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Opened 2 years ago
Closed 2 years ago
#9789 closed defect (duplicate)
MemoryError opening mmCIF files
| 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_J707_class_01_00030_volume.mrc
Opened cryosparc_P122_J707_class_01_00030_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.0261, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_00_00030_volume.mrc
Opened cryosparc_P122_J707_class_00_00030_volume.mrc as #2, grid size
100,100,100, pixel 2.78, shown at level 0.0301, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_02_00030_volume.mrc
Opened cryosparc_P122_J707_class_02_00030_volume.mrc as #3, grid size
100,100,100, pixel 2.78, shown at level 0.0294, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_05_00030_volume.mrc
Opened cryosparc_P122_J707_class_05_00030_volume.mrc as #4, grid size
100,100,100, pixel 2.78, shown at level 0.0312, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_04_00030_volume.mrc
Opened cryosparc_P122_J707_class_04_00030_volume.mrc as #5, grid size
100,100,100, pixel 2.78, shown at level 0.0292, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_03_00030_volume.mrc
Opened cryosparc_P122_J707_class_03_00030_volume.mrc as #6, grid size
100,100,100, pixel 2.78, shown at level 0.0269, step 1, values float32
> volume level 0.2
> volume level 0.1
> tile
6 models tiled
> volume #1 level 0.05503
> volume level 0.055
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_00_00011_volume.mrc
Opened cryosparc_P122_J709_class_00_00011_volume.mrc as #7, grid size
100,100,100, pixel 2.78, shown at level 0.0424, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_01_00011_volume.mrc
Opened cryosparc_P122_J709_class_01_00011_volume.mrc as #8, grid size
100,100,100, pixel 2.78, shown at level 0.0422, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_03_00011_volume.mrc
Opened cryosparc_P122_J709_class_03_00011_volume.mrc as #9, grid size
100,100,100, pixel 2.78, shown at level 0.0444, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_02_00011_volume.mrc
Opened cryosparc_P122_J709_class_02_00011_volume.mrc as #10, grid size
100,100,100, pixel 2.78, shown at level 0.0397, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_04_00011_volume.mrc
Opened cryosparc_P122_J709_class_04_00011_volume.mrc as #11, grid size
100,100,100, pixel 2.78, shown at level 0.0502, step 1, values float32
> volume level 0.055
> volume level 0.1
> tile
5 models tiled
> volume level 0.08
> show #!1 models
> volume level 0.08
> open C:/Users/lilyh/Downloads/cryosparc_P122_J745_class_00_00012_volume.mrc
Opened cryosparc_P122_J745_class_00_00012_volume.mrc as #12, grid size
80,80,80, pixel 3.47, shown at level 0.0582, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J745_class_01_00012_volume.mrc
Opened cryosparc_P122_J745_class_01_00012_volume.mrc as #13, grid size
80,80,80, pixel 3.47, shown at level 0.0634, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J745_class_02_00012_volume.mrc
Opened cryosparc_P122_J745_class_02_00012_volume.mrc as #14, grid size
80,80,80, pixel 3.47, shown at level 0.0648, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J745_class_03_00012_volume.mrc
Opened cryosparc_P122_J745_class_03_00012_volume.mrc as #15, grid size
80,80,80, pixel 3.47, shown at level 0.0633, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J745_class_04_00012_volume.mrc
Opened cryosparc_P122_J745_class_04_00012_volume.mrc as #16, grid size
80,80,80, pixel 3.47, shown at level 0.0562, step 1, values float32
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J745_class_02_00012_volume.mrc
Opened cryosparc_P122_J745_class_02_00012_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.0648, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J745_class_03_00012_volume.mrc
Opened cryosparc_P122_J745_class_03_00012_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.0633, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J745_class_04_00012_volume.mrc
Opened cryosparc_P122_J745_class_04_00012_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.0562, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J745_class_00_00012_volume.mrc
Opened cryosparc_P122_J745_class_00_00012_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.0582, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J745_class_01_00012_volume.mrc
Opened cryosparc_P122_J745_class_01_00012_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.0634, step 1, values float32
> volume level 0.08
> volume level 0.1
> tile
5 models tiled
> tile
5 models tiled
> ~tile
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_01_00030_volume.mrc
Opened cryosparc_P122_J707_class_01_00030_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.0261, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_00_00030_volume.mrc
Opened cryosparc_P122_J707_class_00_00030_volume.mrc as #2, grid size
100,100,100, pixel 2.78, shown at level 0.0301, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_02_00030_volume.mrc
Opened cryosparc_P122_J707_class_02_00030_volume.mrc as #3, grid size
100,100,100, pixel 2.78, shown at level 0.0294, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_05_00030_volume.mrc
Opened cryosparc_P122_J707_class_05_00030_volume.mrc as #4, grid size
100,100,100, pixel 2.78, shown at level 0.0312, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_04_00030_volume.mrc
Opened cryosparc_P122_J707_class_04_00030_volume.mrc as #5, grid size
100,100,100, pixel 2.78, shown at level 0.0292, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_03_00030_volume.mrc
Opened cryosparc_P122_J707_class_03_00030_volume.mrc as #6, grid size
100,100,100, pixel 2.78, shown at level 0.0269, step 1, values float32
> volume level 0.1
> volume level 0.08
> tile
6 models tiled
> volume level 0.06
> hide #!3 models
> hide #!4 models
> volume #6 level 0.05511
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_00_00039_volume.mrc
Opened cryosparc_P122_J747_class_00_00039_volume.mrc as #7, grid size
60,60,60, pixel 4.63, shown at level 0.0389, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_01_00039_volume.mrc
Opened cryosparc_P122_J747_class_01_00039_volume.mrc as #8, grid size
60,60,60, pixel 4.63, shown at level 0.0418, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_02_00039_volume.mrc
Opened cryosparc_P122_J747_class_02_00039_volume.mrc as #9, grid size
60,60,60, pixel 4.63, shown at level 0.0402, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_03_00039_volume.mrc
Opened cryosparc_P122_J747_class_03_00039_volume.mrc as #10, grid size
60,60,60, pixel 4.63, shown at level 0.0407, step 1, values float32
> hide #!2 models
> hide #!1 models
> hide #!5 models
> hide #!6 models
> volume level 0.06
> volume level 0.1
> tile
4 models tiled
> volume level 0.08
> volume #9 level 0.04752
> volume #9 level 0.06051
> volume level 0.06
> hide #!7 models
> hide #!8 models
> hide #!10 models
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_02_00039_volume.mrc
Opened cryosparc_P122_J747_class_02_00039_volume.mrc as #1, grid size
60,60,60, pixel 4.63, shown at level 0.0402, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1051_003_volume_map_sharp.mrc
Opened cryosparc_P122_J1051_003_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.09, shown at level 0.0588, step 1, values float32
> volume #1 level 0.0675
> volume #1 level 0.057
> volume #1 level 0.0528
> volume #2 level 0.4777
> volume #2 level 0.3444
> volume #1 level 0.057
> volume #1 level 0.0486
> open C:/Users/lilyh/Downloads/cryosparc_P122_J749_class_00_00023_volume.mrc
Opened cryosparc_P122_J749_class_00_00023_volume.mrc as #3, grid size
60,60,60, pixel 4.63, shown at level 0.0521, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J749_class_01_00023_volume.mrc
Opened cryosparc_P122_J749_class_01_00023_volume.mrc as #4, grid size
60,60,60, pixel 4.63, shown at level 0.0472, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J749_class_02_00023_volume.mrc
Opened cryosparc_P122_J749_class_02_00023_volume.mrc as #5, grid size
60,60,60, pixel 4.63, shown at level 0.0486, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J749_class_03_00023_volume.mrc
Opened cryosparc_P122_J749_class_03_00023_volume.mrc as #6, grid size
60,60,60, pixel 4.63, shown at level 0.054, step 1, values float32
> hide #!1 models
> volume level 0.06
> hide #!2 models
> volume level 0.08
> hide #!5 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> volume #4 level 0.09566
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> volume #6 level 0.07202
> show #!1 models
> volume level 0.08
> tile
2 models tiled
> volume #6 level 0.1066
> volume level 0.107
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_01_00030_volume.mrc
Opened cryosparc_P122_J707_class_01_00030_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.0261, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_02_00039_volume.mrc
Opened cryosparc_P122_J747_class_02_00039_volume.mrc as #2, grid size
60,60,60, pixel 4.63, shown at level 0.0402, step 1, values float32
> volume level 0.107
> volume level 0.1
> volume level 0.08
> volume level 0.06
> volume level 0.07
> tile
2 models tiled
> volume #1 level 0.04638
> volume #1 level 0.03912
> volume #2 level 0.0595
> volume #2 level 0.04691
> volume #2 level 0.05531
> volume #2 level 0.05111
> open C:/Users/lilyh/Downloads/cryosparc_P122_J757_class_00_00016_volume.mrc
Opened cryosparc_P122_J757_class_00_00016_volume.mrc as #3, grid size
60,60,60, pixel 4.63, shown at level 0.0682, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J757_class_01_00016_volume.mrc
Opened cryosparc_P122_J757_class_01_00016_volume.mrc as #4, grid size
60,60,60, pixel 4.63, shown at level 0.0511, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J757_class_02_00016_volume.mrc
Opened cryosparc_P122_J757_class_02_00016_volume.mrc as #5, grid size
60,60,60, pixel 4.63, shown at level 0.0681, step 1, values float32
> tile
5 models tiled
> volume level 0.07
> volume level 0.1
> hide #!1 models
> hide #!2 models
> volume level 0.2
> tile
3 models tiled
> volume level 0.08
> volume #5 level 0.07726
> volume #4 level 0.05275
> volume #3 level 0.08637
> hide #!4 models
> ~tile
> hide #!5 models
> hide #!3 models
> show #!5 models
> volume #5 level 0.1374
> hide #!5 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_02_00039_volume.mrc
Opened cryosparc_P122_J747_class_02_00039_volume.mrc as #6, grid size
60,60,60, pixel 4.63, shown at level 0.0402, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_00_00039_volume.mrc
Opened cryosparc_P122_J747_class_00_00039_volume.mrc as #7, grid size
60,60,60, pixel 4.63, shown at level 0.0389, step 1, values float32
> volume level 0.08
> volume level 0.1
> tile
2 models tiled
> volume #6 level 0.04371
> volume #7 level 0.03476
> volume #7 level 0.07101
> ~tile
> hide #!7 models
> close session
> open C:/Users/lilyh/Desktop/P122/MapToModel_8/map_to_model.pdb
Summary of feedback from opening
C:/Users/lilyh/Desktop/P122/MapToModel_8/map_to_model.pdb
---
warnings | Ignored bad PDB record found on line 1
Ignored bad PDB record found on line 2
REMARK MODEL FROM PHENIX.MAP_TO_MODEL
Ignored bad PDB record found on line 3
REMARK MAP FILE:
C:\Users\lilyh\Downloads\cryosparc_P122_J1051_003_volume_map_sharp.mrc
Ignored bad PDB record found on line 4
Ignored bad PDB record found on line 852
Chain information for map_to_model.pdb #1
---
Chain | Description
A | No description available
U | No description available
> open
> C:/Users/lilyh/Desktop/P122/MapToModel_8/map_to_model_0/final_model_PROTEIN_shifted.pdb
Summary of feedback from opening
C:/Users/lilyh/Desktop/P122/MapToModel_8/map_to_model_0/final_model_PROTEIN_shifted.pdb
---
warning | Ignored bad PDB record found on line 849
Chain information for final_model_PROTEIN_shifted.pdb #2
---
Chain | Description
A | No description available
U | No description available
> open
> C:/Users/lilyh/Desktop/P122/MapToModel_8/map_to_model_0/TEMP_BUILD_ONE_trace_and_build_PROTEIN_1/tnb/trace_and_build/trace_and_build.pdb
Summary of feedback from opening
C:/Users/lilyh/Desktop/P122/MapToModel_8/map_to_model_0/TEMP_BUILD_ONE_trace_and_build_PROTEIN_1/tnb/trace_and_build/trace_and_build.pdb
---
warning | Ignored bad PDB record found on line 854
Chain information for trace_and_build.pdb #3
---
Chain | Description
A | No description available
U | No description available
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1051_003_volume_map_sharp.mrc
Opened cryosparc_P122_J1051_003_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.09, shown at level 0.0588, step 1, values float32
> volume #4 level 0.5665
> select #4
2 models selected
> transparency #4.1 30
> select clear
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> close session
> 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
#1
---
Chain | Description
B | No description available
C | No description available
> hide #1/B target r
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
Drag select of 425 residues
> copy #1/C
Unknown command: copy #1/C
> copy model #1/C
Unknown command: copy model #1/C
> copy model #1/C target r
Unknown command: copy model #1/C target r
> copy model #1/C
Unknown command: copy model #1/C
> split
Split
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#1) into 2 models
Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
B #1.1
---
Chain | Description
B | No description available
Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
C #1.2
---
Chain | Description
C | No description available
> hide #1.1 models
> hide #1.2 models
> hide #!1 models
> show #!1 models
> show #1.2 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> hide #1.1 models
> hide #1.2 models
> show #1.2 models
> show #1.2 cartoons
[Repeated 1 time(s)]Drag select of 425 residues
> show sel cartoons
> select clear
> show #1/B
> show #1/B tarrget r
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #1/B target r
> hide #!1 models
> show #!1 models
> show #1.1 models
> hide #1.2 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> hide #1.1 atoms
> hide #1.1 models
> show #1.2 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> hide #1.2 models
> save "C:/Users/lilyh/Desktop/Myo2 only afold 1150-1574.pdb" models #1.2
> show #1.2 models
> show #1.1 models
> hide #1.2 models
> save "C:/Users/lilyh/Desktop/Vac17 only afold 1-160.pdb" models #1.1
> hide #1.1 models
> hide #!1 models
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J805_class_01_00014_volume.mrc
Opened cryosparc_P122_J805_class_01_00014_volume.mrc as #1, grid size
72,72,72, pixel 3.86, shown at level 0.0607, step 1, values float32
> volume #1 level 0.07874
> volume #1 level 0.07197
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J802_class_00_00013_volume.mrc
Opened cryosparc_P122_J802_class_00_00013_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.037, step 1, values float32
> volume #1 level 0.05121
> volume #1 level 0.06024
> volume #1 level 0.05121
> open C:/Users/lilyh/Downloads/cryosparc_P122_J802_class_01_00013_volume.mrc
Opened cryosparc_P122_J802_class_01_00013_volume.mrc as #2, grid size
100,100,100, pixel 2.78, shown at level 0.0345, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J802_class_02_00013_volume.mrc
Opened cryosparc_P122_J802_class_02_00013_volume.mrc as #3, grid size
100,100,100, pixel 2.78, shown at level 0.0361, step 1, values float32
> volume level 0.08
> tile
3 models tiled
> volume #1 level 0.05471
> volume level 0.06
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_00_00011_volume.mrc
Opened cryosparc_P122_J709_class_00_00011_volume.mrc as #4, grid size
100,100,100, pixel 2.78, shown at level 0.0424, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_01_00011_volume.mrc
Opened cryosparc_P122_J709_class_01_00011_volume.mrc as #5, grid size
100,100,100, pixel 2.78, shown at level 0.0422, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_03_00011_volume.mrc
Opened cryosparc_P122_J709_class_03_00011_volume.mrc as #6, grid size
100,100,100, pixel 2.78, shown at level 0.0444, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_02_00011_volume.mrc
Opened cryosparc_P122_J709_class_02_00011_volume.mrc as #7, grid size
100,100,100, pixel 2.78, shown at level 0.0397, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_04_00011_volume.mrc
Opened cryosparc_P122_J709_class_04_00011_volume.mrc as #8, grid size
100,100,100, pixel 2.78, shown at level 0.0502, step 1, values float32
> volume level 0.06
> volume level 0.1
> tile
8 models tiled
> volume level 0.06
> volume level 0.07
> volume #1 level 0.08331
> volume #1 level 0.08464
> volume #1 level 0.1046
[Repeated 1 time(s)]
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1206_mask.mrc
Opened cryosparc_P122_J1206_mask.mrc as #9, grid size 100,100,100, pixel 2.78,
shown at level 0.692, step 1, values float32
> volume #9 level 0.746
> volume #9 level 0.1407
> volume #1 level 0.1059
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J813_class_00_00028_volume.mrc
Opened cryosparc_P122_J813_class_00_00028_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.0244, step 1, values float32
> 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 1149 residues
> ui mousemode right zoom
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #2,1,0,0,145.58,0,1,0,-20.095,0,0,1,161.13,#3,1,0,0,145.58,0,1,0,-20.095,0,0,1,161.13
> view matrix models
> #2,1,0,0,141.38,0,1,0,124.21,0,0,1,202.14,#3,1,0,0,141.38,0,1,0,124.21,0,0,1,202.14
> view matrix models
> #2,1,0,0,125.87,0,1,0,137.14,0,0,1,184.47,#3,1,0,0,125.87,0,1,0,137.14,0,0,1,184.47
> volume #1 level 0.1219
> volume #1 level 0.03899
Drag select of 1 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.92657,0.34898,-0.14033,123.8,0.27484,-0.88286,-0.38081,144.48,-0.25679,0.31428,-0.91394,176.59
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J802_class_02_00013_volume.mrc
Opened cryosparc_P122_J802_class_02_00013_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.0361, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J802_class_01_00013_volume.mrc
Opened cryosparc_P122_J802_class_01_00013_volume.mrc as #2, grid size
100,100,100, pixel 2.78, shown at level 0.0345, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J802_class_00_00013_volume.mrc
Opened cryosparc_P122_J802_class_00_00013_volume.mrc as #3, grid size
100,100,100, pixel 2.78, shown at level 0.037, step 1, values float32
> volume level 0.07
> tile
3 models tiled
> volume #3 level 0.05669
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J863_class_00_00017_volume.mrc
Opened cryosparc_P122_J863_class_00_00017_volume.mrc as #1, grid size
72,72,72, pixel 3.86, shown at level 0.0925, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J863_class_01_00017_volume.mrc
Opened cryosparc_P122_J863_class_01_00017_volume.mrc as #2, grid size
72,72,72, pixel 3.86, shown at level 0.0916, step 1, values float32
> volume level 0.07
> volume level 0.1
> volume level 0.2
> tile
2 models tiled
> volume #1 level 0.1733
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_00_00011_volume.mrc
Opened cryosparc_P122_J843_class_00_00011_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.14, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_01_00011_volume.mrc
Opened cryosparc_P122_J843_class_01_00011_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.138, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_02_00011_volume.mrc
Opened cryosparc_P122_J843_class_02_00011_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.129, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_03_00011_volume.mrc
Opened cryosparc_P122_J843_class_03_00011_volume.mrc as #6, grid size
80,80,80, pixel 3.47, shown at level 0.134, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_04_00011_volume.mrc
Opened cryosparc_P122_J843_class_04_00011_volume.mrc as #7, grid size
80,80,80, pixel 3.47, shown at level 0.133, step 1, values float32
> volume level 0.2
> volume level 0.3
> tile
7 models tiled
Drag select of 1 cryosparc_P122_J863_class_00_00017_volume.mrc , 2
cryosparc_P122_J863_class_01_00017_volume.mrc
Drag select of 1 cryosparc_P122_J863_class_00_00017_volume.mrc
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.037512,-0.99866,0.035569,260.27,0.99922,0.037057,-0.013373,-10.645,0.012037,0.036043,0.99928,0.91359
> view matrix models
> #1,0.005527,-0.0035948,-0.99998,285.95,0.23996,-0.97077,0.0048161,224.32,-0.97077,-0.23998,-0.0045029,320.7
Drag select of 2 cryosparc_P122_J863_class_01_00017_volume.mrc
> view matrix models
> #2,-0.049168,0.31515,0.94777,184.67,0.42977,-0.8499,0.30491,138.32,0.9016,0.42231,-0.093654,-14.857
> view matrix models
> #2,-0.098409,-0.054285,-0.99366,522.9,0.16568,-0.98547,0.037429,232.04,-0.98126,-0.16095,0.10597,296.07
> select clear
> volume level 02
> volume level 0.2
> volume level 0.24
> volume #3 level 0.2141
> volume level 0.2
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_00_00011_volume.mrc
Opened cryosparc_P122_J843_class_00_00011_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.14, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_01_00011_volume.mrc
Opened cryosparc_P122_J843_class_01_00011_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.138, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_02_00011_volume.mrc
Opened cryosparc_P122_J843_class_02_00011_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.129, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_03_00011_volume.mrc
Opened cryosparc_P122_J843_class_03_00011_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.134, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_04_00011_volume.mrc
Opened cryosparc_P122_J843_class_04_00011_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.133, step 1, values float32
> volume level 0.2
> volume level 0.3
> tile
5 models tiled
> volume level 0.2
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_00_00011_volume.mrc
Opened cryosparc_P122_J709_class_00_00011_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.0424, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_01_00011_volume.mrc
Opened cryosparc_P122_J709_class_01_00011_volume.mrc as #2, grid size
100,100,100, pixel 2.78, shown at level 0.0422, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_03_00011_volume.mrc
Opened cryosparc_P122_J709_class_03_00011_volume.mrc as #3, grid size
100,100,100, pixel 2.78, shown at level 0.0444, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_02_00011_volume.mrc
Opened cryosparc_P122_J709_class_02_00011_volume.mrc as #4, grid size
100,100,100, pixel 2.78, shown at level 0.0397, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J709_class_04_00011_volume.mrc
Opened cryosparc_P122_J709_class_04_00011_volume.mrc as #5, grid size
100,100,100, pixel 2.78, shown at level 0.0502, step 1, values float32
> volume level 0.2
> tile
5 models tiled
> volume level 0.07
> close session
> open C:/Users/lilyh/Desktop/P122/MapToModel_10/map_to_model.pdb
Summary of feedback from opening
C:/Users/lilyh/Desktop/P122/MapToModel_10/map_to_model.pdb
---
warnings | Ignored bad PDB record found on line 1
Ignored bad PDB record found on line 2
REMARK MODEL FROM PHENIX.MAP_TO_MODEL
Ignored bad PDB record found on line 3
REMARK MAP FILE:
C:\Users\lilyh\Downloads\cryosparc_P122_J1051_003_volume_map_sharp.mrc
Ignored bad PDB record found on line 4
Ignored bad PDB record found on line 1308
Chain information for map_to_model.pdb #1
---
Chain | Description
A | No description available
U | No description available
> open C:/Users/lilyh/Desktop/P122/MapToModel_8/map_to_model.pdb
Summary of feedback from opening
C:/Users/lilyh/Desktop/P122/MapToModel_8/map_to_model.pdb
---
warnings | Ignored bad PDB record found on line 1
Ignored bad PDB record found on line 2
REMARK MODEL FROM PHENIX.MAP_TO_MODEL
Ignored bad PDB record found on line 3
REMARK MAP FILE:
C:\Users\lilyh\Downloads\cryosparc_P122_J1051_003_volume_map_sharp.mrc
Ignored bad PDB record found on line 4
Ignored bad PDB record found on line 852
Chain information for map_to_model.pdb #2
---
Chain | Description
A | No description available
U | No description available
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1051_003_volume_map_sharp.mrc
Opened cryosparc_P122_J1051_003_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.09, shown at level 0.0588, step 1, values float32
> volume #3 level 0.3761
> select #3
2 models selected
> transparency #3.1 60
> select clear
> set bgColor white
> set bgColor #ffffff00
> lighting soft
> lighting full
> graphics silhouettes true
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1188__localfilter.mrc
Opened cryosparc_P122_J1188__localfilter.mrc as #4, grid size 256,256,256,
pixel 1.09, shown at level 0.000312, step 1, values float32
> volume #4 level 0.3089
> volume #4 level 0.4508
> volume #3 level 0.4269
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> open "C:/Users/lilyh/Desktop/Myo2 only afold 1150-1574.pdb"
Chain information for Myo2 only afold 1150-1574.pdb #5
---
Chain | Description
C | No description available
Drag select of 93 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.98756,0.0019069,0.15721,0.48104,0.15138,-0.28137,-0.94758,-8.5919,0.042426,0.9596,-0.27816,0.45978
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.98756,0.0019069,0.15721,-21.607,0.15138,-0.28137,-0.94758,139.75,0.042426,0.9596,-0.27816,168.37
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.18764,0.015182,-0.98212,-25.208,-0.9096,-0.38005,0.16791,142.47,-0.3707,0.92484,0.08512,169.24
> view matrix models
> #5,-0.77944,0.015043,-0.6263,-24.244,-0.3427,-0.84712,0.40615,141.2,-0.52444,0.5312,0.66543,169.19
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.77944,0.015043,-0.6263,134.37,-0.3427,-0.84712,0.40615,131.55,-0.52444,0.5312,0.66543,170.38
> fitmap #5 inMap #3
Fit molecule Myo2 only afold 1150-1574.pdb (#5) to map
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#3) using 3429 atoms
average map value = 0.09601, steps = 216
shifted from previous position = 10.6
rotated from previous position = 15.4 degrees
atoms outside contour = 2981, contour level = 0.42689
Position of Myo2 only afold 1150-1574.pdb (#5) relative to
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.88559795 -0.08958627 -0.45573081 142.82166750
-0.23821556 -0.75471820 0.61127226 136.60160196
-0.39870993 0.64990363 0.64703605 166.90115570
Axis 0.23582722 -0.34808689 -0.90731529
Axis point 94.88842102 32.17551071 0.00000000
Rotation angle (degrees) 175.30186382
Shift along axis -165.29996179
> select clear
Drag select of 7 residues
> view matrix models
> #5,-0.8856,-0.089586,-0.45573,131.03,-0.23822,-0.75472,0.61127,132.31,-0.39871,0.6499,0.64704,158
> fitmap #5 inMap #3
Fit molecule Myo2 only afold 1150-1574.pdb (#5) to map
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#3) using 3429 atoms
average map value = 0.3429, steps = 264
shifted from previous position = 17
rotated from previous position = 19.2 degrees
atoms outside contour = 2051, contour level = 0.42689
Position of Myo2 only afold 1150-1574.pdb (#5) relative to
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.81581392 0.19861668 -0.54313815 140.01278366
-0.52361727 -0.65237995 0.54792823 134.78420894
-0.24550476 0.73140400 0.63621977 143.31332288
Axis 0.22865428 -0.37092172 -0.90007461
Axis point 97.54717369 17.66634320 0.00000000
Rotation angle (degrees) 156.34629274
Shift along axis -146.97255206
> select clear
Drag select of 2 residues
> view matrix models
> #5,-0.81581,0.19862,-0.54314,140.05,-0.52362,-0.65238,0.54793,133.91,-0.2455,0.7314,0.63622,146.03
> select clear
> fitmap #5 inMap #3
Fit molecule Myo2 only afold 1150-1574.pdb (#5) to map
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#3) using 3429 atoms
average map value = 0.3429, steps = 60
shifted from previous position = 2.86
rotated from previous position = 0.0315 degrees
atoms outside contour = 2048, contour level = 0.42689
Position of Myo2 only afold 1150-1574.pdb (#5) relative to
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.81602314 0.19829043 -0.54294302 139.99440386
-0.52318417 -0.65271171 0.54794683 134.77141763
-0.24573266 0.73119649 0.63637028 143.29772558
Axis 0.22862667 -0.37080676 -0.90012899
Axis point 97.52208135 17.70291832 0.00000000
Rotation angle (degrees) 156.37418995
Shift along axis -146.95413572
> save "C:/Users/lilyh/Desktop/J1051_afold docked.cif" models #5 relModel #3
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1204_002_volume_map_sharp.mrc
Opened cryosparc_P122_J1204_002_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.09, shown at level 0.0461, step 1, values float32
> open "C:/Users/lilyh/Desktop/cryoEM/Best Myo2-Vac17 site I
> map/cryosparc_P122_J657_003_volume_map_sharp.mrc"
Opened cryosparc_P122_J657_003_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.09, shown at level 0.0499, step 1, values float32
> open "C:/Users/lilyh/Desktop/cryoEM/Best Myo2-Vac17 site I
> map/cryosparc_P122_J817_003_volume_map_sharp.mrc"
Opened cryosparc_P122_J817_003_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.09, shown at level 0.0574, step 1, values float32
> open "C:/Users/lilyh/Desktop/cryoEM/Best Myo2-Vac17 site I
> map/cryosparc_P122_J657_003_volume_map_sharp.mrc"
Opened cryosparc_P122_J657_003_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.09, shown at level 0.0499, step 1, values float32
> open "C:/Users/lilyh/Desktop/cryoEM/Best Myo2-Vac17 site I
> map/cryosparc_P122_J817_003_volume_map_sharp.mrc"
Opened cryosparc_P122_J817_003_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 1.09, shown at level 0.0574, step 1, values float32
> open "C:/Users/lilyh/Desktop/cryoEM/Best Myo2-Vac17 site I
> map/cryosparc_P122_J1051_003_volume_map_sharp.mrc"
Opened cryosparc_P122_J1051_003_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.09, shown at level 0.0588, step 1, values float32
> volume level 0.07
> volume level 0.1
> volume level 0.2
> volume level 0.3
> volume level 0.4
> volume level 0.3
> tile
6 models tiled
> tile
6 models tiled
> volume level 0.4
> tile
6 models tiled
> volume level 0.6
> tile
6 models tiled
> volume level 0.4
> close #2
> close #3
> volume level 0.4
> tile
4 models tiled
> color dark gray
> lighting full
> set bgColor white
> graphics silhouettes true
> volume level 0.3
> volume level 0.2
> volume level 0.25
> volume level 0.26
> volume level 0.28
> volume level 0.29
> volume level 0.3
> volume level 0.35
> volume level 0.34
> volume level 0.36
> hide #!1 models
> show #!1 models
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1207_002_volume_map.mrc
Opened cryosparc_P122_J1207_002_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.09, shown at level 0.0049, step 1, values float32
> volume #1 level 0.02332
> volume #1 level 0.008775
> volume #1 level 0.03011
> volume #1 level 0.02526
> hide #!1 models
> ~tile
No models found for tiling.
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_03_00039_volume.mrc
Opened cryosparc_P122_J1129_class_03_00039_volume.mrc as #1, grid size
60,60,60, pixel 4.63, shown at level 0.0416, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_01_00039_volume.mrc
Opened cryosparc_P122_J1129_class_01_00039_volume.mrc as #2, grid size
60,60,60, pixel 4.63, shown at level 0.0415, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_00_00039_volume.mrc
Opened cryosparc_P122_J1129_class_00_00039_volume.mrc as #3, grid size
60,60,60, pixel 4.63, shown at level 0.04, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_02_00039_volume.mrc
Opened cryosparc_P122_J1129_class_02_00039_volume.mrc as #4, grid size
60,60,60, pixel 4.63, shown at level 0.0395, step 1, values float32
> volume level 0.34
> volume level 0.3
> volume level 0.1
> volume level 0.15
> volume level 0.1
> volume level 0.12
> tile
4 models tiled
> volume #1 level 0.104
> volume level 0.104
> close #2-4
> hide #!1 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_07_00025_volume.mrc
Opened cryosparc_P122_J1079_class_07_00025_volume.mrc as #2, grid size
72,72,72, pixel 3.86, shown at level 0.0502, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_00_00025_volume.mrc
Opened cryosparc_P122_J1079_class_00_00025_volume.mrc as #3, grid size
72,72,72, pixel 3.86, shown at level 0.0499, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_01_00025_volume.mrc
Opened cryosparc_P122_J1079_class_01_00025_volume.mrc as #4, grid size
72,72,72, pixel 3.86, shown at level 0.0502, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_02_00025_volume.mrc
Opened cryosparc_P122_J1079_class_02_00025_volume.mrc as #5, grid size
72,72,72, pixel 3.86, shown at level 0.0503, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_03_00025_volume.mrc
Opened cryosparc_P122_J1079_class_03_00025_volume.mrc as #6, grid size
72,72,72, pixel 3.86, shown at level 0.0532, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_04_00025_volume.mrc
Opened cryosparc_P122_J1079_class_04_00025_volume.mrc as #7, grid size
72,72,72, pixel 3.86, shown at level 0.0524, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_05_00025_volume.mrc
Opened cryosparc_P122_J1079_class_05_00025_volume.mrc as #8, grid size
72,72,72, pixel 3.86, shown at level 0.052, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_06_00025_volume.mrc
Opened cryosparc_P122_J1079_class_06_00025_volume.mrc as #9, grid size
72,72,72, pixel 3.86, shown at level 0.051, step 1, values float32
> volume level 0.104
> tile
8 models tiled
> volume #3 level 0.05958
> volume level 0.05
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_01_00039_volume.mrc
Opened cryosparc_P122_J1129_class_01_00039_volume.mrc as #1, grid size
60,60,60, pixel 4.63, shown at level 0.0415, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_00_00039_volume.mrc
Opened cryosparc_P122_J1129_class_00_00039_volume.mrc as #2, grid size
60,60,60, pixel 4.63, shown at level 0.04, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_02_00039_volume.mrc
Opened cryosparc_P122_J1129_class_02_00039_volume.mrc as #3, grid size
60,60,60, pixel 4.63, shown at level 0.0395, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_03_00039_volume.mrc
Opened cryosparc_P122_J1129_class_03_00039_volume.mrc as #4, grid size
60,60,60, pixel 4.63, shown at level 0.0416, step 1, values float32
> volume level 0.05
> tile
4 models tiled
> hide #!1 models
> hide #!3 models
> hide #!4 models
> volume level 0.08
> volume #2 level 0.05668
> show #!4 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> ~tile
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_03_00039_volume.mrc
Opened cryosparc_P122_J1129_class_03_00039_volume.mrc as #1, grid size
60,60,60, pixel 4.63, shown at level 0.0416, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_00_00039_volume.mrc
Opened cryosparc_P122_J1129_class_00_00039_volume.mrc as #2, grid size
60,60,60, pixel 4.63, shown at level 0.04, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1051_003_volume_map_sharp.mrc
Opened cryosparc_P122_J1051_003_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.09, shown at level 0.0588, step 1, values float32
> volume #3 level 0.2936
> volume #2 level 0.1006
> volume #1 level 0.1534
> volume #2 level 0.1347
> volume #2 level 0.08548
> volume #1 level 0.1274
> volume #1 level 0.0754
> hide #!3 models
> hide #!1 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_00_00025_volume.mrc
Opened cryosparc_P122_J1079_class_00_00025_volume.mrc as #4, grid size
72,72,72, pixel 3.86, shown at level 0.0499, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_01_00025_volume.mrc
Opened cryosparc_P122_J1079_class_01_00025_volume.mrc as #5, grid size
72,72,72, pixel 3.86, shown at level 0.0502, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_02_00025_volume.mrc
Opened cryosparc_P122_J1079_class_02_00025_volume.mrc as #6, grid size
72,72,72, pixel 3.86, shown at level 0.0503, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_03_00025_volume.mrc
Opened cryosparc_P122_J1079_class_03_00025_volume.mrc as #7, grid size
72,72,72, pixel 3.86, shown at level 0.0532, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_04_00025_volume.mrc
Opened cryosparc_P122_J1079_class_04_00025_volume.mrc as #8, grid size
72,72,72, pixel 3.86, shown at level 0.0524, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_05_00025_volume.mrc
Opened cryosparc_P122_J1079_class_05_00025_volume.mrc as #9, grid size
72,72,72, pixel 3.86, shown at level 0.052, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_06_00025_volume.mrc
Opened cryosparc_P122_J1079_class_06_00025_volume.mrc as #10, grid size
72,72,72, pixel 3.86, shown at level 0.051, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1079_class_07_00025_volume.mrc
Opened cryosparc_P122_J1079_class_07_00025_volume.mrc as #11, grid size
72,72,72, pixel 3.86, shown at level 0.0502, step 1, values float32
> volume level 0.08
> volume level 0.1
> volume level 0.13
> tile
8 models tiled
> volume level 0.08
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1055_class_09_00022_volume.mrc
Opened cryosparc_P122_J1055_class_09_00022_volume.mrc as #1, grid size
72,72,72, pixel 3.86, shown at level 0.089, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1055_class_00_00022_volume.mrc
Opened cryosparc_P122_J1055_class_00_00022_volume.mrc as #2, grid size
72,72,72, pixel 3.86, shown at level 0.0893, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1055_class_01_00022_volume.mrc
Opened cryosparc_P122_J1055_class_01_00022_volume.mrc as #3, grid size
72,72,72, pixel 3.86, shown at level 0.0922, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1055_class_02_00022_volume.mrc
Opened cryosparc_P122_J1055_class_02_00022_volume.mrc as #4, grid size
72,72,72, pixel 3.86, shown at level 0.0823, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1055_class_03_00022_volume.mrc
Opened cryosparc_P122_J1055_class_03_00022_volume.mrc as #5, grid size
72,72,72, pixel 3.86, shown at level 0.0882, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1055_class_04_00022_volume.mrc
Opened cryosparc_P122_J1055_class_04_00022_volume.mrc as #6, grid size
72,72,72, pixel 3.86, shown at level 0.0885, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1055_class_05_00022_volume.mrc
Opened cryosparc_P122_J1055_class_05_00022_volume.mrc as #7, grid size
72,72,72, pixel 3.86, shown at level 0.0858, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1055_class_06_00022_volume.mrc
Opened cryosparc_P122_J1055_class_06_00022_volume.mrc as #8, grid size
72,72,72, pixel 3.86, shown at level 0.0867, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1055_class_07_00022_volume.mrc
Opened cryosparc_P122_J1055_class_07_00022_volume.mrc as #9, grid size
72,72,72, pixel 3.86, shown at level 0.0927, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1055_class_08_00022_volume.mrc
Opened cryosparc_P122_J1055_class_08_00022_volume.mrc as #10, grid size
72,72,72, pixel 3.86, shown at level 0.0905, step 1, values float32
> volume level 0.1
[Repeated 1 time(s)]
> volume level 0.2
> tile
10 models tiled
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_05_00028_volume.mrc
Opened cryosparc_P122_J1078_class_05_00028_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.0728, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_00_00028_volume.mrc
Opened cryosparc_P122_J1078_class_00_00028_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.074, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_01_00028_volume.mrc
Opened cryosparc_P122_J1078_class_01_00028_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.075, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_03_00028_volume.mrc
Opened cryosparc_P122_J1078_class_03_00028_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.076, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_02_00028_volume.mrc
Opened cryosparc_P122_J1078_class_02_00028_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.0758, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_04_00028_volume.mrc
Opened cryosparc_P122_J1078_class_04_00028_volume.mrc as #6, grid size
80,80,80, pixel 3.47, shown at level 0.0714, step 1, values float32
> volume level 0.2
> tile
6 models tiled
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1081_class_00_00022_volume.mrc
Opened cryosparc_P122_J1081_class_00_00022_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.0766, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1081_class_01_00022_volume.mrc
Opened cryosparc_P122_J1081_class_01_00022_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.0859, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1081_class_02_00022_volume.mrc
Opened cryosparc_P122_J1081_class_02_00022_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.0822, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1081_class_03_00022_volume.mrc
Opened cryosparc_P122_J1081_class_03_00022_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.092, step 1, values float32
> volume level 0.2
> tile
4 models tiled
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_00_00028_volume.mrc
Opened cryosparc_P122_J1078_class_00_00028_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.074, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_02_00028_volume.mrc
Opened cryosparc_P122_J1078_class_02_00028_volume.mrc as #6, grid size
80,80,80, pixel 3.47, shown at level 0.0758, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_04_00028_volume.mrc
Opened cryosparc_P122_J1078_class_04_00028_volume.mrc as #7, grid size
80,80,80, pixel 3.47, shown at level 0.0714, step 1, values float32
> volume level 0.2
> tile
7 models tiled
Drag select of 5 cryosparc_P122_J1078_class_00_00028_volume.mrc , 6
cryosparc_P122_J1078_class_02_00028_volume.mrc
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.34388,-0.25889,-0.90262,674.73,0.51294,-0.85695,0.050367,-69.61,-0.78654,-0.44567,0.42748,350.45,#6,-0.34388,-0.25889,-0.90262,593.72,0.51294,-0.85695,0.050367,37.598,-0.78654,-0.44567,0.42748,213.17
> select clear
Drag select of 7 cryosparc_P122_J1078_class_04_00028_volume.mrc
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.96127,-0.043578,-0.27216,48.944,0.048708,-0.94502,0.32335,-165.43,-0.27129,-0.32408,-0.9063,350.85
> view matrix models
> #7,-0.069619,-0.035558,-0.99694,292.28,-0.047361,-0.99812,0.038907,-104.72,-0.99645,0.049925,0.067804,261.85
> select clear
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_00_00028_volume.mrc
Opened cryosparc_P122_J1078_class_00_00028_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.074, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_01_00028_volume.mrc
Opened cryosparc_P122_J1078_class_01_00028_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.075, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_03_00028_volume.mrc
Opened cryosparc_P122_J1078_class_03_00028_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.076, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_02_00028_volume.mrc
Opened cryosparc_P122_J1078_class_02_00028_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.0758, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_04_00028_volume.mrc
Opened cryosparc_P122_J1078_class_04_00028_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.0714, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_05_00028_volume.mrc
Opened cryosparc_P122_J1078_class_05_00028_volume.mrc as #6, grid size
80,80,80, pixel 3.47, shown at level 0.0728, step 1, values float32
> volume level 0.2
> tile
6 models tiled
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_03_00039_volume.mrc
Opened cryosparc_P122_J1129_class_03_00039_volume.mrc as #1, grid size
60,60,60, pixel 4.63, shown at level 0.0416, step 1, values float32
> volume #1 level 0.1259
> volume #1 level 0.1203
> close session
> open
> C:/Users/lilyh/Desktop/P122/MapToModel_11/map_to_model_0/shifted_input_model_1.pdb
Summary of feedback from opening
C:/Users/lilyh/Desktop/P122/MapToModel_11/map_to_model_0/shifted_input_model_1.pdb
---
warning | Ignored bad PDB record found on line 3431
Chain information for shifted_input_model_1.pdb #1
---
Chain | Description
C | No description available
> open
> C:/Users/lilyh/Desktop/P122/MapToModel_11/map_to_model_0/TEMP_BUILD_ONE_trace_and_build_PROTEIN_1/tnb/trace_and_build/path_68.pdb
Summary of feedback from opening
C:/Users/lilyh/Desktop/P122/MapToModel_11/map_to_model_0/TEMP_BUILD_ONE_trace_and_build_PROTEIN_1/tnb/trace_and_build/path_68.pdb
---
warning | Ignored bad PDB record found on line 62
> hide #2 models
> open "C:/Users/lilyh/Desktop/P122/RebuildPredictedModel_12/Myo2 only afold
> 1150-1574_processed.pdb"
Summary of feedback from opening
C:/Users/lilyh/Desktop/P122/RebuildPredictedModel_12/Myo2 only afold
1150-1574_processed.pdb
---
warning | Ignored bad PDB record found on line 2983
Chain information for Myo2 only afold 1150-1574_processed.pdb #3
---
Chain | Description
C1 | No description available
C2 | No description available
C3 | No description available
> hide #1 models
> close #1-2
> open C:/Users/lilyh/Downloads/2f6h.pdb
2f6h.pdb title:
Myosin V cargo binding domain [more info...]
Chain information for 2f6h.pdb #1
---
Chain | Description | UniProt
X | class V unconventional myosin MYO2; TYPE V myosin heavy chain MYO2; myosin
V MYO2; cell divison control protein 66 | MYO2_YEAST 22-440
> matchmaker #1 to #3
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 Myo2 only afold 1150-1574_processed.pdb, chain C1 (#3) with
2f6h.pdb, chain X (#1), sequence alignment score = 777.1
RMSD between 200 pruned atom pairs is 0.524 angstroms; (across all 200 pairs:
0.524)
> select clear
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> open "C:/Users/lilyh/Desktop/Myo2 only afold 1150-1574.pdb"
Chain information for Myo2 only afold 1150-1574.pdb #2
---
Chain | Description
C | No description available
> hide #!1 models
> matchmaker #2 to #3
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 Myo2 only afold 1150-1574_processed.pdb, chain C1 (#3) with Myo2
only afold 1150-1574.pdb, chain C (#2), sequence alignment score = 771.1
RMSD between 200 pruned atom pairs is 0.000 angstroms; (across all 200 pairs:
0.000)
> select clear
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> open "C:/Users/lilyh/Desktop/cryoEM/Best Myo2-Vac17 site I
> map/cryosparc_P122_J1051_003_volume_map_sharp.mrc"
Opened cryosparc_P122_J1051_003_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.09, shown at level 0.0588, step 1, values float32
> ui mousemode right "translate selected models"
Drag select of 4 cryosparc_P122_J1051_003_volume_map_sharp.mrc
> view matrix models #4,1,0,0,-39.489,0,1,0,-205.95,0,0,1,-67.513
> volume #4 level 0.402
Drag select of 257 residues, 5 pseudobonds
> view matrix models #3,1,0,0,54.323,0,1,0,-42.71,0,0,1,94.416
> view matrix models #3,1,0,0,93.395,0,1,0,-75.504,0,0,1,111.19
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.79743,-0.50865,0.32461,90.91,0.57555,-0.4796,0.66237,-81.627,-0.18123,0.71502,0.6752,114.16
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.79743,-0.50865,0.32461,97.857,0.57555,-0.4796,0.66237,-75.742,-0.18123,0.71502,0.6752,73.286
Must specify one map, got 0
Must specify one map, got 0
> fitmap #3 inMap #4
Fit molecule Myo2 only afold 1150-1574_processed.pdb (#3) to map
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#4) using 2974 atoms
average map value = 0.1355, steps = 80
shifted from previous position = 3.02
rotated from previous position = 4.84 degrees
atoms outside contour = 2353, contour level = 0.402
Position of Myo2 only afold 1150-1574_processed.pdb (#3) relative to
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.80616824 -0.53569056 0.25125367 139.54059163
0.53542571 -0.47975025 0.69509641 131.57074721
-0.25181757 0.69489232 0.67358192 142.12050673
Axis -0.00017247 0.42511651 0.90513862
Axis point 60.17174597 57.66785285 0.00000000
Rotation angle (degrees) 143.72323448
Shift along axis 184.54758974
> select clear
Drag select of 4 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.92996,-0.11935,-0.34775,101.33,-0.17051,-0.69798,0.69552,-75.582,-0.32574,0.7061,0.62875,74.593
> fitmap #3 inMap #4
Fit molecule Myo2 only afold 1150-1574_processed.pdb (#3) to map
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#4) using 2974 atoms
average map value = 0.3766, steps = 96
shifted from previous position = 4.72
rotated from previous position = 21.9 degrees
atoms outside contour = 1569, contour level = 0.402
Position of Myo2 only afold 1150-1574_processed.pdb (#3) relative to
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.82227572 0.18885561 -0.53683910 139.96779430
-0.51341838 -0.65310667 0.55664466 134.79990744
-0.24548773 0.73333844 0.63399570 143.26891418
Axis 0.22636403 -0.37325294 -0.89968971
Axis point 97.01158296 18.10348170 0.00000000
Rotation angle (degrees) 157.02765534
Shift along axis -147.52835440
> select clear
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> select #4
2 models selected
> transparency #4.1 40
> select clear
> hide #!4 models
> show #!4 models
> hide #!4 models
Drag select of 364 residues, 9 pseudobonds
> show sel atoms
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> show #2 models
> hide #2 models
> show #!1 models
> hide #!1 models
> matchmaker #1 to #3
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 Myo2 only afold 1150-1574_processed.pdb, chain C1 (#3) with
2f6h.pdb, chain X (#1), sequence alignment score = 777.1
RMSD between 200 pruned atom pairs is 0.524 angstroms; (across all 200 pairs:
0.524)
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 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
> hide #!4 models
> hide #!3 atoms
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> color #3 dark gray
[Repeated 1 time(s)]
> set bgColor white
> lighting soft
> graphics silhouettes true
> show #!1 models
> hide #!1 models
> show #!1 models
> matchmaker #1 to #3
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 Myo2 only afold 1150-1574_processed.pdb, chain C1 (#3) with
2f6h.pdb, chain X (#1), sequence alignment score = 777.1
RMSD between 200 pruned atom pairs is 0.524 angstroms; (across all 200 pairs:
0.524)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #2 models
> hide #2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> matchmaker #2 to #3
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 Myo2 only afold 1150-1574_processed.pdb, chain C1 (#3) with Myo2
only afold 1150-1574.pdb, chain C (#2), sequence alignment score = 771.1
RMSD between 200 pruned atom pairs is 0.000 angstroms; (across all 200 pairs:
0.000)
> show #2 models
> hide #!1 models
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> transparency #2 80 target r
> hide #!3 models
> show #!3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> transparency #2 0 target r
> difference #2 #3
Unknown command: difference #2 #3
> subtract #2 #3
Unknown command: subtract #2 #3
> subtract #2 #3 target r
Unknown command: subtract #2 #3 target r
> subtract model #2 #3
Unknown command: subtract model #2 #3
> show #!4 models
> hide #!4 models
> hide #2 models
> show #!4 models
> hide #!4 models
> show #!1 models
> show #2 models
> hide #2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> save C:\Users\lilyh\Desktop\image148.png supersample 3
> show #!3 models
> save C:\Users\lilyh\Desktop\image149.png supersample 3
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> transparency #1 80 target r
> color #1,3 dim gray
> transparency #1 60 target r
> color #1 #8d8d8d33
> color #1 #84848433
> color #3 #999999ff
> color #3 #8d8d8dff
> color #1 #55555533
> color #1 #2c2c2c33
> color #1 #34343433
> color #1 #5a5a5a33
> color #1 #aa55ff33
> color #1 #ffaa7f33
> color #1 #ffaa0033
> color #1 #462f0033
> color #1 #00000033
> color #1 #53535333
> transparency #1 50 target r
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> transparency #1 ]0 target r
Missing or invalid "percent" argument: Expected a number
> transparency #1 0 target r
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_00_00028_volume.mrc
Opened cryosparc_P122_J1078_class_00_00028_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.074, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_01_00028_volume.mrc
Opened cryosparc_P122_J1078_class_01_00028_volume.mrc as #6, grid size
80,80,80, pixel 3.47, shown at level 0.075, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_03_00028_volume.mrc
Opened cryosparc_P122_J1078_class_03_00028_volume.mrc as #7, grid size
80,80,80, pixel 3.47, shown at level 0.076, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_02_00028_volume.mrc
Opened cryosparc_P122_J1078_class_02_00028_volume.mrc as #8, grid size
80,80,80, pixel 3.47, shown at level 0.0758, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_04_00028_volume.mrc
Opened cryosparc_P122_J1078_class_04_00028_volume.mrc as #9, grid size
80,80,80, pixel 3.47, shown at level 0.0714, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_05_00028_volume.mrc
Opened cryosparc_P122_J1078_class_05_00028_volume.mrc as #10, grid size
80,80,80, pixel 3.47, shown at level 0.0728, step 1, values float32
> tile
6 models tiled
> volume level 0.2
> volume level 0.1
> volume level 0.12
> volume level 0.13
> volume level 0.14
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1081_class_03_00022_volume.mrc
Opened cryosparc_P122_J1081_class_03_00022_volume.mrc as #11, grid size
80,80,80, pixel 3.47, shown at level 0.092, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1081_class_00_00022_volume.mrc
Opened cryosparc_P122_J1081_class_00_00022_volume.mrc as #12, grid size
80,80,80, pixel 3.47, shown at level 0.0766, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1081_class_01_00022_volume.mrc
Opened cryosparc_P122_J1081_class_01_00022_volume.mrc as #13, grid size
80,80,80, pixel 3.47, shown at level 0.0859, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1081_class_02_00022_volume.mrc
Opened cryosparc_P122_J1081_class_02_00022_volume.mrc as #14, grid size
80,80,80, pixel 3.47, shown at level 0.0822, step 1, values float32
> volume level 0.14
> tile
10 models tiled
> open "C:/Users/lilyh/Desktop/cryoEM/Best Myo2-Vac17
> map/cryosparc_P122_J863_class_01_00017_volume.mrc"
Opened cryosparc_P122_J863_class_01_00017_volume.mrc as #15, grid size
72,72,72, pixel 3.86, shown at level 0.0916, step 1, values float32
> open "C:/Users/lilyh/Desktop/cryoEM/Best Myo2-Vac17
> map/cryosparc_P122_J863_class_00_00017_volume.mrc"
Opened cryosparc_P122_J863_class_00_00017_volume.mrc as #16, grid size
72,72,72, pixel 3.86, shown at level 0.0925, step 1, values float32
> close #5-16
> open C:/Users/lilyh/Downloads/cryosparc_P122_J658_class_05_00029_volume.mrc
Opened cryosparc_P122_J658_class_05_00029_volume.mrc as #5, grid size
100,100,100, pixel 2.78, shown at level 0.0285, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J658_class_00_00029_volume.mrc
Opened cryosparc_P122_J658_class_00_00029_volume.mrc as #6, grid size
100,100,100, pixel 2.78, shown at level 0.0294, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J658_class_01_00029_volume.mrc
Opened cryosparc_P122_J658_class_01_00029_volume.mrc as #7, grid size
100,100,100, pixel 2.78, shown at level 0.0304, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J658_class_02_00029_volume.mrc
Opened cryosparc_P122_J658_class_02_00029_volume.mrc as #8, grid size
100,100,100, pixel 2.78, shown at level 0.0274, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J658_class_03_00029_volume.mrc
Opened cryosparc_P122_J658_class_03_00029_volume.mrc as #9, grid size
100,100,100, pixel 2.78, shown at level 0.0286, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J658_class_04_00029_volume.mrc
Opened cryosparc_P122_J658_class_04_00029_volume.mrc as #10, grid size
100,100,100, pixel 2.78, shown at level 0.0279, step 1, values float32
> volume level 0.14
> volume level 0.1
> tile
6 models tiled
> volume #8 level 0.08873
> volume level 0.08
> tile
6 models tiled
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_00_00030_volume.mrc
Opened cryosparc_P122_J707_class_00_00030_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.0301, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_02_00030_volume.mrc
Opened cryosparc_P122_J707_class_02_00030_volume.mrc as #2, grid size
100,100,100, pixel 2.78, shown at level 0.0294, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_05_00030_volume.mrc
Opened cryosparc_P122_J707_class_05_00030_volume.mrc as #3, grid size
100,100,100, pixel 2.78, shown at level 0.0312, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_04_00030_volume.mrc
Opened cryosparc_P122_J707_class_04_00030_volume.mrc as #4, grid size
100,100,100, pixel 2.78, shown at level 0.0292, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_03_00030_volume.mrc
Opened cryosparc_P122_J707_class_03_00030_volume.mrc as #5, grid size
100,100,100, pixel 2.78, shown at level 0.0269, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J707_class_01_00030_volume.mrc
Opened cryosparc_P122_J707_class_01_00030_volume.mrc as #6, grid size
100,100,100, pixel 2.78, shown at level 0.0261, step 1, values float32
> tile
6 models tiled
> volume level 0.08
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_00_00039_volume.mrc
Opened cryosparc_P122_J747_class_00_00039_volume.mrc as #7, grid size
60,60,60, pixel 4.63, shown at level 0.0389, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_01_00039_volume.mrc
Opened cryosparc_P122_J747_class_01_00039_volume.mrc as #8, grid size
60,60,60, pixel 4.63, shown at level 0.0418, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_02_00039_volume.mrc
Opened cryosparc_P122_J747_class_02_00039_volume.mrc as #9, grid size
60,60,60, pixel 4.63, shown at level 0.0402, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J747_class_03_00039_volume.mrc
Opened cryosparc_P122_J747_class_03_00039_volume.mrc as #10, grid size
60,60,60, pixel 4.63, shown at level 0.0407, step 1, values float32
> volume level 0.08
> tile
10 models tiled
> volume level 0.04
> volume level 0.05
> volume level 0.06
> volume level 0.07
> hide #!6 models
> show #!6 models
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_00_00011_volume.mrc
Opened cryosparc_P122_J843_class_00_00011_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.14, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_01_00011_volume.mrc
Opened cryosparc_P122_J843_class_01_00011_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.138, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_02_00011_volume.mrc
Opened cryosparc_P122_J843_class_02_00011_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.129, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_03_00011_volume.mrc
Opened cryosparc_P122_J843_class_03_00011_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.134, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_04_00011_volume.mrc
Opened cryosparc_P122_J843_class_04_00011_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.133, step 1, values float32
> tile
5 models tiled
> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J880_class_00_00024_volume_sharp.mrc
Opened cryosparc_P122_J880_class_00_00024_volume_sharp.mrc as #6, grid size
128,128,128, pixel 2.17, shown at level 0.0618, step 1, values float32
> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J872_class_01_00044_volume_sharp.mrc
Opened cryosparc_P122_J872_class_01_00044_volume_sharp.mrc as #7, grid size
128,128,128, pixel 2.17, shown at level 0.0633, step 1, values float32
> tile
7 models tiled
> volume #6 level 0.1133
> volume #7 level 0.1191
> ~tile
> volume level 0.07
> volume level 0.1
> volume level 0.4
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> tile
2 models tiled
> volume #6 level 0.0796
> volume #7 level 0.06874
> volume #7 level 0.07672
> volume #6 level 0.05983
> ~tile
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J880_class_00_00024_volume.mrc
Opened cryosparc_P122_J880_class_00_00024_volume.mrc as #8, grid size
128,128,128, pixel 2.17, shown at level 0.0511, step 1, values float32
> volume #8 level 0.06749
> volume #8 level 0.05768
> hide #!8 models
> show #!8 models
> volume #8 level 0.1296
[Repeated 1 time(s)]
> volume #8 level 0.1231
> volume #8 level 0.125
> volume #8 level 0.128
> volume #8 level 0.129
> volume #8 level 0.13
> open C:/Users/lilyh/Downloads/cryosparc_P122_J740_mask.mrc
Opened cryosparc_P122_J740_mask.mrc as #9, grid size 256,256,256, pixel 1.09,
shown at level 1, step 1, values float32
> volume #9 level 0.9861
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J740_mask.mrc
Opened cryosparc_P122_J740_mask.mrc as #1, grid size 256,256,256, pixel 1.09,
shown at level 1, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J880_class_00_00024_volume.mrc
Opened cryosparc_P122_J880_class_00_00024_volume.mrc as #2, grid size
128,128,128, pixel 2.17, shown at level 0.0511, step 1, values float32
> volume #1 level 1
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J880_class_00_00024_volume.mrc
Opened cryosparc_P122_J880_class_00_00024_volume.mrc as #1, grid size
128,128,128, pixel 2.17, shown at level 0.0511, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1209_mask.mrc
Opened cryosparc_P122_J1209_mask.mrc as #2, grid size 128,128,128, pixel 2.17,
shown at level 1, step 1, values float32
> volume #1 level 0.1307
> volume #2 level 0.8505
> select #2
2 models selected
> surface style #2 mesh
> select clear
> volume #1 level 0.1339
> hide #!1 models
> hide #!2 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_05_00028_volume.mrc
Opened cryosparc_P122_J1078_class_05_00028_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.0728, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_00_00028_volume.mrc
Opened cryosparc_P122_J1078_class_00_00028_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.074, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_01_00028_volume.mrc
Opened cryosparc_P122_J1078_class_01_00028_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.075, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_03_00028_volume.mrc
Opened cryosparc_P122_J1078_class_03_00028_volume.mrc as #6, grid size
80,80,80, pixel 3.47, shown at level 0.076, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_02_00028_volume.mrc
Opened cryosparc_P122_J1078_class_02_00028_volume.mrc as #7, grid size
80,80,80, pixel 3.47, shown at level 0.0758, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_04_00028_volume.mrc
Opened cryosparc_P122_J1078_class_04_00028_volume.mrc as #8, grid size
80,80,80, pixel 3.47, shown at level 0.0714, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J705_mask.mrc
Opened cryosparc_P122_J705_mask.mrc as #9, grid size 256,256,256, pixel 1.09,
shown at level 0.0227, step 1, values float32
> volume level 0.4
> hide #!9 models
> tile
6 models tiled
> volume level 0.2
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1208_class_00_00050_volume.mrc
Opened cryosparc_P122_J1208_class_00_00050_volume.mrc as #10, grid size
80,80,80, pixel 3.47, shown at level 0.056, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1208_class_02_00050_volume.mrc
Opened cryosparc_P122_J1208_class_02_00050_volume.mrc as #11, grid size
80,80,80, pixel 3.47, shown at level 0.0548, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1208_class_01_00050_volume.mrc
Opened cryosparc_P122_J1208_class_01_00050_volume.mrc as #12, grid size
80,80,80, pixel 3.47, shown at level 0.0566, step 1, values float32
> volume level 0.2
> tile
9 models tiled
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1208_class_00_00050_volume.mrc
Opened cryosparc_P122_J1208_class_00_00050_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.056, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1208_class_02_00050_volume.mrc
Opened cryosparc_P122_J1208_class_02_00050_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.0548, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1208_class_01_00050_volume.mrc
Opened cryosparc_P122_J1208_class_01_00050_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.0566, step 1, values float32
> volume level 0.2
> tile
3 models tiled
> tile
3 models tiled
> volume #1 level 0.1239
> volume level 0.1
> volume #3 level 0.08258
> close session
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1208_class_00_00050_volume
> (1).mrc"
Opened cryosparc_P122_J1208_class_00_00050_volume (1).mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.056, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1208_class_02_00050_volume
> (1).mrc"
Opened cryosparc_P122_J1208_class_02_00050_volume (1).mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.0548, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1208_class_01_00050_volume
> (1).mrc"
Opened cryosparc_P122_J1208_class_01_00050_volume (1).mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.0566, step 1, values float32
> volume level 0.1
> tile
3 models tiled
> volume #1 level 0.1351
> volume level 0.135
> close session
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_00_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_00_00028_volume (1).mrc as #1, grid size
72,72,72, pixel 3.86, shown at level 0.069, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_05_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_05_00028_volume (1).mrc as #2, grid size
72,72,72, pixel 3.86, shown at level 0.0724, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_04_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_04_00028_volume (1).mrc as #3, grid size
72,72,72, pixel 3.86, shown at level 0.0698, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_03_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_03_00028_volume (1).mrc as #4, grid size
72,72,72, pixel 3.86, shown at level 0.0701, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_02_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_02_00028_volume (1).mrc as #5, grid size
72,72,72, pixel 3.86, shown at level 0.0705, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_01_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_01_00028_volume (1).mrc as #6, grid size
72,72,72, pixel 3.86, shown at level 0.078, step 1, values float32
> tile
6 models tiled
> volume level 0.135
> volume level 0.1
> volume level 0.12
> tile
6 models tiled
> ~tile
> tile
6 models tiled
> volume #1 level 0.1766
> volume #4 level 0.1028
> volume level 0.1
> volume #4 level 0.1402
> volume level 0.14
> tile
6 models tiled
> tile
6 models tiled
> hide #!1 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> tile
3 models tiled
> volume #4 level 0.1745
> volume #4 level 0.1802
> show #!3 models
> show #!1 models
> close session
> open C:/Users/lilyh/Desktop/cryoEM/map_to_model-coot-J1051.pdb
Summary of feedback from opening C:/Users/lilyh/Desktop/cryoEM/map_to_model-
coot-J1051.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK MODEL FROM PHENIX.MAP_TO_MODEL
Ignored bad PDB record found on line 2
REMARK MAP FILE: C:\Users\lilyh\Downloads\cryosparc_P122_J1051_003_volume_map
Chain information for map_to_model-coot-J1051.pdb #1
---
Chain | Description
U | No description available
> show atoms
> hide atoms
> open C:/Users/lilyh/Downloads/2f6h.pdb
2f6h.pdb title:
Myosin V cargo binding domain [more info...]
Chain information for 2f6h.pdb #2
---
Chain | Description | UniProt
X | class V unconventional myosin MYO2; TYPE V myosin heavy chain MYO2; myosin
V MYO2; cell divison control protein 66 | MYO2_YEAST 22-440
Drag select of 159 residues, 1 pseudobonds
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,2.5931,0,1,0,77.6,0,0,1,73.375
> view matrix models #2,1,0,0,54.664,0,1,0,119.43,0,0,1,45.014
> view matrix models #2,1,0,0,64.542,0,1,0,79.41,0,0,1,74.498
> view matrix models #2,1,0,0,65.617,0,1,0,79.114,0,0,1,64.375
> view matrix models #2,1,0,0,65.72,0,1,0,79.344,0,0,1,63.356
> view matrix models #2,1,0,0,112.04,0,1,0,87.325,0,0,1,76.197
> matchmaker #2 to #1
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 map_to_model-coot-J1051.pdb, chain U (#1) with 2f6h.pdb, chain X
(#2), sequence alignment score = 782.2
RMSD between 6 pruned atom pairs is 1.194 angstroms; (across all 293 pairs:
30.730)
> ui mousemode right "translate selected models"
> select clear
Drag select of 2 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.91451,0.36328,-0.17807,-13.493,-0.38503,0.91664,-0.10735,80.356,0.12423,0.16673,0.97814,-37.405
> hide #!2 models
> hide #2.1 models
> select clear
> ui mousemode right "translate selected atoms"
> open "C:/Users/lilyh/Desktop/P122/RebuildPredictedModel_12/Myo2 only afold
> 1150-1574_processed.pdb"
Summary of feedback from opening
C:/Users/lilyh/Desktop/P122/RebuildPredictedModel_12/Myo2 only afold
1150-1574_processed.pdb
---
warning | Ignored bad PDB record found on line 2983
Chain information for Myo2 only afold 1150-1574_processed.pdb #3
---
Chain | Description
C1 | No description available
C2 | No description available
C3 | No description available
> hide #!3 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1051_003_volume_map_sharp.mrc
Opened cryosparc_P122_J1051_003_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.09, shown at level 0.0588, step 1, values float32
> volume #4 level 0.3196
> fitmap #1 inMap #4
Fit molecule map_to_model-coot-J1051.pdb (#1) to map
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#4) using 2009 atoms
average map value = 0.4714, steps = 120
shifted from previous position = 0.818
rotated from previous position = 25.3 degrees
atoms outside contour = 741, contour level = 0.31962
Position of map_to_model-coot-J1051.pdb (#1) relative to
cryosparc_P122_J1051_003_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99999706 0.00031628 -0.00240477 0.37708329
-0.00030363 0.99998612 0.00525979 -0.56706714
0.00240641 -0.00525905 0.99998328 0.47590248
Axis -0.90808733 -0.41534721 -0.05351724
Axis point 0.00000000 88.76834363 118.49821194
Rotation angle (degrees) 0.33184503
Shift along axis -0.13236379
> select clear
> ui mousemode right "translate selected models"
> select #4
2 models selected
> surface style mesh
> select clear
> select #4
2 models selected
> surface style solid
> transparency #4.1 40
> select clear
> set bgColor white
> lighting soft
> lighting full
> hide #!4 models
> style #!1 stick
Changed 2009 atom styles
> show #!1 atoms
> show #!4 models
> hide #!4 models
> hide #!1 models
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_03_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_03_00028_volume (1).mrc as #5, grid size
72,72,72, pixel 3.86, shown at level 0.0701, step 1, values float32
> open "C:/Users/lilyh/Desktop/Myo2 only afold 1150-1574.pdb"
Chain information for Myo2 only afold 1150-1574.pdb #6
---
Chain | Description
C | No description available
> volume #5 level 0.1707
> lighting full
> lighting soft
> lighting simple
> set bgColor white
> set bgColor black
> set bgColor transparent
> lighting soft
Drag select of 146 residues
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,10.21,0,1,0,107.33,0,0,1,73.012
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.68602,0.21156,-0.69615,8.7434,-0.59367,-0.71591,0.36746,100.62,-0.42064,0.66536,0.61673,74.766
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.68602,0.21156,-0.69615,137.1,-0.59367,-0.71591,0.36746,131.8,-0.42064,0.66536,0.61673,144.44
> fitmap #3 inMap #5
Fit molecule Myo2 only afold 1150-1574_processed.pdb (#3) to map
cryosparc_P122_J1152_class_03_00028_volume (1).mrc (#5) using 2974 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 2974, contour level = 0.17074
Position of Myo2 only afold 1150-1574_processed.pdb (#3) relative to
cryosparc_P122_J1152_class_03_00028_volume (1).mrc (#5) 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
> show #!3 models
> hide #!3 models
> hide #6 models
> show #6 models
> fitmap #6 inMap #5
Fit molecule Myo2 only afold 1150-1574.pdb (#6) to map
cryosparc_P122_J1152_class_03_00028_volume (1).mrc (#5) using 3429 atoms
average map value = 0.7167, steps = 56
shifted from previous position = 4.18
rotated from previous position = 13.8 degrees
atoms outside contour = 236, contour level = 0.17074
Position of Myo2 only afold 1150-1574.pdb (#6) relative to
cryosparc_P122_J1152_class_03_00028_volume (1).mrc (#5) coordinates:
Matrix rotation and translation
-0.81305627 0.21178200 -0.54229872 139.93158036
-0.53047848 -0.65326820 0.54021593 134.97348205
-0.23985850 0.72690375 0.64348959 143.37790708
Axis 0.22684755 -0.36750026 -0.90193334
Axis point 97.64951610 17.59239128 0.00000000
Rotation angle (degrees) 155.70197127
Shift along axis -147.17696867
> select clear
> select #5
2 models selected
> color #5.1 dark gray
> select clear
> select #5
2 models selected
> transparency #5.1 40
> select clear
> set bgColor white
> set bgColor #ffffff00
> lighting soft
> lighting full
> volume #5 level 0.2378
> volume #5 level 0.3217
> volume #5 level 0.2994
> hide #6 models
> hide #!5 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1160_class_02_00012_volume.mrc
Opened cryosparc_P122_J1160_class_02_00012_volume.mrc as #7, grid size
72,72,72, pixel 3.86, shown at level 0.109, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1160_class_00_00012_volume.mrc
Opened cryosparc_P122_J1160_class_00_00012_volume.mrc as #8, grid size
72,72,72, pixel 3.86, shown at level 0.114, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1160_class_01_00012_volume.mrc
Opened cryosparc_P122_J1160_class_01_00012_volume.mrc as #9, grid size
72,72,72, pixel 3.86, shown at level 0.112, step 1, values float32
> volume level 0.12
> volume level 0.2
> volume level 0.26
> hide #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> volume #7 level 0.1963
> volume #7 level 0.3121
> volume #8 level 0.2198
> volume #9 level 0.3922
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_05_00028_volume.mrc
Opened cryosparc_P122_J1078_class_05_00028_volume.mrc as #10, grid size
80,80,80, pixel 3.47, shown at level 0.0728, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_00_00028_volume.mrc
Opened cryosparc_P122_J1078_class_00_00028_volume.mrc as #11, grid size
80,80,80, pixel 3.47, shown at level 0.074, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_01_00028_volume.mrc
Opened cryosparc_P122_J1078_class_01_00028_volume.mrc as #12, grid size
80,80,80, pixel 3.47, shown at level 0.075, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_03_00028_volume.mrc
Opened cryosparc_P122_J1078_class_03_00028_volume.mrc as #13, grid size
80,80,80, pixel 3.47, shown at level 0.076, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_02_00028_volume.mrc
Opened cryosparc_P122_J1078_class_02_00028_volume.mrc as #14, grid size
80,80,80, pixel 3.47, shown at level 0.0758, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_04_00028_volume.mrc
Opened cryosparc_P122_J1078_class_04_00028_volume.mrc as #15, grid size
80,80,80, pixel 3.47, shown at level 0.0714, step 1, values float32
> tile
6 models tiled
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> set bgColor white
> lighting soft
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting full
> lighting simple
> lighting full
> volume level 0.3
> volume level 0.25
> volume level 0.24
> volume level 0.23
> volume level 0.2
> volume level 0.18
> tile
6 models tiled
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_05_00028_volume.mrc
Opened cryosparc_P122_J1078_class_05_00028_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.0728, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_00_00028_volume.mrc
Opened cryosparc_P122_J1078_class_00_00028_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.074, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_01_00028_volume.mrc
Opened cryosparc_P122_J1078_class_01_00028_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.075, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_03_00028_volume.mrc
Opened cryosparc_P122_J1078_class_03_00028_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.076, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_02_00028_volume.mrc
Opened cryosparc_P122_J1078_class_02_00028_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.0758, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_04_00028_volume.mrc
Opened cryosparc_P122_J1078_class_04_00028_volume.mrc as #6, grid size
80,80,80, pixel 3.47, shown at level 0.0714, step 1, values float32
> tile
6 models tiled
> volume level 0.2
> tile
6 models tiled
> tile
6 models tiled
> volume #1 level 0.1584
> volume #1 level 0.2297
> volume level 0.23
> volume #2 level 0.3723
> volume #2 level 0.4407
> volume #2 level 0.4293
> volume level 0.429
> ~tile
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!6 models
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_01_00039_volume.mrc
Opened cryosparc_P122_J1129_class_01_00039_volume.mrc as #1, grid size
60,60,60, pixel 4.63, shown at level 0.0415, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_00_00039_volume.mrc
Opened cryosparc_P122_J1129_class_00_00039_volume.mrc as #2, grid size
60,60,60, pixel 4.63, shown at level 0.04, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_02_00039_volume.mrc
Opened cryosparc_P122_J1129_class_02_00039_volume.mrc as #3, grid size
60,60,60, pixel 4.63, shown at level 0.0395, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1129_class_03_00039_volume.mrc
Opened cryosparc_P122_J1129_class_03_00039_volume.mrc as #4, grid size
60,60,60, pixel 4.63, shown at level 0.0416, step 1, values float32
> tile
4 models tiled
> volume level 0.429
> volume level 0.05
> volume level 0.09
> volume #2 level 0.08157
> volume #4 level 0.116
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_00_00028_volume.mrc
Opened cryosparc_P122_J1078_class_00_00028_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.074, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_01_00028_volume.mrc
Opened cryosparc_P122_J1078_class_01_00028_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.075, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_03_00028_volume.mrc
Opened cryosparc_P122_J1078_class_03_00028_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.076, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_02_00028_volume.mrc
Opened cryosparc_P122_J1078_class_02_00028_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.0758, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_04_00028_volume.mrc
Opened cryosparc_P122_J1078_class_04_00028_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.0714, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1078_class_05_00028_volume.mrc
Opened cryosparc_P122_J1078_class_05_00028_volume.mrc as #6, grid size
80,80,80, pixel 3.47, shown at level 0.0728, step 1, values float32
> volume level 0.09
> volume level 0.1
> volume level 0.15
> volume level 0.2
> tile
6 models tiled
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> volume level 0.1
> volume level 0.15
> volume level 0.1
> tile
6 models tiled
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> volume level 0.15
> tile
6 models tiled
> color dark gray
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1153_class_00_00039_volume.mrc
Opened cryosparc_P122_J1153_class_00_00039_volume.mrc as #1, grid size
72,72,72, pixel 3.86, shown at level 0.0608, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1153_class_01_00039_volume.mrc
Opened cryosparc_P122_J1153_class_01_00039_volume.mrc as #2, grid size
72,72,72, pixel 3.86, shown at level 0.0614, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1153_class_02_00039_volume.mrc
Opened cryosparc_P122_J1153_class_02_00039_volume.mrc as #3, grid size
72,72,72, pixel 3.86, shown at level 0.0625, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1153_class_03_00039_volume.mrc
Opened cryosparc_P122_J1153_class_03_00039_volume.mrc as #4, grid size
72,72,72, pixel 3.86, shown at level 0.0616, step 1, values float32
> tile
4 models tiled
> volume level 0.15
> tile
4 models tiled
> tile
4 models tiled
> volume level 0.1
> volume level 0.08
> close session
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_00_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_00_00028_volume (1).mrc as #1, grid size
72,72,72, pixel 3.86, shown at level 0.069, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_01_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_01_00028_volume (1).mrc as #2, grid size
72,72,72, pixel 3.86, shown at level 0.078, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_02_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_02_00028_volume (1).mrc as #3, grid size
72,72,72, pixel 3.86, shown at level 0.0705, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_03_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_03_00028_volume (1).mrc as #4, grid size
72,72,72, pixel 3.86, shown at level 0.0701, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_04_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_04_00028_volume (1).mrc as #5, grid size
72,72,72, pixel 3.86, shown at level 0.0698, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1152_class_05_00028_volume
> (1).mrc"
Opened cryosparc_P122_J1152_class_05_00028_volume (1).mrc as #6, grid size
72,72,72, pixel 3.86, shown at level 0.0724, step 1, values float32
> volume level 0.08
> tile
6 models tiled
> volume level 0.1
> tile
6 models tiled
> volume level 0.15
> tile
6 models tiled
> volume #5 level 0.1735
> close session
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1155_001_volume_map_sharp
> (1).mrc"
Opened cryosparc_P122_J1155_001_volume_map_sharp (1).mrc as #1, grid size
256,256,256, pixel 1.09, shown at level 0.0195, step 1, values float32
> volume #1 level 0.06944
> volume #1 level 0.07684
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1096_class_00_00022_volume.mrc
Opened cryosparc_P122_J1096_class_00_00022_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.0913, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1096_class_03_00022_volume.mrc
Opened cryosparc_P122_J1096_class_03_00022_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.0889, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1096_class_02_00022_volume.mrc
Opened cryosparc_P122_J1096_class_02_00022_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.0962, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1096_class_01_00022_volume.mrc
Opened cryosparc_P122_J1096_class_01_00022_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.0971, step 1, values float32
> volume level 0.15
> tile
4 models tiled
> volume level 0.3
> tile
4 models tiled
> tile
4 models tiled
> volume #1 level 0.2031
> volume #2 level 0.1215
> volume #3 level 0.1541
> volume #4 level 0.3286
> hide #!3 models
> show #!3 models
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1102_002_volume_map_sharp.mrc
Opened cryosparc_P122_J1102_002_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.09, shown at level 0.0346, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1105_001_volume_map_sharp.mrc
Opened cryosparc_P122_J1105_001_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.09, shown at level 0.0237, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1103_002_volume_map_sharp.mrc
Opened cryosparc_P122_J1103_002_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.09, shown at level 0.0386, step 1, values float32
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1104_002_volume_map_sharp
> (1).mrc"
Opened cryosparc_P122_J1104_002_volume_map_sharp (1).mrc as #4, grid size
256,256,256, pixel 1.09, shown at level 0.0272, step 1, values float32
> volume level 0.3
> tile
4 models tiled
> volume #1 level 0.1779
> volume #1 level 0.1845
> volume level 0.18
> tile
4 models tiled
> volume #1 level 0.1569
> volume level 0.15
> volume #2 level 0.09835
> volume level 0.09
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1116_class_00_00023_volume.mrc
Opened cryosparc_P122_J1116_class_00_00023_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.0861, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1116_class_01_00023_volume.mrc
Opened cryosparc_P122_J1116_class_01_00023_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.0864, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1116_class_02_00023_volume.mrc
Opened cryosparc_P122_J1116_class_02_00023_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.0859, step 1, values float32
> volume level 0.09
> volume level 0.1
> volume level 0.3
> tile
3 models tiled
> tile
3 models tiled
> volume level 0.1
> volume level 0.15
[Repeated 1 time(s)]
> volume #2 level 0.173
> volume #2 level 0.15
> ~tile
> hide #!2 models
> hide #!3 models
> volume #1 level 0.5119
> show #!2 models
> show #!3 models
> volume level 0.5
> tile
3 models tiled
> hide #!2 models
> ~tile
> volume #1 level 0.4152
> show #!2 models
> hide #!1 models
> hide #!3 models
> volume #2 level 0.3906
> volume #2 level 0.6209
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ~tile
> volume level 0.5
> tile
3 models tiled
> volume #1 level 0.2116
> volume level 0.2
> tile
3 models tiled
> hide #!2 models
> tile
2 models tiled
> ~tile
> volume #3 level 0.3842
> hide #!3 models
> volume #1 level 0.2226
> volume #2 level 0.1942
> hide #!1 models
> volume #3 level 0.5051
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> close session
> open C:/Users/lilyh/Desktop/P122/MapToModel_11/map_to_model.pdb
Summary of feedback from opening
C:/Users/lilyh/Desktop/P122/MapToModel_11/map_to_model.pdb
---
warnings | Ignored bad PDB record found on line 1
Ignored bad PDB record found on line 2
REMARK MODEL FROM PHENIX.MAP_TO_MODEL
Ignored bad PDB record found on line 3
REMARK MAP FILE:
C:\Users\lilyh\Downloads\cryosparc_P122_J1051_003_volume_map_sharp.mrc
Ignored bad PDB record found on line 4
Ignored bad PDB record found on line 2015
Chain information for map_to_model.pdb #1
---
Chain | Description
U | No description available
> close session
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1089_002_volume_map_sharp
> (1).mrc"
Opened cryosparc_P122_J1089_002_volume_map_sharp (1).mrc as #1, grid size
256,256,256, pixel 1.09, shown at level 0.0447, step 1, values float32
> volume #1 level 0.2579
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1051_003_volume_map_sharp.mrc
Opened cryosparc_P122_J1051_003_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.09, shown at level 0.0588, step 1, values float32
> volume #2 level 0.2647
> 0.265
Unknown command: 0.265
> volume #2 level 0.3814
> volume #2 color black
> volume #2 color #6d6d6d
> volume #1 level 0.2456
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1042_class_00_00010_volume.mrc
Opened cryosparc_P122_J1042_class_00_00010_volume.mrc as #1, grid size
72,72,72, pixel 3.86, shown at level 0.114, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1042_class_01_00010_volume.mrc
Opened cryosparc_P122_J1042_class_01_00010_volume.mrc as #2, grid size
72,72,72, pixel 3.86, shown at level 0.129, step 1, values float32
> 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
#3
---
Chain | Description
B | No description available
C | No description available
Drag select of 27 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.2549,0.92463,-0.28299,-6.9764,0.53822,-0.3788,-0.75288,5.0223,-0.80333,0.039604,-0.59421,-7.5446
> view matrix models
> #3,0.11376,0.98962,-0.087837,-7.1012,0.58456,-0.13816,-0.7995,4.0569,-0.80333,0.039604,-0.59421,-7.5446
> view matrix models
> #3,-0.42843,-0.73148,0.53046,-0.0093898,-0.41364,0.68071,0.60459,1.7938,-0.80333,0.039604,-0.59421,-7.5446
> view matrix models
> #3,-0.39273,-0.7853,0.4786,0.16583,-0.44768,0.61784,0.64642,2.0655,-0.80333,0.039604,-0.59421,-7.5446
> view matrix models
> #3,0.42214,-0.66593,-0.61509,-1.0136,-0.42006,-0.74496,0.51825,7.2768,-0.80333,0.039604,-0.59421,-7.5446
> view matrix models
> #3,0.5383,-0.37849,-0.75298,-2.2207,-0.25473,-0.92476,0.28274,7.8213,-0.80333,0.039604,-0.59421,-7.5446
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.5383,-0.37849,-0.75298,135.77,-0.25473,-0.92476,0.28274,131.51,-0.80333,0.039604,-0.59421,135.26
> select clear
> select /B:59
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.62848,0.025224,-0.77742,134.36,-0.7778,0.02808,-0.62788,123.23,0.0059917,0.99929,0.037267,135.88
> view matrix models
> #3,-0.88593,0.17348,-0.43016,129.96,-0.4077,-0.73348,0.54387,131.03,-0.22117,0.6572,0.72053,138.6
> fitmap #1 inMap #2
Fit map cryosparc_P122_J1042_class_00_00010_volume.mrc in map
cryosparc_P122_J1042_class_01_00010_volume.mrc using 3728 points
correlation = 0.9631, correlation about mean = 0.9592, overlap = 837.2
steps = 40, shift = 0.101, angle = 0.327 degrees
Position of cryosparc_P122_J1042_class_00_00010_volume.mrc (#1) relative to
cryosparc_P122_J1042_class_01_00010_volume.mrc (#2) coordinates:
Matrix rotation and translation
0.99998745 -0.00495926 0.00071517 0.63612991
0.00496118 0.99998401 -0.00271530 -0.37162468
-0.00070169 0.00271881 0.99999606 -0.25532189
Axis 0.47669018 0.12428963 0.87024052
Axis point 76.18176737 124.72789415 0.00000000
Rotation angle (degrees) 0.32657787
Shift along axis 0.03485633
> fitmap #1 inMap #2
Fit map cryosparc_P122_J1042_class_00_00010_volume.mrc in map
cryosparc_P122_J1042_class_01_00010_volume.mrc using 3728 points
correlation = 0.9631, correlation about mean = 0.9592, overlap = 837.6
steps = 36, shift = 0.00926, angle = 0.0114 degrees
Position of cryosparc_P122_J1042_class_00_00010_volume.mrc (#1) relative to
cryosparc_P122_J1042_class_01_00010_volume.mrc (#2) coordinates:
Matrix rotation and translation
0.99998797 -0.00484205 0.00078657 0.60180728
0.00484406 0.99998496 -0.00257051 -0.38000057
-0.00077411 0.00257428 0.99999639 -0.22930589
Axis 0.46440919 0.14087978 0.87434375
Axis point 79.56479030 121.64829425 0.00000000
Rotation angle (degrees) 0.31736700
Shift along axis 0.02545826
Must specify one map, got 0
> select /B:90
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.19076,0.52767,-0.82775,129.55,-0.84806,-0.51327,-0.13175,126.69,-0.49438,0.67685,0.5454,137.12
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.19076,0.52767,-0.82775,146.04,-0.84806,-0.51327,-0.13175,140.94,-0.49438,0.67685,0.5454,149.69
Must specify one map, got 0
> fitmap #3 inMap #1
Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) to map cryosparc_P122_J1042_class_00_00010_volume.mrc (#1) using 4737
atoms
average map value = 0.5359, steps = 104
shifted from previous position = 12
rotated from previous position = 45.8 degrees
atoms outside contour = 1061, contour level = 0.11382
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#3) relative to cryosparc_P122_J1042_class_00_00010_volume.mrc (#1)
coordinates:
Matrix rotation and translation
-0.81457406 0.20678226 -0.54195037 139.99847739
-0.52748698 -0.65272927 0.54378489 134.90080452
-0.24130181 0.72882485 0.64077126 143.63080783
Axis 0.22711888 -0.36901740 -0.90124535
Axis point 97.60556122 17.55309842 0.00000000
Rotation angle (degrees) 155.96066783
Shift along axis -147.43104438
> select clear
> hide #!2 models
> volume #1 level 0.2378
> volume #1 level 0.1138
> volume #1 level 0.2378
> show #!2 models
> hide #!1 models
> volume #2 level 0.2088
[Repeated 1 time(s)]
> show #!1 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J863_class_01_00017_volume.mrc
Opened cryosparc_P122_J863_class_01_00017_volume.mrc as #4, grid size
72,72,72, pixel 3.86, shown at level 0.0916, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J863_class_00_00017_volume.mrc
Opened cryosparc_P122_J863_class_00_00017_volume.mrc as #5, grid size
72,72,72, pixel 3.86, shown at level 0.0925, step 1, values float32
> show #!2 models
> show #!1 models
> 0.265
Unknown command: 0.265
> 0.265
Unknown command: 0.265
> volume level 0.265
> tile
4 models tiled
> volume level 0.2
> volume level 0.15
> volume level 0.16
> volume level 0.18
> volume level 0.16
> volume level 0.15
> volume level 0.13
> volume level 0.14
> volume level 0.12
> volume level 0.1
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #!5 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J876_001_volume_map_sharp.mrc
Opened cryosparc_P122_J876_001_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.09, shown at level 0.0597, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J905_004_volume_map_sharp.mrc
Opened cryosparc_P122_J905_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.09, shown at level 0.0176, step 1, values float32
> volume level 0.1
> volume level 0.4
> tile
1 model tiled
> ~tile
> tile
1 model tiled
> volume level 0.08
> tile
2 models tiled
> volume #7 level 0.04361
> volume #6 level 0.2405
> volume #5 level 0.1491
> volume #7 level 0.04641
> close #7
> hide #!5 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J898_class_00_00008_volume.mrc
Opened cryosparc_P122_J898_class_00_00008_volume.mrc as #7, grid size
72,72,72, pixel 3.86, shown at level 0.143, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J898_class_01_00008_volume.mrc
Opened cryosparc_P122_J898_class_01_00008_volume.mrc as #8, grid size
72,72,72, pixel 3.86, shown at level 0.142, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J898_class_02_00008_volume.mrc
Opened cryosparc_P122_J898_class_02_00008_volume.mrc as #9, grid size
72,72,72, pixel 3.86, shown at level 0.143, step 1, values float32
> tile
3 models tiled
> volume level 0.4
> volume level 0.09
> volume level 0.1
[Repeated 1 time(s)]
> volume level 0.17
> volume level 0.19
> volume #9 level 0.2124
> volume #7 level 0.1955
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1212_003_volume_map.mrc
Opened cryosparc_P122_J1212_003_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.09, shown at level 0.0104, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1211_001_volume_map.mrc
Opened cryosparc_P122_J1211_001_volume_map.mrc as #2, grid size 256,256,256,
pixel 1.09, shown at level 0.0132, step 1, values float32
> hide #!2 models
> volume #1 level 0.0482
> volume #1 level 0.07112
> volume #1 level 0.07786
> hide #!1 models
> volume #2 level 0.09416
> volume #2 level 0.1137
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #1 level 0.08191
> volume #1 level 0.06708
> volume #1 level 0.0482
> volume #1 level 0.02528
> volume #1 level 0.02393
> volume #1 level 0.03202
> volume #1 level 0.04146
> volume #1 level 0.04415
> volume #1 level 0.0482
> volume #1 level 0.05629
> volume #1 level 0.05764
> volume #1 level 0.05899
> volume #1 level 0.06033
> volume #1 level 0.06303
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_00_00011_volume.mrc
Opened cryosparc_P122_J843_class_00_00011_volume.mrc as #1, grid size
80,80,80, pixel 3.47, shown at level 0.14, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_01_00011_volume.mrc
Opened cryosparc_P122_J843_class_01_00011_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.138, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_02_00011_volume.mrc
Opened cryosparc_P122_J843_class_02_00011_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.129, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_03_00011_volume.mrc
Opened cryosparc_P122_J843_class_03_00011_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.134, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_04_00011_volume.mrc
Opened cryosparc_P122_J843_class_04_00011_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.133, step 1, values float32
> volume level 0.19
> volume level 0.3
> tile
5 models tiled
> volume #1 level 0.1718
> volume #1 level 0.1495
> volume level 0.149
> ~tile
> volume level 0.3
> volume level 0.2
> volume level 0.25
> volume level 0.26
> volume level 0.28
> volume level 0.3
> volume level 0.4
> volume level 0.35
> volume level 0.3
> volume level 0.31
> volume level 0.32
> volume level 0.33
> hide #!4 models
> hide #!3 models
> hide #!1 models
> hide #!2 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!3 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1213_mask.mrc
Opened cryosparc_P122_J1213_mask.mrc as #6, grid size 80,80,80, pixel 3.47,
shown at level 1, step 1, values float32
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1213_mask.mrc
Opened cryosparc_P122_J1213_mask.mrc as #1, grid size 80,80,80, pixel 3.47,
shown at level 1, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_00_00011_volume.mrc
Opened cryosparc_P122_J843_class_00_00011_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.14, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_01_00011_volume.mrc
Opened cryosparc_P122_J843_class_01_00011_volume.mrc as #3, grid size
80,80,80, pixel 3.47, shown at level 0.138, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_02_00011_volume.mrc
Opened cryosparc_P122_J843_class_02_00011_volume.mrc as #4, grid size
80,80,80, pixel 3.47, shown at level 0.129, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_03_00011_volume.mrc
Opened cryosparc_P122_J843_class_03_00011_volume.mrc as #5, grid size
80,80,80, pixel 3.47, shown at level 0.134, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_04_00011_volume.mrc
Opened cryosparc_P122_J843_class_04_00011_volume.mrc as #6, grid size
80,80,80, pixel 3.47, shown at level 0.133, step 1, values float32
> hide #!3 models
> hide #!5 models
> hide #!4 models
> hide #!6 models
> volume #2 level 0.3296
> hide #!2 models
> volume #1 level 0.02994
> show #!2 models
> volume #1 level 1
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #1 level 0.9601
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1210_001_volume_map_sharp.mrc
Opened cryosparc_P122_J1210_001_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.09, shown at level 0.0276, step 1, values float32
> volume #1 level 0.1561
> volume #1 level 0.06554
> hide #!1 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1211_001_volume_map.mrc
Opened cryosparc_P122_J1211_001_volume_map.mrc as #2, grid size 256,256,256,
pixel 1.09, shown at level 0.0132, step 1, values float32
> volume #2 level 0.03756
> close session
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1210_002_volume_map (1).mrc"
Opened cryosparc_P122_J1210_002_volume_map (1).mrc as #1, grid size
256,256,256, pixel 1.09, shown at level 0.00467, step 1, values float32
> volume #1 level 0.03164
> volume #1 level 0.02306
> volume #1 level 0.05002
> hide #!1 models
> open C:/Users/lilyh/Downloads/cryosparc_P122_J843_class_00_00011_volume.mrc
Opened cryosparc_P122_J843_class_00_00011_volume.mrc as #2, grid size
80,80,80, pixel 3.47, shown at level 0.14, step 1, values float32
> volume #2 level 0.319
> volume #2 level 0.1997
> close session
> open
> C:/Users/lilyh/Downloads/cryosparc_P122_J880_class_00_00024_volume_sharp.mrc
Opened cryosparc_P122_J880_class_00_00024_volume_sharp.mrc as #1, grid size
128,128,128, pixel 2.17, shown at level 0.0618, step 1, values float32
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1209_mask.mrc
Opened cryosparc_P122_J1209_mask.mrc as #2, grid size 128,128,128, pixel 2.17,
shown at level 1, step 1, values float32
> volume #1 level 0.1696
> volume #2 level 1
> volume #1 level 0.07338
> volume #1 level 0.1542
> volume #1 level 0.1657
> open C:/Users/lilyh/Downloads/cryosparc_P122_J880_class_00_00024_volume.mrc
Opened cryosparc_P122_J880_class_00_00024_volume.mrc as #3, grid size
128,128,128, pixel 2.17, shown at level 0.0511, step 1, values float32
> volume #3 level 0.05114
> volume #3 level 0.1339
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1209_mask (1).mrc"
Opened cryosparc_P122_J1209_mask (1).mrc as #4, grid size 128,128,128, pixel
2.17, shown at level 1, step 1, values float32
> volume #4 level 1
> volume #3 level 0.1437
> volume #3 level 0.06191
> ui tool show "Hide Dust"
> volume #3 level 0.06191
> surface dust #3 size 7.84
[Repeated 1 time(s)]
> surface dust #3 size 11.48
> surface dust #3 size 11.56
> surface dust #3 size 11.64
> surface dust #3 size 30.35
> volume #3 level 0.06845
> volume #3 level 0.134
> volume #3 level 0.05877
> surface dust #3 size 30.35
> surface undust #3
[Repeated 1 time(s)]
> close #3
> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1155_001_volume_map_sharp
> (2).mrc"
Opened cryosparc_P122_J1155_001_volume_map_sharp (2).mrc as #3, grid size
256,256,256, pixel 1.09, shown at level 0.0195, step 1, values float32
> volume #3 level 0.06894
[Repeated 1 time(s)]
> volume #3 level 0.1165
> close session
> open C:/Users/lilyh/Downloads/cryosparc_P122_J1051_003_volume_map_sharp.mrc
Opened cryosparc_P122_J1051_003_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.09, shown at level 0.0588, step 1, values float32
> open 6IXP
Summary of feedback from opening 6IXP fetched from pdb
---
note | Fetching compressed mmCIF 6ixp from
http://files.rcsb.org/download/6ixp.cif
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 files |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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