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Opened 4 years ago
Closed 4 years ago
#6749 closed defect (can't reproduce)
MemoryError saving session
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.17763
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Current thread 0x000428b8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 235 in swap_buffers
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 496 in swap_buffers
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 179 in draw
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\sideview\tool.py", line 276 in render
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\sideview\tool.py", line 112 in _redraw
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 134 in invoke
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 217 in _activate
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 186 in activate
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 354 in activate_trigger
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 89 in draw_new_frame
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 139 in _redraw_timer_callback
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open
> C:/Users/user/Desktop/장송이_채용관련/구조분석/Refinement_88_big/run_it018_half1_class001_unfil.mrc
Opened run_it018_half1_class001_unfil.mrc as #1, grid size 320,320,320, pixel
0.855, shown at level 0.00307, step 2, values float32
> open C:/Users/user/Desktop/장송이_채용관련/구조분석/Postpocess_93_big/postprocess.mrc
Opened postprocess.mrc as #2, grid size 320,320,320, pixel 0.855, shown at
level 0.00268, step 2, values float32
> open
> C:/Users/user/Desktop/장송이_채용관련/구조분석/Postprocess_87_small/postprocess.mrc
Opened postprocess.mrc as #3, grid size 320,320,320, pixel 0.855, shown at
level 0.00854, step 2, values float32
> volume #3 level 0.009838
> ui tool show "Color Actions"
> set bgColor white
> volume #3 level 0.006592
> volume #1 level 0.002901
> close #2
> volume #1 step 1
> volume #1 level 0.003128
> volume #1 level 0.003355
> volume #1 level 0.003128
> ui tool show "Hide Dust"
> surface dust #1 size 6.39
> volume #1 level 0.002731
> volume #3 level 0.003346
> surface dust #3 size 21.9
> volume #3 level 0.004969
> volume #3 level 0.003995
> surface dust #3 size 26.83
> volume #3 level 0.01049
> volume #3 level 0.008215
> volume #3 level 0.006267
> surface dust #3 size 93.43
> volume #3 level 0.005943
> volume #1 level 0.004093
> volume #3 level 0.004644
> surface dust #3 size 206.9
> surface dust #3 size 205.48
> surface dust #3 size 204.06
> surface dust #3 size 153.84
> surface dust #3 size 152.78
> surface dust #3 size 151.73
> surface dust #3 size 150.68
> surface dust #3 size 149.65
> surface dust #3 size 148.62
> surface dust #3 size 147.59
> surface dust #3 size 146.58
> surface dust #3 size 67.34
> surface dust #3 size 81.15
> surface dust #3 size 94.86
> surface dust #3 size 102.56
> surface dust #3 size 119.89
> surface dust #3 size 119.06
> surface dust #3 size 118.24
> surface dust #3 size 117.43
> surface dust #3 size 100.94
> volume #3 level 0.005293
> volume #1 level 0.004434
> vop add #1 #3
Opened volume sum as #2, grid size 320,320,320, pixel 0.855, shown at step 1,
values float32
> volume #2 level 0.00481
> volume #2 level 0.006317
> volume #2 level 0.01574
> close #2
> close #3
> close #1
> open
> C:/Users/user/Desktop/장송이_채용관련/구조분석/coot_Test/cryosparc_P8_J147_005_volume_map_half_A.mrc
> C:/Users/user/Desktop/장송이_채용관련/구조분석/coot_Test/PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb
Opened cryosparc_P8_J147_005_volume_map_half_A.mrc as #1, grid size
250,250,250, pixel 0.85, shown at level 0.152, step 1, values float32
Chain information for
PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb #2
---
Chain | Description
A | No description available
B | No description available
> transparency 60
> volume #1 level 0.1931
> volume #1 level 0.1866
> volume #1 level 0.1405
> show cartoons
> hide cartoons
> show cartoons
> hide atoms
> show atoms
> hide atoms
> style stick
Changed 4968 atom styles
> show atoms
> style stick
Changed 4968 atom styles
> hide atoms
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\user\Desktop\movie1.mp4
Movie saved to \C:Users\\...\Desktop\movie1.mp4
> volume style surface
> volume style mesh
> volume style image
> volume style surface
> transparency #2#1.1#!1 0
> volume style image
> volume style surface
> transparency 50
> volume showOutlineBox true
> volume showOutlineBox false
> volume showOutlineBox true
> volume showOutlineBox false
> volume showOutlineBox true
> volume showOutlineBox false
> volume zone #1 nearAtoms #2 range 5.1
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> vop gaussian #1 sdev 2.55
Opened cryosparc_P8_J147_005_volume_map_half_A.mrc gaussian as #3, grid size
250,250,250, pixel 0.85, shown at step 1, values float32
> vop gaussian #3 sdev 2.55
Opened cryosparc_P8_J147_005_volume_map_half_A.mrc gaussian as #4, grid size
250,250,250, pixel 0.85, shown at step 1, values float32
> vop gaussian #4 sdev 2.55
Opened cryosparc_P8_J147_005_volume_map_half_A.mrc gaussian as #5, grid size
250,250,250, pixel 0.85, shown at step 1, values float32
> vop gaussian #5 sdev 2.55
Opened cryosparc_P8_J147_005_volume_map_half_A.mrc gaussian as #6, grid size
250,250,250, pixel 0.85, shown at step 1, values float32
> vop gaussian #6 sdev 2.55
Opened cryosparc_P8_J147_005_volume_map_half_A.mrc gaussian as #7, grid size
250,250,250, pixel 0.85, shown at step 1, values float32
> vop gaussian #7 sdev 2.55
Opened cryosparc_P8_J147_005_volume_map_half_A.mrc gaussian as #8, grid size
250,250,250, pixel 0.85, shown at step 1, values float32
> close #2,4#1,3,5-8
> open
> C:/Users/user/Desktop/장송이_채용관련/구조분석/Postprocess_87_small/postprocess.mrc
Opened postprocess.mrc as #1, grid size 320,320,320, pixel 0.855, shown at
level 0.00854, step 2, values float32
> surface dust #1 size 5.13
> volume #1 level 0.01016
> open
> C:/Users/user/Desktop/장송이_채용관련/구조분석/coot_Test/PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb
Chain information for
PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide #!1 models
> show #!1 models
> mlp
Map values for surface
"PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb_A SES surface":
minimum -26.6, mean -9.021, maximum 5.938
Map values for surface
"PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb_B SES surface":
minimum -25.66, mean -9.1, maximum 6.193
To also show corresponding color key, enter the above mlp command and add key
true
> mlp
Map values for surface
"PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb_A SES surface":
minimum -26.6, mean -9.021, maximum 5.938
Map values for surface
"PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb_B SES surface":
minimum -25.66, mean -9.1, maximum 6.193
To also show corresponding color key, enter the above mlp command and add key
true
> rainbow
> hide cartoons
> hide surfaces
> show cartoons
> select #1
2 models selected
> ~select #1
Nothing selected
> select #1
2 models selected
> ~select #1
Nothing selected
> select #1
2 models selected
> ~select #1
Nothing selected
> ui tool show "Model Panel"
> view clip false
> show target m
> select #1
2 models selected
> ~select #1
Nothing selected
> select #2.1
2484 atoms, 502 residues, 1 model selected
> ~select #2.1
1 model selected
> select #2.1
2484 atoms, 502 residues, 1 model selected
> ~select #2.1
1 model selected
> ui windowfill toggle
> ui tool show "Model Panel"
> ui autostart false "Model Panel"
> ui autostart true "Model Panel"
> ui dockable false "Model Panel"
> ui dockable true "Model Panel"
> ui favorite true "Model Panel"
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui tool show "Selection Inspector"
> ui tool show ViewDockX
No suitable models found for ViewDockX
> show #!1 models
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Basic Actions"
> ui tool show "Model Panel"
> ui tool show Registration
> toolshed show
> ui tool show "Command Line Interface"
> hide /A target abp
> hide #!1 models
> show #!1 models
> volume #1 region 0,0,0,319,319,214
> volume #1 region 0,0,0,319,319,100
> show surfaces
> hide surfaces
> volume style surface
> close #1
> open
> C:/Users/user/Desktop/장송이_채용관련/구조분석/Postprocess_87_small/postprocess.mrc
Opened postprocess.mrc as #1, grid size 320,320,320, pixel 0.855, shown at
level 0.00854, step 2, values float32
> volume #1 level 0.01633
> volume #1 region 0,0,0,319,319,319
> select #2.2
2484 atoms, 502 residues, 1 model selected
> select #2.1
2484 atoms, 502 residues, 1 model selected
> ui tool show "Fit in Map"
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.004103, steps = 80
shifted from previous position = 2.32
rotated from previous position = 3.32 degrees
atoms outside contour = 4468, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.99866169 -0.04460666 0.02617392 2.41233135
0.04527499 0.99864847 -0.02552286 -0.23216369
-0.02500006 0.02667372 0.99933153 1.52628424
Axis 0.45054057 0.44171393 0.77582343
Axis point 27.21979087 31.36162142 0.00000000
Rotation angle (degrees) 3.32080940
Shift along axis 2.16843028
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.004104, steps = 44
shifted from previous position = 0.0176
rotated from previous position = 0.00784 degrees
atoms outside contour = 4468, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.99866795 -0.04450169 0.02611371 2.40692388
0.04517008 0.99865152 -0.02558915 -0.19844414
-0.02493973 0.02673462 0.99933141 1.50523160
Axis 0.45225735 0.44127739 0.77507261
Axis point 26.50282869 31.26370787 0.00000000
Rotation angle (degrees) 3.31625947
Shift along axis 2.16764389
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.004103, steps = 28
shifted from previous position = 0.019
rotated from previous position = 0.0175 degrees
atoms outside contour = 4466, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.99865397 -0.04471677 0.02628029 2.41062764
0.04538601 0.99864540 -0.02544559 -0.25400871
-0.02510685 0.02660410 0.99933071 1.54436944
Axis 0.44849900 0.44278992 0.77639277
Axis point 27.68038222 31.33376720 0.00000000
Rotation angle (degrees) 3.32654453
Shift along axis 2.16772885
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.004103, steps = 64
shifted from previous position = 0.0024
rotated from previous position = 0.002 degrees
atoms outside contour = 4467, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.99865524 -0.04468504 0.02628592 2.40704300
0.04535411 0.99864717 -0.02543298 -0.25040274
-0.02511389 0.02659095 0.99933088 1.54797574
Axis 0.44849085 0.44311036 0.77621464
Axis point 27.65561604 31.25350075 0.00000000
Rotation angle (degrees) 3.32495681
Shift along axis 2.17014215
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.004104, steps = 40
shifted from previous position = 0.0113
rotated from previous position = 0.0123 degrees
atoms outside contour = 4468, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.99866548 -0.04453137 0.02615769 2.40611078
0.04519907 0.99865212 -0.02551450 -0.21498421
-0.02498623 0.02666275 0.99933217 1.52294305
Axis 0.45091579 0.44198581 0.77545051
Axis point 26.91655727 31.24307013 0.00000000
Rotation angle (degrees) 3.31681258
Shift along axis 2.17090034
> fitmap #2 inMap #1
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.004103, steps = 44
shifted from previous position = 0.00309
rotated from previous position = 0.00324 degrees
atoms outside contour = 4469, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.99866287 -0.04456253 0.02620394 2.40306695
0.04523167 0.99865042 -0.02552309 -0.21582029
-0.02503120 0.02667421 0.99933074 1.52439831
Axis 0.45070426 0.44239631 0.77533940
Axis point 26.92099901 31.17547683 0.00000000
Rotation angle (degrees) 3.31964837
Shift along axis 2.16952046
> select #2
4968 atoms, 4966 bonds, 1004 residues, 1 model selected
> ~select #2
2 models selected
> select #2
4968 atoms, 4966 bonds, 1004 residues, 1 model selected
> ~select #2
2 models selected
> ui tool show "Model Panel"
> lighting soft
> lighting simple
> lighting soft
Drag select of 69 residues
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99866,-0.044563,0.026204,-19.863,0.045232,0.99865,-0.025523,-1.8859,-0.025031,0.026674,0.99933,16.21
> view matrix models
> #2,0.99866,-0.044563,0.026204,-34.471,0.045232,0.99865,-0.025523,3.5323,-0.025031,0.026674,0.99933,28.544
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.79577,0.32952,0.50811,-105.2,-0.39619,0.91782,0.025266,53.69,-0.45803,-0.22141,0.86092,116.24
> view matrix models
> #2,0.94794,0.20768,-0.2414,-26.765,0.31829,-0.64118,0.69827,70.206,-0.0097664,-0.73875,-0.67391,290.81
> view matrix models
> #2,0.83116,0.12733,0.54125,-91.049,-0.16855,-0.86993,0.46348,172.09,0.52986,-0.47646,-0.70159,208.33
> view matrix models
> #2,0.88547,0.081898,0.45743,-82.866,-0.26742,-0.71522,0.64571,146.29,0.38004,-0.69408,-0.6114,237.67
> view matrix models
> #2,0.66829,-0.73031,0.14154,61.247,-0.73929,-0.63086,0.23551,232.34,-0.082703,-0.26202,-0.96151,279.16
> view matrix models
> #2,0.84779,-0.52973,-0.025132,38.898,-0.53032,-0.84665,-0.044003,263.51,0.0020318,0.050633,-0.99872,240.87
> view matrix models
> #2,0.90603,-0.087628,0.41405,-62.273,-0.18701,-0.96053,0.20595,211.78,0.37966,-0.26403,-0.88665,221.89
> view matrix models
> #2,0.77436,-0.09826,0.62507,-70.095,-0.23237,-0.963,0.13648,224.45,0.58853,-0.25093,-0.76854,185.35
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.77436,-0.09826,0.62507,2.1067,-0.23237,-0.963,0.13648,239.39,0.58853,-0.25093,-0.76854,173.19
> view matrix models
> #2,0.77436,-0.09826,0.62507,-16.385,-0.23237,-0.963,0.13648,230.58,0.58853,-0.25093,-0.76854,170.47
> view matrix models
> #2,0.77436,-0.09826,0.62507,4.1152,-0.23237,-0.963,0.13648,242.37,0.58853,-0.25093,-0.76854,175.85
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.45077,-0.31396,0.8356,38.661,-0.84352,-0.45608,0.28368,237.51,0.29203,-0.83272,-0.47042,236.95
> view matrix models
> #2,0.97607,-0.14358,0.16335,37.75,-0.21053,-0.8121,0.54421,179.53,0.05452,-0.56558,-0.82289,272.24
> view matrix models
> #2,0.74029,-0.313,0.59498,33.903,-0.43505,-0.89776,0.069015,264.39,0.51255,-0.30994,-0.80077,193.75
> view matrix models
> #2,0.67931,-0.39438,0.61887,46.473,-0.63477,-0.73896,0.22585,251.68,0.36824,-0.54626,-0.75233,229.03
> view matrix models
> #2,0.93954,-0.2412,0.24307,43.357,-0.32499,-0.85172,0.41103,210.47,0.10788,-0.46518,-0.87862,261.93
> view matrix models
> #2,0.82316,-0.30568,0.4785,36.979,-0.43964,-0.87643,0.19643,248.72,0.35933,-0.37206,-0.85583,222.71
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.82316,-0.30568,0.4785,37.081,-0.43964,-0.87643,0.19643,245.75,0.35933,-0.37206,-0.85583,219.2
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.009013, steps = 128
shifted from previous position = 4.3
rotated from previous position = 5.48 degrees
atoms outside contour = 3761, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.84415497 -0.33696476 0.41696179 41.65737275
-0.46260506 -0.85090636 0.24890746 240.72233122
0.27092240 -0.40300510 -0.87417843 231.45412241
Axis -0.95900300 0.21483282 -0.18482452
Axis point 0.00000000 145.64093287 89.12072542
Rotation angle (degrees) 160.12977994
Shift along axis -31.01288640
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.009012, steps = 84
shifted from previous position = 0.0183
rotated from previous position = 0.0182 degrees
atoms outside contour = 3760, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.84426669 -0.33672621 0.41692830 41.63087873
-0.46233616 -0.85106464 0.24886593 240.73124512
0.27103325 -0.40287025 -0.87420623 231.43641652
Axis -0.95903382 0.21468546 -0.18483582
Axis point 0.00000000 145.62998105 89.12173733
Rotation angle (degrees) 160.13604759
Shift along axis -31.02166336
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.009012, steps = 64
shifted from previous position = 0.00823
rotated from previous position = 0.0153 degrees
atoms outside contour = 3763, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.84432423 -0.33685829 0.41670502 41.66977010
-0.46236909 -0.85104346 0.24887719 240.73167173
0.27079774 -0.40280457 -0.87430948 231.46048399
Axis -0.95904955 0.21472492 -0.18470836
Axis point 0.00000000 145.63530411 89.13541133
Rotation angle (degrees) 160.13811519
Shift along axis -31.02497289
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.009012, steps = 100
shifted from previous position = 0.00945
rotated from previous position = 0.0195 degrees
atoms outside contour = 3763, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.84420017 -0.33683247 0.41697715 41.64204691
-0.46249971 -0.85094394 0.24897476 240.71898817
0.27096140 -0.40303635 -0.87415194 231.44965334
Axis -0.95901478 0.21476822 -0.18483848
Axis point 0.00000000 145.63835275 89.11705584
Rotation angle (degrees) 160.12690408
Shift along axis -31.01735280
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.009012, steps = 84
shifted from previous position = 0.0071
rotated from previous position = 0.014 degrees
atoms outside contour = 3762, contour level = 0.016329
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.84423226 -0.33668236 0.41703342 41.61399384
-0.46234221 -0.85106002 0.24887049 240.72909955
0.27113016 -0.40291666 -0.87415479 231.42530965
Axis -0.95902434 0.21467863 -0.18489296
Axis point 0.00000000 145.62793007 89.11447287
Rotation angle (degrees) 160.13422393
Shift along axis -31.01835180
> ui mousemode right select
> transparency (#!2 & sel) 60
> volume gaussian #1 sDev 2
Opened postprocess.mrc gaussian as #3, grid size 320,320,320, pixel 0.855,
shown at step 1, values float32
> volume #3 level 0.003488
> transparency (#!2 & sel) 70
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc gaussian (#3) using 4968 atoms
average map value = 0.01735, steps = 208
shifted from previous position = 16.6
rotated from previous position = 35.9 degrees
atoms outside contour = 21, contour level = 0.0034883
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc gaussian (#3) coordinates:
Matrix rotation and translation
0.99754015 -0.07009727 -0.00013686 38.26598500
-0.07009737 -0.99753974 -0.00090859 250.36037263
-0.00007283 0.00091594 -0.99999957 217.70689975
Axis 0.99938477 -0.03507241 -0.00005416
Axis point 0.00000000 125.80192634 108.91189182
Rotation angle (degrees) 179.94769879
Shift along axis 29.44991006
> hide sel surfaces
> transparency (#!2 & sel) 40
Drag select of 1 postprocess.mrc
> select clear
> lighting simple
> transparency #1-2 80
Drag select of 13 residues, 1 postprocess.mrc
> select clear
Drag select of 33 residues, 1 postprocess.mrc
> select clear
> color #2.1 #5c845c transparency 0
> color #2.1 #005500 transparency 0
> color #2.1 #005d00 transparency 0
> color #2.1 #006100 transparency 0
> color #2.2 #007c00 transparency 0
> color /A #438663 target c
> color /B #00946d target c
> volume #1 color #c8c8c833
> lighting soft
> lighting simple
> lighting soft
Drag select of 160 residues, 1 postprocess.mrc
> select clear
> save
> C:/Users/user/Desktop/장송이_채용관련/구조분석/Postprocess_87_small/PRSdimer_fit.cxs
> open
> C:/Users/user/Desktop/장송이_채용관련/구조분석/Refinement_88_big/run_it018_half1_class001_unfil.mrc
Opened run_it018_half1_class001_unfil.mrc as #4, grid size 320,320,320, pixel
0.855, shown at level 0.00307, step 2, values float32
Drag select of 4 run_it018_half1_class001_unfil.mrc
> select clear
> hide #!2 models
> hide #!1 models
> ui tool show "Hide Dust"
> surface dust #4 size 5.13
> ui tool show "Map Eraser"
> volume erase #4 center 158.09,166.16,104.33 radius 29.058
Opened run_it018_half1_class001_unfil.mrc copy as #6, grid size 320,320,320,
pixel 0.855, shown at step 1, values float32
> volume erase #6 center 156.52,132.57,110.22 radius 29.002
> surface dust #4 size 5.13
> surface dust #4 size 5.05
> surface dust #6 size 8.33
> volume erase #6 center 161.46,104.71,100.58 radius 29.002
> volume erase #6 center 135.99,115.33,102.51 radius 29.002
> volume erase #6 center 113.69,124.1,108.92 radius 29.002
> volume erase #6 center 150.28,110.3,93.176 radius 29.002
> volume erase #6 center 154.76,95.911,92.943 radius 29.002
> volume erase #6 center 139.66,152.94,85.359 radius 29.002
> volume erase #6 center 132.33,172.57,89.586 radius 29.002
> volume erase #6 center 132.79,149,111.3 radius 29.002
> volume erase #6 center 144.07,133.63,143.8 radius 25.171
> volume erase #6 center 162.3,148.63,145.97 radius 25.171
> volume erase #6 center 124.52,109.6,143.93 radius 19.426
> volume erase #6 center 107.72,122.7,137.68 radius 19.426
> volume erase #6 center 118.22,144.64,131.71 radius 19.426
> volume erase #6 center 102,137.3,121.35 radius 19.426
> volume erase #6 center 120.23,158.19,110.81 radius 19.426
> volume erase #6 center 139.99,174.22,129.14 radius 19.426
> volume erase #6 center 140.19,162.03,145.42 radius 19.426
> volume #4 level 0.002628
> close #6
> volume #4 level 0.002866
> ui tool show "Map Eraser"
> volume erase #4 center 146.06,149.25,87.773 radius 35.158
Opened run_it018_half1_class001_unfil.mrc copy as #6, grid size 320,320,320,
pixel 0.855, shown at step 1, values float32
> surface dust #6 size 5.13
> surface dust #6 size 6.04
> volume erase #6 center 160.68,114.39,90.654 radius 35.158
> volume erase #6 center 141.61,108.59,103.56 radius 30.37
> volume erase #6 center 112.16,127.83,99.158 radius 30.37
> volume erase #6 center 128.57,134.87,130.04 radius 30.37
> volume erase #6 center 160.62,142.83,115.16 radius 30.37
> volume erase #6 center 149.74,168.81,111.1 radius 30.37
> volume erase #6 center 144.71,173.74,88.531 radius 30.37
> volume erase #6 center 129.07,169.17,87.638 radius 30.37
> volume erase #6 center 103.06,129.12,122.3 radius 23.94
> volume #6 level 0.002441
> surface dust #6 size 7.23
> surface dust #6 size 10.92
> close session
> open
> C:\Users\user\Desktop\장송이_채용관련\구조분석\Postprocess_87_small\PRSdimer_fit.cxs
> format session
Opened postprocess.mrc as #1, grid size 320,320,320, pixel 0.855, shown at
level 0.0163, step 2, values float32
Opened postprocess.mrc gaussian as #3, grid size 320,320,320, pixel 0.855,
shown at level 0.00349, step 1, values float32
opened ChimeraX session
> open
> C:/Users/user/Desktop/장송이_채용관련/구조분석/Refinement_88_big/run_it018_half1_class001_unfil.mrc
Opened run_it018_half1_class001_unfil.mrc as #5, grid size 320,320,320, pixel
0.855, shown at level 0.00307, step 2, values float32
> ui tool show "Map Eraser"
> hide #!2 models
> hide #!1 models
> volume erase #5 center 136.02,107.3,91.884 radius 29.412
Opened run_it018_half1_class001_unfil.mrc copy as #6, grid size 320,320,320,
pixel 0.855, shown at step 1, values float32
> ui tool show "Hide Dust"
> volume #5 level 0.003117
> surface dust #6 size 5.13
> volume erase #6 center 161.52,130.11,91.695 radius 29.412
> volume erase #6 center 139.87,161.56,87.601 radius 29.412
> volume erase #6 center 144.92,151.48,120.27 radius 29.412
> volume erase #6 center 115.96,123.62,105.73 radius 29.412
> volume erase #6 center 117.66,118.67,132.32 radius 29.412
> volume erase #6 center 145.77,111.48,120.5 radius 14.09
> volume erase #6 center 144.98,119.1,130.66 radius 12.996
> volume erase #6 center 131.83,136.35,76.924 radius 12.996
> volume erase #6 center 131.09,196.07,103.2 radius 12.996
> volume erase #6 center 172.76,142.91,111.94 radius 12.996
> volume erase #6 center 172.01,140.04,134.35 radius 12.996
> volume erase #6 center 166.43,137.92,146.3 radius 12.996
> volume erase #6 center 178.65,133.4,125.37 radius 12.996
> volume erase #6 center 161.45,138.66,142.55 radius 12.996
> volume erase #6 center 161.84,134.4,134.49 radius 12.996
> volume erase #6 center 154.58,126.06,153.1 radius 12.996
> volume erase #6 center 146.31,120.76,151.74 radius 12.996
> volume erase #6 center 151.68,135.54,169.67 radius 12.996
> volume erase #6 center 100.1,135.63,120.6 radius 12.996
> volume erase #6 center 99.167,140.22,124.53 radius 12.996
> volume erase #6 center 105.35,136.96,134.19 radius 7.6608
> volume erase #6 center 98.102,135.94,135.57 radius 7.6608
> volume erase #6 center 107.73,143.5,133.09 radius 7.6608
> volume erase #6 center 113.62,139.07,132.52 radius 7.6608
> volume erase #6 center 134.55,136.1,149.35 radius 7.6608
> volume erase #6 center 137.31,138.86,164.95 radius 7.6608
> volume erase #6 center 127.53,137.81,174.25 radius 7.6608
> volume erase #6 center 112.18,156.46,107.34 radius 7.6608
> volume erase #6 center 115.83,164.19,106.59 radius 7.6608
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right translate
> volume #6 level 0.002884
> save "C:/Users/user/Desktop/장송이_채용관련/구조분석/model merge.cxs"
> surface dust #6 size 5.96
> ui tool show "Volume Viewer"
> save #6
Cannot determine format for '#6'
> save crop.mrc #6
QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: "data"
> open C:/Users/user/Desktop/crop.mrc
Opened crop.mrc as #7, grid size 320,320,320, pixel 0.855, shown at level
0.00231, step 2, values float32
> volume #7 level 0.002489
> surface dust #7 size 5.13
> close #7
> transparency #1,6 0
> save merge.mrc #6,1
Cannot write multiple volumes using format mrc
> save merge%d.mrc #6,1
> lighting simple
> lighting soft
> volume #1 level 0.01804
> volume #1 level 0.0149
> volume #1 level 0.01291
> save "C:/Users/user/Desktop/장송이_채용관련/구조분석/model merge.cxs"
> open C:/Users/user/Desktop/장송이_채용관련/구조분석/W3_Nb
'C:/Users/user/Desktop/장송이_채용관련/구조분석/W3_Nb' has no suffix
> open C:/Users/user/Desktop/장송이_채용관련/구조분석/autobuild_r52_refine_52-coot-0.pdb
Chain information for autobuild_r52_refine_52-coot-0.pdb #7
---
Chain | Description
A D | No description available
B C | No description available
> select #2/A
2484 atoms, 2483 bonds, 502 residues, 1 model selected
> close #7
> open C:/Users/user/Desktop/XL-MS/EPRS/EPRS_CX_template.pdb
Chain information for EPRS_CX_template.pdb #7
---
Chain | Description
A B | No description available
Drag select of 1 postprocess.mrc , 493 residues
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,-1.5108,0,1,0,2.5161,0,0,1,4.6518,#7,1,0,0,-1.5108,0,1,0,2.5161,0,0,1,4.6518
> select clear
Drag select of 653 residues
> view matrix models #7,1,0,0,-5.5277,0,1,0,40.185,0,0,1,15.2
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.87653,-0.37309,0.30413,82.249,-0.27934,0.90883,0.30983,24.916,-0.392,0.18662,-0.90084,243.92
> view matrix models
> #7,0.9214,-0.37349,0.10733,-11.808,-0.045264,-0.37745,-0.92492,142.9,0.38596,0.84737,-0.36469,136.31
> view matrix models
> #7,0.92921,-0.19553,0.31358,-34.501,0.26429,-0.24146,-0.93373,123.95,0.25829,0.95051,-0.17269,123.85
> view matrix models
> #7,0.093765,0.44678,0.88972,-43.064,0.99198,0.034125,-0.12168,-9.8187,-0.084726,0.89399,-0.44,174.5
> view matrix models
> #7,-0.84984,-0.45621,0.26389,84.894,0.22158,0.14502,0.9643,-76.918,-0.47819,0.87798,-0.022155,154.93
> view matrix models
> #7,-0.25763,0.056826,0.96457,-28.384,0.88871,0.40574,0.21347,-39.31,-0.37923,0.91222,-0.15503,162.81
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.25763,0.056826,0.96457,-39.512,0.88871,0.40574,0.21347,67.962,-0.37923,0.91222,-0.15503,187.85
> view matrix models
> #7,-0.25763,0.056826,0.96457,49.932,0.88871,0.40574,0.21347,52.631,-0.37923,0.91222,-0.15503,222.71
> view matrix models
> #7,-0.25763,0.056826,0.96457,43.724,0.88871,0.40574,0.21347,52.627,-0.37923,0.91222,-0.15503,210.68
> view matrix models
> #7,-0.25763,0.056826,0.96457,41.97,0.88871,0.40574,0.21347,52.636,-0.37923,0.91222,-0.15503,207.37
> view matrix models
> #7,-0.25763,0.056826,0.96457,46.12,0.88871,0.40574,0.21347,52.788,-0.37923,0.91222,-0.15503,216.76
> view matrix models
> #7,-0.25763,0.056826,0.96457,40.453,0.88871,0.40574,0.21347,66.432,-0.37923,0.91222,-0.15503,198.29
> open C:/Users/user/Desktop/장송이_채용관련/구조분석/W3_NB.pdb
Chain information for W3_NB.pdb #8
---
Chain | Description
A | No description available
C | No description available
> view matrix models
> #7,-0.25763,0.056826,0.96457,40.212,0.88871,0.40574,0.21347,64.76,-0.37923,0.91222,-0.15503,195.36
> select clear
Drag select of 156 residues
> view matrix models #8,1,0,0,16.194,0,1,0,60.339,0,0,1,170.85
> view matrix models #8,1,0,0,145.7,0,1,0,87.107,0,0,1,140.63
> view matrix models #8,1,0,0,143.1,0,1,0,80.547,0,0,1,123.59
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.56323,-0.58462,-0.58394,172.32,0.8263,-0.39615,-0.40037,93.074,0.0027338,-0.70801,0.7062,135.18
> view matrix models
> #8,-0.0090322,-0.86743,-0.49747,168.74,0.91837,0.18963,-0.34733,85.504,0.39562,-0.46,0.79491,127.69
> view matrix models
> #8,-0.30104,-0.73799,-0.60395,171.75,0.91592,-0.047446,-0.39856,88.698,0.26548,-0.67315,0.69021,132.64
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.30104,-0.73799,-0.60395,180.44,0.91592,-0.047446,-0.39856,110.43,0.26548,-0.67315,0.69021,144.63
> view matrix models
> #8,-0.30104,-0.73799,-0.60395,181.3,0.91592,-0.047446,-0.39856,112.59,0.26548,-0.67315,0.69021,143.25
> view matrix models
> #8,-0.30104,-0.73799,-0.60395,185.78,0.91592,-0.047446,-0.39856,118.08,0.26548,-0.67315,0.69021,145.8
> view matrix models
> #8,-0.30104,-0.73799,-0.60395,186.44,0.91592,-0.047446,-0.39856,117.5,0.26548,-0.67315,0.69021,145.4
> view matrix models
> #8,-0.30104,-0.73799,-0.60395,195.44,0.91592,-0.047446,-0.39856,119.19,0.26548,-0.67315,0.69021,138.27
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.49816,0.355,0.79108,155.83,-0.0066114,0.91388,-0.40594,118.14,-0.86706,0.19699,0.45761,143.5
> view matrix models
> #8,0.84503,-0.19654,0.49728,162.65,-0.52525,-0.13088,0.84082,114.55,-0.10017,-0.97172,-0.21383,158.39
> view matrix models
> #8,0.56966,0.82161,-0.020975,162.79,-0.32105,0.24595,0.91457,107.74,0.75658,-0.51426,0.40389,136.47
> view matrix models
> #8,0.59351,0.79234,-0.14124,164.69,-0.15222,0.28284,0.94701,105.31,0.7903,-0.54056,0.28848,138.18
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.59351,0.79234,-0.14124,151.98,-0.15222,0.28284,0.94701,71.267,0.7903,-0.54056,0.28848,153.75
> open C:/Users/user/Desktop/merge2.mrc
Opened merge2.mrc as #9, grid size 320,320,320, pixel 0.855, shown at level
0.00854, step 2, values float32
> view matrix models
> #8,0.59351,0.79234,-0.14124,146.81,-0.15222,0.28284,0.94701,45.8,0.7903,-0.54056,0.28848,149.45
> ui mousemode right translate
> surface dust #9 size 5.13
> open C:/Users/user/Desktop/merge1.mrc
Opened merge1.mrc as #10, grid size 320,320,320, pixel 0.855, shown at level
0.00231, step 2, values float32
> close #9
> close #10
> volume #1 level 0.01205
> volume #1 level 0.01547
> volume #5 level 0.004291
> ui tool show "Fit in Map"
Fit molecule EPRS_CX_template.pdb (#7) to map postprocess.mrc gaussian (#3)
using 19350 atoms
average map value = 0.005658, steps = 536
shifted from previous position = 9.94
rotated from previous position = 37.8 degrees
atoms outside contour = 12157, contour level = 0.0034883
Position of EPRS_CX_template.pdb (#7) relative to postprocess.mrc gaussian
(#3) coordinates:
Matrix rotation and translation
-0.20930098 -0.50978795 0.83445150 36.30410601
0.94700351 0.10697667 0.30288659 51.50143040
-0.24367477 0.85362299 0.46038067 126.79656042
Axis 0.29075227 0.56917913 0.76908922
Axis point 6.62797384 -22.86571353 0.00000000
Rotation angle (degrees) 108.72170687
Shift along axis 137.38690895
> lighting simple
> transparency sel 80
> transparency sel 70
> lighting simple
> lighting soft
> lighting simple
> transparency sel 80
> save "C:/Users/user/Desktop/장송이_채용관련/구조분석/model merge.cxs"
> lighting simple
> select clear
> transparency #1,6-8 80
> lighting soft
> transparency #1,6-8 60
> color #7 #005500 transparency 0
> color #7 darkgreen transparency 0
> volume #6 level 0.002608
> volume #6 level 0.002332
> surface dust #6 size 5.96
> surface dust #6 size 7.71
> surface dust #6 size 10.64
> hide #8 models
Drag select of 1 postprocess.mrc , 6 crop.mrc , 248 residues
> select clear
Drag select of 1 postprocess.mrc , 110 residues
Drag select of 1 postprocess.mrc , 112 residues
Drag select of 257 residues
Drag select of 1 postprocess.mrc , 236 residues
Drag select of 1 residues
> select add #7/B:1252
3868 atoms, 10 bonds, 483 residues, 3 models selected
Drag select of 1 postprocess.mrc , 112 residues
> select #1
2 models selected
Drag select of 1 postprocess.mrc , 167 residues
> select clear
Drag select of 1 postprocess.mrc , 22 residues
Drag select of 1 postprocess.mrc , 131 residues
Drag select of 1 postprocess.mrc , 151 residues
Drag select of 1 postprocess.mrc , 180 residues
Drag select of 1 postprocess.mrc , 254 residues
Drag select of 1 postprocess.mrc , 47 residues
Drag select of 1 postprocess.mrc , 22 residues
Drag select of 5 residues
> select clear
> volume gaussian #6 sDev 2
Opened crop.mrc gaussian as #9, grid size 320,320,320, pixel 0.855, shown at
step 1, values float32
> surface dust #6 size 15.85
> surface dust #9 size 21.3
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A #7/B
Alignment identifier is 1
> select #7/A-B:197
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #7/A-B:197-576
6218 atoms, 6378 bonds, 760 residues, 1 model selected
> hide #!9 models
> select #7/A-B:577
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #7/A-B:577-684
1750 atoms, 1784 bonds, 216 residues, 1 model selected
> select #7/A-B:932-933
22 atoms, 20 bonds, 4 residues, 1 model selected
> select #7/A-B:932-973
660 atoms, 670 bonds, 84 residues, 1 model selected
> select #7/A-B:954-955
32 atoms, 30 bonds, 4 residues, 1 model selected
> select #7/A-B:954-960
122 atoms, 126 bonds, 14 residues, 1 model selected
> select #7/A-B:950
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #7/A-B:950-952
54 atoms, 52 bonds, 6 residues, 1 model selected
> select #7/A-B:945
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/A-B:945-947
40 atoms, 38 bonds, 6 residues, 1 model selected
> select #7/A-B:944
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #7/A-B:941-944
54 atoms, 50 bonds, 8 residues, 1 model selected
> select #7/A-B:941
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #7/A-B:941-943
32 atoms, 30 bonds, 6 residues, 1 model selected
> select #7/A-B:943
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #7/A-B:943
10 atoms, 8 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:197-446
2071 atoms, 2122 bonds, 250 residues, 1 model selected
> select #7/A:942-943
9 atoms, 8 bonds, 2 residues, 1 model selected
> select #7/A:520-943
3300 atoms, 3360 bonds, 424 residues, 1 model selected
> select #7/A:197-943
5956 atoms, 6083 bonds, 747 residues, 1 model selected
> ui mousemode right "translate selected models"
> show #!9 models
> view matrix models
> #7,-0.2093,-0.50979,0.83445,34.833,0.947,0.10698,0.30289,53.862,-0.24367,0.85362,0.46038,126.14
> view matrix models
> #7,-0.2093,-0.50979,0.83445,34.711,0.947,0.10698,0.30289,53.918,-0.24367,0.85362,0.46038,126.85
Fit molecule EPRS_CX_template.pdb (#7) to map crop.mrc gaussian (#9) using
5956 atoms
average map value = 0.0006404, steps = 444
shifted from previous position = 42.7
rotated from previous position = 56.2 degrees
atoms outside contour = 5154, contour level = 0.0005537
Fit molecule EPRS_CX_template.pdb (#7) to map crop.mrc gaussian (#9) using
5956 atoms
average map value = 0.0006403, steps = 48
shifted from previous position = 0.0857
rotated from previous position = 0.125 degrees
atoms outside contour = 5155, contour level = 0.0005537
Fit molecule EPRS_CX_template.pdb (#7) to map crop.mrc gaussian (#9) using
5956 atoms
average map value = 0.0006403, steps = 84
shifted from previous position = 0.0341
rotated from previous position = 0.0903 degrees
atoms outside contour = 5155, contour level = 0.0005537
Fit molecule EPRS_CX_template.pdb (#7) to map crop.mrc gaussian (#9) using
5956 atoms
average map value = 0.0006403, steps = 64
shifted from previous position = 0.0444
rotated from previous position = 0.0884 degrees
atoms outside contour = 5155, contour level = 0.0005537
Fit molecule EPRS_CX_template.pdb (#7) to map crop.mrc gaussian (#9) using
5956 atoms
average map value = 0.0006404, steps = 60
shifted from previous position = 0.0431
rotated from previous position = 0.0605 degrees
atoms outside contour = 5155, contour level = 0.0005537
> view matrix models
> #7,-0.2093,-0.50979,0.83445,37.642,0.947,0.10698,0.30289,52.871,-0.24367,0.85362,0.46038,128.11
> view matrix models
> #7,-0.2093,-0.50979,0.83445,39.144,0.947,0.10698,0.30289,52.439,-0.24367,0.85362,0.46038,125.57
> view matrix models
> #7,-0.2093,-0.50979,0.83445,34.966,0.947,0.10698,0.30289,51.566,-0.24367,0.85362,0.46038,134.43
Fit molecule EPRS_CX_template.pdb (#7) to map postprocess.mrc gaussian (#3)
using 19350 atoms
average map value = 0.005453, steps = 2000
shifted from previous position = 7.71
rotated from previous position = 0.301 degrees
atoms outside contour = 12166, contour level = 0.0034883
> show #8 models
> hide #8 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
Fit molecule EPRS_CX_template.pdb (#7) to map crop.mrc gaussian (#9) using
5956 atoms
average map value = 0.0006404, steps = 96
shifted from previous position = 2.76
rotated from previous position = 0.368 degrees
atoms outside contour = 5154, contour level = 0.0005537
> ui tool show "Show Sequence Viewer"
> sequence chain #7/B
Alignment identifier is 7/B
> select #7/B:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/B:197-514
2619 atoms, 2684 bonds, 318 residues, 1 model selected
> select #7/B:197-636
3582 atoms, 3672 bonds, 440 residues, 1 model selected
> select #7/B:197-796
4842 atoms, 4954 bonds, 600 residues, 1 model selected
> select #7/B:197-956
6058 atoms, 6184 bonds, 760 residues, 1 model selected
> select #7/B:197-956
6058 atoms, 6184 bonds, 760 residues, 1 model selected
> select #7/B:197-956
6058 atoms, 6184 bonds, 760 residues, 1 model selected
> select
> #7/B:212-227,246-258,269-285,296-304,310-313,316-328,333-335,349-351,377-388,397-413,435-443,458-464,468-478,489-503,512-514,537-539,554-559,641-644,659-663,717-723,731-754,759-780,800-827,832-853,884-905,910-931,955-965,982-1001,1015-1020,1048-1058,1104-1125,1172-1176,1202-1212,1236-1256,1270-1280,1290-1294,1313-1341,1349-1357,1370-1382
3982 atoms, 4016 bonds, 491 residues, 1 model selected
> select #7/B:197-956
6058 atoms, 6184 bonds, 760 residues, 1 model selected
> select #7/B:943
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/B:877-943
510 atoms, 516 bonds, 67 residues, 1 model selected
> select #7/B:876
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/B:838-876
296 atoms, 301 bonds, 39 residues, 1 model selected
> select #7/B:837
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/B:837
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/B:837-943
815 atoms, 827 bonds, 107 residues, 1 model selected
> select #7/B:717-943
1732 atoms, 1752 bonds, 227 residues, 1 model selected
> select #7/B:562-943
2968 atoms, 3017 bonds, 382 residues, 1 model selected
> select #7/B:437-943
3970 atoms, 4048 bonds, 507 residues, 1 model selected
> select #7/B:197-943
5956 atoms, 6083 bonds, 747 residues, 1 model selected
> select #7/B:197-1076
7020 atoms, 7177 bonds, 880 residues, 1 model selected
> select #7/B:197-1352
9203 atoms, 9406 bonds, 1156 residues, 1 model selected
> select #7/B:197-1352
9203 atoms, 9406 bonds, 1156 residues, 1 model selected
> select
> #7/B:199-202,231-236,265-268,289-292,337-340,357-359,373-375,392-396,419-423,509-511,515-519,526-531,541-546,549-553,565-568,572-580,589-594,605-607,609-611,619-626,650-657,669-672,676-682,697-702,969-971,978-980,1067-1076,1091-1101,1130-1134,1146-1154,1159-1170,1180-1182,1190-1192,1194-1201,1229-1233,1260-1262,1284-1288,1297-1302,1308-1312,1343-1345,1361-1366,1387-1390,1411-1416
1919 atoms, 1931 bonds, 231 residues, 1 model selected
> select #7/B:197-1352
9203 atoms, 9406 bonds, 1156 residues, 1 model selected
> select #7/B:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/B:197-436
1986 atoms, 2034 bonds, 240 residues, 1 model selected
> select #7/B:197-676
3912 atoms, 4006 bonds, 480 residues, 1 model selected
> select #7/B:197-916
5750 atoms, 5874 bonds, 720 residues, 1 model selected
> select #7/B:197-943
5956 atoms, 6083 bonds, 747 residues, 1 model selected
Fit molecule EPRS_CX_template.pdb (#7) to map crop.mrc gaussian (#9) using
5956 atoms
average map value = 0.001191, steps = 424
shifted from previous position = 38
rotated from previous position = 26.2 degrees
atoms outside contour = 3268, contour level = 0.0005537
> select clear
> transparency #1,7,9 60
> color #9 #ffff7f models transparency 0
> transparency #1,7,9 60
> save "C:/Users/user/Desktop/장송이_채용관련/구조분석/model merge.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 694, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 694, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
> save "C:/Users/user/Desktop/장송이_채용관련/구조분석/model merge.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 694, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 694, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
> save "D:/장송이/장송이/Documents/Songlee/취업, 퇴사/입사 서류/Fig/EPRS_tem.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 694, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 694, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
> close #8
> close #4
> save "D:/장송이/장송이/Documents/Songlee/취업, 퇴사/입사 서류/Fig/ets.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 694, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 624, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\safesave.py", line 130, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 694, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
> save "D:/장송이/장송이/Documents/Songlee/취업, 퇴사/입사 서류/Fig/test.cxs" includeMaps
> true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 295, in process
return copy_state(data, convert=convert)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\state.py", line 219, in copy_state
return _copy(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\state.py", line 207, in _copy
return data.copy()
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 5.42 MiB for an
array with shape (473172, 3) and data type int32
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> ->
'PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb_A SES surface':
Unable to allocate 5.42 MiB for an array with shape (473172, 3) and data type
int32
ValueError: error processing: 'models' -> ->
'PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb_A SES surface':
Unable to allocate 5.42 MiB for an array with shape (473172, 3) and data type
int32
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 295, in process
return copy_state(data, convert=convert)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\state.py", line 219, in copy_state
return _copy(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\state.py", line 207, in _copy
return data.copy()
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 5.42 MiB for an
array with shape (473172, 3) and data type int32
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> ->
'PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb_A SES surface':
Unable to allocate 5.42 MiB for an array with shape (473172, 3) and data type
int32
ValueError: error processing: 'models' -> ->
'PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb_A SES surface':
Unable to allocate 5.42 MiB for an array with shape (473172, 3) and data type
int32
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> hide #7 models
> transparency #1,9 0
> show #!6 models
> hide #!9 models
> transparency #1,6 0
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> show #!3 models
> volume #3 level 0.001944
> surface dust #3 size 8.89
> volume #3 level 0.001759
> volume #3 level 0.001944
> volume #3 level 0.002191
> volume #3 level 0.002253
> hide #!1 models
> show #!1 models
> hide #!6 models
> hide #!1 models
> transparency #3 60
> transparency #3 40
> show #!1 models
> volume #1 level 0.02032
> transparency #3 70
> color #3 #324832 models transparency 0
> transparency #3 70
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> show #!9 models
> hide #!1 models
> color #9 #aaff7f models transparency 0
> transparency #3,9 70
> transparency #3,9 50
> show #!1 models
> show #!6 models
> volume #6 level 0.002608
> volume #6 level 0.003528
> transparency #3,6 80
> transparency #3,6 60
> color #6 #aaff7f models transparency 0
> color #6 springgreen models transparency 0
> color #6 #aaff00 models transparency 0
> transparency #3,6 80
> color #6 white models transparency 0
> color #6 #838383 models transparency 0
> color #6 #919191 models transparency 0
> transparency #3,6 0
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!9 models
> hide #!9 models
> show #!9 models
> transparency #3,9 80
> show #!6 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> transparency #3 70
> transparency #3 80
> show #!9 models
> show #7 models
> hide #7 models
> show #!6 models
> show #!1 models
> color #9 #00ffff33 models
> color #9 #aaffff33 models
> color #9 #83c5c533 models
> color #9 #aaff7f33 models
> volume #6 level 0.002332
> hide #!3 models
> hide #!9 models
> color #1 #b3b3b3 models transparency 0
> color #6 #adadad models transparency 0
> turn x 0-
Expected a number or a keyword
> turn x 90
> turn x -90
> turn x 90
> turn x -90
> turn x 90
> show #!2 models
> ui tool show "Fit in Map"
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc gaussian (#3) using 4968 atoms
average map value = 0.01735, steps = 44
shifted from previous position = 0.0145
rotated from previous position = 0.0103 degrees
atoms outside contour = 4, contour level = 0.0022532
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc gaussian (#3) coordinates:
Matrix rotation and translation
0.99754475 -0.07003185 -0.00008778 38.24687178
-0.07003189 -0.99754447 -0.00074828 250.32306570
-0.00003515 0.00075258 -0.99999971 217.71957420
Axis 0.99938591 -0.03504009 -0.00003282
Axis point 0.00000000 125.79113529 108.90762919
Rotation angle (degrees) 179.95697714
Shift along axis 29.44489574
> show #!3 models
> hide #!3 models
> transparency #1-2,6 40
> transparency #1-2,6 70
Fit molecule PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
to map postprocess.mrc (#1) using 4968 atoms
average map value = 0.03486, steps = 72
shifted from previous position = 5.53
rotated from previous position = 0.172 degrees
atoms outside contour = 1310, contour level = 0.020322
Position of PRS_dimer_test_chainsaw1_real_space_refined_017-coot-4.pdb (#2)
relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.99774913 -0.06705665 -0.00028331 37.94191431
-0.06705678 -0.99774905 -0.00046295 250.00583266
-0.00025163 0.00048090 -0.99999985 217.80403661
Axis 0.99943698 -0.03355142 -0.00013711
Axis point 0.00000000 125.61405129 108.93426710
Rotation angle (degrees) 179.97294544
Shift along axis 29.50263685
> turn x -90
> transparency #1-2,6 20
> transparency #1-2,6 70
> ui tool show "Side View"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 419.67
OpenGL renderer: Quadro K2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Pro (Build 17763)
Memory: 8,521,994,240
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz
OSLanguage: ko-KR
Locale: ('ko_KR', 'cp949')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving session |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Note:
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The memory error saving a session does not appear to have caused the crash. That was a "Windows fatal exception: access violation". But it could be related.