morpholino)-ethanesulfonic acid
> hide #2-3 target a
> cartoon #2-3
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 39891 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> delete /F,G,H,I,J,K,L,W
> delete /v
> select add #3
16715 atoms, 16897 bonds, 21 pseudobonds, 2156 residues, 3 models selected
> view matrix models #3,1,0,0,-21.857,0,1,0,120.05,0,0,1,64.361
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.82271,0.064653,0.56478,-60.805,0.006114,0.99245,-0.12252,131.33,-0.56843,0.10425,0.8161,131.8
> ui mousemode right "translate selected models"
> volume #2 level 0.0452
> view matrix models
> #3,0.82271,0.064653,0.56478,18.813,0.006114,0.99245,-0.12252,109.69,-0.56843,0.10425,0.8161,153.26
> view matrix models
> #3,0.82271,0.064653,0.56478,21.485,0.006114,0.99245,-0.12252,133.93,-0.56843,0.10425,0.8161,152.28
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.81312,0.10619,0.57233,19.217,-0.10483,0.99386,-0.035467,136.77,-0.57258,-0.031161,0.81925,160.61
> view matrix models
> #3,0.8356,0.098814,0.54038,20.406,0.061782,0.96054,-0.27118,144.19,-0.54585,0.25998,0.79653,142.41
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.8356,0.098814,0.54038,23.069,0.061782,0.96054,-0.27118,156.71,-0.54585,0.25998,0.79653,146.65
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.83231,-0.041817,0.55273,30.77,0.15851,0.97347,-0.16504,136.4,-0.53116,0.22498,0.81686,145.41
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.83231,-0.041817,0.55273,34.025,0.15851,0.97347,-0.16504,128.56,-0.53116,0.22498,0.81686,145.01
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.69965,-0.12603,0.70328,38.297,0.26126,0.96128,-0.087656,111.85,-0.66501,0.24507,0.70548,167.51
> hide #!3 models
> show #!3 models
> view matrix models
> #3,0.7681,-0.232,0.59682,47.837,0.60092,0.58308,-0.54672,143.78,-0.22115,0.77858,0.58728,101.99
> view matrix models
> #3,0.86189,-0.30951,0.40168,61.399,0.50699,0.5102,-0.69473,171.35,0.01009,0.80243,0.59666,76.644
> view matrix models
> #3,0.93347,0.082778,0.34897,35.405,-0.034936,0.98936,-0.14123,144.64,-0.35695,0.11964,0.92643,123.83
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.93347,0.082778,0.34897,36.86,-0.034936,0.98936,-0.14123,147.35,-0.35695,0.11964,0.92643,119.39
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.91542,0.10681,0.38808,33.553,-0.040219,0.9836,-0.17585,151.45,-0.4005,0.14537,0.90469,124.2
> view matrix models
> #3,-0.1062,-0.54062,0.83454,132.89,-0.34072,-0.76869,-0.54132,321.7,0.93415,-0.34183,-0.10257,114.79
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.1062,-0.54062,0.83454,124.38,-0.34072,-0.76869,-0.54132,308.35,0.93415,-0.34183,-0.10257,120.52
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.049023,-0.64077,0.76617,131.13,0.19418,-0.75857,-0.62199,262,0.97974,0.11828,0.16161,63.445
> view matrix models
> #3,0.24948,-0.38479,0.88865,74.464,0.20436,-0.87608,-0.43672,250.83,0.94657,0.29056,-0.13993,84.43
> view matrix models
> #3,0.21783,-0.41673,0.88254,80.121,0.20002,-0.866,-0.45829,252.66,0.95527,0.27636,-0.10529,81.194
> view matrix models
> #3,0.46824,-0.38401,0.79579,61.294,0.87419,0.33242,-0.35396,103.14,-0.12861,0.86141,0.49135,97.999
> view matrix models
> #3,0.23561,-0.20948,0.949,59.587,0.93788,-0.20691,-0.27852,122.46,0.2547,0.95567,0.14772,86.169
> view matrix models
> #3,0.46907,0.022913,0.88286,28.419,0.87406,-0.15514,-0.46037,142.64,0.12642,0.98763,-0.0928,119.44
> view matrix models
> #3,0.24606,-0.10051,0.96403,50.538,0.91366,0.35607,-0.19607,83.047,-0.32355,0.92904,0.17945,142.41
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.24606,-0.10051,0.96403,50.207,0.91366,0.35607,-0.19607,83.37,-0.32355,0.92904,0.17945,141.84
> select /A
3286 atoms, 3318 bonds, 8 pseudobonds, 426 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.40644,0.022826,0.91339,31.482,0.81602,0.44062,-0.37412,104.57,-0.41099,0.89741,0.16046,154.24
> view matrix models
> #3,0.4841,-0.20273,0.8512,43.224,0.7873,0.52544,-0.32262,97.489,-0.38185,0.82633,0.41397,132
> view matrix models
> #3,-0.29045,-0.078983,0.95363,103.3,-0.93173,-0.20368,-0.30065,310.82,0.21798,-0.97585,-0.014433,221.49
> view matrix models
> #3,-0.072914,-0.025465,0.99701,74.343,-0.91505,-0.39593,-0.077032,299.96,0.39671,-0.91793,0.0055665,198.32
> view matrix models
> #3,-0.074872,-0.053808,0.99574,76.375,-0.92308,-0.37403,-0.08962,300.6,0.37725,-0.92586,-0.021665,203.27
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.074872,-0.053808,0.99574,77.775,-0.92308,-0.37403,-0.08962,306.92,0.37725,-0.92586,-0.021665,194.13
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.60598,-0.29188,0.74,48.267,0.58037,0.79841,-0.16034,92.725,-0.54402,0.52664,0.65322,134.85
> view matrix models
> #3,0.57253,-0.20289,0.79438,41.13,0.72304,0.58176,-0.37252,111.44,-0.38656,0.78765,0.47977,119.53
> view matrix models
> #3,0.56543,-0.1057,0.81799,33.741,0.76327,0.44292,-0.47037,124.98,-0.31259,0.89031,0.33112,119.81
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.56543,-0.1057,0.81799,37.289,0.76327,0.44292,-0.47037,120,-0.31259,0.89031,0.33112,123.78
> hide #!3 models
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.59963,-0.018023,0.80008,30.24,0.074411,0.99667,-0.033317,114.26,-0.79681,0.079512,0.59897,196.17
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.59963,-0.018023,0.80008,31.382,0.074411,0.99667,-0.033317,121.38,-0.79681,0.079512,0.59897,198.88
Opened 4esv.pdb.gz map 2 as #4, grid size 214,239,209, pixel 0.667, shown at
level 0.188, step 1, values float32
Opened 4esv.pdb.gz map 2 as #5, grid size 214,239,209, pixel 0.667, shown at
level 0.188, step 1, values float32
> fitmap #3 inMap #2 resolution 2 moveWholeMolecules false
Fit map 4esv.pdb.gz map 2 in map cryosparc_P5_J167_005_volume_map_sharp_RNA-
DNA-Hybrid (1).mrc gaussian using 301658 points
correlation = 0.6583, correlation about mean = 0.003665, overlap = 1.85e+04
steps = 136, shift = 2.56, angle = 17 degrees
Position of 4esv.pdb.gz map 2 (#5) relative to
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
coordinates:
Matrix rotation and translation
0.77480920 -0.10103496 0.62406945 35.15086863
0.08124071 0.99487463 0.06020336 108.93106154
-0.62695350 0.00405373 0.77904616 163.94598936
Axis -0.04437027 0.98857707 0.14403697
Axis point 226.04459407 0.00000000 16.01686672
Rotation angle (degrees) 39.25250559
Shift along axis 129.74137989
Average map value = 0.05204 for 16715 atoms, 6877 outside contour
> delete :1-152
> volume #2 level 0.06879
> select
11155 atoms, 11256 bonds, 19 pseudobonds, 1435 residues, 11 models selected
> select subtract #1
11155 atoms, 11256 bonds, 19 pseudobonds, 1435 residues, 9 models selected
> select subtract #2
11155 atoms, 11256 bonds, 19 pseudobonds, 1435 residues, 7 models selected
> select add #2
11155 atoms, 11256 bonds, 19 pseudobonds, 1435 residues, 9 models selected
> select add #1
11155 atoms, 11256 bonds, 19 pseudobonds, 1435 residues, 11 models selected
> select clear
> select /B
2218 atoms, 2239 bonds, 2 pseudobonds, 285 residues, 2 models selected
> select clear
> select /C
2300 atoms, 2323 bonds, 2 pseudobonds, 294 residues, 2 models selected
> select clear
> select /D
2253 atoms, 2273 bonds, 5 pseudobonds, 291 residues, 3 models selected
> select /E
2232 atoms, 2253 bonds, 3 pseudobonds, 286 residues, 3 models selected
> delete :157-178
> delete :153-157
> delete :178-183
> volume #2 level 0.07858
Opened 4esv.pdb.gz map 2 as #4, grid size 182,190,152, pixel 0.667, shown at
level 0.187, step 1, values float32
> view matrix models
> #3,0.59963,-0.018023,0.80008,31.429,0.074411,0.99667,-0.033317,122.2,-0.79681,0.079512,0.59897,201.72
Opened 4esv.pdb.gz map 2 as #5, grid size 86,96,141, pixel 0.667, shown at
level 0.189, step 1, values float32
> fitmap sel inMap #2 resolution 2 moveWholeMolecules false
Fit map 4esv.pdb.gz map 2 in map cryosparc_P5_J167_005_volume_map_sharp_RNA-
DNA-Hybrid (1).mrc gaussian using 37227 points
correlation = 0.7194, correlation about mean = 0.01547, overlap = 3322
steps = 252, shift = 7.8, angle = 43.7 degrees
Position of 4esv.pdb.gz map 2 (#5) relative to
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
coordinates:
Matrix rotation and translation
0.79085760 0.50961653 0.33887356 36.67591428
-0.35727074 0.83401602 -0.42044609 212.82024234
-0.49689226 0.21144338 0.84165897 137.42677989
Axis 0.46466451 0.61458647 -0.63747185
Axis point 419.92533661 155.28597730 0.00000000
Rotation angle (degrees) 42.83907883
Shift along axis 60.23273336
Average map value = 0.07556 for 2059 atoms, 1050 outside contour
Opened 4esv.pdb.gz map 2 as #5, grid size 121,124,95, pixel 0.667, shown at
level 0.187, step 1, values float32
Opened 4esv.pdb.gz map 2 as #5, grid size 86,96,141, pixel 0.667, shown at
level 0.189, step 1, values float32
> select /A/B/C/D/E
10194 atoms, 10287 bonds, 14 pseudobonds, 1311 residues, 3 models selected
> fitmap sel inMap #2 resolution 2 moveWholeMolecules false
Fit map 4esv.pdb.gz map 2 in map cryosparc_P5_J167_005_volume_map_sharp_RNA-
DNA-Hybrid (1).mrc gaussian using 184188 points
correlation = 0.6947, correlation about mean = 0.004128, overlap = 1.381e+04
steps = 68, shift = 3.95, angle = 4.64 degrees
Position of 4esv.pdb.gz map 2 (#4) relative to
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian (#2)
coordinates:
Matrix rotation and translation
0.54545031 0.02202850 0.83785365 32.74804945
0.00804917 0.99947080 -0.03151776 130.93536904
-0.83810453 0.02393540 0.54498434 212.58828413
Axis 0.03306819 0.99941833 -0.00833625
Axis point 211.17896610 0.00000000 80.62001107
Rotation angle (degrees) 56.97856800
Shift along axis 130.16993852
Average map value = 0.06353 for 10194 atoms, 7020 outside contour
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> select subtract #3
Nothing selected
> open
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb
> /Users/wkeliason/Downloads/ChimeraX/AlphaFold/prediction_16/af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
Chain information for
af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #6
---
Chain | Description
A | No description available
Chain information for
af454_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb #7
---
Chain | Description
A | No description available
Chain information for
af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb #8
---
Chain | Description
A | No description available
Chain information for
af454_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb #9
---
Chain | Description
A | No description available
Chain information for
af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb #10
---
Chain | Description
A | No description available
> select add #10
3553 atoms, 3599 bonds, 454 residues, 1 model selected
> select add #9
7106 atoms, 7198 bonds, 908 residues, 2 models selected
> select add #8
10659 atoms, 10797 bonds, 1362 residues, 3 models selected
> select add #7
14212 atoms, 14396 bonds, 1816 residues, 4 models selected
> select add #6
17765 atoms, 17995 bonds, 2270 residues, 5 models selected
Opened map 2 as #11, grid size 152,170,161, pixel 0.667, shown at level 0.326,
step 1, values float32
> view matrix models
> #6,1,0,0,93.777,0,1,0,109.61,0,0,1,236.9,#7,1,0,0,93.777,0,1,0,109.61,0,0,1,236.9,#8,1,0,0,93.777,0,1,0,109.61,0,0,1,236.9,#9,1,0,0,93.777,0,1,0,109.61,0,0,1,236.9,#10,1,0,0,93.777,0,1,0,109.61,0,0,1,236.9
> select clear
> select add #6
3553 atoms, 3599 bonds, 454 residues, 1 model selected
Opened af454_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb map 2 as
#12, grid size 147,115,155, pixel 0.667, shown at level 0.188, step 1, values
float32
> view matrix models #6,1,0,0,228.47,0,1,0,37.301,0,0,1,299.34
> select add #7
7106 atoms, 7198 bonds, 908 residues, 2 models selected
> select subtract #6
3553 atoms, 3599 bonds, 454 residues, 1 model selected
Opened af454_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb map 2 as
#13, grid size 152,109,136, pixel 0.667, shown at level 0.188, step 1, values
float32
> view matrix models #7,1,0,0,129.49,0,1,0,14.701,0,0,1,280.78
> select subtract #7
Nothing selected
> select add #8
3553 atoms, 3599 bonds, 454 residues, 1 model selected
Opened af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb map 2 as
#14, grid size 116,109,161, pixel 0.667, shown at level 0.189, step 1, values
float32
> view matrix models #8,1,0,0,7.2032,0,1,0,76.39,0,0,1,225.52
> select subtract #8
Nothing selected
> select add #9
3553 atoms, 3599 bonds, 454 residues, 1 model selected
Opened af454_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb map 2 as
#15, grid size 141,170,128, pixel 0.667, shown at level 0.188, step 1, values
float32
> view matrix models #9,1,0,0,15.004,0,1,0,174.12,0,0,1,192.37
> select subtract #9
Nothing selected
> select add #10
3553 atoms, 3599 bonds, 454 residues, 1 model selected
Opened af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 as
#16, grid size 138,116,153, pixel 0.667, shown at level 0.187, step 1, values
float32
> view matrix models #10,1,0,0,118.46,0,1,0,104.22,0,0,1,245.51
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> select add #9
7106 atoms, 7198 bonds, 908 residues, 2 models selected
> select add #8
10659 atoms, 10797 bonds, 1362 residues, 3 models selected
> select add #7
14212 atoms, 14396 bonds, 1816 residues, 4 models selected
> select add #6
17765 atoms, 17995 bonds, 2270 residues, 5 models selected
> delete :1-180
Opened map 2 as #11, grid size 450,330,258, pixel 0.667, shown at level 0.188,
step 1, values float32
> view matrix models
> #6,1,0,0,274.66,0,1,0,82.566,0,0,1,221.71,#7,1,0,0,175.67,0,1,0,59.965,0,0,1,203.15,#8,1,0,0,53.388,0,1,0,121.65,0,0,1,147.89,#9,1,0,0,61.189,0,1,0,219.39,0,0,1,114.73,#10,1,0,0,164.64,0,1,0,149.49,0,0,1,167.87
> select clear
> select add #6
2138 atoms, 2162 bonds, 274 residues, 1 model selected
> select add #7
4276 atoms, 4324 bonds, 548 residues, 2 models selected
> select add #8
6414 atoms, 6486 bonds, 822 residues, 3 models selected
> select add #9
8552 atoms, 8648 bonds, 1096 residues, 4 models selected
> select add #10
10690 atoms, 10810 bonds, 1370 residues, 5 models selected
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select clear
> select add #7
2138 atoms, 2162 bonds, 274 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7
2138 atoms, 2162 bonds, 274 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #10
2138 atoms, 2162 bonds, 274 residues, 1 model selected
Opened af454_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb map 2 as
#16, grid size 96,96,116, pixel 0.667, shown at level 0.188, step 1, values
float32
> view matrix models #10,1,0,0,169.46,0,1,0,147.75,0,0,1,170.66
> select subtract #10
Nothing selected
> select add #10
2138 atoms, 2162 bonds, 274 residues, 1 model selected
> view matrix models #10,1,0,0,147.2,0,1,0,155.45,0,0,1,203.07
> view matrix models #10,1,0,0,171.5,0,1,0,154.37,0,0,1,206.05
> view matrix models #10,1,0,0,166.67,0,1,0,163.25,0,0,1,286.63
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.24064,-0.79839,0.55196,173.17,0.95598,0.096584,-0.27708,151.06,0.16791,0.59434,0.78649,286.07
> view matrix models
> #10,-0.34288,-0.28295,0.89575,182.1,-0.00014944,-0.95354,-0.30126,152.27,0.93938,-0.10343,0.32691,274.14
> view matrix models
> #10,0.42131,0.48592,0.76575,179.43,0.88887,-0.053656,-0.45501,149.17,-0.18001,0.87235,-0.45453,277.65
> view matrix models
> #10,0.71579,0.47264,0.51407,175.22,0.63069,-0.12151,-0.76646,147.52,-0.29979,0.87284,-0.38506,279.04
> view matrix models
> #10,0.83106,0.39493,0.39162,173.04,0.51108,-0.26452,-0.81782,147.17,-0.21939,0.87981,-0.42167,278.23
> view matrix models
> #10,0.61951,0.78449,-0.027948,171.99,0.58226,-0.4831,-0.65391,147.37,-0.52649,0.38883,-0.75606,274.9
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.61951,0.78449,-0.027948,165.03,0.58226,-0.4831,-0.65391,145.03,-0.52649,0.38883,-0.75606,208.29
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.49752,0.86739,-0.010434,166.28,0.63357,-0.37157,-0.67862,144.95,-0.5925,0.33102,-0.73442,208.65
> view matrix models
> #10,0.53183,0.84678,-0.010923,165.98,0.4143,-0.27141,-0.86873,144.91,-0.73859,0.45749,-0.49516,212.32
> view matrix models
> #10,0.52608,0.85038,-0.0099709,166.04,0.45475,-0.2912,-0.84167,144.84,-0.71864,0.43825,-0.5399,211.7
> view matrix models
> #10,0.68965,0.62489,-0.36592,160.75,0.19969,-0.64983,-0.73338,145.91,-0.69606,0.43271,-0.57294,211.23
> view matrix models
> #10,0.71141,0.59693,-0.37091,160.46,-0.0094234,-0.51963,-0.85434,146.59,-0.70272,0.61128,-0.36404,213.98
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.71141,0.59693,-0.37091,160.78,-0.0094234,-0.51963,-0.85434,144.61,-0.70272,0.61128,-0.36404,212.57
> view matrix models
> #10,0.71141,0.59693,-0.37091,166.06,-0.0094234,-0.51963,-0.85434,144.07,-0.70272,0.61128,-0.36404,211.21
> view matrix models
> #10,0.71141,0.59693,-0.37091,176.83,-0.0094234,-0.51963,-0.85434,155.78,-0.70272,0.61128,-0.36404,268.53
> view matrix models
> #10,0.71141,0.59693,-0.37091,166.74,-0.0094234,-0.51963,-0.85434,143.02,-0.70272,0.61128,-0.36404,211.77
> view matrix models
> #10,0.71141,0.59693,-0.37091,165.54,-0.0094234,-0.51963,-0.85434,144.39,-0.70272,0.61128,-0.36404,209.94
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.52426,0.67718,-0.51631,165.64,-0.019432,-0.59665,-0.80227,144.63,-0.85133,0.43063,-0.29964,210.69
> view matrix models
> #10,0.5794,0.65727,-0.48196,165.55,-0.027927,-0.57498,-0.81769,144.62,-0.81457,0.48723,-0.31478,210.56
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.5794,0.65727,-0.48196,169.44,-0.027927,-0.57498,-0.81769,143.96,-0.81457,0.48723,-0.31478,209.61
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/fitgui.py", line 651, in _undo
position_history.undo()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/move.py", line 41, in undo
if restore_position(ps):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/move.py", line 93, in restore_position
atoms.coords = xyz
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
ValueError: Values array length 16715 does not match objects array length
10194
ValueError: Values array length 16715 does not match objects array length
10194
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
See log for complete Python traceback.
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.51249,0.69858,-0.49934,169.86,-0.064745,-0.54842,-0.83369,144.14,-0.85625,0.45959,-0.23583,210.49
> view matrix models
> #10,-0.89541,-0.40652,0.18163,180.23,-0.11567,0.6063,0.78678,164.53,-0.42996,0.68348,-0.58991,205.49
> view matrix models
> #10,0.63739,0.73039,0.24548,176.25,0.43052,-0.073356,-0.89959,142.49,-0.63905,0.67908,-0.36121,208.9
> view matrix models
> #10,0.79674,0.48357,-0.36245,168.52,-0.054831,-0.53945,-0.84023,144.06,-0.60183,0.68932,-0.40328,208.32
> view matrix models
> #10,0.83568,0.36587,-0.4096,167.35,-0.14147,-0.57723,-0.80423,144.77,-0.53068,0.73003,-0.43062,207.8
> view matrix models
> #10,0.72296,0.44347,-0.52977,167.23,-0.11282,-0.68073,-0.7238,144.92,-0.68161,0.58304,-0.44211,208
> view matrix models
> #10,0.61725,0.60103,-0.5077,168.73,-0.14792,-0.54514,-0.82519,144.74,-0.77273,0.58445,-0.24758,210.39
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.61725,0.60103,-0.5077,170.15,-0.14792,-0.54514,-0.82519,145.76,-0.77273,0.58445,-0.24758,210.44
> volume #2 level 0.08991
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/fitgui.py", line 651, in _undo
position_history.undo()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/move.py", line 41, in undo
if restore_position(ps):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/move.py", line 93, in restore_position
atoms.coords = xyz
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
ValueError: Values array length 16715 does not match objects array length
10194
ValueError: Values array length 16715 does not match objects array length
10194
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
See log for complete Python traceback.
> view matrix models
> #10,0.61725,0.60103,-0.5077,239.51,-0.14792,-0.54514,-0.82519,138.03,-0.77273,0.58445,-0.24758,312.12
> select subtract #10
Nothing selected
> select add #9
2138 atoms, 2162 bonds, 274 residues, 1 model selected
> select subtract #9
Nothing selected
> select add #8
2138 atoms, 2162 bonds, 274 residues, 1 model selected
> view matrix models #8,1,0,0,114.98,0,1,0,97.71,0,0,1,282.28
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.8632,0.50431,-0.023504,116.94,0.16352,-0.32332,-0.93206,81.51,-0.47765,0.80071,-0.36155,270.66
> view matrix models
> #8,0.87482,0.46717,-0.1282,115.6,0.043044,-0.33854,-0.93997,81.393,-0.48253,0.81679,-0.31627,271.24
> view matrix models
> #8,-0.52837,-0.00094745,-0.84901,105.94,0.82983,-0.21194,-0.5162,86.44,-0.17945,-0.97728,0.11277,268.18
> view matrix models
> #8,-0.20079,0.35755,-0.91205,106.69,0.94101,0.32925,-0.078093,93.648,0.27238,-0.87393,-0.40257,262.73
> view matrix models
> #8,-0.56911,0.29706,-0.76673,108.17,0.64976,0.73391,-0.19794,94.147,0.50391,-0.61084,-0.6107,261.47
> view matrix models
> #8,-0.51081,-0.19753,-0.8367,105.23,0.85151,0.017726,-0.52403,87.339,0.11834,-0.98014,0.15914,268.6
> view matrix models
> #8,-0.56839,-0.36343,-0.73814,105.63,0.81815,-0.15483,-0.55377,86.27,0.086975,-0.91866,0.38535,271.4
> view matrix models
> #8,-0.30779,-0.8274,-0.46977,106.54,0.71484,0.12474,-0.68807,86.009,0.6279,-0.54759,0.55306,274.72
> view matrix models
> #8,-0.19233,-0.77457,-0.60254,105.25,0.74686,0.28275,-0.60187,87.647,0.63656,-0.56577,0.52412,274.31
> view matrix models
> #8,0.75132,0.60059,-0.27352,114.59,-0.64703,0.5888,-0.48442,90.711,-0.12989,0.54093,0.83098,282.77
> view matrix models
> #8,0.23147,0.6413,-0.73154,109.8,-0.97074,0.20165,-0.13039,93.094,0.063899,0.74032,0.66921,281.76
> view matrix models
> #8,0.40229,0.33563,-0.85178,107.09,-0.88117,-0.11049,-0.4597,88.033,-0.2484,0.93549,0.2513,278.03
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.40229,0.33563,-0.85178,174.37,-0.88117,-0.11049,-0.4597,145.57,-0.2484,0.93549,0.2513,208.32
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.60913,0.20294,-0.76667,174.68,-0.77548,-0.050072,-0.62938,143.9,-0.16612,0.97791,0.12688,207.09
> view matrix models
> #8,0.59908,0.53874,-0.59234,178.09,-0.72165,0.042786,-0.69094,143.6,-0.34689,0.84138,0.41441,209.77
> view matrix models
> #8,0.61856,0.59836,-0.50926,179.27,-0.36711,-0.35296,-0.86061,139.88,-0.6947,0.7193,0.0013312,204.72
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.61856,0.59836,-0.50926,175.41,-0.36711,-0.35296,-0.86061,142.84,-0.6947,0.7193,0.0013312,205.33
> view matrix models
> #8,0.61856,0.59836,-0.50926,173.14,-0.36711,-0.35296,-0.86061,145.7,-0.6947,0.7193,0.0013312,211.65
> view matrix models
> #8,0.61856,0.59836,-0.50926,171.63,-0.36711,-0.35296,-0.86061,144.06,-0.6947,0.7193,0.0013312,211.98
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.24048,-0.75476,-0.61034,164.76,0.80183,0.50883,-0.31331,153.55,0.54703,-0.41404,0.72755,214.82
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.24048,-0.75476,-0.61034,172.44,0.80183,0.50883,-0.31331,141.47,0.54703,-0.41404,0.72755,213.93
> view matrix models
> #8,0.24048,-0.75476,-0.61034,171.4,0.80183,0.50883,-0.31331,141.93,0.54703,-0.41404,0.72755,206.28
> view matrix models
> #8,0.24048,-0.75476,-0.61034,169.82,0.80183,0.50883,-0.31331,142.38,0.54703,-0.41404,0.72755,204.61
> fitmap #8 inMap #2 moveWholeMolecules false
Fit molecule af454_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000.pdb (#8)
to map cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc gaussian
(#2) using 2138 atoms
average map value = 0.07129, steps = 236
shifted from previous position = 10
rotated from previous position = 25.1 degrees
atoms outside contour = 1624, contour level = 0.089914
> close #3
> close #4
> close #5
> close #6
> close #7
> close #8
> close #9
> close #10
> close #11
> close #12
> close #13
> close #14
> close #15
> close #16
> open /Users/wkeliason/Downloads/output_raw.cif
Summary of feedback from opening /Users/wkeliason/Downloads/output_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for output_raw.cif #3
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A8 CF | No description available
AA | No description available
AB | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
AP | No description available
AQ | No description available
AR | No description available
AS | No description available
AT | No description available
AU | No description available
AV | No description available
AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
Al | No description available
Am | No description available
An | No description available
Ao | No description available
Ap | No description available
Aq | No description available
Ar | No description available
As | No description available
At | No description available
Au | No description available
Av | No description available
Aw | No description available
Ax | No description available
Ay | No description available
Az | No description available
B | No description available
B0 | No description available
B1 | No description available
B2 | No description available
B7 | No description available
BC DN | No description available
BH | No description available
BK | No description available
BO | No description available
BQ | No description available
BT | No description available
BU | No description available
BW | No description available
Ba | No description available
Bk | No description available
Bl | No description available
Bn | No description available
Br | No description available
Bs | No description available
Bw | No description available
C | No description available
C2 | No description available
CD | No description available
CG | No description available
CH | No description available
CI | No description available
CM | No description available
CN | No description available
CO | No description available
CQ | No description available
CS | No description available
CW | No description available
Ca | No description available
Ce DC | No description available
Cp | No description available
Cs | No description available
Cw | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> hide surfaces
> hide atoms
> show surfaces
> hide surfaces
> show cartoons
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 9993 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select add #3
14223 atoms, 14113 bonds, 1763 residues, 1 model selected
> select subtract #3
160 models selected
> select /0
27 atoms, 27 bonds, 4 residues, 1 model selected
> select clear
> volume #2 level 0.08401
> close #3
> ui tool show AlphaFold
> volume #2 level 0.0797
> ui tool show AlphaFold
> fetch 2R6D
Unknown command: fetch 2R6D
> fetch: 2R6D
Unknown command: fetch: 2R6D
> ui tool show AlphaFold
No sequence chosen for AlphaFold match
[Repeated 1 time(s)]
> alphafold match 2R6D
Missing or invalid "sequences" argument: Sequences argument "2R6D" is not a
chain specifier, alignment id, UniProt id, or sequence characters
> alphafold match 2R6D
Missing or invalid "sequences" argument: Sequences argument "2R6D" is not a
chain specifier, alignment id, UniProt id, or sequence characters
> help help:user
> fetch 2R6D
Unknown command: fetch 2R6D
> fetch
Unknown command: fetch
> oped 2r6d
Unknown command: oped 2r6d
> oped: 2r6d
Unknown command: oped: 2r6d
> open /Users/wkeliason/Downloads/2r6d.cif.gz
File reader requires uncompressed file;
'/Users/wkeliason/Downloads/2r6d.cif.gz' is compressed
> open /Users/wkeliason/Downloads/2r6d.pdb
2r6d.pdb title:
Crystal form B1 [more info...]
Chain information for 2r6d.pdb #3
---
Chain | Description | UniProt
A B C D E F | DNAB helicase | Q9X4C9_BACST 1-454
> hide atoms
> show cartoons
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 18085 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select add #3
18085 atoms, 18282 bonds, 26 pseudobonds, 2340 residues, 2 models selected
> view matrix models #3,1,0,0,66.035,0,1,0,151.38,0,0,1,130.42
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.91245,0.2309,-0.33782,61.275,-0.27249,0.95877,-0.080694,164.77,0.30526,0.16568,0.93775,110.98
> view matrix models
> #3,0.6363,0.74904,0.18457,81.201,-0.76306,0.64628,0.0078503,196.28,-0.1134,-0.14583,0.98279,137.73
> view matrix models
> #3,0.76677,0.3309,0.55006,86.261,-0.49612,0.84925,0.18069,183.32,-0.40735,-0.41144,0.81534,152.93
> view matrix models
> #3,0.767,0.33202,0.54906,86.216,-0.50014,0.84541,0.18744,183.72,-0.40195,-0.41837,0.81449,152.7
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.767,0.33202,0.54906,80.202,-0.50014,0.84541,0.18744,229.58,-0.40195,-0.41837,0.81449,217.96
> color #3 #fffb00ff
> view matrix models
> #3,0.767,0.33202,0.54906,123.12,-0.50014,0.84541,0.18744,238.47,-0.40195,-0.41837,0.81449,218.15
> view matrix models
> #3,0.767,0.33202,0.54906,134.28,-0.50014,0.84541,0.18744,204.19,-0.40195,-0.41837,0.81449,218.6
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.69733,0.37262,0.61229,138.87,-0.21263,0.92334,-0.31975,177.5,-0.68449,0.09278,0.72309,226.32
> view matrix models
> #3,0.63132,0.49083,0.60043,140.88,0.67694,-0.72654,-0.11786,151.87,0.37839,0.48087,-0.79094,134
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.63132,0.49083,0.60043,141.83,0.67694,-0.72654,-0.11786,138.59,0.37839,0.48087,-0.79094,140.61
> view matrix models
> #3,0.63132,0.49083,0.60043,142.38,0.67694,-0.72654,-0.11786,136.24,0.37839,0.48087,-0.79094,143.23
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.60662,0.39325,0.69092,146.63,0.79334,-0.35552,-0.49419,118.24,0.051298,0.84791,-0.52765,162.19
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.60662,0.39325,0.69092,145.46,0.79334,-0.35552,-0.49419,121.2,0.051298,0.84791,-0.52765,160.46
> cartoon hide (#!3 & sel)
> select /A
3138 atoms, 3173 bonds, 4 pseudobonds, 405 residues, 2 models selected
> cartoon (#!3 & sel)
> select /B
2897 atoms, 2929 bonds, 4 pseudobonds, 376 residues, 2 models selected
> cartoon (#!3 & sel)
> view matrix models
> #3,0.60662,0.39325,0.69092,144.02,0.79334,-0.35552,-0.49419,126.76,0.051298,0.84791,-0.52765,163.54
> select add #3
18085 atoms, 18282 bonds, 26 pseudobonds, 2340 residues, 2 models selected
> view matrix models
> #3,0.60662,0.39325,0.69092,153.95,0.79334,-0.35552,-0.49419,126.03,0.051298,0.84791,-0.52765,161.11
> select subtract #3
Nothing selected
> ui mousemode right "rotate selected models"
> select add #3
18085 atoms, 18282 bonds, 26 pseudobonds, 2340 residues, 2 models selected
> view matrix models
> #3,0.61679,0.43745,0.65438,151.27,0.7842,-0.41316,-0.46295,128.61,0.067846,0.79871,-0.59789,157.99
> view matrix models
> #3,0.6403,0.41845,0.64414,149.67,0.76446,-0.42901,-0.4812,129.33,0.074983,0.80053,-0.59459,157.65
> delete: 1-150
Unknown command: delete: 1-150
> delete:1-150
Unknown command: delete:1-150
> delete :1-152
> view matrix models
> #3,0.6614,0.42722,0.61646,146.94,0.73189,-0.54731,-0.40594,137.58,0.16397,0.71967,-0.67467,150.65
> select /B
1815 atoms, 1831 bonds, 3 pseudobonds, 236 residues, 2 models selected
> cartoon hide (#!3 & sel)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #2 level 0.09183
> view matrix models
> #3,-0.22439,0.94254,-0.24751,163.64,0.41545,0.32228,0.85061,205.39,0.88151,0.08804,-0.46389,117.8
> hide #!3 models
> show #!3 models
> view matrix models
> #3,-0.38686,0.35962,-0.84912,159.16,0.10128,0.93182,0.3485,193.02,0.91656,0.048819,-0.39691,119.12
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.38686,0.35962,-0.84912,168.32,0.10128,0.93182,0.3485,179.29,0.91656,0.048819,-0.39691,120.13
> view matrix models
> #3,-0.38686,0.35962,-0.84912,167.76,0.10128,0.93182,0.3485,178.17,0.91656,0.048819,-0.39691,120.25
> view matrix models
> #3,-0.38686,0.35962,-0.84912,149.95,0.10128,0.93182,0.3485,182.15,0.91656,0.048819,-0.39691,122.68
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.58964,0.7988,0.11938,203.76,0.69758,0.57817,-0.42319,105.36,-0.40707,-0.16625,-0.89814,206.27
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.58964,0.7988,0.11938,157.09,0.69758,0.57817,-0.42319,93.513,-0.40707,-0.16625,-0.89814,205.42
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.66559,0.74068,0.091572,162.87,0.68199,0.65345,-0.32845,97.779,-0.30312,-0.15616,-0.94007,195.05
> view matrix models
> #3,-0.55635,0.78666,0.26767,161.93,0.73855,0.61575,-0.27457,96.749,-0.38081,0.04493,-0.92356,197.78
> view matrix models
> #3,-0.34108,0.93634,0.083246,133.06,0.9087,0.35109,-0.22585,91.265,-0.2407,-0.0013876,-0.9706,185.49
> view matrix models
> #3,-0.5476,0.68037,-0.48706,126.8,0.78347,0.21255,-0.58395,86.53,-0.29378,-0.70137,-0.64944,219.66
> view matrix models
> #3,-0.61182,0.71136,-0.34591,138.04,0.65299,0.20742,-0.72841,89.826,-0.44641,-0.67153,-0.59141,233.79
> view matrix models
> #3,-0.59949,0.79471,0.095162,156.76,0.24534,0.29563,-0.92326,110.42,-0.76185,-0.53014,-0.3722,266.18
> view matrix models
> #3,-0.25078,0.91118,-0.32689,106.61,0.21957,-0.27534,-0.93594,123.59,-0.94281,-0.30649,-0.13102,287.43
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.25078,0.91118,-0.32689,119.06,0.21957,-0.27534,-0.93594,144.34,-0.94281,-0.30649,-0.13102,277.74
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.01906,0.7899,-0.61293,89.556,0.24367,-0.59089,-0.76907,157.05,-0.96967,-0.16401,-0.18121,274.47
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.01906,0.7899,-0.61293,123.14,0.24367,-0.59089,-0.76907,143.31,-0.96967,-0.16401,-0.18121,277.88
> view matrix models
> #3,-0.01906,0.7899,-0.61293,121.13,0.24367,-0.59089,-0.76907,147.34,-0.96967,-0.16401,-0.18121,286.62
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.12704,0.86351,-0.48806,114.25,0.36208,-0.49847,-0.78768,135.28,-0.92345,-0.076653,-0.37598,271.75
> ui tool show "Fit in Map"
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule 2r6d.pdb (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-
DNA-Hybrid (1).mrc (#1) using 1815 atoms
average map value = 0.08333, steps = 160
shifted from previous position = 1.75
rotated from previous position = 13.9 degrees
atoms outside contour = 1588, contour level = 0.26541
> fitmap sel inMap #1
Fit molecule 2r6d.pdb (#3) to map cryosparc_P5_J167_005_volume_map_sharp_RNA-
DNA-Hybrid (1).mrc (#1) using 1815 atoms
average map value = 0.08331, steps = 80
shifted from previous position = 0.00358
rotated from previous position = 0.00589 degrees
atoms outside contour = 1588, contour level = 0.26541
Position of 2r6d.pdb (#3) relative to
cryosparc_P5_J167_005_volume_map_sharp_RNA-DNA-Hybrid (1).mrc (#1)
coordinates:
Matrix rotation and translation
0.12703210 0.86354283 -0.48801296 114.24496459
0.36216061 -0.49841152 -0.78767104 135.26517643
-0.92341895 -0.07667956 -0.37605546 271.75285952
Axis 0.73082038 0.44754906 -0.51536531
Axis point 0.00000000 -15.98028024 199.86732761
Rotation angle (degrees) 150.89354619
Shift along axis 3.97835495
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/fitgui.py", line 651, in _undo
position_history.undo()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/move.py", line 41, in undo
if restore_position(ps):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/move.py", line 93, in restore_position
atoms.coords = xyz
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
ValueError: Values array length 2138 does not match objects array length 0
ValueError: Values array length 2138 does not match objects array length 0
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 210, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-20.2.48
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,4
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0)
OS Loader Version: 564.40.4~55
Software:
System Software Overview:
System Version: macOS 13.1 (22C65)
Kernel Version: Darwin 22.2.0
Time since boot: 93 days, 1 hour, 21 minutes
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL S2721Q:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 30.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: BM0F513
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 0.00
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → fitmap: mismatch coordinate array sizes |
comment:2 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
User fit atoms into a map with moveWholeMolecules false, then deleted the atoms or whole model and tried to undo the fit. I made the undo code not raise an error if any of the moved atoms have been deleted. It also cannot move the undeleted atoms if any are deleted since it does not know how the coordinates pair up with the atoms.