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Opened 2 years ago
Closed 2 years ago
#9475 closed defect (can't reproduce)
MemoryError opening mmCIF
| 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-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/lilyh/Downloads/cryosparc_P122_J494_class_00_00024_volume.mrc
Opened cryosparc_P122_J494_class_00_00024_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.0705, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J494_class_03_00024_volume.mrc
Opened cryosparc_P122_J494_class_03_00024_volume.mrc as #2, grid size
100,100,100, pixel 2.78, shown at level 0.0742, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J494_class_02_00024_volume.mrc
Opened cryosparc_P122_J494_class_02_00024_volume.mrc as #3, grid size
100,100,100, pixel 2.78, shown at level 0.068, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J494_class_01_00024_volume.mrc
Opened cryosparc_P122_J494_class_01_00024_volume.mrc as #4, grid size
100,100,100, pixel 2.78, shown at level 0.0709, step 1, values float32
> volume level .25
> hide #!3 models
> hide #!4 models
> hide #!2 models
> volume #1 level 0.1791
> volume #2 level 0.1606
> volume #3 level 0.1714
> volume #4 level 0.1737
> volume level .174
> show #!3 models
> show #!2 models
> show #!1 models
> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
#5
---
Chain | Description
B | No description available
C | No description available
> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
#6
---
Chain | Description
B | No description available
C | No description available
> ~tile
> fitmap #5 inMap #1
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#5) to map cryosparc_P122_J494_class_00_00024_volume.mrc (#1) using 4737
atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 4737, contour level = 0.174
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#5) relative to cryosparc_P122_J494_class_00_00024_volume.mrc (#1)
coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
Drag select of 785 residues
> ui mousemode right "translate selected models"
> view matrix models
> #5,1,0,0,-3.4308,0,1,0,106.04,0,0,1,145.18,#6,1,0,0,-3.4308,0,1,0,106.04,0,0,1,145.18
> view matrix models
> #5,1,0,0,121.68,0,1,0,111.29,0,0,1,69.047,#6,1,0,0,121.68,0,1,0,111.29,0,0,1,69.047
> view matrix models
> #5,1,0,0,157.36,0,1,0,145.93,0,0,1,136.97,#6,1,0,0,157.36,0,1,0,145.93,0,0,1,136.97
> select clear
Drag select of 3 residues
> view matrix models #6,1,0,0,152.46,0,1,0,143.32,0,0,1,166.32
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.17813,0.7129,-0.67827,157.25,0.93113,0.1008,0.35048,137.3,0.31823,-0.69398,-0.64585,161.72
Drag select of 6 residues
> view matrix models
> #5,-0.82353,0.0085243,-0.5672,149.78,-0.42753,-0.66651,0.61072,153.15,-0.37284,0.74545,0.55254,131.41
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.82353,0.0085243,-0.5672,145.55,-0.42753,-0.66651,0.61072,132.96,-0.37284,0.74545,0.55254,150.76
Drag select of 11 residues
> view matrix models
> #6,0.17813,0.7129,-0.67827,158.57,0.93113,0.1008,0.35048,135.86,0.31823,-0.69398,-0.64585,153.11
> view matrix models
> #6,0.17813,0.7129,-0.67827,144.19,0.93113,0.1008,0.35048,143.55,0.31823,-0.69398,-0.64585,148.48
> fitmap #5 inMap #1
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#5) to map cryosparc_P122_J494_class_00_00024_volume.mrc (#1) using 4737
atoms
average map value = 0.3487, steps = 80
shifted from previous position = 9.74
rotated from previous position = 10.2 degrees
atoms outside contour = 1670, contour level = 0.174
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#5) relative to cryosparc_P122_J494_class_00_00024_volume.mrc (#1)
coordinates:
Matrix rotation and translation
-0.83340597 0.18019999 -0.52245810 140.48395792
-0.49729999 -0.65692279 0.56669673 134.92258149
-0.24109588 0.73210684 0.63709682 142.50381770
Axis 0.21995492 -0.37414281 -0.90090898
Axis point 96.25593848 19.12892879 0.00000000
Rotation angle (degrees) 157.91330405
Shift along axis -147.96314593
> fitmap #6 inMap #1
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#6) to map cryosparc_P122_J494_class_00_00024_volume.mrc (#1) using 4737
atoms
average map value = 0.3485, steps = 116
shifted from previous position = 9.73
rotated from previous position = 23.7 degrees
atoms outside contour = 1720, contour level = 0.174
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#6) relative to cryosparc_P122_J494_class_00_00024_volume.mrc (#1)
coordinates:
Matrix rotation and translation
0.21769849 0.37151397 -0.90254348 140.07406500
0.94775122 0.14046379 0.28642196 135.99949794
0.23318443 -0.91774032 -0.32152407 143.29435818
Axis -0.68703533 -0.64799008 0.32877243
Axis point 0.00000000 83.04588306 84.90509156
Rotation angle (degrees) 118.79524163
Shift along axis -137.25092364
> select clear
> select #1
2 models selected
> transparency #1.1 30
> select clear
> volume #1 level 0.4136
> volume #1 level 0.3056
> volume #1 level 0.2449
> volume #1 level 0.147
> volume level .147
Drag select of 1 cryosparc_P122_J494_class_00_00024_volume.mrc , 2
cryosparc_P122_J494_class_03_00024_volume.mrc , 3
cryosparc_P122_J494_class_02_00024_volume.mrc , 4
cryosparc_P122_J494_class_01_00024_volume.mrc , 10 residues
> transparency (#5-6 & sel) 50
> select clear
Drag select of 1 cryosparc_P122_J494_class_00_00024_volume.mrc , 2
cryosparc_P122_J494_class_03_00024_volume.mrc , 3
cryosparc_P122_J494_class_02_00024_volume.mrc , 4
cryosparc_P122_J494_class_01_00024_volume.mrc
> transparency #1.1#2.1#3.1#4.1 40
> select clear
> select #4
2 models selected
> select #4
2 models selected
> select #4
2 models selected
> show atoms
> select clear
> volume #4 level 0.4557
> volume #4 level 0.3135
> hide #6 models
> hide #5 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #5 models
> hide #5 atoms
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!4 models
> volume #4 level 0.147
> volume #4 level 0.2511
> volume level .251
> select clear
> select #5/B:18
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #5/B:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
Drag select of 1 cryosparc_P122_J494_class_00_00024_volume.mrc , 6 residues
> show sel atoms
> select clear
> select #1
2 models selected
> select clear
> select #5/B:103
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #5/B:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
[Repeated 1 time(s)]Drag select of 1 residues
> select #5/B:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #5/B:111
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]Drag select of 4
cryosparc_P122_J494_class_01_00024_volume.mrc , 27 atoms, 45 residues, 25
bonds
> show sel atoms
> select clear
> hide #5 models
> show #6 models
> select #6/B:4
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> hide #6 models
> hide #!1 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J495_001_volume_map_sharp.mrc
Opened cryosparc_P122_J495_001_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.09, shown at level 0.13, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J498_001_volume_map_sharp.mrc
Opened cryosparc_P122_J498_001_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 1.09, shown at level 0.136, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J496_001_volume_map_sharp.mrc
Opened cryosparc_P122_J496_001_volume_map_sharp.mrc as #9, grid size
256,256,256, pixel 1.09, shown at level 0.11, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J497_001_volume_map_sharp.mrc
Opened cryosparc_P122_J497_001_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 1.09, shown at level 0.0962, step 1, values float32
> volume level .251
> volume level .1
> volume level .4
> volume level .5
[Repeated 1 time(s)]
> volume level .6
> hide #!8 models
> hide #!9 models
> hide #!10 models
> volume #7 level 0.5832
> volume #7 level 0.5664
> volume #7 level 0.457
> volume #7 level 0.3981
> volume #7 level 0.3561
> volume #7 level 0.3729
> volume #7 level 0.4234
> volume #7 level 0.457
> volume #7 level 0.4822
> volume #7 level 0.5075
> volume #7 level 0.5243
> volume #7 level 0.5579
> volume #7 level 0.5832
> volume #7 level 0.6
> volume #7 level 0.6168
> volume #7 level 0.6
> volume #7 level 0.5243
> volume #7 level 0.5075
> volume #7 level 0.5243
> volume #7 level 0.5411
> volume #7 level 0.5579
> volume #7 level 0.5916
> volume #7 level 0.6
> volume #7 level 0.6084
> hide #!7 models
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J500_class_03_00024_volume.mrc
Opened cryosparc_P122_J500_class_03_00024_volume.mrc as #11, grid size
100,100,100, pixel 2.78, shown at level 0.0703, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J500_class_02_00024_volume.mrc
Opened cryosparc_P122_J500_class_02_00024_volume.mrc as #12, grid size
100,100,100, pixel 2.78, shown at level 0.0736, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J500_class_01_00024_volume.mrc
Opened cryosparc_P122_J500_class_01_00024_volume.mrc as #13, grid size
100,100,100, pixel 2.78, shown at level 0.0749, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J500_class_00_00024_volume.mrc
Opened cryosparc_P122_J500_class_00_00024_volume.mrc as #14, grid size
100,100,100, pixel 2.78, shown at level 0.0755, step 1, values float32
> volume level .6
> volume level .4
> volume level .3
> volume level .2
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J499_class_01_00044_volume_sharp.mrc
Opened cryosparc_P122_J499_class_01_00044_volume_sharp.mrc as #15, grid size
128,128,128, pixel 2.17, shown at level 0.0558, step 1, values float32
> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J499_class_03_00044_volume_sharp.mrc
Opened cryosparc_P122_J499_class_03_00044_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.17, shown at level 0.0579, step 1, values float32
> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J499_class_00_00044_volume_sharp.mrc
Opened cryosparc_P122_J499_class_00_00044_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.17, shown at level 0.0574, step 1, values float32
> volume level .2
> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J499_class_02_00044_volume_sharp.mrc
Opened cryosparc_P122_J499_class_02_00044_volume_sharp.mrc as #18, grid size
128,128,128, pixel 2.17, shown at level 0.0567, step 1, values float32
> volume level .2
> volume #17 level 0.287
> volume #16 level 0.2588
> volume level .259
> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
#19
---
Chain | Description
B | No description available
C | No description available
> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
#20
---
Chain | Description
B | No description available
C | No description available
Drag select of 131 residues
> view matrix models
> #19,1,0,0,-22.441,0,1,0,91.22,0,0,1,164.18,#20,1,0,0,-22.441,0,1,0,91.22,0,0,1,164.18
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.63841,0.61966,-0.45657,-22.631,-0.74284,-0.34069,0.5763,98.422,0.20156,0.70707,0.6778,162.88,#20,-0.63841,0.61966,-0.45657,-22.631,-0.74284,-0.34069,0.5763,98.422,0.20156,0.70707,0.6778,162.88
Drag select of 4 residues
> view matrix models
> #20,-0.68013,0.2234,-0.69823,-23.082,0.72999,0.29395,-0.61701,88.869,0.067405,-0.92935,-0.36301,160.74
Drag select of 27 residues
Drag select of 18 residues
> view matrix models
> #19,-0.67232,0.48958,-0.55524,-21.664,-0.7381,-0.50061,0.45233,99.96,-0.056502,0.71393,0.69793,162.64,#20,-0.6726,0.37799,-0.63618,-21.875,0.73278,0.46005,-0.50139,91.044,0.10315,-0.80341,-0.58642,158.58
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.67232,0.48958,-0.55524,-20.895,-0.7381,-0.50061,0.45233,97.627,-0.056502,0.71393,0.69793,144.13,#20,-0.6726,0.37799,-0.63618,-21.105,0.73278,0.46005,-0.50139,88.711,0.10315,-0.80341,-0.58642,140.06
> view matrix models
> #19,-0.67232,0.48958,-0.55524,108.28,-0.7381,-0.50061,0.45233,182.26,-0.056502,0.71393,0.69793,175.79,#20,-0.6726,0.37799,-0.63618,108.07,0.73278,0.46005,-0.50139,173.34,0.10315,-0.80341,-0.58642,171.73
> view matrix models
> #19,-0.67232,0.48958,-0.55524,152.28,-0.7381,-0.50061,0.45233,150.32,-0.056502,0.71393,0.69793,140.07,#20,-0.6726,0.37799,-0.63618,152.07,0.73278,0.46005,-0.50139,141.41,0.10315,-0.80341,-0.58642,136.01
Drag select of 6 residues
> view matrix models
> #19,-0.67232,0.48958,-0.55524,152.53,-0.7381,-0.50061,0.45233,149.49,-0.056502,0.71393,0.69793,146.41
> fitmap #19 to #18
Expected a keyword
> hide #!18 models
> show #!18 models
> fitmap #19 inMap #18
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#19) to map cryosparc_P122_J499_class_02_00044_volume_sharp.mrc (#18) using
4737 atoms
average map value = 0.3506, steps = 108
shifted from previous position = 20.3
rotated from previous position = 20.1 degrees
atoms outside contour = 2031, contour level = 0.259
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#19) relative to cryosparc_P122_J499_class_02_00044_volume_sharp.mrc (#18)
coordinates:
Matrix rotation and translation
-0.82690186 0.18689325 -0.53038122 140.52509992
-0.50704684 -0.65565095 0.55948670 134.80377205
-0.24318067 0.73156870 0.63692262 142.68153315
Axis 0.22334206 -0.37275229 -0.90065202
Axis point 96.83736324 18.58502570 0.00000000
Rotation angle (degrees) 157.34116237
Shift along axis -147.36966089
> fitmap #20 inMap #18
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#20) to map cryosparc_P122_J499_class_02_00044_volume_sharp.mrc (#18) using
4737 atoms
average map value = 0.2578, steps = 104
shifted from previous position = 14.1
rotated from previous position = 17.5 degrees
atoms outside contour = 2706, contour level = 0.259
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#20) relative to cryosparc_P122_J499_class_02_00044_volume_sharp.mrc (#18)
coordinates:
Matrix rotation and translation
-0.83999778 0.16259715 -0.51765427 140.23208438
0.52531883 0.48250233 -0.70087924 135.49174411
0.13580843 -0.86067050 -0.49071622 141.85973467
Axis -0.20907606 -0.85501175 0.47459678
Axis point 32.78375418 0.00000000 122.93062684
Rotation angle (degrees) 157.53390383
Shift along axis -77.84003183
> select #20/C:1504
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #20,-0.059567,0.40774,-0.91115,135.37,0.96383,0.26105,0.053808,133.58,0.25979,-0.87499,-0.40854,141.21
> select clear
Drag select of 1 residues
> view matrix models
> #19,-0.63632,0.42607,-0.64309,139.83,-0.76087,-0.48408,0.43214,132.91,-0.12718,0.76429,0.63221,142.91
> fitmap #20 inMap #18
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#20) to map cryosparc_P122_J499_class_02_00044_volume_sharp.mrc (#18) using
4737 atoms
average map value = 0.3539, steps = 92
shifted from previous position = 5.41
rotated from previous position = 16.6 degrees
atoms outside contour = 2041, contour level = 0.259
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#20) relative to cryosparc_P122_J499_class_02_00044_volume_sharp.mrc (#18)
coordinates:
Matrix rotation and translation
0.22672785 0.37371377 -0.89940679 140.00859826
0.94434149 0.14164527 0.29691046 135.85506804
0.23835625 -0.91666498 -0.32079849 143.27542322
Axis -0.69005677 -0.64694872 0.32446728
Axis point 0.00000000 83.46326811 84.45615234
Rotation angle (degrees) 118.43833652
Shift along axis -138.01695672
> fitmap #19 inMap #18
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#19) to map cryosparc_P122_J499_class_02_00044_volume_sharp.mrc (#18) using
4737 atoms
average map value = 0.3506, steps = 96
shifted from previous position = 1.38
rotated from previous position = 19.6 degrees
atoms outside contour = 2029, contour level = 0.259
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#19) relative to cryosparc_P122_J499_class_02_00044_volume_sharp.mrc (#18)
coordinates:
Matrix rotation and translation
-0.82739090 0.18640764 -0.52978911 140.52756961
-0.50631534 -0.65578548 0.55999126 134.79646379
-0.24304136 0.73157201 0.63697198 142.68187659
Axis 0.22309016 -0.37283087 -0.90068192
Axis point 96.79655335 18.61671991 0.00000000
Rotation angle (degrees) 157.38390007
Shift along axis -147.41695142
> hide #!16 models
> hide #!18 models
> hide #!17 models
> hide #!12 models
> hide #!14 models
> select #19/C: 1458, 1338, 1462, 1448, 1449
43 atoms, 39 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel cyan
> select #19/B: 60, 132
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel magenta
> select #20/B:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #19/C: 1458, 1338, 1462, 1448, 1449, 1408, 1407
66 atoms, 63 bonds, 7 residues, 1 model selected
> show sel atoms
> color sel light sea green
> color sel cyan
> select #20/B:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/B:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J382_003_volume_map_sharp.mrc
Opened cryosparc_P122_J382_003_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.09, shown at level 0.0922, step 1, values float32
> volume #1 level 0.5735
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map_sharp.mrc
Opened cryosparc_P122_J482_003_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.09, shown at level 0.0359, step 1, values float32
> volume #1 level 0.1838
> volume #1 level 0.2113
> volume #1 level 0.1941
> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
#2
---
Chain | Description
B | No description available
C | No description available
> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
#3
---
Chain | Description
B | No description available
C | No description available
> ~tile
Drag select of 30 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.81841,0.014512,-0.57446,-7.61,-0.47688,-0.57493,0.66486,6.8504,-0.32063,0.81807,0.47745,-5.9114
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.81841,0.014512,-0.57446,-20.959,-0.47688,-0.57493,0.66486,116.76,-0.32063,0.81807,0.47745,123.87
Drag select of 58 residues
> view matrix models #3,1,0,0,-34.165,0,1,0,-4.5316,0,0,1,274.42
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.97464,-0.13741,0.17663,-33.941,0.058092,-0.60686,-0.79269,-7.484,0.21611,0.78284,-0.58348,272.01
> view matrix models
> #3,0.99705,-0.076327,0.0083769,-34.216,0.067093,0.81294,-0.57847,-5.8247,0.037343,0.57733,0.81566,274.56
> view matrix models
> #3,0.99998,0.0060532,0.0013779,-34.157,-0.0061135,0.99878,0.049021,-4.4369,-0.0010794,-0.049029,0.9988,274.37
> view matrix models
> #3,0.98974,-0.13137,0.056128,-34.171,0.099292,0.3501,-0.93143,-6.9186,0.10272,0.92745,0.35955,273.98
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98974,-0.13137,0.056128,-28.783,0.099292,0.3501,-0.93143,40.695,0.10272,0.92745,0.35955,240.18
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99524,-0.095568,0.019054,-28.824,0.080682,0.69844,-0.71111,41.43,0.054651,0.70926,0.70283,240.66
> view matrix models
> #3,0.98067,-0.15016,0.12544,-28.664,0.089711,-0.22465,-0.9703,40.117,0.17388,0.9628,-0.20684,239.1
> view matrix models
> #3,-0.058069,0.23271,-0.97081,-23.433,0.98347,0.18043,-0.015577,36.382,0.17154,-0.95566,-0.23934,237.11
Drag select of 163 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.058069,0.23271,-0.97081,17.819,0.98347,0.18043,-0.015577,134.03,0.17154,-0.95566,-0.23934,157.89
Drag select of 1 cryosparc_P122_J482_003_volume_map_sharp.mrc
> view matrix models #1,1,0,0,-126.15,0,1,0,3.8379,0,0,1,60.81
> view matrix models #1,1,0,0,-173.22,0,1,0,-10.418,0,0,1,22.622
> view matrix models #1,1,0,0,-135.67,0,1,0,-8.5881,0,0,1,32.538
Drag select of 6 residues
> view matrix models
> #3,-0.058069,0.23271,-0.97081,-1.9339,0.98347,0.18043,-0.015577,125.31,0.17154,-0.95566,-0.23934,152.94
> view matrix models
> #3,-0.058069,0.23271,-0.97081,-0.73894,0.98347,0.18043,-0.015577,124.25,0.17154,-0.95566,-0.23934,178.74
Drag select of 39 residues
> view matrix models
> #2,-0.81841,0.014512,-0.57446,-19.448,-0.47688,-0.57493,0.66486,119.74,-0.32063,0.81807,0.47745,180.35
> view matrix models
> #2,-0.81841,0.014512,-0.57446,-1.1402,-0.47688,-0.57493,0.66486,123.78,-0.32063,0.81807,0.47745,175.46
> fitmap #2 #3 inMap #1
Fit molecules
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#2),
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#3) to map cryosparc_P122_J482_003_volume_map_sharp.mrc (#1) using 9474 atoms
average map value = 0.1355, steps = 136
shifted from previous position = 6.92
rotated from previous position = 10.9 degrees
atoms outside contour = 6405, contour level = 0.19413
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#2) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.84114037 0.15266103 -0.51882317 140.43652036
-0.47662323 -0.66258792 0.57776080 134.74623851
-0.25556441 0.73326111 0.63009125 142.20325939
Axis 0.22226031 -0.37628204 -0.89945104
Axis point 95.74827856 20.23873163 0.00000000
Rotation angle (degrees) 159.52395457
Shift along axis -147.39399498
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#3) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.06328922 0.08401013 -0.99445305 141.30122841
0.95368871 0.29869793 -0.03546126 134.85284941
0.29406196 -0.95064291 -0.09902387 145.43088432
Axis -0.50732614 -0.71428152 0.48210175
Axis point -62.18178244 0.00000000 158.63307109
Rotation angle (degrees) 115.58232713
Shift along axis -97.89622157
> fitmap #3 inMap #1
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#3) to map cryosparc_P122_J482_003_volume_map_sharp.mrc (#1) using 4737 atoms
average map value = 0.1868, steps = 176
shifted from previous position = 2.68
rotated from previous position = 24.5 degrees
atoms outside contour = 2738, contour level = 0.19413
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#3) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.22137531 0.37386489 -0.90067648 140.03979458
0.94570995 0.14306661 0.29183000 135.77520351
0.23796172 -0.91638261 -0.32189631 143.25068226
Axis -0.68807659 -0.64845399 0.32566553
Axis point 0.00000000 83.05871411 84.72498208
Rotation angle (degrees) 118.60230471
Shift along axis -137.75026642
> color zone #2 near #1 distance 2.5
color zone: No surfaces specified.
> color zone #1 near #2 distance 2.5
[Repeated 1 time(s)]
> hide #3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> undo color zone
Expected fewer arguments
> undo color zone #1
Expected fewer arguments
> ~colordef zone
Unknown color 'zone'
> color single #1
> volume copy #1
Opened cryosparc_P122_J482_003_volume_map_sharp.mrc copy as #4, grid size
256,256,256, pixel 1.09, shown at step 1, values float32
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!1 models
> color #4 #aa00ffff models
> color #4 red models
> color #4 #0055ffff models
> color #4 #aa00ffff models
> color #4 #aa55ffff models
> color #4 #aaaaffff models
> color #4 #aa55ffff models
> color #4 #8844ccff models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> close #4
> ui tool show "Color Zone"
> color zone #1 near #2 distance 1.28
> color zone #1 near #2 distance 1.61
> color single #1
> select #1
2 models selected
> select clear
> select #1
2 models selected
> select clear
Need to color zone map before it can be split
> select #1
2 models selected
Need to color zone map before it can be split
> select clear
> color zone #1 near #2 distance 3.2
> color zone #1 near #2 distance 8
[Repeated 4 time(s)]
> color single #1
> select #1
2 models selected
> select clear
> hide #!1 models
> hide #2 models
> show #!1 models
> volume #1 level 0.2028
> ui mousemode right "map eraser"
> select #4
1 model selected
> volume erase #1 center -14.206,148.15,164.49 radius 12.349
Opened cryosparc_P122_J482_003_volume_map_sharp.mrc copy as #5, grid size
256,256,256, pixel 1.09, shown at step 1, values float32
> volume erase #5 center -11.214,150.15,155.17 radius 12.221
> volume erase #5 center -17.564,140.01,169.8 radius 12.221
> volume erase #5 center -17.249,149.71,145.42 radius 12.221
> volume erase #5 center -14.752,146.28,156.52 radius 12.221
> volume erase #5 center -14.813,144.96,164.6 radius 12.221
[Repeated 1 time(s)]Drag select of 5
cryosparc_P122_J482_003_volume_map_sharp.mrc copy
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> color #1 #55aa00ff models
> color #1 #55aa7fff models
> color #1 #4c9971ff models
> color #1 #aa55ffff models
> color #1 #8543c8ff models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> color #1 black models
> color #1 #8b8b8bff models
> hide #!5 models
> show #!5 models
> hide #!1 models
> color #5 #ff557fff models
> hide #!5 models
> show #!1 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> color #5 black models
> color #5 #949494ff models
> show #!1 models
> color #1 #aa55ffff models
> hide #!1 models
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!5 models
> ui tool show "Map Eraser"
> volume erase #1 center -6.142,135.78,214.78 radius 35.681
Opened cryosparc_P122_J482_003_volume_map_sharp.mrc copy as #6, grid size
256,256,256, pixel 1.09, shown at step 1, values float32
> volume erase #6 center 4.3298,98.191,146.39 radius 35.553
> volume erase #6 center 13.696,141.96,111 radius 35.553
> volume erase #6 center 9.4219,102.73,159.88 radius 35.553
> volume erase #6 center 9.7275,103.77,171.61 radius 35.553
> volume erase #6 center 27.901,112.19,143.91 radius 35.553
> volume erase #6 center 22.926,116.74,140.28 radius 35.553
> volume erase #6 center 24.719,115.85,164.24 radius 35.553
> volume erase #6 center 23.13,118.24,182.16 radius 35.553
> volume erase #6 center 24.815,117.94,173.15 radius 35.553
[Repeated 2 time(s)]
> volume erase #6 center 24.485,118.15,172.48 radius 35.553
[Repeated 1 time(s)]
> volume erase #6 center 4.3389,101.93,147.38 radius 35.553
> volume erase #6 center 33.327,163.58,176.87 radius 35.553
[Repeated 1 time(s)]
> volume erase #6 center 32.657,166.19,172.4 radius 35.553
[Repeated 1 time(s)]
> volume erase #6 center 20.777,175.79,175.32 radius 35.553
[Repeated 1 time(s)]
> volume erase #6 center 12.779,174.61,176.9 radius 35.553
[Repeated 2 time(s)]
> show #!1 models
> color #1 black models
> color #1 #aaaaaaff models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #4 models
> show #4 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!5 models
> volume #6 level 0.2003
> volume #6 level 0.2052
> set bgColor white
> set bgColor #ffffff00
> save C:\Users\lilyh\Desktop\image98.png supersample 3
> show #3 models
> hide #3 models
> show #3 models
> fitmap #3 inMap #6
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#3) to map cryosparc_P122_J482_003_volume_map_sharp.mrc copy (#6) using 4737
atoms
average map value = 0.004253, steps = 144
shifted from previous position = 2.89
rotated from previous position = 3.22 degrees
atoms outside contour = 4695, contour level = 0.20523
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#3) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc copy (#6)
coordinates:
Matrix rotation and translation
0.16670464 0.38518017 -0.90765957 140.25282221
0.95560267 0.16372116 0.24498782 138.37399571
0.24296752 -0.90820246 -0.34078611 142.20231994
Axis -0.66811798 -0.66663296 0.33048278
Axis point 0.00000000 79.93836255 86.16157097
Rotation angle (degrees) 120.34331093
Shift along axis -138.95468057
> show #2 models
> hide #3 models
> fitmap 23 in #6
Missing or invalid "atomsOrMap" argument: invalid objects specifier
> fitmap #2 inMap #6
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#2) to map cryosparc_P122_J482_003_volume_map_sharp.mrc copy (#6) using 4737
atoms
average map value = 0.005185, steps = 56
shifted from previous position = 1.64
rotated from previous position = 2.92 degrees
atoms outside contour = 4695, contour level = 0.20523
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#2) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc copy (#6)
coordinates:
Matrix rotation and translation
-0.83562575 0.20150595 -0.51100387 140.47427610
-0.49969822 -0.66517447 0.55483747 135.94309947
-0.22810367 0.71898420 0.65652908 143.35637974
Axis 0.21214885 -0.36562989 -0.90626026
Axis point 96.02922277 19.92476845 0.00000000
Rotation angle (degrees) 157.24031195
Shift along axis -149.82159284
> hide #2 models
> save C:\Users\lilyh\Desktop\image99.png supersample 3
> show #2 models
> show #3 models
> select #5
2 models selected
> transparency #5.1 50
> select clear
> hide #!6 models
> show #!1 models
> hide #!5 models
> color #1 #949494ff models
> fitmap #2 inMap #1
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#2) to map cryosparc_P122_J482_003_volume_map_sharp.mrc (#1) using 4737 atoms
average map value = 0.1856, steps = 68
shifted from previous position = 1.49
rotated from previous position = 1.56 degrees
atoms outside contour = 2809, contour level = 0.20279
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#2) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.83218488 0.18002363 -0.52446146 140.51845915
-0.49774911 -0.65934975 0.56347469 134.65604500
-0.24436477 0.72996534 0.63830750 142.53443690
Axis 0.22138830 -0.37245411 -0.90125754
Axis point 96.39705566 19.12551338 0.00000000
Rotation angle (degrees) 157.91293892
Shift along axis -147.50429074
> fitmap #3 inMap #1
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#3) to map cryosparc_P122_J482_003_volume_map_sharp.mrc (#1) using 4737 atoms
average map value = 0.1868, steps = 88
shifted from previous position = 2.89
rotated from previous position = 3.22 degrees
atoms outside contour = 2784, contour level = 0.20279
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
(#3) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.22134410 0.37367246 -0.90076400 140.05364861
0.94574976 0.14301455 0.29172650 135.77625379
0.23783251 -0.91646922 -0.32174519 143.25909034
Axis -0.68805247 -0.64841659 0.32579092
Axis point 0.00000000 83.06903866 84.73682788
Rotation angle (degrees) 118.60009092
Shift along axis -137.73132259
> select #1
2 models selected
> transparency #1.1 50
> select clear
> color #3 #00aaffff
> color #2 #ffff7fff
> lighting flat
> lighting full
> lighting simple
> lighting full
> color #2 yellow
> show #!6 models
> hide #!6 models
> show #!6 models
> save C:\Users\lilyh\Desktop\image100.png supersample 3
> hide #3 models
> hide #2 models
> open 2f6h
Traceback (most recent call last):
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open
models, status = collated_open(session, database_name, ident,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data
return provider_open(self.session, [path], _return_status=True,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
> open 2f6h
Traceback (most recent call last):
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open
models, status = collated_open(session, database_name, ident,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data
return provider_open(self.session, [path], _return_status=True,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
> open 2f6h
Traceback (most recent call last):
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open
models, status = collated_open(session, database_name, ident,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data
return provider_open(self.session, [path], _return_status=True,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
> undo
> hide #2 models
> open 2f6h
Traceback (most recent call last):
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open
models, status = collated_open(session, database_name, ident,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data
return provider_open(self.session, [path], _return_status=True,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
OpenGL version: 3.3.14756 Core Profile Forward-Compatible Context 20.40.68.03 27.20.14068.3000
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: Microsoft Corporation
Model: Surface Laptop 4
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 8,002,093,056
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 Microsoft Surface (R) Edition
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
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 → MemoryError opening mmCIF |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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