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Opened 2 years ago
Closed 2 years ago
#9940 closed defect (duplicate)
Save mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets'
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.5rc202210270150 (2022-10-27 01:50:44 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5rc202210270150 (2022-10-27)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:\\\DeepEMhancer_test\\\P1_J26\\\denoised\\\J26_009_volume_map.mrc
Opened J26_009_volume_map.mrc as #1, grid size 400,400,400, pixel 0.834, shown
at level 0.0619, step 2, values float32
> volume #1 level 0.1632
> volume #1 step 1
> volume #1 level 0.3331
> volume #1 level 0.2017
> volume #1 level 0.2786
> open Z:/Arjun/relion/RY80/csparc/CS-cs-ry80/J28/J28_map.mrc
Opened J28_map.mrc as #2, grid size 400,400,400, pixel 0.834, shown at level
0.0793, step 2, values float32
> volume #2 level 0.08875
> volume #2 step 1
> volume #2 level 0.08954
> volume #2 level 0.04383
> volume #2 level 0.04462
> volume #2 level 0.045
> volume #2 level 0.04736
> volume #2 level 0.048
> volume #1 level 0.1857
> volume #1 level 0.1152
> open Z:/Arjun/relion/RY80/csparc/CS-cs-ry80/J34/J34_mask.mrc
Opened J34_mask.mrc as #3, grid size 400,400,400, pixel 0.834, shown at level
1, step 2, values float32
> volume #3 step 1
> volume #3 level 0.2549
> volume #3 level 0.2172
> volume #3 level 0.2819
> volume #2 level 0.04564
> volume #2 level 0.05115
> volume #2 level 0.1008
> volume #2 level 0.08504
> hide #!2 models
> open Z:/Arjun/relion/RY80/csparc/CS-cs-ry80/J31/J31_005_volume_map_sharp.mrc
Opened J31_005_volume_map_sharp.mrc as #4, grid size 400,400,400, pixel 0.834,
shown at level 0.0511, step 2, values float32
> volume #4 level 0.1795
> volume #4 step 1
> volume #4 level 0.2038
> volume #4 level 0.2007
> hide target m
> open D:/DeepEMhancer_test/P1_J26/denoised/J26_009_volume_map.mrc
Opened J26_009_volume_map.mrc as #5, grid size 400,400,400, pixel 0.834, shown
at level 0.0619, step 2, values float32
> volume #5 level 0.1818
> volume #5 step 1
> volume #5 level 0.238
> volume #4 level 0.3355
> volume #4 level 0.2295
> hide target m
> open volume series
'volume' has no suffix
> open series
'series' has no suffix
> ui tool show "Volume Viewer"
>
Incomplete command: vseries
>
Incomplete command: vseries
> Z:\Arjun\relion\RY80\csparc\CS-cs-ry80\J27\J27_component_000\\*.mrc
Unknown command: vseries Z:\Arjun\relion\RY80\csparc\CS-cs-
ry80\J27\J27_component_000\\*.mrc
> "Z:\Arjun\relion\RY80\csparc\CS-cs-ry80\J27\J27_component_000\\*.mrc"
Unknown command: vseries "Z:\Arjun\relion\RY80\csparc\CS-cs-
ry80\J27\J27_component_000\\*.mrc"
> toolshed show
> open Z:/Arjun/relion/RY80/relion/Refine3D/job001/run_class001.mrc
Opened run_class001.mrc as #6, grid size 400,400,400, pixel 0.834, shown at
level 0.0014, step 2, values float32
> volume #6 level 0.002499
> volume #6 step 1
> volume #6 level 0.00364
> volume #6 level 0.002291
> volume #6 level 0.003536
> hide #!6 models
> show #!5 models
> volume #3 level 0.4444
> volume #3 level 0.2815
> hide #!4 target m
> close #4
> close
> open Z:/Arjun/relion/RY80/Class3D/job003/run_it025_class001.mrc
Opened run_it025_class001.mrc as #1, grid size 140,140,140, pixel 2.5, shown
at level 0.0212, step 1, values float32
> open Z:/Arjun/relion/RY80/Class3D/job003/run_it025_class002.mrc
Opened run_it025_class002.mrc as #2, grid size 140,140,140, pixel 2.5, shown
at level 0.0221, step 1, values float32
> open Z:/Arjun/relion/RY80/Class3D/job003/run_it025_class003.mrc
Opened run_it025_class003.mrc as #3, grid size 140,140,140, pixel 2.5, shown
at level 0.0171, step 1, values float32
> open Z:/Arjun/relion/RY80/Class3D/job003/run_it025_class004.mrc
Opened run_it025_class004.mrc as #4, grid size 140,140,140, pixel 2.5, shown
at level 0.0276, step 1, values float32
> open Z:/Arjun/relion/RY80/Class3D/job003/run_it025_class005.mrc
Opened run_it025_class005.mrc as #5, grid size 140,140,140, pixel 2.5, shown
at level 0.0219, step 1, values float32
> open Z:/Arjun/relion/RY80/Class3D/job003/run_it025_class006.mrc
Opened run_it025_class006.mrc as #6, grid size 140,140,140, pixel 2.5, shown
at level 0.0253, step 1, values float32
> ~tile
> tile
6 models tiled
> volume #1 level 0.03419
> volume #1 level 0.03875
> volume #1 level 0.01699
> volume #1 level 0.04717
> volume #1 level 0.04121
> volume #6 level 0.07976
> volume #6 level 0.03317
> volume #6 level 0.04301
> volume #6 level 0.0499
> volume #6 level 0.007244
> volume #1 level 0.03524
> volume #2 level 0.02893
> volume #6 level 0.001009
> volume #6 level 0.03645
> volume #6 level 0.04137
> volume #5 level 0.01146
> volume #4 level 0.02598
> volume #3 level 0.03409
> volume #1 level 0.05735
> volume #1 level 0.01734
> volume #1 level 0.04296
> volume #1 level 0.04086
> volume #1 level 0.02647
> volume #1 level 0.04963
> volume #6 level 0.0627
> volume #6 level 0.03317
> volume #6 level 0.02923
> volume rmsLevel 6
> volume #6 level 0.03297
> ~tile
> volume rmsLevel 5
> volume rmsLevel 6
> volume #6 level 0.03593
[Repeated 1 time(s)]
> volume #6 level 0.03625
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job013/run_it025_class001.mrc
Opened run_it025_class001.mrc as #7, grid size 160,160,160, pixel 2.09, shown
at level 0.0238, step 1, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job013/run_it025_class002.mrc
Opened run_it025_class002.mrc as #8, grid size 160,160,160, pixel 2.09, shown
at level 0.0167, step 1, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job013/run_it025_class003.mrc
Opened run_it025_class003.mrc as #9, grid size 160,160,160, pixel 2.09, shown
at level 0.019, step 1, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job013/run_it025_class004.mrc
Opened run_it025_class004.mrc as #10, grid size 160,160,160, pixel 2.09, shown
at level 0.0269, step 1, values float32
> ~tile
> tile
5 models tiled
> close #7
> close #8-10
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job014/run_it009_class001.mrc
Opened run_it009_class001.mrc as #7, grid size 160,160,160, pixel 2.09, shown
at level 0.0321, step 1, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job014/run_it009_class002.mrc
Opened run_it009_class002.mrc as #8, grid size 160,160,160, pixel 2.09, shown
at level 0.0252, step 1, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job014/run_it009_class003.mrc
Opened run_it009_class003.mrc as #9, grid size 160,160,160, pixel 2.09, shown
at level 0.0222, step 1, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job014/run_it009_class004.mrc
Opened run_it009_class004.mrc as #10, grid size 160,160,160, pixel 2.09, shown
at level 0.0256, step 1, values float32
> tile
5 models tiled
> close #7-10
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job022/run_ct13_it025_class001.mrc
Opened run_ct13_it025_class001.mrc as #7, grid size 160,160,160, pixel 2.09,
shown at level 0.0246, step 1, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job022/run_ct13_it025_class002.mrc
Opened run_ct13_it025_class002.mrc as #8, grid size 160,160,160, pixel 2.09,
shown at level 0.0169, step 1, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job022/run_ct13_it025_class003.mrc
Opened run_ct13_it025_class003.mrc as #9, grid size 160,160,160, pixel 2.09,
shown at level 0.0838, step 1, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job022/run_ct13_it025_class004.mrc
Opened run_ct13_it025_class004.mrc as #10, grid size 160,160,160, pixel 2.09,
shown at level 0.0506, step 1, values float32
> tile
5 models tiled
> close #7-10
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job044/run_it025_class001.mrc
Opened run_it025_class001.mrc as #7, grid size 400,400,400, pixel 0.834, shown
at level 8.2e-05, step 2, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job044/run_it025_class002.mrc
Opened run_it025_class002.mrc as #8, grid size 400,400,400, pixel 0.834, shown
at level 1.82e-05, step 2, values float32
> open
> Z:/Arjun/fs01/relion/20201012_AB74_Krios/Class3D/job044/run_it025_class003.mrc
Opened run_it025_class003.mrc as #9, grid size 400,400,400, pixel 0.834, shown
at level 0.000531, step 2, values float32
> close
> open D:/DeepEMhancer_test/P1_J26/J26_009_volume_map_enhanced_tight.mrc
Opened J26_009_volume_map_enhanced_tight.mrc as #1, grid size 400,400,400,
pixel 0.834, shown at level 0.000155, step 2, values float32
> volume #1 level 0.09943
> volume #1 step 1
> open Z:/Arjun/relion/RY80/csparc/CS-cs-ry80/J26/J26_009_volume_map_sharp.mrc
Opened J26_009_volume_map_sharp.mrc as #2, grid size 400,400,400, pixel 0.834,
shown at level 0.0736, step 2, values float32
> ~tile
> tile
2 models tiled
> volume #2 step 1
> volume #2 level 0.282
> ~tile
> tile
2 models tiled
> volume #2 level 0.271
> volume #1 level 0.01256
> volume #1 level 0.0622
> open D:/RNaseZ-tyr_map.pdb
Summary of feedback from opening D:/RNaseZ-tyr_map.pdb
---
warning | Ignored bad PDB record found on line 15194
Chain information for RNaseZ-tyr_map.pdb #3
---
Chain | Description
A B C D | No description available
F | No description available
G | No description available
T | No description available
> ~tile
> hide all atoms
> show all ribbons
> select /F:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
254 atoms, 256 bonds, 30 residues, 1 model selected
> select up
540 atoms, 547 bonds, 65 residues, 1 model selected
> select up
614 atoms, 622 bonds, 73 residues, 1 model selected
> select up
2287 atoms, 2335 bonds, 276 residues, 1 model selected
> select up
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> select up
15181 atoms, 15584 bonds, 1885 residues, 5 models selected
> select down
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.59517,-0.80299,0.031449,201.01,0.78745,0.57495,-0.22218,21.701,0.16033,0.157,0.9745,-41.963
> view matrix models
> #3,0.58975,-0.80647,-0.042407,210.72,0.73319,0.55669,-0.39053,51.614,0.33856,0.19922,0.91961,-68.532
> view matrix models
> #3,0.59259,-0.80519,-0.022427,207.84,0.75108,0.5624,-0.34581,43.023,0.29106,0.18808,0.93804,-61.898
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.59259,-0.80519,-0.022427,204.44,0.75108,0.5624,-0.34581,23.263,0.29106,0.18808,0.93804,-12.169
> view matrix models
> #3,0.59259,-0.80519,-0.022427,203.21,0.75108,0.5624,-0.34581,22.947,0.29106,0.18808,0.93804,-21.421
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.09938,-0.92195,0.37435,278.34,0.9552,-0.19379,-0.22368,93.825,0.27877,0.33535,0.8999,-37.662
> view matrix models
> #3,0.053336,-0.93447,0.35202,260.18,0.96105,-0.047693,-0.27222,76.26,0.27117,0.35283,0.89553,-38.698
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.053336,-0.93447,0.35202,247.91,0.96105,-0.047693,-0.27222,66.948,0.27117,0.35283,0.89553,-37.581
> fitmap #2 inMap #1
Fit map J26_009_volume_map_sharp.mrc in map
J26_009_volume_map_enhanced_tight.mrc using 130544 points
correlation = -0.5904, correlation about mean = -0.01262, overlap = -0.3379
steps = 244, shift = 11.7, angle = 16.9 degrees
Position of J26_009_volume_map_sharp.mrc (#2) relative to
J26_009_volume_map_enhanced_tight.mrc (#1) coordinates:
Matrix rotation and translation
-0.97991685 0.12071352 -0.15871739 321.79719105
-0.07633905 -0.96240998 -0.26065184 556.52227449
-0.18421540 -0.24330079 0.95229691 105.77284878
Axis 0.08699377 0.12784062 -0.98797210
Axis point 179.65164549 276.95185209 0.00000000
Rotation angle (degrees) 174.27662034
Shift along axis -5.36012123
> fitmap #3 inMap #1
Fit molecule RNaseZ-tyr_map.pdb (#3) to map
J26_009_volume_map_enhanced_tight.mrc (#1) using 15181 atoms
average map value = 0.09641, steps = 124
shifted from previous position = 3.06
rotated from previous position = 5.94 degrees
atoms outside contour = 10407, contour level = 0.062203
Position of RNaseZ-tyr_map.pdb (#3) relative to
J26_009_volume_map_enhanced_tight.mrc (#1) coordinates:
Matrix rotation and translation
-0.26628162 0.94962836 -0.16522737 86.23796286
-0.95902906 -0.24381307 0.14428604 329.41796736
0.09673352 0.19687857 0.97564412 4.78525961
Axis 0.02728864 -0.13592343 -0.99034345
Axis point 167.19450273 130.77789021 0.00000000
Rotation angle (degrees) 105.49922137
Shift along axis -47.16135296
> fitmap #3 inMap #1
Fit molecule RNaseZ-tyr_map.pdb (#3) to map
J26_009_volume_map_enhanced_tight.mrc (#1) using 15181 atoms
average map value = 0.09638, steps = 64
shifted from previous position = 0.0285
rotated from previous position = 0.0332 degrees
atoms outside contour = 10403, contour level = 0.062203
Position of RNaseZ-tyr_map.pdb (#3) relative to
J26_009_volume_map_enhanced_tight.mrc (#1) coordinates:
Matrix rotation and translation
-0.26599866 0.94978351 -0.16479077 86.10917832
-0.95911416 -0.24361899 0.14404796 329.42948541
0.09666822 0.19636972 0.97575314 4.88243011
Axis 0.02714586 -0.13565157 -0.99038465
Axis point 167.17315331 130.82024862 0.00000000
Rotation angle (degrees) 105.48179933
Shift along axis -47.18560357
> select clear
> select /G:626
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
54 atoms, 53 bonds, 7 residues, 1 model selected
> select up
1151 atoms, 1178 bonds, 148 residues, 1 model selected
> select up
1184 atoms, 1210 bonds, 152 residues, 1 model selected
> select up
1335 atoms, 1366 bonds, 170 residues, 1 model selected
> select up
1343 atoms, 1373 bonds, 171 residues, 1 model selected
> select up
1387 atoms, 1417 bonds, 177 residues, 1 model selected
> select up
1396 atoms, 1425 bonds, 178 residues, 1 model selected
> select up
2006 atoms, 2049 bonds, 259 residues, 1 model selected
> select up
2023 atoms, 2065 bonds, 261 residues, 1 model selected
> select up
2340 atoms, 2389 bonds, 299 residues, 1 model selected
> select up
2414 atoms, 2465 bonds, 308 residues, 1 model selected
> select up
2854 atoms, 2915 bonds, 363 residues, 1 model selected
> select up
2863 atoms, 2923 bonds, 364 residues, 1 model selected
> select up
2989 atoms, 3053 bonds, 380 residues, 1 model selected
> select up
3251 atoms, 3320 bonds, 413 residues, 1 model selected
> select up
3942 atoms, 4026 bonds, 501 residues, 1 model selected
> select up
3955 atoms, 4037 bonds, 503 residues, 1 model selected
> select down
3942 atoms, 4026 bonds, 501 residues, 1 model selected
> select up
3955 atoms, 4037 bonds, 503 residues, 1 model selected
> select up
4084 atoms, 4168 bonds, 521 residues, 1 model selected
> select up
4086 atoms, 4168 bonds, 523 residues, 1 model selected
> select up
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> select up
15181 atoms, 15584 bonds, 1885 residues, 5 models selected
> select down
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> select down
4086 atoms, 4168 bonds, 523 residues, 1 model selected
> select up
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> select up
15181 atoms, 15584 bonds, 1885 residues, 5 models selected
> select down
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> select down
4086 atoms, 4168 bonds, 523 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> fitmap #3 inMap #1
Fit molecule RNaseZ-tyr_map.pdb (#3) to map
J26_009_volume_map_enhanced_tight.mrc (#1) using 11095 atoms
average map value = 0.1067, steps = 84
shifted from previous position = 2.33
rotated from previous position = 2.18 degrees
atoms outside contour = 7495, contour level = 0.062203
Position of RNaseZ-tyr_map.pdb (#3) relative to
J26_009_volume_map_enhanced_tight.mrc (#1) coordinates:
Matrix rotation and translation
-0.23650167 0.95470083 -0.18059147 83.28586918
-0.96858064 -0.21693480 0.12161761 330.49058103
0.07693186 0.20368017 0.97601018 4.39409600
Axis 0.04225280 -0.13259497 -0.99026929
Axis point 170.21016130 131.23748566 0.00000000
Rotation angle (degrees) 103.81060149
Shift along axis -44.65366463
> hide #!1 models
> show #!1 models
> select add #3
11095 atoms, 11416 bonds, 2 pseudobonds, 1362 residues, 2 models selected
> view matrix models
> #3,0.11473,-0.93973,0.32208,244.06,0.95872,0.019826,-0.28368,61.695,0.26019,0.34133,0.90321,-30.682
> view matrix models
> #3,0.11473,-0.93973,0.32208,242.19,0.95872,0.019826,-0.28368,65.253,0.26019,0.34133,0.90321,-34.826
> select clear
> select /T:13
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1416 atoms, 1585 bonds, 66 residues, 1 model selected
> select up
11095 atoms, 11416 bonds, 1362 residues, 1 model selected
> select up
11095 atoms, 11416 bonds, 1362 residues, 5 models selected
> select down
11095 atoms, 11416 bonds, 1362 residues, 1 model selected
> close #1
> close #2-3
> open D:/DeepEMhancer_test/P1_J26/J26_009_volume_map_enhanced_tight.mrc
Opened J26_009_volume_map_enhanced_tight.mrc as #1, grid size 400,400,400,
pixel 0.834, shown at level 0.000155, step 2, values float32
> volume #1 step 1
> volume #1 level 0.07875
> open 7onu
7onu title:
Structure of human mitochondrial RNase P in complex with mitochondrial pre-
tRNA-Tyr [more info...]
Chain information for 7onu #2
---
Chain | Description | UniProt
A B C D | 3-hydroxyacyl-CoA dehydrogenase type-2 | HCD2_HUMAN
E | Mitochondrial ribonuclease P catalytic subunit | MRPP3_HUMAN
F | tRNA methyltransferase 10 homolog C | TM10C_HUMAN
T | Mitochondrial Precursor tRNA-Tyr |
Non-standard residues in 7onu #2
---
MG — magnesium ion
NAD — nicotinamide-adenine-dinucleotide
ZN — zinc ion
> hide all atoms
> show all ribbons
> fitmap #3 inMap #1
No atoms or maps for #3
Must specify one map, got 0
> fitmap #2 inMap #1
Fit molecule 7onu (#2) to map J26_009_volume_map_enhanced_tight.mrc (#1) using
15083 atoms
average map value = 0.07732, steps = 212
shifted from previous position = 14.9
rotated from previous position = 9.45 degrees
atoms outside contour = 11707, contour level = 0.078749
Position of 7onu (#2) relative to J26_009_volume_map_enhanced_tight.mrc (#1)
coordinates:
Matrix rotation and translation
0.99762434 -0.04954102 -0.04786819 19.27490969
0.05613084 0.98740603 0.14791434 -28.54659145
0.03993751 -0.15024983 0.98784107 34.82933148
Axis -0.90821754 -0.26745893 0.32187983
Axis point 0.00000000 212.05557527 208.62610614
Rotation angle (degrees) 9.44774325
Shift along axis 1.34008904
> select add #2
15083 atoms, 15505 bonds, 65 pseudobonds, 1835 residues, 4 models selected
> view matrix models
> #2,0.99762,-0.049541,-0.047868,20.631,0.056131,0.98741,0.14791,-26.853,0.039938,-0.15025,0.98784,43.557
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.84468,0.53245,0.054996,212.4,-0.52307,-0.79922,-0.29606,429.62,-0.11368,-0.27885,0.95358,95.177
> view matrix models
> #2,-0.90567,0.41548,0.084519,238.25,-0.42034,-0.85371,-0.3074,423.4,-0.055566,-0.31393,0.94782,92.287
> view matrix models
> #2,-0.81133,0.56249,0.15922,187.89,-0.58315,-0.75968,-0.28779,431.75,-0.040928,-0.32634,0.94436,92.431
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.81133,0.56249,0.15922,187.59,-0.58315,-0.75968,-0.28779,438.4,-0.040928,-0.32634,0.94436,95.246
> view matrix models
> #2,-0.81133,0.56249,0.15922,180.08,-0.58315,-0.75968,-0.28779,435.72,-0.040928,-0.32634,0.94436,97.173
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.73399,0.66121,0.15515,151.21,-0.67708,-0.69452,-0.24332,434.25,-0.053126,-0.28364,0.95746,90.224
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.73399,0.66121,0.15515,160.06,-0.67708,-0.69452,-0.24332,434.83,-0.053126,-0.28364,0.95746,100.74
> view matrix models
> #2,-0.73399,0.66121,0.15515,159.65,-0.67708,-0.69452,-0.24332,432.97,-0.053126,-0.28364,0.95746,88.402
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.72093,0.67009,0.17674,153.11,-0.68246,-0.64217,-0.34908,439.17,-0.12041,-0.37228,0.92028,119.43
> view matrix models
> #2,-0.72729,0.6842,-0.054089,182.66,-0.62205,-0.69042,-0.3693,440.06,-0.29002,-0.23494,0.92774,123.22
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.72729,0.6842,-0.054089,185.31,-0.62205,-0.69042,-0.3693,439.14,-0.29002,-0.23494,0.92774,126.33
> fitmap #2 inMap #1
Fit molecule 7onu (#2) to map J26_009_volume_map_enhanced_tight.mrc (#1) using
15083 atoms
average map value = 0.156, steps = 304
shifted from previous position = 5.17
rotated from previous position = 18.5 degrees
atoms outside contour = 8832, contour level = 0.078749
Position of 7onu (#2) relative to J26_009_volume_map_enhanced_tight.mrc (#1)
coordinates:
Matrix rotation and translation
-0.89767014 0.44052340 -0.01128934 244.61266784
-0.42379776 -0.87004161 -0.25183932 421.86180188
-0.12076331 -0.22128424 0.96770321 87.40591800
Axis 0.03504979 0.12557780 -0.99146444
Axis point 173.02247538 188.06452744 0.00000000
Rotation angle (degrees) 154.15862890
Shift along axis -25.10976039
> select clear
> select /E:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
142 atoms, 143 bonds, 17 residues, 1 model selected
> select up
3810 atoms, 3897 bonds, 467 residues, 1 model selected
> select up
3812 atoms, 3897 bonds, 469 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> fitmap #2 inMap #1
Fit molecule 7onu (#2) to map J26_009_volume_map_enhanced_tight.mrc (#1) using
11271 atoms
average map value = 0.1866, steps = 52
shifted from previous position = 0.0697
rotated from previous position = 0.0754 degrees
atoms outside contour = 5862, contour level = 0.078749
Position of 7onu (#2) relative to J26_009_volume_map_enhanced_tight.mrc (#1)
coordinates:
Matrix rotation and translation
-0.89776114 0.44034254 -0.01110786 244.62577143
-0.42350732 -0.86982199 -0.25308351 421.99905204
-0.12110530 -0.22250428 0.96738066 87.64924439
Axis 0.03509362 0.12623626 -0.99137926
Axis point 173.03124857 188.18885679 0.00000000
Rotation angle (degrees) 154.17137663
Shift along axis -25.03725646
> select add #2
11271 atoms, 11608 bonds, 58 pseudobonds, 1366 residues, 3 models selected
> fitmap #2 inMap #1
Fit molecule 7onu (#2) to map J26_009_volume_map_enhanced_tight.mrc (#1) using
11271 atoms
average map value = 0.1866, steps = 40
shifted from previous position = 0.0234
rotated from previous position = 0.0599 degrees
atoms outside contour = 5870, contour level = 0.078749
Position of 7onu (#2) relative to J26_009_volume_map_enhanced_tight.mrc (#1)
coordinates:
Matrix rotation and translation
-0.89773299 0.44039344 -0.01136224 244.65006022
-0.42362259 -0.87005029 -0.25210395 421.87468566
-0.12091064 -0.22150873 0.96763345 87.41407587
Axis 0.03510758 0.12570525 -0.99144624
Axis point 173.02743411 188.08301556 0.00000000
Rotation angle (degrees) 154.16791590
Shift along axis -25.04542033
> hide #!1 models
> show #!1 models
> select clear
> select /T:14
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1416 atoms, 1585 bonds, 66 residues, 1 model selected
> select up
11271 atoms, 11608 bonds, 1366 residues, 1 model selected
> select down
1416 atoms, 1585 bonds, 66 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> fitmap #2 inMap #1
Fit molecule 7onu (#2) to map J26_009_volume_map_enhanced_tight.mrc (#1) using
9855 atoms
average map value = 0.2015, steps = 80
shifted from previous position = 0.118
rotated from previous position = 0.556 degrees
atoms outside contour = 4787, contour level = 0.078749
Position of 7onu (#2) relative to J26_009_volume_map_enhanced_tight.mrc (#1)
coordinates:
Matrix rotation and translation
-0.89786543 0.44015242 -0.01017400 244.48828928
-0.42247978 -0.86785745 -0.26140828 422.96484039
-0.12388907 -0.23041115 0.96517470 89.70902767
Axis 0.03560241 0.13060984 -0.99079440
Axis point 173.12991449 189.02822034 0.00000000
Rotation angle (degrees) 154.19411866
Shift along axis -24.93546077
> select clear
> volume #1 level 0.207
> volume #1 level 0.04979
> volume #1 level 0.1036
> volume #1 level 0.1595
> fitmap #2/A-D inMap #1
Fit molecule 7onu (#2) to map J26_009_volume_map_enhanced_tight.mrc (#1) using
7568 atoms
average map value = 0.2295, steps = 60
shifted from previous position = 0.182
rotated from previous position = 0.366 degrees
atoms outside contour = 4232, contour level = 0.15952
Position of 7onu (#2) relative to J26_009_volume_map_enhanced_tight.mrc (#1)
coordinates:
Matrix rotation and translation
-0.89739788 0.44104283 -0.01258043 244.69073392
-0.42204259 -0.86635482 -0.26703813 423.64558372
-0.12867437 -0.23432998 0.96360384 91.23987465
Axis 0.03753206 0.13321586 -0.99037613
Axis point 173.50429350 189.52203947 0.00000000
Rotation angle (degrees) 154.16785258
Shift along axis -24.74173613
> fitmap #2/F inMap #1
Fit molecule 7onu (#2) to map J26_009_volume_map_enhanced_tight.mrc (#1) using
2287 atoms
average map value = 0.2566, steps = 76
shifted from previous position = 4.92
rotated from previous position = 2.58 degrees
atoms outside contour = 1186, contour level = 0.15952
Position of 7onu (#2) relative to J26_009_volume_map_enhanced_tight.mrc (#1)
coordinates:
Matrix rotation and translation
-0.88857205 0.45842892 0.01681179 236.20852800
-0.44263455 -0.84718088 -0.29386937 427.46348401
-0.12047559 -0.26856558 0.95569773 101.62039020
Axis 0.02775106 0.15056523 -0.98821050
Axis point 172.24411152 192.54470115 0.00000000
Rotation angle (degrees) 152.87671529
Shift along axis -29.50616232
> volume #1 level -0.001803
> volume #1 level 0.1678
> open D:/DeepEMhancer_test/P1_J26/denoised_unmasked/J26_009_volume_map.mrc
Opened J26_009_volume_map.mrc as #3, grid size 400,400,400, pixel 0.834, shown
at level 0.0619, step 2, values float32
> close #3
> open D:/DeepEMhancer_test/P1_J26/denoised/J26_009_volume_map.mrc
Opened J26_009_volume_map.mrc as #3, grid size 178,210,272, pixel
0.834,0.834,0.834, shown at level 0.271, step 1, values float32
> volume #3 level 0.2899
> open D:/DeepEMhancer_test/P1_J26/denoised_unmasked/J26_009_volume_map.mrc
Opened J26_009_volume_map.mrc as #4, grid size 400,400,400, pixel 0.834, shown
at level 0.0619, step 2, values float32
> volume #4 level 0.1483
> volume #4 step 1
> volume #4 level 0.1099
> close #4
> open Z:/Arjun/relion/RY80/csparc/CS-cs-ry80/J26/J26_009_volume_map.mrc
Opened J26_009_volume_map.mrc as #4, grid size 400,400,400, pixel 0.834, shown
at level 0.06, step 2, values float32
> open Z:/Arjun/relion/RY80/csparc/CS-cs-ry80/J26/J26_009_volume_map_sharp.mrc
Opened J26_009_volume_map_sharp.mrc as #5, grid size 400,400,400, pixel 0.834,
shown at level 0.0736, step 2, values float32
> volume #4 level 0.08819
> volume #4 step 1
> volume #5 step 1
> volume #5 level 0.1641
> volume #4 level 0.1436
> ~tile
> select /B:234
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
110 atoms, 112 bonds, 14 residues, 1 model selected
> select up
1848 atoms, 1874 bonds, 255 residues, 1 model selected
> select up
1892 atoms, 1922 bonds, 256 residues, 1 model selected
> select up
9855 atoms, 10023 bonds, 1300 residues, 1 model selected
> select up
9855 atoms, 10023 bonds, 1300 residues, 9 models selected
> select down
9855 atoms, 10023 bonds, 1300 residues, 1 model selected
> view matrix models
> #2,1,5.6379e-17,1.3878e-17,19.644,8.6736e-18,1,-1.3364e-50,-50.914,1.0408e-17,8.5528e-50,1,4.6503
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.90291,0.42047,0.089179,250.46,-0.42857,-0.86483,-0.26153,366.88,-0.03284,-0.27436,0.96107,61.206
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.90291,0.42047,0.089179,226.21,-0.42857,-0.86483,-0.26153,422.61,-0.03284,-0.27436,0.96107,83.426
> view matrix models
> #2,-0.90291,0.42047,0.089179,227.22,-0.42857,-0.86483,-0.26153,420.58,-0.03284,-0.27436,0.96107,82.735
> view matrix models
> #2,-0.90291,0.42047,0.089179,227.42,-0.42857,-0.86483,-0.26153,421.94,-0.03284,-0.27436,0.96107,81.754
> volume #4 level 0.1951
> fitmap 32 in #4
Missing or invalid "atomsOrMap" argument: invalid objects specifier
> fitmap #2 inMap #4
Fit molecule 7onu (#2) to map J26_009_volume_map.mrc (#4) using 9855 atoms
average map value = 0.1881, steps = 112
shifted from previous position = 4.86
rotated from previous position = 5.69 degrees
atoms outside contour = 5550, contour level = 0.19509
Position of 7onu (#2) relative to J26_009_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.89768263 0.44057667 -0.00762222 243.91089866
-0.42251270 -0.86553016 -0.26896199 423.87466668
-0.12509564 -0.23822202 0.96312063 91.70744854
Axis 0.03526886 0.13478068 -0.99024758
Axis point 173.06876241 189.82876332 0.00000000
Rotation angle (degrees) 154.16412504
Shift along axis -25.08050479
> volume #4 level 0.1852
> volume #4 level 0.1832
> volume #4 level 0.2129
> volume #4 level 0.1832
> volume #4 level 0.1674
> volume #4 level 0.1258
> volume #4 level 0.1872
> volume #4 level 0.1278
> volume #4 level 0.2228
> select clear
> select /F:328
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Fit in Map"
> select /F:323
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
72 atoms, 71 bonds, 10 residues, 1 model selected
> select up
1747 atoms, 1788 bonds, 211 residues, 1 model selected
> select up
2287 atoms, 2335 bonds, 276 residues, 1 model selected
> fitmap sel inMap #4
Fit molecule 7onu (#2) to map J26_009_volume_map.mrc (#4) using 2287 atoms
average map value = 0.2399, steps = 92
shifted from previous position = 4.45
rotated from previous position = 1.15 degrees
atoms outside contour = 1067, contour level = 0.2228
Position of 7onu (#2) relative to J26_009_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.89187028 0.45228617 0.00215092 239.79058013
-0.43469845 -0.85585592 -0.28026398 425.74328956
-0.12491865 -0.25089412 0.95992055 98.68204284
Axis 0.03275980 0.14173620 -0.98936224
Axis point 172.95361396 191.14222109 0.00000000
Rotation angle (degrees) 153.36784662
Shift along axis -29.43355911
> undo
> select up
2287 atoms, 2335 bonds, 276 residues, 1 model selected
> fitmap sel inMap #4
Fit molecule 7onu (#2) to map J26_009_volume_map.mrc (#4) using 2287 atoms
average map value = 0.2399, steps = 92
shifted from previous position = 4.45
rotated from previous position = 1.15 degrees
atoms outside contour = 1067, contour level = 0.2228
Position of 7onu (#2) relative to J26_009_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.89187028 0.45228617 0.00215092 239.79058013
-0.43469845 -0.85585592 -0.28026398 425.74328956
-0.12491865 -0.25089412 0.95992055 98.68204284
Axis 0.03275980 0.14173620 -0.98936224
Axis point 172.95361396 191.14222109 0.00000000
Rotation angle (degrees) 153.36784662
Shift along axis -29.43355911
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule 7onu (#2) to map J26_009_volume_map.mrc (#4) using 2287 atoms
average map value = 0.2399, steps = 92
shifted from previous position = 4.45
rotated from previous position = 1.15 degrees
atoms outside contour = 1067, contour level = 0.2228
> color sel blue
> color /A-D beige
> color /A-D darkgrey
> select clear
> volume #5 level 0.4469
> volume #5 level 0.2772
> volume #5 level 0.2659
> volume #5 level 0.2376
> volume #5 level 0.2602
> volume #5 level 0.1358
> volume #5 level 0.379
> open 7onu
7onu title:
Structure of human mitochondrial RNase P in complex with mitochondrial pre-
tRNA-Tyr [more info...]
Chain information for 7onu #6
---
Chain | Description | UniProt
A B C D | 3-hydroxyacyl-CoA dehydrogenase type-2 | HCD2_HUMAN
E | Mitochondrial ribonuclease P catalytic subunit | MRPP3_HUMAN
F | tRNA methyltransferase 10 homolog C | TM10C_HUMAN
T | Mitochondrial Precursor tRNA-Tyr |
Non-standard residues in 7onu #6
---
MG — magnesium ion
NAD — nicotinamide-adenine-dinucleotide
ZN — zinc ion
> select #6/D:7@N
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
34 atoms, 33 bonds, 5 residues, 1 model selected
> select up
1848 atoms, 1874 bonds, 255 residues, 1 model selected
> select up
1892 atoms, 1922 bonds, 256 residues, 1 model selected
> select up
15083 atoms, 15505 bonds, 1835 residues, 1 model selected
> select up
24938 atoms, 25528 bonds, 3135 residues, 10 models selected
> select down
15083 atoms, 15505 bonds, 1835 residues, 1 model selected
> hide all atoms
> show all ribbons
> align #6 toAtoms #2
Unequal number of atoms to pair, 15083 and 9855
> select clear
> select #6/E:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
134 atoms, 135 bonds, 16 residues, 1 model selected
> select up
3810 atoms, 3897 bonds, 467 residues, 1 model selected
> select up
3812 atoms, 3897 bonds, 469 residues, 1 model selected
> select up
15083 atoms, 15505 bonds, 1835 residues, 1 model selected
> ui tool show Matchmaker
No reference and/or match structure/chain chosen
> matchmaker #!6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7onu, chain F (#2) with 7onu, chain F (#6), sequence alignment
score = 1788.7
RMSD between 276 pruned atom pairs is 0.000 angstroms; (across all 276 pairs:
0.000)
> select clear
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> volume #5 level 0.4469
> volume #5 level 0.2207
> volume #5 level 0.3338
> show #!6 models
> select #6/C:81
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/D:112
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #6/A:138
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #6/B:21
31 atoms, 27 bonds, 4 residues, 1 model selected
> select up
546 atoms, 546 bonds, 72 residues, 1 model selected
> select up
7392 atoms, 7496 bonds, 1020 residues, 1 model selected
> select up
7568 atoms, 7688 bonds, 1024 residues, 1 model selected
> select up
15083 atoms, 15505 bonds, 1835 residues, 1 model selected
> select down
7568 atoms, 7688 bonds, 1024 residues, 1 model selected
> delete sel
> hide #!2 models
> select #6/F:152
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
265 atoms, 267 bonds, 32 residues, 1 model selected
> select up
540 atoms, 547 bonds, 65 residues, 1 model selected
> select up
2287 atoms, 2335 bonds, 276 residues, 1 model selected
> delete sel
> show #!2 models
> select #6/E:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
142 atoms, 143 bonds, 17 residues, 1 model selected
> select up
3810 atoms, 3897 bonds, 467 residues, 1 model selected
> select up
3812 atoms, 3897 bonds, 469 residues, 1 model selected
> select up
5228 atoms, 5482 bonds, 535 residues, 1 model selected
> select down
3812 atoms, 3897 bonds, 469 residues, 1 model selected
> delete sel
> select clear
> open D:/RNaseZ-tyr_map.pdb
Summary of feedback from opening D:/RNaseZ-tyr_map.pdb
---
warning | Ignored bad PDB record found on line 15194
Chain information for RNaseZ-tyr_map.pdb #7
---
Chain | Description
A B C D | No description available
F | No description available
G | No description available
T | No description available
> hide all atoms
> show all ribbons
> ui tool show Matchmaker
> matchmaker #!7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7onu, chain F (#2) with RNaseZ-tyr_map.pdb, chain F (#7), sequence
alignment score = 1336.1
RMSD between 276 pruned atom pairs is 0.001 angstroms; (across all 276 pairs:
0.001)
> matchmaker #!7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7onu, chain F (#2) with RNaseZ-tyr_map.pdb, chain F (#7), sequence
alignment score = 1336.1
RMSD between 276 pruned atom pairs is 0.001 angstroms; (across all 276 pairs:
0.001)
> matchmaker #!7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7onu, chain F (#2) with RNaseZ-tyr_map.pdb, chain F (#7), sequence
alignment score = 1336.1
RMSD between 276 pruned atom pairs is 0.001 angstroms; (across all 276 pairs:
0.001)
> volume #5 level 0.2885
> select #7/T:5
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1416 atoms, 1585 bonds, 66 residues, 1 model selected
> select up
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> select down
1416 atoms, 1585 bonds, 66 residues, 1 model selected
> select up
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> select up
26452 atoms, 27192 bonds, 3251 residues, 11 models selected
> select down
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> select down
1416 atoms, 1585 bonds, 66 residues, 1 model selected
> select up
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> select down
1416 atoms, 1585 bonds, 66 residues, 1 model selected
> select down
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1416 atoms, 1585 bonds, 66 residues, 1 model selected
> select up
15181 atoms, 15584 bonds, 1885 residues, 1 model selected
> select down
1416 atoms, 1585 bonds, 66 residues, 1 model selected
> delete sel
> select clear
> select #7/B:213
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #7/D:212
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #7/D:52
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add #7/A:80
29 atoms, 25 bonds, 4 residues, 1 model selected
> select add #7/B:44
37 atoms, 32 bonds, 5 residues, 1 model selected
> select up
339 atoms, 338 bonds, 45 residues, 1 model selected
> select up
5544 atoms, 5622 bonds, 765 residues, 1 model selected
> select up
13765 atoms, 13999 bonds, 1819 residues, 1 model selected
> select down
5544 atoms, 5622 bonds, 765 residues, 1 model selected
> delete sel
> select #7/F:213
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
46 atoms, 47 bonds, 5 residues, 1 model selected
> select up
1747 atoms, 1788 bonds, 211 residues, 1 model selected
> select up
1752 atoms, 1792 bonds, 212 residues, 1 model selected
> select up
2287 atoms, 2335 bonds, 276 residues, 1 model selected
> delete sel
> select clear
> select #7/C:137
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
21 atoms, 20 bonds, 3 residues, 1 model selected
> select up
1848 atoms, 1874 bonds, 255 residues, 1 model selected
> select up
5934 atoms, 6042 bonds, 778 residues, 1 model selected
> select down
1848 atoms, 1874 bonds, 255 residues, 1 model selected
> delete sel
> select clear
> show #!4 models
> hide #!5 models
> fitmap #7 inMap #4
Fit molecule RNaseZ-tyr_map.pdb (#7) to map J26_009_volume_map.mrc (#4) using
4086 atoms
average map value = 0.164, steps = 104
shifted from previous position = 9.26
rotated from previous position = 8.1 degrees
atoms outside contour = 3224, contour level = 0.2228
Position of RNaseZ-tyr_map.pdb (#7) relative to J26_009_volume_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.14337675 0.96787681 -0.20653712 67.41744020
-0.98124020 -0.11184788 0.15702778 305.50435206
0.12888281 0.22517666 0.96575602 7.79990621
Axis 0.03443704 -0.16949465 -0.98492926
Axis point 163.64945081 121.63503933 0.00000000
Rotation angle (degrees) 98.32189364
Shift along axis -57.14205181
> fitmap #7 inMap #4
Fit molecule RNaseZ-tyr_map.pdb (#7) to map J26_009_volume_map.mrc (#4) using
4086 atoms
average map value = 0.164, steps = 104
shifted from previous position = 9.26
rotated from previous position = 8.1 degrees
atoms outside contour = 3224, contour level = 0.2228
Position of RNaseZ-tyr_map.pdb (#7) relative to J26_009_volume_map.mrc (#4)
coordinates:
Matrix rotation and translation
-0.14337675 0.96787681 -0.20653712 67.41744020
-0.98124020 -0.11184788 0.15702778 305.50435206
0.12888281 0.22517666 0.96575602 7.79990621
Axis 0.03443704 -0.16949465 -0.98492926
Axis point 163.64945081 121.63503933 0.00000000
Rotation angle (degrees) 98.32189364
Shift along axis -57.14205181
> volume #4 level 0.1753
> volume #4 level 0.1891
> volume #4 level 0.1911
> volume #4 level 0.2149
> hide #!6 models
> show #!6 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!7 models
> show #!7 models
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display
cmd += ' ' + save_mgr.save_args_string_from_widget(fmt, self._current_option)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\manager.py", line 110, in
save_args_string_from_widget
return provider_info.bundle_info.run_provider(self.session,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 111, in
save_args_string_from_widget
return widget.options_string()
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mmcif\gui.py",
line 130, in options_string
if self.compute_sheets.isChecked():
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mmcif\gui.py",
line 130, in options_string
if self.compute_sheets.isChecked():
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display
cmd += ' ' + save_mgr.save_args_string_from_widget(fmt, self._current_option)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\manager.py", line 110, in
save_args_string_from_widget
return provider_info.bundle_info.run_provider(self.session,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 111, in
save_args_string_from_widget
return widget.options_string()
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mmcif\gui.py",
line 130, in options_string
if self.compute_sheets.isChecked():
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mmcif\gui.py",
line 130, in options_string
if self.compute_sheets.isChecked():
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 537.42
OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Supermicro
Model: M12SWA-TF
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 137,301,839,872
MaxProcessMemory: 137,438,953,344
CPU: 32 AMD Ryzen Threadripper PRO 3955WX 16-Cores
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.0.8
Babel: 2.10.3
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-ArtiaX: 0.3
ChimeraX-Atomic: 1.41.4
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5rc202210270150
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.2
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.3
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.1.1
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.0
geomdl: 5.3.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.0.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 4.11.2
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
pandas: 1.5.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
prompt-toolkit: 3.0.31
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.5
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.2.1
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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
stack-data: 0.5.1
starfile: 0.4.11
superqt: 0.3.8
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.12
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.10.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Save mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets' |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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