Context Navigation

← Previous Ticket
Next Ticket →

#9541 closed defect (duplicate)

MemoryError open mmCIF

Reported by:	chimerax-bug-report@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Input/Output	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description (last modified by pett)

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/Class3D_Job147/run_it025_class001.mrc

Opened run_it025_class001.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 5.66e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job147/run_it025_class004.mrc

Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 1.49e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job147/run_it025_class003.mrc

Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 1.86e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job147/run_it025_class002.mrc

Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 9.88e-07, step 1, values float32  

> color red

> open C:/Users/lilyh/Downloads/Class3D_Job148/run_it025_class004.mrc

Opened run_it025_class004.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 7.05e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job148/run_it025_class003.mrc

Opened run_it025_class003.mrc as #6, grid size 256,256,256, pixel 1.09, shown
at level 6.04e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job148/run_it025_class002.mrc

Opened run_it025_class002.mrc as #7, grid size 256,256,256, pixel 1.09, shown
at level 1.46e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job148/run_it025_class001.mrc

Opened run_it025_class001.mrc as #8, grid size 256,256,256, pixel 1.09, shown
at level 1.79e-06, step 1, values float32  

> select add #5

2 models selected  

> select add #6

4 models selected  

> select add #7

6 models selected  

> select add #8

8 models selected  

> color #5.1#6.1#7.1#8.1 orange

> tile

8 models tiled  

> volume level 0.03

> volume level 0.3

> volume level 0.03

> volume #6 level 0.0006345

> volume level 0.000635

> select clear

> set bgColor white

> lighting flat

> lighting full

[Repeated 1 time(s)]

> lighting soft

> volume showOutlineBox true

> volume showOutlineBox false

> volume #2 level 0.002014

> volume level 0.00201

> volume #3 level 0.003119

> volume level 0.00312

> open C:/Users/lilyh/Downloads/Class3D_Job148/run_it025_class003.mrc

Opened run_it025_class003.mrc as #9, grid size 256,256,256, pixel 1.09, shown
at level 6.04e-07, step 1, values float32  

> volume #9 level 0.00312

> select #9

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #9,1,0,0,179.4,0,1,0,-149.38,0,0,1,0

> select clear

> volume #9 level 0.0006087

> ui mousemode right "rotate selected models"

> select #9

2 models selected  

> view matrix models
> #9,0.66964,0.16837,-0.72334,329.01,-0.57203,-0.50424,-0.64693,242.97,-0.47367,0.84699,-0.24135,169.56

> view matrix models
> #9,0.4012,0.45178,-0.79682,344.13,0.51845,0.60515,0.60415,-276.98,0.75514,-0.6555,0.0085597,141.95

> volume #9 level 0.0008467

> volume #9 level 0.0009658

> volume #9 level 0.00312

> select clear

> close #9

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> show #!4 models

> volume #1 level 0.00361

> volume #2 level 0.00381

> volume #3 level 0.003397

> volume level 0.0034

> select clear

Drag select of 1 run_it025_class001.mrc , 2 run_it025_class004.mrc , 3
run_it025_class003.mrc  

> color #1.1#2.1#3.1 orange red

> select clear

Drag select of 4 run_it025_class002.mrc  

> color #4.1 orange red

> select clear

> save C:\Users\lilyh\Desktop\image106.png supersample 3

> open "C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map (1).mrc"

Opened cryosparc_P122_J482_003_volume_map (1).mrc as #9, grid size
256,256,256, pixel 1.09, shown at level 0.00334, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J505_mask.mrc

Opened cryosparc_P122_J505_mask.mrc as #10, grid size 256,256,256, pixel 1.09,
shown at level 5e-05, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J520_mask.mrc

Opened cryosparc_P122_J520_mask.mrc as #11, grid size 256,256,256, pixel 1.09,
shown at level 5e-05, step 1, values float32  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> volume #9 level 0.0579

> ~tile

> volume #9 level 0.08961

> select #10

2 models selected  

> select #9

2 models selected  

> color #9.1 dark gray

> select #10

2 models selected  

> color #10.1 red

> transparency #10.1 80

> select clear

> hide #!11 models

> hide #!10 models

> show #!10 models

> save C:\Users\lilyh\Desktop\image107.png supersample 3

> hide #!10 models

> show #!11 models

> select #11

2 models selected  

> transparency #11.1 50

> color #11.1 orange

> show #!10 models

> select #10

2 models selected  

> surface style #10 mesh

> select clear

> select #11

2 models selected  

> transparency #11.1 70

> select clear

> save C:\Users\lilyh\Desktop\image108.png supersample 3

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!11 models

> show #!11 models

> hide #!10 models

> hide #!11 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #!9 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class004.mrc

Opened run_it025_class004.mrc as #12, grid size 256,256,256, pixel 1.09, shown
at level 1.52e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class003.mrc

Opened run_it025_class003.mrc as #13, grid size 256,256,256, pixel 1.09, shown
at level 5.8e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class002.mrc

Opened run_it025_class002.mrc as #14, grid size 256,256,256, pixel 1.09, shown
at level 1.22e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class001.mrc

Opened run_it025_class001.mrc as #15, grid size 256,256,256, pixel 1.09, shown
at level 6.64e-08, step 1, values float32  

> tile

4 models tiled  

> volume level 0.0034

> lighting flat

> lighting full

> lighting shadows false

> lighting soft

> color #12-15 yellow

> color #12-15 #ffff00ff

> color #12-15 #ffff7fff

> color #12-15 #eaea75ff

> color #12-15 #f0f078ff

> color #12-15 #f3f379ff

> color #12-15 #ffff7fff

> color #12-15 #f9ff7eff

> color #12-15 #fdff7cff

> color #12-15 #f2ff7cff

> color #12-15 #eaff80ff

> color #12-15 #e1ff80ff

> color #12-15 #ddff81ff

> color #12-15 #d7ff81ff

> color #12-15 #ddff81ff

> color #12-15 #e2ff81ff

> color #12-15 #e4ff81ff

> color #12-15 #e8ff81ff

> color #12-15 #eeff81ff

> color #12-15 #f5ff81ff

> color #12-15 #f9ff81ff

> color #12-15 #fdff81ff

> color #12-15 #ffff81ff

> color #12-15 #fffb81ff

> color #12-15 #fff581ff

> color #12-15 #fff585ff

> color #12-15 #fff587ff

> color #12-15 #fff58cff

> color #12-15 #fff68eff

> color #12-15 #fff690ff

> color #12-15 #fff692ff

> color #12-15 #fff695ff

> color #12-15 #fff799ff

> color #12-15 #fff79bff

> color #12-15 #fff79cff

> color #12-15 #fff7a1ff

> color #12-15 #fff7a4ff

> color #12-15 #fff8a5ff

> color #12-15 #fff7a4ff

> color #12-15 #fff7a1ff

> color #12-15 #fff79eff

> color #12-15 #fff79dff

> select clear

> hide #!12 models

> show #!12 models

> hide #!13 models

> show #!13 models

> hide #!14 models

> show #!14 models

> hide #!15 models

> show #!15 models

> hide #!12 models

> show #!12 models

> save C:\Users\lilyh\Desktop\image109.png supersample 3

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> open C:/Users/lilyh/Downloads/Class3D_Job153/run_it025_class004.mrc

Opened run_it025_class004.mrc as #16, grid size 256,256,256, pixel 1.09, shown
at level 5.91e-07, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job153/run_it025_class003.mrc

Opened run_it025_class003.mrc as #17, grid size 256,256,256, pixel 1.09, shown
at level 1.36e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job153/run_it025_class002.mrc

Opened run_it025_class002.mrc as #18, grid size 256,256,256, pixel 1.09, shown
at level 2.03e-06, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job153/run_it025_class001.mrc

Opened run_it025_class001.mrc as #19, grid size 256,256,256, pixel 1.09, shown
at level 1.39e-06, step 1, values float32  

> volume level 0.0034

> tile

4 models tiled  

> lighting shadows true

> lighting soft

> color #16-19 #aaff00ff

> color #16-19 #aaff7fff

> color #16-19 #55ff7fff

> color #16-19 #aaff7fff

> color #16-19 #a5ff7cff

> color #16-19 #9fff7cff

> color #16-19 #98ff7cff

> color #16-19 #8dff7cff

> color #16-19 #89ff7cff

> color #16-19 #85ff7cff

> color #16-19 #83ff7cff

> color #16-19 #83ff7dff

> color #16-19 #7dff7dff

> color #16-19 #7eff7eff

> color #16-19 #80ff7eff

> color #16-19 #8bff7eff

> color #16-19 #a7ff7eff


[deleted a bunch to fit within ticket limits]

> transparency #7.1 50

> select clear

> volume #7 level 0.2812

> fitmap #3 inMap #7

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7) using
4737 atoms  
average map value = 0.2552, steps = 44  
shifted from previous position = 0.0269  
rotated from previous position = 0.429 degrees  
atoms outside contour = 2734, contour level = 0.28116  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7)
coordinates:  
Matrix rotation and translation  
-0.25509729 0.56550088 -0.78430490 140.42174494  
0.94831869 0.30464485 -0.08878766 140.55147930  
0.18872495 -0.76642047 -0.61398912 132.41045159  
Axis -0.54384537 -0.78092113 0.30723673  
Axis point -18.36724619 0.00000000 107.57844873  
Rotation angle (degrees) 141.46435832  
Shift along axis -145.44598047  
  

> select clear

> select #3/B:100

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.91714,-0.176,-0.35761,134.82,-0.098454,-0.76939,0.63115,135.49,-0.38623,0.61406,0.6883,143.89

> fitmap #3 inMap #7

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7) using
4737 atoms  
average map value = 0.2621, steps = 160  
shifted from previous position = 2.36  
rotated from previous position = 12.9 degrees  
atoms outside contour = 2676, contour level = 0.28116  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7)
coordinates:  
Matrix rotation and translation  
-0.61122751 0.36402006 -0.70277334 140.39505130  
0.76369176 0.50438723 -0.40294975 141.17512270  
0.20778810 -0.78299616 -0.58629446 132.33946309  
Axis -0.35699750 -0.85533805 0.37543256  
Axis point 10.76974698 0.00000000 113.51955199  
Rotation angle (degrees) 147.84025622  
Shift along axis -121.18859343  
  

> hide #3 models

> hide #!7 models

> show #!5 models

> hide #!5 models

> show #!6 models

> volume #2 level 0.2966

> close session

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class003.mrc

Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.000799, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class002.mrc

Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.000869, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class001.mrc

Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.000826, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class004.mrc

Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.00106, step 1, values float32  

> volume level 0.2

> volume level 0.02

> volume level 0.01

> tile

4 models tiled  

> volume #1 level 0.003781

> volume level 0.003

> tile

4 models tiled  

> volume #2 level 0.003072

> volume #3 level 0.002963

> volume #3 level 0.00183

> volume #3 level 0.001684

> volume #3 level 0.0009525

> volume #3 level 0.0007696

> volume #3 level 0.0006234

> volume #3 level 0.00066

> volume #3 level 0.001172

> volume #3 level 0.001208

> volume #3 level 0.001647

> volume #3 level 0.001684

> volume #3 level 0.002159

> volume #3 level 0.002196

> volume #3 level 0.002452

> volume #3 level 0.002525

> volume #3 level 0.002707

> volume #3 level 0.002744

> volume #3 level 0.002781

> volume #3 level 0.002854

> volume #3 level 0.003219

> volume #3 level 0.003256

> volume #3 level 0.003329

> volume #3 level 0.005925

> volume level 0.006

> volume #4 level 0.00359

> volume #4 level 0.005905

> volume level 0.006

> volume #2 level 0.002526

> volume level 0.002

> volume #4 level 0.003205

> volume level 0.0032

> hide #!4 models

> ui hideFloating toggle

> tile

3 models tiled  

> ~tile

> volume #1 level 0.005461

> close session

> open C:/Users/lilyh/Downloads/Class3D_Job220/run_it025_class002.mrc

Opened run_it025_class002.mrc as #1, grid size 256,256,256, pixel 1.09, shown
at level 0.000898, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job220/run_it025_class001.mrc

Opened run_it025_class001.mrc as #2, grid size 256,256,256, pixel 1.09, shown
at level 0.000933, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job220/run_it025_class003.mrc

Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.00118, step 1, values float32  

> tile

3 models tiled  

> volume level 0.0032

> volume #1 level 0.005225

> volume level 0.005

> volume #3 level 0.006761

> volume #2 level 0.005889

> volume level 0.00589

> volume #3 level 0.005749

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J586_class_01_00144_volume_sharp.mrc

Opened cryosparc_P122_J586_class_01_00144_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.17, shown at level 0.0602, step 1, values float32  

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J587_class_01_00163_volume_sharp.mrc

Opened cryosparc_P122_J587_class_01_00163_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.17, shown at level 0.056, step 1, values float32  

> volume #5 level 0.2687

> volume #4 level 0.2037

> ui mousemode right "rotate selected models"

> select #4

2 models selected  

> view matrix models
> #4,0.021877,-0.024926,-0.99945,276.72,0.17372,-0.98439,0.028353,257.1,-0.98455,-0.17425,-0.017206,301.51

> select #5

2 models selected  

> view matrix models
> #5,0.20848,0.28289,0.93622,-62.447,0.16421,-0.95379,0.25163,221.01,0.96414,0.10127,-0.2453,27.116

> view matrix models
> #5,0.32816,0.039176,-0.94381,218.11,0.0048989,-0.9992,-0.039771,289.96,-0.94461,0.0084276,-0.32809,313.46

> hide #!3 models

> hide #!2 models

> hide #!1 models

> close session

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J586_class_01_00144_volume_sharp.mrc

Opened cryosparc_P122_J586_class_01_00144_volume_sharp.mrc as #1, grid size
128,128,128, pixel 2.17, shown at level 0.0602, step 1, values float32  

> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J587_class_01_00163_volume_sharp.mrc

Opened cryosparc_P122_J587_class_01_00163_volume_sharp.mrc as #2, grid size
128,128,128, pixel 2.17, shown at level 0.056, step 1, values float32  

> volume level 0.2

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class003.mrc

Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
at level 0.000799, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class002.mrc

Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
at level 0.000869, step 1, values float32  

> open C:/Users/lilyh/Downloads/Class3D_Job219/run_it025_class001.mrc

Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
at level 0.000826, step 1, values float32  

> hide #!3 models

> hide #!2 models

> hide #!1 models

> hide #!4 models

> hide #!5 models

> show #!3 models

> volume #3 level 0.002495

> volume #4 level 0.003945

> volume #3 level 0.005145

> volume #4 level 0.005899

> volume #4 level 0.00561

> volume #5 level 0.005506

> volume #5 level 0.006128

> fitmap #3 inMap #2

Fit map run_it025_class003.mrc in map
cryosparc_P122_J587_class_01_00163_volume_sharp.mrc using 32143 points  
correlation = 0.949, correlation about mean = 0.6576, overlap = 133.9  
steps = 64, shift = 0.9, angle = 2.44 degrees  
  
Position of run_it025_class003.mrc (#3) relative to
cryosparc_P122_J587_class_01_00163_volume_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99913921 -0.03934563 -0.01314413 7.14587444  
0.03946968 0.99917734 0.00931547 -6.53061788  
0.01276680 -0.00982625 0.99987022 0.45256795  
Axis -0.22481375 -0.30431613 0.92566218  
Axis point 163.09879041 182.61971920 0.00000000  
Rotation angle (degrees) 2.43995581  
Shift along axis 0.79980652  
  

> select clear

> fitmap #3 inMap #1

Fit map run_it025_class003.mrc in map
cryosparc_P122_J586_class_01_00144_volume_sharp.mrc using 32143 points  
correlation = 0.956, correlation about mean = 0.6745, overlap = 129.2  
steps = 44, shift = 0.136, angle = 0.4 degrees  
  
Position of run_it025_class003.mrc (#3) relative to
cryosparc_P122_J586_class_01_00144_volume_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99885143 -0.04625382 -0.01250607 8.12141889  
0.04636230 0.99888829 0.00852814 -7.27175418  
0.01209771 -0.00909815 0.99988543 0.53410225  
Axis -0.18090112 -0.25251222 0.95053267  
Axis point 156.28140350 175.12403655 0.00000000  
Rotation angle (degrees) 2.79244185  
Shift along axis 0.87471463  
  

> hide #!1 models

> show #!1 models

> hide #!3 models

> volume #1 level 0.3754

> show #!2 models

> hide #!2 models

> show #!3 models

> select #1

2 models selected  

> surface style #1 mesh

> select clear

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

Drag select of 1 cryosparc_P122_J586_class_01_00144_volume_sharp.mrc  

> transparency #1.1 0

> surface style #1 solid

> select clear

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 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.  
  




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 pett, 2 years ago

Component:	Unassigned → Input/Output
Description:	modified (diff)
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → MemoryError open mmCIF

comment:2 by pett, 2 years ago

Resolution:	→ duplicate
Status:	assigned → closed

Note: See TracTickets for help on using tickets.

Download in other formats: