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Opened 2 years ago
Closed 2 years ago
#10322 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.
> open "D:\Back-up\Baker Lab\Structures\Data Processing\NCCAT Oct
> 2023\Colored_sandwich.cxs" format session
Opened cryosparc_P123_J94_map_sharp_not as clean.mrc z flip as #11, grid size
300,300,300, pixel 1.06, shown at level 0.0168, step 1, values float32
Opened cryosparc_P123_J243_map_sharp(1).mrc as #13, grid size 400,400,400,
pixel 1.06, shown at level 0.0121, step 2, values float32
Log from Fri Dec 1 15:07:38 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:\Back-up\Baker Lab\Structures\Data Processing\NCCAT Oct
> 2023\WTF_HighestRes.cxs" format session
Opened cryosparc_P67_J843_map_sharp_merge.mrc as #4, grid size 200,200,200,
pixel 1.24, shown at level 0.0231, step 1, values float32
Opened cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip as #8, grid size
300,300,300, pixel 1.06, shown at level 0.0191, step 1, values float32
Opened cryosparc_P123_J94_map_sharp_not as clean.mrc z flip as #11, grid size
300,300,300, pixel 1.06, shown at level 0.0168, step 1, values float32
Log from Sun Nov 26 15:48:41 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\mbegl\OneDrive\transfer\HAILMARY.cxs format session
Opened cryosparc_P67_J843_map_sharp_merge.mrc as #4, grid size 200,200,200,
pixel 1.24, shown at level 0.0231, step 1, values float32
Opened cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip as #8, grid size
300,300,300, pixel 1.06, shown at level 0.0571, step 1, values float32
Opened AP3D1.pdb map 5 as #11, grid size 94,59,67, pixel 1.67, shown at level
0.0923, step 1, values float32
Opened AP3D1.pdb map 5 as #12, grid size 94,59,67, pixel 1.67, shown at level
0.0923, step 1, values float32
Opened AP3B1.pdb map 5 as #13, grid size 89,74,61, pixel 1.67, shown at level
0.0869, step 1, values float32
Opened AP3B1.pdb map 5 as #14, grid size 89,74,61, pixel 1.67, shown at level
0.0869, step 1, values float32
Opened AP3M1.pdb map 5 as #15, grid size 40,36,49, pixel 1.67, shown at level
0.0932, step 1, values float32
Opened AP3M1.pdb map 5 as #16, grid size 40,36,49, pixel 1.67, shown at level
0.0932, step 1, values float32
Opened AP3S1.pdb map 5 as #17, grid size 60,54,44, pixel 1.67, shown at level
0.082, step 1, values float32
Log from Sat Nov 25 18:56:35 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\Back-up\Baker Lab\Structures\Data Processing\NCCAT Oct
> 2023\WTF.cxs" format session
Opened cryosparc_P67_J843_map_sharp_merge.mrc as #4, grid size 200,200,200,
pixel 1.24, shown at level 0.0231, step 1, values float32
Opened chaos.mrc as #7, grid size 80,80,80, pixel 3.97, shown at level 0.335,
step 1, values float32
Log from Sat Nov 25 00:24:07 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Dec
> 2022/Rick_processing/merged_AFdocked.cxs"
Opened cryosparc_P67_J843_map_sharp_merge.mrc as #4, grid size 200,200,200,
pixel 1.24, shown at level 0.0231, step 1, values float32
Log from Wed Oct 11 18:52:50 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\Back-up\Baker Lab\Structures\Data Processing\NCCAT Dec
> 2022\Apo_AP3\40Tilt\AF_docked_2.cxs" format session
Opened cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc as
#3, grid size 300,300,300, pixel 0.826, shown at level 0.0422, step 1, values
float32
Opened Apo_40degree_EMhancer.mrc as #1, grid size 128,128,128, pixel 1.65,
shown at level 0.267, step 1, values float32
Log from Wed Mar 8 12:55:44 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\Back-up\Baker Lab\Structures\Data
> Processing\RB_AFintoChameleon_colored.cxs" format session
Opened cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc as
#3, grid size 300,300,300, pixel 0.826, shown at level 0.0422, step 1, values
float32
Log from Sun Nov 13 22:44:10 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\Back-up\Baker Lab\Structures\Data
> Processing\RB_AFintoChameleon.cxs" format session
Opened cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc as
#3, grid size 300,300,300, pixel 0.826, shown at level 0.0422, step 1, values
float32
Log from Wed Aug 17 02:02:43 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\Back-up\Baker Lab\Structures\Data Processing\RB_AP3_NCCAT_it2.cxs"
> format session
Opened RB_AP3_NCCAT.mrc as #1, grid size 300,300,300, pixel 0.826, shown at
level 0.131, step 2, values float32
Opened AP3.cif map 5 as #4, grid size 43,61,54, pixel 1.67, shown at level
0.0818, step 1, values float32
Log from Thu Jun 30 14:01:38 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\Back-up\Baker Lab\Structures\Data Processing\RB_AP3_NCCAT_it1.cxs"
> format session
Opened RB_AP3_NCCAT.mrc as #1, grid size 300,300,300, pixel 0.826, shown at
level 0.131, step 2, values float32
Opened AP3.cif map 5 as #3, grid size 36,42,42, pixel 1.67, shown at level
0.093, step 1, values float32
Opened AP3.cif map 5 as #4, grid size 36,42,42, pixel 1.67, shown at level
0.093, step 1, values float32
Log from Thu Jun 30 13:49:22 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\Back-up\Baker Lab\Structures\RB_AP3_NCCAT.cxs" format session
Opened RB_AP3_NCCAT.mrc as #1, grid size 300,300,300, pixel 0.826, shown at
level 0.131, step 2, values float32
Log from Thu Jun 30 12:34:46 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\\\Users\\\mbegl\\\OneDrive\\\Desktop\\\RB_AP3_NCCAT.mrc
Opened RB_AP3_NCCAT.mrc as #1, grid size 300,300,300, pixel 0.826, shown at
level 0.0561, step 2, values float32
> volume #1 level 0.1312
> save "D:/Back-up/Baker Lab/Structures/RB_AP3_NCCAT.cxs"
——— End of log from Thu Jun 30 12:34:46 2022 ———
opened ChimeraX session
> open "D:/Back-up/Baker Lab/Structures/AlphaFold/AP3.cif"
Summary of feedback from opening D:/Back-up/Baker
Lab/Structures/AlphaFold/AP3.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for AP3.cif
---
Chain | Description
2.1/A | No description available
2.2/A | No description available
2.3/A | No description available
2.4/A | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #2.3/A
Alignment identifier is 2.3/A
> select #2.3/A:165
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.3/A:165-418
2009 atoms, 2055 bonds, 254 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2
13051 atoms, 13277 bonds, 1651 residues, 5 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-16.468,0,1,0,8.3387,0,0,1,-61.47
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.15155,-0.29634,-0.94298,500.26,0.50467,0.79709,-0.3316,11.405,0.84991,-0.52615,0.028753,70.899
> view matrix models
> #2,-0.14972,-0.97977,-0.13279,445.16,0.33215,0.07666,-0.9401,322.4,0.93127,-0.18486,0.31396,-75.505
> view matrix models
> #2,-0.3334,-0.94274,-0.0089029,450.6,0.18641,-0.056659,-0.98084,389.06,0.92417,-0.32867,0.19462,-19.838
> view matrix models
> #2,-0.61406,-0.7636,-0.1996,520.3,0.17404,0.11567,-0.97792,358.46,0.76983,-0.63524,0.061873,100.56
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.61406,-0.7636,-0.1996,487.89,0.17404,0.11567,-0.97792,283.35,0.76983,-0.63524,0.061873,73.894
> view matrix models
> #2,-0.61406,-0.7636,-0.1996,455.83,0.17404,0.11567,-0.97792,300.22,0.76983,-0.63524,0.061873,86.581
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.72726,-0.42945,0.53541,252.71,-0.32674,-0.4694,-0.82031,481.16,0.60361,-0.77152,0.20106,116.1
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.72726,-0.42945,0.53541,235.81,-0.32674,-0.4694,-0.82031,483.95,0.60361,-0.77152,0.20106,115.48
> ui tool show "Fit in Map"
Fit molecule AP3.cif (#2.1) to map RB_AP3_NCCAT.mrc (#1) using 4858 atoms
average map value = 0.0787, steps = 552
shifted from previous position = 16.7
rotated from previous position = 42.1 degrees
atoms outside contour = 3529, contour level = 0.1312
Position of AP3.cif (#2.1) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.74882746 -0.49019706 -0.44605412 132.04750561
0.42854293 0.87151940 -0.23833776 -14.40025342
0.50557729 -0.01267948 0.86268814 -58.48992974
Axis 0.16816739 -0.70918458 0.68467289
Axis point 161.79731822 -0.00000000 207.80266020
Rotation angle (degrees) 42.13915575
Shift along axis -7.62794739
> view matrix models
> #2,-0.72726,-0.42945,0.53541,232.43,-0.32674,-0.4694,-0.82031,491.51,0.60361,-0.77152,0.20106,105.3
> view matrix models
> #2,-0.72726,-0.42945,0.53541,229.98,-0.32674,-0.4694,-0.82031,489.19,0.60361,-0.77152,0.20106,101.65
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.6333,-0.64164,0.43269,273.04,-0.15183,-0.44523,-0.88245,461.48,0.75887,-0.62455,0.18455,44.537
Fit molecule AP3.cif (#2.1) to map RB_AP3_NCCAT.mrc (#1) using 4858 atoms
average map value = 0.1199, steps = 176
shifted from previous position = 5.48
rotated from previous position = 16.4 degrees
atoms outside contour = 3076, contour level = 0.1312
Position of AP3.cif (#2.1) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.95928347 -0.27512031 -0.06390648 47.83767096
0.27577720 0.96122038 0.00152181 -27.63963106
0.06100953 -0.01908380 0.99795473 -8.52885845
Axis -0.03645347 -0.22098936 0.97459471
Axis point 125.16062468 154.83279769 0.00000000
Rotation angle (degrees) 16.41717606
Shift along axis -3.94796495
> ~select #2
Nothing selected
> select #2.1
4858 atoms, 4939 bonds, 617 residues, 1 model selected
Opened AP3.cif map 5 as #3, grid size 68,77,81, pixel 1.67, shown at level
0.0919, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 19093 points
correlation = 0.02291, correlation about mean = 0.02673, overlap = 0.05535
steps = 620, shift = 2.49, angle = 12 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.97822241 0.20457086 0.03509531 -49.46370760
-0.20528665 0.97853384 0.01813616 40.70003056
-0.03063181 -0.02494580 0.99921939 11.93248331
Axis -0.10323386 0.15749663 -0.98210874
Axis point 171.21484405 260.12142587 0.00000000
Rotation angle (degrees) 12.04395256
Shift along axis -0.20254925
Average map value = 0.04617 for 4858 atoms, 4057 outside contour
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 19093 points
correlation = 0.02293, correlation about mean = 0.02664, overlap = 0.05538
steps = 108, shift = 0.0241, angle = 0.0283 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.97825297 0.20447431 0.03480499 -49.38195754
-0.20519464 0.97854584 0.01852547 40.60043007
-0.03027029 -0.02526439 0.99922241 11.93848503
Axis -0.10498387 0.15601456 -0.98215979
Axis point 170.85849666 259.78494409 0.00000000
Rotation angle (degrees) 12.03769339
Shift along axis -0.20693270
Average map value = 0.04603 for 4858 atoms, 4057 outside contour
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 19093 points
correlation = 0.02297, correlation about mean = 0.02691, overlap = 0.05547
steps = 144, shift = 0.052, angle = 0.0717 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.97834387 0.20400787 0.03498658 -49.37176437
-0.20469821 0.97867047 0.01739974 40.71355079
-0.03069065 -0.02418462 0.99923630 11.80151226
Axis -0.09995448 0.15786544 -0.98238872
Axis point 171.94298149 260.37486020 0.00000000
Rotation angle (degrees) 12.00613805
Shift along axis -0.23148086
Average map value = 0.04636 for 4858 atoms, 4055 outside contour
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,0.97834,0.20401,0.034987,-57.242,-0.2047,0.97867,0.0174,41.027,-0.030691,-0.024185,0.99924,9.9688
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 19093 points
correlation = 0.0213, correlation about mean = 0.0253, overlap = 0.06031
steps = 112, shift = 2.89, angle = 2.61 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.98479477 0.16778496 0.04502734 -50.95170436
-0.16973794 0.98451782 0.04374569 27.12497814
-0.03699035 -0.05072337 0.99802748 16.19439573
Axis -0.26244138 0.22785065 -0.93766124
Axis point 125.82671547 308.24416599 0.00000000
Rotation angle (degrees) 10.36866829
Shift along axis 4.36742212
Average map value = 0.05664 for 4858 atoms, 3855 outside contour
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 19093 points
correlation = 0.02125, correlation about mean = 0.02542, overlap = 0.06017
steps = 96, shift = 0.00977, angle = 0.00897 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.98479579 0.16776617 0.04507520 -50.96015951
-0.16971614 0.98452810 0.04359888 27.15464995
-0.03706339 -0.05058598 0.99803174 16.16963311
Axis -0.26171365 0.22824039 -0.93776985
Axis point 126.01068086 308.35780492 0.00000000
Rotation angle (degrees) 10.36619331
Shift along axis 4.37136306
Average map value = 0.05666 for 4858 atoms, 3856 outside contour
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 19093 points
correlation = 0.02125, correlation about mean = 0.02543, overlap = 0.06018
steps = 184, shift = 0.00984, angle = 0.0102 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.98478668 0.16785228 0.04495330 -50.95168100
-0.16979239 0.98451932 0.04350001 27.18979474
-0.03695582 -0.05047096 0.99804156 16.12496501
Axis -0.26108732 0.22757489 -0.93810612
Axis point 126.18701518 308.20026692 0.00000000
Rotation angle (degrees) 10.36747685
Shift along axis 4.36362389
Average map value = 0.0567 for 4858 atoms, 3853 outside contour
> ~select #2.1
Nothing selected
> select #2.4
1525 atoms, 1551 bonds, 193 residues, 1 model selected
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 19093 points
correlation = 0.02125, correlation about mean = 0.02544, overlap = 0.06017
steps = 120, shift = 0.00583, angle = 0.00996 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.98478290 0.16791727 0.04479318 -50.92886628
-0.16984849 0.98451057 0.04347903 27.20954856
-0.03679848 -0.05042546 0.99804967 16.07919092
Axis -0.26088507 0.22667766 -0.93837957
Axis point 126.28767674 307.95864930 0.00000000
Rotation angle (degrees) 10.36818066
Shift along axis 4.36599339
Average map value = 0.05675 for 4858 atoms, 3851 outside contour
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 19093 points
correlation = 0.02126, correlation about mean = 0.02542, overlap = 0.0602
steps = 76, shift = 0.00509, angle = 0.00613 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.98478546 0.16787605 0.04489129 -50.94397503
-0.16981267 0.98451624 0.04349058 27.19727826
-0.03689518 -0.05045200 0.99804476 16.10998552
Axis -0.26100408 0.22723030 -0.93821280
Axis point 126.22871321 308.12005270 0.00000000
Rotation angle (degrees) 10.36765238
Shift along axis 4.36203667
Average map value = 0.05672 for 4858 atoms, 3853 outside contour
> view matrix models
> #2.4,1,-3.8858e-16,-1.3878e-16,0.041235,-5.5511e-17,1,-5.5511e-17,-0.1567,3.0815e-32,-2.7756e-17,1,0.34064
> ui mousemode right "rotate selected models"
> view matrix models
> #2.4,0.91226,-0.40194,0.07895,90.75,0.37437,0.89634,0.23752,-101.19,-0.16624,-0.18713,0.96817,81.87
> ui mousemode right "translate selected models"
> view matrix models
> #2.4,0.91226,-0.40194,0.07895,87.774,0.37437,0.89634,0.23752,-98.36,-0.16624,-0.18713,0.96817,83.178
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 19093 points
correlation = 0.02129, correlation about mean = 0.02529, overlap = 0.06029
steps = 172, shift = 0.0214, angle = 0.0288 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.98482300 0.16758782 0.04514410 -50.93753139
-0.16954975 0.98454671 0.04382532 27.06490286
-0.03710188 -0.05081435 0.99801871 16.23691119
Axis -0.26310855 0.22865273 -0.93727895
Axis point 125.61822732 308.45747570 0.00000000
Rotation angle (degrees) 10.36097112
Shift along axis 4.37204860
Average map value = 0.05656 for 4858 atoms, 3854 outside contour
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 424116 points
correlation = 0.0003396, correlation about mean = 0.01038, overlap = 0.05487
steps = 112, shift = 0.732, angle = 1.12 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.98735196 0.15184557 0.04559631 -47.80055973
-0.15428488 0.98644758 0.05583317 20.87846469
-0.03650035 -0.06216181 0.99739843 18.94620957
Axis -0.34889219 0.24274664 -0.90517860
Axis point 100.63276248 312.61997169 0.00000000
Rotation angle (degrees) 9.73546462
Shift along axis 4.59571592
Average map value = 0.05125 for 4858 atoms, 3892 outside contour
Fit molecule AP3.cif (#2.1) to map RB_AP3_NCCAT.mrc (#1) using 4858 atoms
average map value = 0.08189, steps = 156
shifted from previous position = 5.51
rotated from previous position = 6.39 degrees
atoms outside contour = 3559, contour level = 0.1312
Position of AP3.cif (#2.1) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.99785675 0.04477700 0.04771709 -38.24276693
-0.04632848 0.99841616 0.03191940 9.39397170
-0.04621226 -0.03406165 0.99835076 13.44688537
Axis -0.45023383 0.64094432 -0.62167506
Axis point 466.81008017 0.00000000 682.01877595
Rotation angle (degrees) 4.20206802
Shift along axis 14.87960677
Fit molecule AP3.cif (#2.1) to map RB_AP3_NCCAT.mrc (#1) using 4858 atoms
average map value = 0.08189, steps = 156
shifted from previous position = 5.51
rotated from previous position = 6.39 degrees
atoms outside contour = 3559, contour level = 0.1312
> ui tool show "Fit in Map"
Average map value = 0.05125 for 4858 atoms, 3892 outside contour
> ~select #2.4
Nothing selected
> select #2.4
1525 atoms, 1551 bonds, 193 residues, 1 model selected
Fit molecule AP3.cif (#2.4) to map RB_AP3_NCCAT.mrc (#1) using 1525 atoms
average map value = 0.09335, steps = 196
shifted from previous position = 4.25
rotated from previous position = 22.8 degrees
atoms outside contour = 1028, contour level = 0.1312
> ui mousemode right "rotate selected models"
> view matrix models
> #2.4,0.90607,-0.37139,-0.20273,145.75,0.40261,0.90411,0.14312,-84.112,0.13013,-0.2113,0.96872,32.409
Opened AP3.cif map 5 as #4, grid size 44,62,52, pixel 1.67, shown at level
0.081, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 6190 points
correlation = 0.03232, correlation about mean = 0.04439, overlap = 0.03757
steps = 992, shift = 1.3, angle = 5.04 degrees
Position of AP3.cif map 5 (#4) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.92032521 -0.32593655 -0.21625651 135.61801279
0.37147214 0.90145719 0.22222373 -95.59962681
0.12251515 -0.28485137 0.95071012 53.23728272
Axis -0.54734386 -0.36567480 0.75279256
Axis point 344.93004568 333.12180196 -0.00000000
Rotation angle (degrees) 27.59472110
Shift along axis 0.80531798
Average map value = 0.0649 for 1525 atoms, 1142 outside contour
> select #2
13051 atoms, 13277 bonds, 1651 residues, 5 models selected
> ~select #2
Nothing selected
> close #4
> close #3
> select #2.3
1300 atoms, 1331 bonds, 164 residues, 1 model selected
> select #2.2
5368 atoms, 5456 bonds, 677 residues, 1 model selected
Opened AP3.cif map 5 as #3, grid size 89,72,99, pixel 1.67, shown at level
0.0834, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 21668 points
correlation = -0.00138, correlation about mean = 0.0246, overlap = -0.03965
steps = 272, shift = 5.61, angle = 4.86 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
Average map value = 0.02287 for 5368 atoms, 4900 outside contour
Opened AP3.cif map 5 as #3, grid size 85,73,101, pixel 1.67, shown at level
0.083, step 1, values float32
> view matrix models
> #2.2,0.9103,0.41012,-0.056173,-42.726,-0.41357,0.89535,-0.16526,145.9,-0.017483,0.17367,0.98465,-24.434
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 21661 points
correlation = 0.01772, correlation about mean = 0.01966, overlap = 0.415
steps = 236, shift = 6.43, angle = 7.21 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.90947002 0.37963408 -0.16953540 -15.13095975
-0.40968314 0.88778485 -0.20975648 155.16304514
0.07088025 0.26022302 0.96294339 -50.27489912
Axis 0.49493409 -0.25318105 -0.83122777
Axis point 344.04948969 115.40417929 0.00000000
Rotation angle (degrees) 28.34567643
Shift along axis -4.98327854
Average map value = 0.03591 for 5368 atoms, 4603 outside contour
Average map value = 0.03591 for 5368 atoms, 4603 outside contour
Opened AP3.cif map 5 as #3, grid size 79,71,105, pixel 1.67, shown at level
0.0841, step 1, values float32
Correlation = 0.005438, Correlation about mean = 0.01489, Overlap = 0.1061
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 21679 points
correlation = 0.01783, correlation about mean = 0.02151, overlap = 0.4183
steps = 92, shift = 1.2, angle = 3.13 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.92002223 0.38922633 -0.04540882 -43.07663108
-0.38954400 0.89581263 -0.21395140 150.95386284
-0.04259772 0.21452878 0.97578832 -24.23137789
Axis 0.48205150 -0.00316257 -0.87613717
Axis point 339.27239280 180.37020537 0.00000000
Rotation angle (degrees) 26.38713316
Shift along axis -0.01254565
Average map value = 0.03686 for 5368 atoms, 4597 outside contour
Opened AP3.cif map 5 as #3, grid size 80,69,106, pixel 1.67, shown at level
0.0838, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 21661 points
correlation = 0.01737, correlation about mean = 0.02319, overlap = 0.4055
steps = 136, shift = 0.724, angle = 1.6 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.90894704 0.41588046 -0.02930397 -49.07067204
-0.41452140 0.89398510 -0.17018417 147.47853960
-0.04457896 0.16683552 0.98497646 -17.43515234
Axis 0.37600533 0.01704196 -0.92646077
Axis point 308.28263688 185.68253609 0.00000000
Rotation angle (degrees) 26.62557298
Shift along axis 0.21547459
Average map value = 0.03718 for 5368 atoms, 4588 outside contour
Opened AP3.cif map 5 as #3, grid size 82,69,105, pixel 1.67, shown at level
0.0841, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 21675 points
correlation = 0.0174, correlation about mean = 0.02306, overlap = 0.4081
steps = 52, shift = 0.451, angle = 0.68 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.90909537 0.41296168 -0.05484757 -43.45091897
-0.41633915 0.89609283 -0.15388093 144.04618568
-0.01439842 0.16272763 0.98656597 -23.35207365
Axis 0.35629885 -0.04551989 -0.93326259
Axis point 303.09755609 171.72693991 0.00000000
Rotation angle (degrees) 26.37868821
Shift along axis -0.24486178
Average map value = 0.03679 for 5368 atoms, 4595 outside contour
Opened AP3.cif map 5 as #3, grid size 82,69,105, pixel 1.67, shown at level
0.0842, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 21680 points
correlation = 0.01761, correlation about mean = 0.0236, overlap = 0.4135
steps = 44, shift = 0.117, angle = 0.239 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.90968310 0.41093873 -0.06005020 -41.88942709
-0.41507812 0.89487688 -0.16402905 145.93354794
-0.01366835 0.17413998 0.98462604 -25.39815119
Axis 0.37836517 -0.05189499 -0.92420058
Axis point 308.58269212 169.80312311 0.00000000
Rotation angle (degrees) 26.54379911
Shift along axis 0.05026620
Average map value = 0.03693 for 5368 atoms, 4585 outside contour
> ui mousemode right "translate selected models"
Opened AP3.cif map 5 as #3, grid size 81,69,105, pixel 1.67, shown at level
0.0836, step 1, values float32
> view matrix models
> #2.2,0.9103,0.41012,-0.056173,-38.93,-0.41357,0.89535,-0.16526,149.37,-0.017483,0.17367,0.98465,-24.051
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 21684 points
correlation = 0.03214, correlation about mean = 0.02612, overlap = 0.5345
steps = 108, shift = 3.35, angle = 2.64 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.92116280 0.38822373 -0.02722913 -41.50347892
-0.38594919 0.90228990 -0.19213577 149.55773725
-0.05002309 0.18749739 0.98099053 -20.40637727
Axis 0.44013121 0.02642639 -0.89754452
Axis point 341.46368295 180.78351687 0.00000000
Rotation angle (degrees) 25.54835678
Shift along axis 4.00092638
Average map value = 0.05829 for 5368 atoms, 4353 outside contour
Opened AP3.cif map 5 as #3, grid size 83,68,104, pixel 1.67, shown at level
0.0843, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 21657 points
correlation = 0.03144, correlation about mean = 0.02859, overlap = 0.5305
steps = 56, shift = 1.12, angle = 1.06 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.90918192 0.41453237 -0.03938472 -43.78070003
-0.41526534 0.89566633 -0.15917455 149.29598099
-0.03070744 0.16107373 0.98646455 -19.48314722
Axis 0.36003446 -0.00975530 -0.93288800
Axis point 315.43505631 175.55279998 0.00000000
Rotation angle (degrees) 26.40713348
Shift along axis 0.95660635
Average map value = 0.05538 for 5368 atoms, 4402 outside contour
Opened AP3.cif map 5 as #3, grid size 84,68,104, pixel 1.67, shown at level
0.0836, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 21671 points
correlation = 0.03222, correlation about mean = 0.02946, overlap = 0.5406
steps = 64, shift = 0.573, angle = 0.484 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.90869998 0.41343764 -0.05773788 -39.32945024
-0.41723040 0.89500958 -0.15772333 148.35680046
-0.01353280 0.16741318 0.98579394 -24.27604125
Axis 0.36404255 -0.04949469 -0.93006629
Axis point 314.08938458 165.29689363 0.00000000
Rotation angle (degrees) 26.52343937
Shift along axis 0.91786081
Average map value = 0.0541 for 5368 atoms, 4433 outside contour
> ~select #2.2
Nothing selected
> select #2.3
1300 atoms, 1331 bonds, 164 residues, 1 model selected
Opened AP3.cif map 5 as #4, grid size 41,45,50, pixel 1.67, shown at level
0.0905, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 5107 points
correlation = 0.02863, correlation about mean = 0.04709, overlap = 0.2576
steps = 160, shift = 4.23, angle = 11.8 degrees
Position of AP3.cif map 5 (#4) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
Average map value = 0.02227 for 1300 atoms, 1212 outside contour
> view matrix models
> #2.3,1,5.5511e-17,-1.3878e-16,3.575,-1.1102e-16,1,-4.1633e-17,9.0924,-1.1102e-16,-3.0531e-16,1,9.1922
> view matrix models
> #2.3,1,9.2445e-33,1.1102e-16,4.6099,-3.8858e-16,1,-2.7756e-17,10.853,-1.1102e-16,-6.1062e-16,1,15.436
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 5107 points
correlation = 0.04968, correlation about mean = 0.06941, overlap = 0.09509
steps = 84, shift = 1.61, angle = 10.9 degrees
Position of AP3.cif map 5 (#4) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.98246953 -0.10358248 -0.15499774 58.42571265
0.10796637 0.99395103 0.02011480 -15.17415581
0.15197663 -0.03649672 0.98771003 -7.28683555
Axis -0.15013041 -0.81407795 0.56101510
Axis point 75.82660542 0.00000000 367.87881911
Rotation angle (degrees) 10.86765901
Shift along axis -0.50655527
Average map value = 0.03438 for 1300 atoms, 1116 outside contour
Opened AP3.cif map 5 as #4, grid size 41,45,50, pixel 1.67, shown at level
0.0911, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 5110 points
correlation = 0.05067, correlation about mean = 0.06669, overlap = 0.09962
steps = 156, shift = 3.6, angle = 0.358 degrees
Position of AP3.cif map 5 (#4) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999449 0.00322026 0.00081119 0.33436022
-0.00322451 0.99998078 0.00529467 11.17086995
-0.00079413 -0.00529726 0.99998565 16.58117230
Axis -0.84721582 0.12840433 -0.51549752
Axis point 0.00000000 2416.53999820 -2280.43702128
Rotation angle (degrees) 0.35815965
Shift along axis -7.39644038
Average map value = 0.03794 for 1300 atoms, 1140 outside contour
Opened AP3.cif map 5 as #4, grid size 41,45,50, pixel 1.67, shown at level
0.0922, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 5110 points
correlation = 0.05038, correlation about mean = 0.06973, overlap = 0.09849
steps = 44, shift = 0.0575, angle = 0.394 degrees
Position of AP3.cif map 5 (#4) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.99998013 -0.00554009 0.00300753 4.99207506
0.00554836 0.99998083 -0.00274696 10.34891180
-0.00299226 0.00276359 0.99999170 15.53476829
Axis 0.40049712 0.43605445 0.80588993
Axis point -371.15397004 -473.37425080 0.00000000
Rotation angle (degrees) 0.39417690
Shift along axis 19.03131399
Average map value = 0.03785 for 1300 atoms, 1143 outside contour
Opened AP3.cif map 5 as #4, grid size 41,45,50, pixel 1.67, shown at level
0.0918, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 5107 points
correlation = 0.05102, correlation about mean = 0.06635, overlap = 0.09997
steps = 48, shift = 0.0533, angle = 0.242 degrees
Position of AP3.cif map 5 (#4) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999415 0.00265062 -0.00216083 4.62199855
-0.00264526 0.99999342 0.00248280 10.85055496
0.00216740 -0.00247707 0.99999458 15.42611987
Axis -0.58705912 -0.51229636 -0.62682855
Axis point 621.65814210 2231.33488412 0.00000000
Rotation angle (degrees) 0.24203781
Shift along axis -17.94161856
Average map value = 0.03793 for 1300 atoms, 1140 outside contour
Opened AP3.cif map 5 as #4, grid size 41,45,50, pixel 1.67, shown at level
0.0918, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 5109 points
correlation = 0.05086, correlation about mean = 0.06782, overlap = 0.09978
steps = 40, shift = 0.0577, angle = 0.0342 degrees
Position of AP3.cif map 5 (#4) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999993 0.00010263 0.00035105 4.49304890
-0.00010247 0.99999988 -0.00047266 11.02492392
-0.00035110 0.00047262 0.99999983 15.42836589
Axis 0.79086172 0.58744594 -0.17159547
Axis point 0.00000000 -35319.32312555 14158.71791426
Rotation angle (degrees) 0.03424153
Shift along axis 7.38248950
Average map value = 0.03782 for 1300 atoms, 1141 outside contour
Opened AP3.cif map 5 as #4, grid size 41,45,50, pixel 1.67, shown at level
0.0918, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 5109 points
correlation = 0.05093, correlation about mean = 0.06779, overlap = 0.09985
steps = 40, shift = 0.011, angle = 0.0519 degrees
Position of AP3.cif map 5 (#4) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999961 -0.00027271 -0.00084444 4.82995493
0.00027255 0.99999995 -0.00018376 10.83162237
0.00084449 0.00018353 0.99999963 15.22118970
Axis 0.20265300 -0.93189070 0.30085126
Axis point -19636.92123805 0.00000000 6817.36542386
Rotation angle (degrees) 0.05192072
Shift along axis -4.53576915
Average map value = 0.03782 for 1300 atoms, 1142 outside contour
> select #2
13051 atoms, 13277 bonds, 1651 residues, 5 models selected
> close #3
> close #4
> ~select #2
Nothing selected
> transparency 50
> color blue
> hide #!2 models
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> select #2.1
4858 atoms, 4939 bonds, 617 residues, 1 model selected
> show #2.1 models
> color sel purple
> ~select #2.1
Nothing selected
> show #2.2 models
> show #2.3 models
> show #2.4 models
> select #2.2
5368 atoms, 5456 bonds, 677 residues, 1 model selected
> ~select #2.2
Nothing selected
> select #2.3
1300 atoms, 1331 bonds, 164 residues, 1 model selected
> color sel lime
> ~select #2.3
Nothing selected
> select #2.4
1525 atoms, 1551 bonds, 193 residues, 1 model selected
> color sel red
> ~select #2.4
Nothing selected
> hide #!1 models
> save "D:/Back-up/Baker Lab/Structures/Data Processing/RB_AP3_NCCAT.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #2.4/A
Alignment identifier is 2.4/A
> select #2.4/A:193
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2.4/A:106-193
669 atoms, 677 bonds, 88 residues, 1 model selected
> select #2.4/A:192-193
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #2.4/A:151-193
315 atoms, 320 bonds, 43 residues, 1 model selected
> select #2.4/A:193
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2.4/A:156-193
284 atoms, 289 bonds, 38 residues, 1 model selected
> color sel yellow
> select #2.4
1525 atoms, 1551 bonds, 193 residues, 1 model selected
> ~select #2.4
Nothing selected
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2.3/A
Alignment identifier is 2.3/A
> select #2.3/A:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.3/A:156-164
64 atoms, 64 bonds, 9 residues, 1 model selected
> select #2.3/A:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.3/A:109-164
422 atoms, 427 bonds, 56 residues, 1 model selected
> select #2.3/A:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.3/A:117-164
352 atoms, 356 bonds, 48 residues, 1 model selected
> select #2.3/A:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.3/A:127-164
277 atoms, 279 bonds, 38 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Fit in Map"
> select #2.3
1023 atoms, 1051 bonds, 126 residues, 1 model selected
Opened AP3.cif map 5 as #3, grid size 36,42,42, pixel 1.67, shown at level
0.093, step 1, values float32
Opened AP3.cif map 5 as #4, grid size 36,42,42, pixel 1.67, shown at level
0.093, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 3990 points
correlation = 0.05792, correlation about mean = 0.1002, overlap = 0.06034
steps = 92, shift = 1.24, angle = 11.4 degrees
Position of AP3.cif map 5 (#4) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.99439479 -0.02082121 -0.10366037 32.40447417
0.03797127 0.98533767 0.16633661 -30.87896072
0.09867714 -0.16934037 0.98060525 30.94447110
Axis -0.84696714 -0.51053017 0.14834290
Axis point 0.00000000 163.54135368 221.81988966
Rotation angle (degrees) 11.42962191
Shift along axis -7.09049106
Average map value = 0.04264 for 1023 atoms, 855 outside contour
> view matrix models
> #2.3,0.99439,-0.020821,-0.10366,32.227,0.037971,0.98534,0.16634,-31.146,0.098677,-0.16934,0.98061,33.48
> ui mousemode right "rotate selected models"
> view matrix models
> #2.3,0.36371,-0.87391,-0.32249,368.26,-0.69647,-0.025229,-0.71714,498.09,0.61858,0.48544,-0.61783,146.71
> view matrix models
> #2.3,0.28528,-0.95331,0.099125,308.89,-0.95743,-0.2787,0.075153,429.38,-0.044018,-0.11634,-0.99223,475.78
> view matrix models
> #2.3,0.74498,-0.51773,-0.42067,244.27,-0.5877,-0.80773,-0.046691,477.98,-0.31561,0.28201,-0.90601,438.97
> view matrix models
> #2.3,0.82517,-0.46755,-0.31701,196.17,-0.41579,-0.88259,0.21943,399.48,-0.38239,-0.049259,-0.92269,518.11
> view matrix models
> #2.3,0.14007,-0.97594,-0.1671,400.09,-0.95504,-0.088636,-0.2829,470.16,0.26128,0.19922,-0.94448,343.75
> view matrix models
> #2.3,-0.12276,-0.91125,0.39313,322.14,-0.91202,-0.052621,-0.40675,481.11,0.39134,-0.40848,-0.82462,404.63
> view matrix models
> #2.3,0.4057,-0.80218,-0.43808,371,-0.90968,-0.30779,-0.27884,500.82,0.088849,0.51164,-0.8546,301.75
> view matrix models
> #2.3,0.28755,-0.50032,-0.8167,420.17,-0.95236,-0.23982,-0.1884,477.56,-0.1016,0.83197,-0.54544,214.99
> view matrix models
> #2.3,0.79586,-0.081868,-0.59991,190.88,-0.28842,-0.92244,-0.25675,482.71,-0.53236,0.37737,-0.75775,434.08
> view matrix models
> #2.3,0.9294,-0.32103,0.1821,40.394,-0.24525,-0.90587,-0.34533,489.7,0.27582,0.27629,-0.92065,321.27
> view matrix models
> #2.3,0.76833,-0.031029,-0.6393,195.52,-0.45779,-0.72471,-0.515,536.07,-0.44733,0.68836,-0.57102,318.52
> view matrix models
> #2.3,0.71639,0.42857,-0.55056,101.46,0.15589,-0.86748,-0.47242,427.09,-0.68006,0.25261,-0.68826,472.91
> view matrix models
> #2.3,0.37858,0.92126,0.089215,-57.932,0.77536,-0.26302,-0.57414,208.45,-0.50547,0.28653,-0.81388,457.51
> view matrix models
> #2.3,-0.71302,0.35937,0.60204,161.99,0.37162,0.92183,-0.11013,-28.819,-0.59456,0.1452,-0.79083,497.3
> view matrix models
> #2.3,-0.81883,-0.15808,0.55184,291.09,0.23857,0.78066,0.57763,-122.45,-0.52211,0.60464,-0.60151,356.09
> view matrix models
> #2.3,-0.86035,-0.49163,0.13451,451.31,0.46238,-0.64176,0.61184,89.457,-0.21447,0.58859,0.77946,-0.26945
> view matrix models
> #2.3,-0.91096,-0.018776,-0.41207,490.65,-0.40704,-0.12101,0.90536,108.6,-0.066862,0.99247,0.10259,39.012
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 3990 points
correlation = 0.04589, correlation about mean = 0.1027, overlap = 0.04327
steps = 116, shift = 1.54, angle = 8.45 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
-0.88851427 -0.00189771 -0.45884505 493.85096976
-0.44311398 -0.25608083 0.85911152 152.07191004
-0.11913177 0.96665350 0.22669057 28.27174270
Axis 0.18962323 -0.59899889 -0.77797388
Axis point 263.43536002 18.86463148 -0.00000000
Rotation angle (degrees) 163.52675785
Shift along axis -19.43996581
Average map value = 0.03268 for 1023 atoms, 855 outside contour
> view matrix models
> #2.3,-0.0024924,0.67844,-0.73465,243.41,-0.69292,0.52852,0.49043,136.19,0.72101,0.51028,0.46879,-111.63
> view matrix models
> #2.3,0.00059857,0.93212,-0.36214,115.62,-0.66345,0.27133,0.69729,133.77,0.74822,0.23984,0.61858,-98.889
> view matrix models
> #2.3,-0.62732,0.63014,-0.4576,321.84,-0.778,-0.533,0.3326,385.59,-0.034315,0.56466,0.82461,-42.349
> view matrix models
> #2.3,0.077634,0.77764,-0.62389,184.66,-0.95695,-0.11743,-0.26545,473.11,-0.27969,0.61764,0.73505,17.534
> view matrix models
> #2.3,0.72665,0.65869,0.19522,-102.46,-0.65416,0.57657,0.48953,119.44,0.20988,-0.48342,0.84985,97.437
> view matrix models
> #2.3,0.38128,0.90674,0.18013,-74.316,-0.85489,0.27167,0.442,227.87,0.35184,-0.32252,0.87874,31.971
> view matrix models
> #2.3,0.99178,0.062099,0.11188,-27.945,-0.059232,0.99783,-0.028772,29.296,-0.11343,0.021909,0.9933,39.06
> view matrix models
> #2.3,0.75971,0.59702,0.25771,-111.16,-0.6489,0.72174,0.24089,144.55,-0.042181,-0.35024,0.93571,106.14
> view matrix models
> #2.3,0.88672,0.38372,0.25783,-97.571,-0.43059,0.88852,0.15849,86.098,-0.16827,-0.25156,0.9531,110
> view matrix models
> #2.3,0.60803,0.67877,0.41179,-128.17,-0.79352,0.53593,0.28828,198.87,-0.025019,-0.50204,0.86448,146.19
> view matrix models
> #2.3,0.18357,0.62583,0.75805,-105.01,-0.76584,0.57451,-0.28885,309.64,-0.61628,-0.52752,0.58475,332.76
> view matrix models
> #2.3,0.59024,0.4927,0.63942,-138.57,-0.22586,0.86129,-0.45516,180.49,-0.77498,0.12423,0.61965,236.4
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 3990 points
correlation = 0.05931, correlation about mean = 0.07317, overlap = 0.06361
steps = 84, shift = 3.87, angle = 4.84 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.53850585 0.55876420 0.63070913 -138.02500210
-0.26792168 0.82320632 -0.50054901 202.26766958
-0.79889262 0.10056792 0.59300647 250.00762581
Axis 0.34204583 0.81346787 -0.47039842
Axis point 146.68823848 0.00000000 326.02417254
Rotation angle (degrees) 61.48692333
Shift along axis -0.27581712
Average map value = 0.04561 for 1023 atoms, 797 outside contour
> view matrix models
> #2.3,0.2878,0.3055,0.90766,-98.453,-0.36965,0.90975,-0.189,140.32,-0.88348,-0.28112,0.37475,385.42
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 3990 points
correlation = 0.04861, correlation about mean = 0.06478, overlap = 0.05029
steps = 100, shift = 1.89, angle = 15.3 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.27957102 0.43828088 0.85425401 -109.29515609
-0.59154667 0.77943169 -0.20629778 213.39882277
-0.75624902 -0.44765623 0.47717010 369.95955556
Axis -0.12526455 0.83584783 -0.53447843
Axis point 250.25512820 0.00000000 339.82534173
Rotation angle (degrees) 74.44957143
Shift along axis -5.67564822
Average map value = 0.05401 for 1023 atoms, 763 outside contour
> view matrix models
> #2.3,0.82594,0.48548,0.28658,-109.06,-0.27371,0.78973,-0.54902,219.41,-0.49286,0.37502,0.78515,96.195
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 3990 points
correlation = 0.05197, correlation about mean = 0.07461, overlap = 0.05523
steps = 160, shift = 2.88, angle = 3.64 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.83050826 0.48050191 0.28173378 -110.60318412
-0.24045639 0.76552411 -0.59678602 227.71561652
-0.50243083 0.42789103 0.75131386 96.86227751
Axis 0.69325861 0.53053679 -0.48777374
Axis point 0.00000000 0.44675341 384.16094363
Rotation angle (degrees) 47.64880478
Shift along axis -3.11197356
Average map value = 0.06961 for 1023 atoms, 740 outside contour
> ~select #2.3
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2.4/A
Alignment identifier is 2.4/A
> select #2.4/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.4/A:1-5
38 atoms, 37 bonds, 5 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2.3/A
Alignment identifier is 2.3/A
> select #2.3/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.3/A:1-4
32 atoms, 32 bonds, 4 residues, 1 model selected
> select #2.3/A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2.3/A:1-4
32 atoms, 32 bonds, 4 residues, 1 model selected
> select #2.3/A:116-117
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2.3/A:116-125
74 atoms, 75 bonds, 10 residues, 1 model selected
> ui mousemode right select
> select clear
> save "D:/Back-up/Baker Lab/Structures/Data Processing/RB_AP3_NCCAT_it1.cxs"
——— End of log from Thu Jun 30 13:49:22 2022 ———
opened ChimeraX session
> select #2.4
1525 atoms, 1551 bonds, 193 residues, 1 model selected
> close #4
> close #3
> ui mousemode right "rotate selected models"
> view matrix models
> #2.4,0.90345,-0.34166,-0.25894,152.07,0.36951,0.92686,0.066284,-65.805,0.21735,-0.15556,0.96362,4.3356
> view matrix models
> #2.4,0.94763,-0.31273,-0.064769,93.5,0.31413,0.9493,0.012464,-48.39,0.057588,-0.032157,0.99782,-1.3945
> view matrix models
> #2.4,0.8383,-0.5451,-0.011459,155.32,0.54286,0.83644,-0.075252,-46.081,0.050605,0.056863,0.9971,-20.271
> ui mousemode right "translate selected models"
> view matrix models
> #2.4,0.8383,-0.5451,-0.011459,151.48,0.54286,0.83644,-0.075252,-46.682,0.050605,0.056863,0.9971,-19.59
> ui tool show "Fit in Map"
Opened AP3.cif map 5 as #3, grid size 43,61,54, pixel 1.67, shown at level
0.0818, step 1, values float32
Opened AP3.cif map 5 as #4, grid size 43,61,54, pixel 1.67, shown at level
0.0818, step 1, values float32
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 6193 points
correlation = 0.03503, correlation about mean = 0.04095, overlap = 0.03835
steps = 164, shift = 3.2, angle = 9.42 degrees
Position of AP3.cif map 5 (#4) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.84437174 -0.52600391 0.10176566 120.21568872
0.52473826 0.85027502 0.04101411 -72.02807874
-0.10810238 0.01876918 0.99396257 22.58107109
Axis -0.02075615 0.19582231 0.98041971
Axis point 188.67727728 172.94004755 0.00000000
Rotation angle (degrees) 32.40248714
Shift along axis 5.53900703
Average map value = 0.06748 for 1525 atoms, 1119 outside contour
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 6193 points
correlation = 0.03491, correlation about mean = 0.04064, overlap = 0.03823
steps = 104, shift = 0.019, angle = 0.022 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.84451889 -0.52581945 0.10149751 120.21440560
0.52456514 0.85038968 0.04085098 -71.99692377
-0.10779268 0.01874263 0.99399671 22.50866684
Axis -0.02063770 0.19536816 0.98051281
Axis point 188.66391954 173.05315577 0.00000000
Rotation angle (degrees) 32.38666177
Shift along axis 5.52318012
Average map value = 0.0675 for 1525 atoms, 1120 outside contour
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 6193 points
correlation = 0.03497, correlation about mean = 0.041, overlap = 0.03828
steps = 64, shift = 0.024, angle = 0.0288 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.84435899 -0.52599272 0.10192915 120.17789446
0.52473394 0.85027938 0.04097888 -72.01601133
-0.10822285 0.01888480 0.99394727 22.58452496
Axis -0.02061468 0.19608044 0.98037110
Axis point 188.64052049 172.87683535 0.00000000
Rotation angle (degrees) 32.40375368
Shift along axis 5.54285583
Average map value = 0.06745 for 1525 atoms, 1120 outside contour
> ui mousemode right "rotate selected models"
> view matrix models
> #2.4,0.80464,-0.49785,0.32358,71.463,0.51667,0.8556,0.031622,-69.608,-0.2926,0.14174,0.94567,40.154
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 6193 points
correlation = 0.03141, correlation about mean = 0.05418, overlap = 0.0357
steps = 108, shift = 1.65, angle = 4.49 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.80224779 -0.49211505 0.33796636 68.43365980
0.53520338 0.84368095 -0.04194984 -53.60559584
-0.26449164 0.21453491 0.94022282 21.03974597
Axis 0.21053609 0.49452903 0.84327670
Axis point 130.02193588 84.39894995 0.00000000
Rotation angle (degrees) 37.52611566
Shift along axis 5.64055940
Average map value = 0.04568 for 1525 atoms, 1229 outside contour
> view matrix models
> #2.4,0.9037,-0.42817,0.0017184,110.17,0.417,0.8792,-0.23047,2.9367,0.097171,0.209,0.97308,-53.379
> ui mousemode right "translate selected models"
> view matrix models
> #2.4,0.9037,-0.42817,0.0017184,108.68,0.417,0.8792,-0.23047,2.4818,0.097171,0.209,0.97308,-52.623
> view matrix models
> #2.4,0.9037,-0.42817,0.0017184,107.56,0.417,0.8792,-0.23047,0.81991,0.097171,0.209,0.97308,-53.788
Fit map AP3.cif map 5 in map RB_AP3_NCCAT.mrc using 6193 points
correlation = 0.03192, correlation about mean = 0.04456, overlap = 0.03752
steps = 132, shift = 2.94, angle = 9.54 degrees
Position of AP3.cif map 5 (#3) relative to RB_AP3_NCCAT.mrc (#1) coordinates:
Matrix rotation and translation
0.82968243 -0.55779042 -0.02229160 155.03558000
0.52688690 0.79565881 -0.29885992 17.14660870
0.18443771 0.23621367 0.95403660 -72.81236329
Axis 0.43607749 -0.16848149 0.88399684
Axis point 67.08752573 257.18543483 0.00000000
Rotation angle (degrees) 37.84355010
Shift along axis 0.35274193
Average map value = 0.06686 for 1525 atoms, 1127 outside contour
> close #3
> ~select #2.4
Nothing selected
> save "D:/Back-up/Baker Lab/Structures/Data Processing/RB_AP3_NCCAT_it2.cxs"
> save "D:/Back-up/Baker Lab/Structures/Data Processing/RB_AP3_NCCAT_it2.cxs"
——— End of log from Thu Jun 30 14:01:38 2022 ———
opened ChimeraX session
> open
> C:/Users/mbegl/Downloads/cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-
> sharpened.mrc
Opened cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc as
#3, grid size 300,300,300, pixel 0.826, shown at level 0.00127, step 2, values
float32
> transparency #1-3 70
> hide #!1 models
> volume #3 step 1
> volume #4 level 0.04831
> volume #3 level 0.001496
> set bgColor white
> lighting soft
> transparency #2-4 40
> transparency #2-4 20
> volume #3 color #fff0e7cc
> volume #3 color #7a736fcc
> volume #3 color #7a7471cc
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> transparency #3 0
> volume #1 step 1
> volume #3 level 0.02341
> volume #3 color #958e8a
> graphics silhouettes true
> volume #3 level 0.04218
> volume #3 color #959595
> open C:/Users/mbegl/Downloads/AP2_af_matt_redocked.pdb
Chain information for AP2_af_matt_redocked.pdb #5
---
Chain | Description
A | No description available
B | No description available
M | No description available
S | No description available
> set bgColor black
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> select #4
2 models selected
> close #4
> color bymodel #5
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #5
> volume #3
> transparency #3,5 70
> select #5/B
5368 atoms, 5456 bonds, 677 residues, 1 model selected
> color sel blue
> select #5/M
1300 atoms, 1331 bonds, 164 residues, 1 model selected
> color sel lime
> select #5/S
1524 atoms, 1550 bonds, 193 residues, 1 model selected
> color sel red
> ui mousemode right select
> select clear
No model chosen to save relative to
> select #5
13106 atoms, 13333 bonds, 1658 residues, 1 model selected
> save "D:/Back-up/Baker Lab/Structures/Data
> Processing/RB_AFintoChameleon.pdb" selectedOnly true relModel #3
> save "D:/Back-up/Baker Lab/Structures/Data
> Processing/RB_AFintoChameleon.cxs"
> close #1
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #2.2/A #5/B
Alignment identifier is 1
> select #2.2/A:677 #5/B:677
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #2.2/A:672-677 #5/B:672-677
104 atoms, 106 bonds, 12 residues, 2 models selected
Seqview [ID: 1] region chains A,B [672-677] RMSD: 32.647
> select #2.2/A:677 #5/B:677
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #2.2/A:461-677 #5/B:461-677
3464 atoms, 3532 bonds, 434 residues, 2 models selected
Seqview [ID: 1] region chains A,B [461-677] RMSD: 9.454
> select #2.2/A:1 #5/B:1
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2.2/A:1-9 #5/B:1-9
144 atoms, 148 bonds, 18 residues, 2 models selected
Seqview [ID: 1] region chains A,B [1-9] RMSD: 103.160
> select #2.2/A:10 #5/B:10
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2.2/A:10-13 #5/B:10-13
56 atoms, 54 bonds, 8 residues, 2 models selected
Seqview [ID: 1] region chains A,B [10-13] RMSD: 72.302
> select #2.2/A:1 #5/B:1
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2.2/A:1-30 #5/B:1-30
428 atoms, 434 bonds, 60 residues, 2 models selected
Seqview [ID: 1] region chains A,B [1-30] RMSD: 71.229
> cartoon hide (#5 & sel)
> select #2.2/A:677 #5/B:677
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #2.2/A:664-677 #5/B:664-677
222 atoms, 224 bonds, 28 residues, 2 models selected
Seqview [ID: 1] region chains A,B [664-677] RMSD: 25.122
> select #2.2/A:677 #5/B:677
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #2.2/A:650-677 #5/B:650-677
446 atoms, 454 bonds, 56 residues, 2 models selected
Seqview [ID: 1] region chains A,B [650-677] RMSD: 18.810
> select #2.2/A:677 #5/B:677
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #2.2/A:655-677 #5/B:655-677
368 atoms, 376 bonds, 46 residues, 2 models selected
Seqview [ID: 1] region chains A,B [655-677] RMSD: 20.679
> cartoon hide (#5 & sel)
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> select #2.2
5368 atoms, 5456 bonds, 677 residues, 1 model selected
> ~select #2.2
Nothing selected
> select #5
13106 atoms, 13333 bonds, 1658 residues, 1 model selected
> ~select #5
Nothing selected
> save "D:/Back-up/Baker Lab/Structures/Data
> Processing/RB_AFintoChameleon.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #2.4/A #5/S
Alignment identifier is 2
> select #2.4/A:1 #5/S:1
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2.4/A:1-5 #5/S:1-5
76 atoms, 74 bonds, 10 residues, 2 models selected
Seqview [ID: 2] region chains A,S [1-5] RMSD: 4.916
> select #2.4/A:193 #5/S:193
19 atoms, 17 bonds, 2 residues, 2 models selected
> select #2.4/A:127-193 #5/S:127-193
1001 atoms, 1011 bonds, 134 residues, 2 models selected
Seqview [ID: 2] region chains A,S [127-193] RMSD: 39.196
> select #2.4/A:124-125 #5/S:124-125
30 atoms, 28 bonds, 4 residues, 2 models selected
> select #2.4/A:124-127 #5/S:124-127
46 atoms, 44 bonds, 8 residues, 2 models selected
Seqview [ID: 2] region chains A,S [124-127] RMSD: 5.869
> select #2.4/A:134 #5/S:134
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2.4/A:134-167 #5/S:134-167
490 atoms, 490 bonds, 68 residues, 2 models selected
Seqview [ID: 2] region chains A,S [134-167] RMSD: 21.849
> select #2.4/A:134 #5/S:134
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2.4/A:134-151 #5/S:134-151
288 atoms, 286 bonds, 36 residues, 2 models selected
Seqview [ID: 2] region chains A,S [134-151] RMSD: 6.428
> ui tool show "Fit in Map"
Fit molecules AP3.cif (#2.4), AP2_af_matt_redocked.pdb (#5) to map
cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc (#3) using
288 atoms
average map value = 0.1693, steps = 112
shifted from previous position = 4.81
rotated from previous position = 8.46 degrees
atoms outside contour = 121, contour level = 0.042185
Position of AP3.cif (#2.4) relative to
cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc (#3)
coordinates:
Matrix rotation and translation
0.81634435 -0.57638177 0.03695887 155.88541995
0.57356268 0.80150443 -0.16916411 -2.63503488
0.06788041 0.15929439 0.98489469 -56.41285633
Axis 0.27455434 -0.02584693 0.96122414
Axis point 90.58693709 247.00136079 0.00000000
Rotation angle (degrees) 36.73870604
Shift along axis -11.35827343
Position of AP2_af_matt_redocked.pdb (#5) relative to
cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc (#3)
coordinates:
Matrix rotation and translation
0.99798292 -0.03952761 0.04967554 5.45731711
0.03257432 0.99048310 0.13372414 -14.93186817
-0.05448858 -0.13183627 0.98977280 26.36305363
Axis -0.90256119 0.35402299 0.24505310
Axis point 0.00000000 197.95659480 115.81832176
Rotation angle (degrees) 8.45976802
Shift along axis -3.75143914
Fit molecules AP3.cif (#2.4), AP2_af_matt_redocked.pdb (#5) to map
cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc (#3) using
288 atoms
average map value = 0.1693, steps = 112
shifted from previous position = 4.81
rotated from previous position = 8.46 degrees
atoms outside contour = 121, contour level = 0.042185
> select #2.4/A:193 #5/S:193
19 atoms, 17 bonds, 2 residues, 2 models selected
> select #2.4/A:187-193 #5/S:187-193
113 atoms, 117 bonds, 14 residues, 2 models selected
Seqview [ID: 2] region chains A,S [187-193] RMSD: 59.999
> select #2.4/A:193 #5/S:193
19 atoms, 17 bonds, 2 residues, 2 models selected
> select #2.4/A:192-193 #5/S:192-193
41 atoms, 41 bonds, 4 residues, 2 models selected
Seqview [ID: 2] region chains A,S [192-193] RMSD: 63.635
> select #2.4/A:193 #5/S:193
19 atoms, 17 bonds, 2 residues, 2 models selected
> select #2.4/A:171-193 #5/S:171-193
361 atoms, 369 bonds, 46 residues, 2 models selected
Seqview [ID: 2] region chains A,S [171-193] RMSD: 57.737
> cartoon hide (#5 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:1-6
45 atoms, 44 bonds, 6 residues, 1 model selected
> select #5/A:624
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:614-624
86 atoms, 87 bonds, 11 residues, 1 model selected
> select #5/A:624
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:593-624
238 atoms, 242 bonds, 32 residues, 1 model selected
> select #5/A:624
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:588-624
276 atoms, 281 bonds, 37 residues, 1 model selected
> select #5/A:624
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:590-624
259 atoms, 264 bonds, 35 residues, 1 model selected
> cartoon hide sel
> select #2.2/A:628 #5/B:628
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2.2/A:612-628 #5/B:612-628
280 atoms, 284 bonds, 34 residues, 2 models selected
Seqview [ID: 1] region chains A,B [612-628] RMSD: 4.327
> select #2.2/A:599 #5/B:599
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2.2/A:599-612 #5/B:599-612
216 atoms, 222 bonds, 28 residues, 2 models selected
Seqview [ID: 1] region chains A,B [599-612] RMSD: 4.855
> select
> #2.2/A:31-52,56-71,77-88,92-105,110-125,129-141,145-160,164-180,182-197,201-214,219-235,238-255,259-262,264-270,283-285,295-309,313-326,329-344,347-363,365-367,369-375,383-396,402-414,418-434,436-451,455-471,477-488,493-505,513-527,530-546,548-564,568-581,589-598,612-614,622-626,646-649
> #5/B:31-52,56-71,77-88,92-105,110-125,129-141,145-160,164-180,182-197,201-214,219-235,238-255,259-262,264-270,283-285,295-309,313-326,329-344,347-363,365-367,369-375,383-396,402-414,418-434,436-451,455-471,477-488,493-505,513-527,530-546,548-564,568-581,589-598,612-614,622-626,646-649
7406 atoms, 7442 bonds, 928 residues, 2 models selected
> select #2.2/A:615-616 #5/B:615-616
36 atoms, 36 bonds, 4 residues, 2 models selected
> select #2.2/A:615-618 #5/B:615-618
76 atoms, 78 bonds, 8 residues, 2 models selected
Seqview [ID: 1] region chains A,B [615-618] RMSD: 4.050
> select #2.2/A:582 #5/B:582
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #2.2/A:582-592 #5/B:582-592
152 atoms, 152 bonds, 22 residues, 2 models selected
Seqview [ID: 1] region chains A,B [582-592] RMSD: 10.467
> select #2.2/A:582 #5/B:582
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #2.2/A:582-607 #5/B:582-607
392 atoms, 400 bonds, 52 residues, 2 models selected
Seqview [ID: 1] region chains A,B [582-607] RMSD: 8.327
> ui tool show "Fit in Map"
Fit molecules AP3.cif (#2.2), AP2_af_matt_redocked.pdb (#5) to map
cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc (#3) using
392 atoms
average map value = 0.1844, steps = 240
shifted from previous position = 8.3
rotated from previous position = 27.2 degrees
atoms outside contour = 188, contour level = 0.042185
> select #2.2/A:582 #5/B:582
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #2.2/A:582-589 #5/B:582-589
106 atoms, 106 bonds, 16 residues, 2 models selected
Seqview [ID: 1] region chains A,B [582-589] RMSD: 10.969
> select #2.2/A:582 #5/B:582
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #2.2/A:582-598 #5/B:582-598
260 atoms, 264 bonds, 34 residues, 2 models selected
Seqview [ID: 1] region chains A,B [582-598] RMSD: 9.519
Fit molecules AP3.cif (#2.2), AP2_af_matt_redocked.pdb (#5) to map
cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc (#3) using
260 atoms
average map value = 0.1433, steps = 128
shifted from previous position = 9.72
rotated from previous position = 28.2 degrees
atoms outside contour = 136, contour level = 0.042185
> select clear
> set bgColor black
> select #5/A
4914 atoms, 4996 bonds, 624 residues, 1 model selected
> select sel :< 5
12229 atoms, 12353 bonds, 1545 residues, 5 models selected
> undo
> transparency sel 30
> set bgColor white
> select clear
> transparency #3,5 50
> transparency #3,5 70
> select clear
> undo
> undo
> select #5/A
4914 atoms, 4996 bonds, 624 residues, 1 model selected
> color sel purple
> select #5/M
1300 atoms, 1331 bonds, 164 residues, 1 model selected
> color sel lime
> select #5/S
1524 atoms, 1550 bonds, 193 residues, 1 model selected
> color sel red
> select clear
> select #3.1
1 model selected
> color #3.1 light gray
> color #3.1 light sea green
> color #3.1 cornflower blue
> color #3.1 blue
> volume #3 color #0000ff4c
> volume #3 color #107cff4c
> volume #3 color #0a58ff4c
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\mbegl\Downloads\movie1.mp4
Movie saved to \C:Users\\...\Downloads\movie1.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\mbegl\Downloads\movie1.mp4
Movie saved to \C:Users\\...\Downloads\movie1.mp4
> save "D:/Back-up/Baker Lab/Structures/Data
> Processing/RB_AFintoChameleon.cxs"
——— End of log from Wed Aug 17 02:02:43 2022 ———
opened ChimeraX session
> set bgColor grey
> select #3
2 models selected
> color zone #3 near #5 distance 4.96
> transparency sel 0
> select up
13106 atoms, 13333 bonds, 1658 residues, 4 models selected
> select up
13106 atoms, 13333 bonds, 1658 residues, 4 models selected
> transparency sel 70
> ui mousemode right select
> select clear
> save C:\ProgramData\ChimeraX\image19.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode C:\ProgramData\ChimeraX\movie3.mp4
Movie saved to C:\ProgramData\ChimeraX\movie3.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode C:\ProgramData\ChimeraX\movie4.mp4
Movie saved to C:\ProgramData\ChimeraX\movie4.mp4
> save "D:/Back-up/Baker Lab/Structures/Data
> Processing/RB_AFintoChameleon_colored.cxs"
——— End of log from Sun Nov 13 22:44:10 2022 ———
opened ChimeraX session
> transparency #3,5 70
> open "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Dec
> 2022/Apo_AP3/40Tilt/Apo_40degree_EMhancer.mrc"
Opened Apo_40degree_EMhancer.mrc as #1, grid size 128,128,128, pixel 1.65,
shown at level 0.267, step 1, values float32
> select #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.55898,0.79903,-0.22156,-3.9482,-0.81146,0.58209,0.051964,117.12,0.17049,0.15074,0.97376,-28.754
> view matrix models
> #1,0.55735,0.82956,-0.034342,-30.517,-0.82999,0.5556,-0.049323,134.45,-0.021836,0.055994,0.99819,-2.9498
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.55735,0.82956,-0.034342,-34.295,-0.82999,0.5556,-0.049323,138.19,-0.021836,0.055994,0.99819,13.326
> view matrix models
> #1,0.55735,0.82956,-0.034342,-28.506,-0.82999,0.5556,-0.049323,160.73,-0.021836,0.055994,0.99819,13.116
> view matrix models
> #1,0.55735,0.82956,-0.034342,-21.982,-0.82999,0.5556,-0.049323,156.96,-0.021836,0.055994,0.99819,12.661
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.32817,0.94454,-0.011932,-12.44,-0.93992,0.32525,-0.10375,197.46,-0.094118,0.045263,0.99453,21.582
> ui tool show "Fit in Map"
Fit map Apo_40degree_EMhancer.mrc in map
cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc using 20968
points
correlation = 0.6888, correlation about mean = 0.3874, overlap = 2320
steps = 308, shift = 4.14, angle = 19.4 degrees
Position of Apo_40degree_EMhancer.mrc (#1) relative to
cryosparc_P67_J82_003_volume_map_half_A_deepEMhancer-sharpened.mrc (#3)
coordinates:
Matrix rotation and translation
0.00859470 0.99944234 0.03226689 13.36108641
-0.99964353 0.00940317 -0.02498791 229.35724981
-0.02527739 -0.03204063 0.99916688 21.46777888
Axis -0.00352649 0.02877320 -0.99957975
Axis point 122.57479805 108.27316546 0.00000000
Rotation angle (degrees) 89.50826009
Shift along axis -14.90653214
> hide #!3 models
> hide #5 models
> show #5 models
> transparency #1.1 70
> surface dust #1 size 16.5
> color zone #1 near #5 distance 9.91
> transparency sel 0
> transparency #1.1 70
> ~select #1
Nothing selected
> save "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Dec
> 2022/Apo_AP3/40Tilt/AF_docked_2.cxs" includeMaps true
——— End of log from Wed Mar 8 12:55:44 2023 ———
opened ChimeraX session
> open "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Dec
> 2022/Rick_processing/cryosparc_P67_J843_map_sharp_merge.mrc"
Opened cryosparc_P67_J843_map_sharp_merge.mrc as #4, grid size 200,200,200,
pixel 1.24, shown at level 0.00202, step 1, values float32
> close #1
> close #3
> select #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.61277,-0.77169,-0.17029,122.26,0.74333,0.636,-0.20728,-8.4823,0.26826,0.00043328,0.96335,-19.217
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.61277,-0.77169,-0.17029,156.16,0.74333,0.636,-0.20728,-27.098,0.26826,0.00043328,0.96335,-35.929
> view matrix models
> #4,0.61277,-0.77169,-0.17029,158.2,0.74333,0.636,-0.20728,-23.033,0.26826,0.00043328,0.96335,-33.856
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.36296,-0.93053,-0.048781,177.78,0.90689,0.3648,-0.21089,-14.427,0.21403,0.032306,0.97629,-33.394
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.36296,-0.93053,-0.048781,196.6,0.90689,0.3648,-0.21089,-13.164,0.21403,0.032306,0.97629,-32.231
> ui tool show "Fit in Map"
Fit molecule AP2_af_matt_redocked.pdb (#5) to map
cryosparc_P67_J843_map_sharp_merge.mrc (#4) using 13106 atoms
average map value = 0.1615, steps = 172
shifted from previous position = 7.47
rotated from previous position = 17.2 degrees
atoms outside contour = 3971, contour level = 0.0020222
Position of AP2_af_matt_redocked.pdb (#5) relative to
cryosparc_P67_J843_map_sharp_merge.mrc (#4) coordinates:
Matrix rotation and translation
0.55333771 0.83294170 -0.00505018 -46.33548188
-0.83212950 0.55304802 0.04121152 153.30095502
0.03711979 -0.01860149 0.99913768 0.48264127
Axis -0.03588755 -0.02530180 -0.99903549
Axis point 119.72069331 119.94480425 0.00000000
Rotation angle (degrees) 56.44331546
Shift along axis -2.69809920
> color zone #4 near #5 distance 7.43
> transparency #4.1 70
> volume #4 level 0.02306
> color zone #4 near #5 distance 7.43
> transparency sel 50
> transparency #4.1 70
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> show #2.2 models
> show #2.3 models
> show #2.4 models
> hide #5 models
> close #2
> show #5 models
> open "D:/Back-up/Baker Lab/Structures/AlphaFold/AP3B1.pdb" "D:/Back-up/Baker
> Lab/Structures/AlphaFold/AP3D1.pdb" "D:/Back-up/Baker
> Lab/Structures/AlphaFold/AP3M1.pdb" "D:/Back-up/Baker
> Lab/Structures/AlphaFold/AP3S1.pdb"
AP3B1.pdb title:
Alphafold monomer V2.0 prediction for ap-3 complex subunit β-1 (O00203) [more
info...]
Chain information for AP3B1.pdb #1
---
Chain | Description
A | ap-3 complex subunit β-1
AP3D1.pdb title:
Alphafold V2.0 prediction for ap-3 complex subunit δ-1 (O14617) [more info...]
Chain information for AP3D1.pdb #2
---
Chain | Description
A | ap-3 complex subunit δ-1
AP3M1.pdb title:
Alphafold monomer V2.0 prediction for ap-3 complex subunit μ-1 (Q9Y2T2) [more
info...]
Chain information for AP3M1.pdb #3
---
Chain | Description
A | ap-3 complex subunit μ-1
AP3S1.pdb title:
Alphafold monomer V2.0 prediction for ap-3 complex subunit σ-1 (Q92572) [more
info...]
Chain information for AP3S1.pdb #6
---
Chain | Description
A | ap-3 complex subunit σ-1
> hide #!4 models
> hide #5 models
> ~select #4
Nothing selected
> select #1
8512 atoms, 8643 bonds, 1094 residues, 1 model selected
Alignment identifier is 1/A
> select #1/A:1094
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:625-1094
3562 atoms, 3615 bonds, 470 residues, 1 model selected
> select #1/A
8512 atoms, 8643 bonds, 1094 residues, 1 model selected
> view matrix models #1,1,0,0,102.13,0,1,0,90.117,0,0,1,-40.777
> select #1/A:1076-1094
143 atoms, 143 bonds, 19 residues, 1 model selected
> select #1/A:1076-1094
143 atoms, 143 bonds, 19 residues, 1 model selected
> select #1/A:1094
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:678-1094
3144 atoms, 3186 bonds, 417 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A
9127 atoms, 9285 bonds, 1153 residues, 1 model selected
Alignment identifier is 2/A
> select #2/A:1153
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:618-1153
4269 atoms, 4345 bonds, 536 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/A
3309 atoms, 3387 bonds, 418 residues, 1 model selected
Alignment identifier is 3/A
> select #3/A:418
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:141-418
2176 atoms, 2223 bonds, 278 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #5 models
> select #1
5368 atoms, 5456 bonds, 677 residues, 1 model selected
> mmaker #1 #5
> matchmaker #1 #5
Missing required "to" argument
> mmaker #1 / #5
> matchmaker #1 / #5
Expected a keyword
> mmaker #1 to #5
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 AP2_af_matt_redocked.pdb, chain B (#5) with AP3B1.pdb, chain A
(#1), sequence alignment score = 3342.1
RMSD between 421 pruned atom pairs is 0.781 angstroms; (across all 677 pairs:
14.928)
> mmaker #2 to #5
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 AP2_af_matt_redocked.pdb, chain A (#5) with AP3D1.pdb, chain A
(#2), sequence alignment score = 3147
RMSD between 364 pruned atom pairs is 0.954 angstroms; (across all 617 pairs:
2.623)
> mmaker #3 to #5
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 AP2_af_matt_redocked.pdb, chain M (#5) with AP3M1.pdb, chain A
(#3), sequence alignment score = 808.2
RMSD between 140 pruned atom pairs is 0.001 angstroms; (across all 140 pairs:
0.001)
> mmaker #6 to #5
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 AP2_af_matt_redocked.pdb, chain S (#5) with AP3S1.pdb, chain A
(#6), sequence alignment score = 927.2
RMSD between 126 pruned atom pairs is 0.432 angstroms; (across all 193 pairs:
21.201)
> show #!4 models
Alignment identifier is 1/A
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1-5
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1-38
269 atoms, 274 bonds, 38 residues, 1 model selected
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1-44
317 atoms, 322 bonds, 44 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Dec
> 2022/Rick_processing/merged_AFdocked.cxs" includeMaps true
——— End of log from Wed Oct 11 18:52:50 2023 ———
opened ChimeraX session
> open "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Oct
> 2023/chaos.mrc"
Opened chaos.mrc as #7, grid size 80,80,80, pixel 3.97, shown at level 0.335,
step 1, values float32
> select #7
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ~select #7
Nothing selected
> select #7
2 models selected
> view matrix models
> #7,-0.38973,0.78156,0.48711,20.268,0.36977,-0.35162,0.86002,-3.6989,0.84343,0.51529,-0.15196,-13.766
> view matrix models
> #7,-0.78911,0.60564,0.10245,178.17,0.06348,-0.085493,0.99431,-18.179,0.61096,0.79113,0.029018,-49.721
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.78911,0.60564,0.10245,168.36,0.06348,-0.085493,0.99431,26.292,0.61096,0.79113,0.029018,-98.127
> view matrix models
> #7,-0.78911,0.60564,0.10245,122.65,0.06348,-0.085493,0.99431,13.296,0.61096,0.79113,0.029018,-103.02
> view matrix models
> #7,-0.78911,0.60564,0.10245,125.16,0.06348,-0.085493,0.99431,13.654,0.61096,0.79113,0.029018,-109.95
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.79642,0.60181,0.059501,134.39,0.028621,-0.060771,0.99774,14.913,0.60407,0.79632,0.031175,-110.01
> ~select #7
Nothing selected
> select #1
5051 atoms, 5133 bonds, 633 residues, 1 model selected
> hide #1 models
> hide #2 models
> hide #3 models
> hide #6 models
> ~select #1
Nothing selected
> save "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Oct
> 2023/WTF.cxs" includeMaps true
——— End of log from Sat Nov 25 00:24:07 2023 ———
opened ChimeraX session
> close #7
> open "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Oct
> 2023/cryosparc_P123_J67_map_sharp_CHAOS.mrc"
Opened cryosparc_P123_J67_map_sharp_CHAOS.mrc as #7, grid size 300,300,300,
pixel 1.06, shown at level 0.0133, step 2, values float32
> select #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.36296,-0.93053,-0.048781,210.17,0.90689,0.3648,-0.21089,-31.449,0.21403,0.032306,0.97629,-28.364
> undo
> ~select #4
Nothing selected
> select #7
2 models selected
> view matrix models #7,1,0,0,-4.8259,0,1,0,-46.279,0,0,1,81.987
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.80643,0.46067,-0.37075,10.682,-0.13813,0.75639,0.63937,-85.848,0.57497,-0.4644,0.67361,115.89
> view matrix models
> #7,0.69863,0.59925,-0.39092,8.8828,-0.097094,0.62072,0.778,-92.498,0.70887,-0.50558,0.49184,129.71
> select up
25673 atoms, 26119 bonds, 3241 residues, 9 models selected
> select down
2 models selected
> volume flip #7
Opened cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip as #8, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> close #7
> select #8
2 models selected
> view matrix models
> #8,-0.052055,0.837,-0.54471,114.65,0.61341,-0.40363,-0.67883,190.55,-0.78805,-0.36947,-0.49241,502.65
> view matrix models
> #8,0.67389,0.42018,-0.60771,75.853,-0.30745,-0.58845,-0.74779,376.48,-0.67182,0.69078,-0.26737,280.51
> view matrix models
> #8,0.79817,0.5886,-0.12837,-47.242,0.20397,-0.46452,-0.86175,294.25,-0.56686,0.66164,-0.49082,304.31
> volume #8 level 0.05707
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.79817,0.5886,-0.12837,-72.408,0.20397,-0.46452,-0.86175,376.41,-0.56686,0.66164,-0.49082,220.94
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.77092,0.53035,-0.35271,-22.883,-0.30705,-0.17572,-0.93533,421.28,-0.55803,0.82937,0.027379,109.63
> view matrix models
> #8,0.92164,0.38413,0.054957,-88.75,-0.021959,0.19303,-0.98095,326.84,-0.38742,0.90288,0.18634,46.232
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.92164,0.38413,0.054957,-77.053,-0.021959,0.19303,-0.98095,298.82,-0.38742,0.90288,0.18634,15.781
> view matrix models
> #8,0.92164,0.38413,0.054957,-98.731,-0.021959,0.19303,-0.98095,313.62,-0.38742,0.90288,0.18634,1.3406
> view matrix models
> #8,0.92164,0.38413,0.054957,-111.31,-0.021959,0.19303,-0.98095,292.8,-0.38742,0.90288,0.18634,-1.6999
> view matrix models
> #8,0.92164,0.38413,0.054957,-112.74,-0.021959,0.19303,-0.98095,294.43,-0.38742,0.90288,0.18634,-6.2619
> open 4ikn
4ikn title:
Crystal structure of adaptor protein complex 3 (AP-3) mu3A subunit C-terminal
domain, in complex with a sorting peptide from TGN38 [more info...]
Chain information for 4ikn #7
---
Chain | Description
A | AP-3 complex subunit mu-1
B | Trans-Golgi network integral membrane protein TGN38
> ~select #8
Nothing selected
> select #7
2161 atoms, 2069 bonds, 2 pseudobonds, 390 residues, 2 models selected
> view matrix models #7,1,0,0,28.557,0,1,0,-16.727,0,0,1,43.404
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.83655,0.084469,0.54133,34.623,0.099874,0.94798,-0.30226,-19.994,-0.5387,0.30692,0.7846,32.649
> view matrix models
> #7,-0.93611,0.33477,-0.10779,0.90271,0.046534,-0.18588,-0.98147,-30.007,-0.34861,-0.92378,0.15843,26.775
> view matrix models
> #7,0.15442,-0.49333,-0.85603,4.6889,-0.6918,-0.67256,0.2628,-20.195,-0.70538,0.55162,-0.44515,11.304
> view matrix models
> #7,-0.18466,-0.6448,-0.74171,2.1008,-0.71788,-0.42694,0.54988,-16.375,-0.67123,0.634,-0.38405,12.613
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.18466,-0.6448,-0.74171,-43.047,-0.71788,-0.42694,0.54988,4.7276,-0.67123,0.634,-0.38405,108.78
> view matrix models
> #7,-0.18466,-0.6448,-0.74171,21.012,-0.71788,-0.42694,0.54988,77.584,-0.67123,0.634,-0.38405,187.27
> view matrix models
> #7,-0.18466,-0.6448,-0.74171,26.3,-0.71788,-0.42694,0.54988,86.09,-0.67123,0.634,-0.38405,113.56
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.28826,-0.58026,-0.76171,24.556,-0.64065,-0.47435,0.60379,87.99,-0.71167,0.66204,-0.235,115.28
> view matrix models
> #7,-0.2768,0.041028,-0.96005,21.042,-0.95733,0.074609,0.27921,78.259,0.083083,0.99637,0.018625,129.38
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.2768,0.041028,-0.96005,36.934,-0.95733,0.074609,0.27921,95.524,0.083083,0.99637,0.018625,99.917
> view matrix models
> #7,-0.2768,0.041028,-0.96005,61.054,-0.95733,0.074609,0.27921,126.71,0.083083,0.99637,0.018625,118.57
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.59688,0.031912,-0.80169,59.252,-0.80207,-0.049133,0.59521,133.75,-0.020396,0.99828,0.054922,117.75
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.59688,0.031912,-0.80169,59.354,-0.80207,-0.049133,0.59521,126.98,-0.020396,0.99828,0.054922,125.89
> ~select #7
Nothing selected
> select #8
2 models selected
> transparency #8.1 70
> ui tool show "Fit in Map"
Fit map cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip in map
cryosparc_P67_J843_map_sharp_merge.mrc using 154622 points
correlation = 0.4851, correlation about mean = 0.2502, overlap = 5339
steps = 168, shift = 4.56, angle = 2.88 degrees
Position of cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) relative to
cryosparc_P67_J843_map_sharp_merge.mrc (#4) coordinates:
Matrix rotation and translation
0.21822188 0.50467487 -0.83527389 171.39904120
-0.86034656 -0.30450480 -0.40875497 406.47754821
-0.46063326 0.80782430 0.36774568 -12.81114391
Axis 0.65180813 -0.20072166 -0.73133917
Axis point 274.50977335 136.62844387 -0.00000000
Rotation angle (degrees) 111.05528636
Shift along axis 39.49973215
Fit map cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip in map
cryosparc_P67_J843_map_sharp_merge.mrc using 154622 points
correlation = 0.485, correlation about mean = 0.25, overlap = 5339
steps = 44, shift = 0.0239, angle = 0.0408 degrees
Position of cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) relative to
cryosparc_P67_J843_map_sharp_merge.mrc (#4) coordinates:
Matrix rotation and translation
0.21863262 0.50508858 -0.83491633 171.19903579
-0.86011710 -0.30435170 -0.40935146 406.53134739
-0.46086696 0.80762340 0.36789412 -12.77877503
Axis 0.65192436 -0.20037546 -0.73133050
Axis point 274.52340101 136.71388587 0.00000000
Rotation angle (degrees) 111.03342286
Shift along axis 39.49542238
Fit molecule 4ikn (#7) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip
(#8) using 2161 atoms
average map value = 0.1409, steps = 144
shifted from previous position = 8.12
rotated from previous position = 22 degrees
atoms outside contour = 959, contour level = 0.057074
Position of 4ikn (#7) relative to cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip (#8) coordinates:
Matrix rotation and translation
-0.65769573 -0.05689029 -0.75113238 114.04128892
-0.12891995 0.99093317 0.03783040 166.25064353
0.74216980 0.12171683 -0.65906680 195.46104215
Axis 0.05602177 -0.99727008 -0.04810347
Axis point 19.40152880 0.00000000 121.59842411
Rotation angle (degrees) 131.52254298
Shift along axis -168.81035326
> hide #!4 models
> open C:/Users/mbegl/Downloads/AF/MZB127/MZB127AF.pdb
Chain information for MZB127AF.pdb #9
---
Chain | Description
A | No description available
> select #9
1461 atoms, 1487 bonds, 182 residues, 1 model selected
> view matrix models #9,1,0,0,35.362,0,1,0,55.121,0,0,1,-41.741
> view matrix models #9,1,0,0,37.336,0,1,0,72.073,0,0,1,-41.985
> view matrix models #9,1,0,0,21.38,0,1,0,62.074,0,0,1,-14.665
> view matrix models #9,1,0,0,61.464,0,1,0,75.583,0,0,1,-0.016986
> view matrix models #9,1,0,0,43.169,0,1,0,113.56,0,0,1,27.423
> view matrix models #9,1,0,0,54.105,0,1,0,98.806,0,0,1,57.421
> view matrix models #9,1,0,0,66.363,0,1,0,105.67,0,0,1,59.353
Fit molecule MZB127AF.pdb (#9) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip (#8) using 1461 atoms
average map value = 0.02489, steps = 116
shifted from previous position = 4.76
rotated from previous position = 9.9 degrees
atoms outside contour = 1228, contour level = 0.057074
Position of MZB127AF.pdb (#9) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.91718116 -0.10553234 -0.38424164 146.83903223
0.38996246 0.03952090 0.91998227 100.19716114
-0.08190231 -0.99363023 0.07740148 205.25004660
Axis -0.95694538 -0.15119165 0.24778343
Axis point 0.00000000 161.38804929 76.80456067
Rotation angle (degrees) 89.02295820
Shift along axis -104.80834735
Fit molecule MZB127AF.pdb (#9) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip (#8) using 1461 atoms
average map value = 0.02489, steps = 36
shifted from previous position = 0.00535
rotated from previous position = 0.0184 degrees
atoms outside contour = 1228, contour level = 0.057074
Position of MZB127AF.pdb (#9) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.91716820 -0.10528432 -0.38434061 146.84090975
0.39002719 0.03933632 0.91996274 100.19252845
-0.08173910 -0.99366387 0.07714177 205.24452130
Axis -0.95694873 -0.15132217 0.24769080
Axis point 0.00000000 161.34359935 76.81782453
Rotation angle (degrees) 89.03605922
Shift along axis -104.84339165
Fit molecule MZB127AF.pdb (#9) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip (#8) using 1461 atoms
average map value = 0.02488, steps = 48
shifted from previous position = 0.0126
rotated from previous position = 0.0327 degrees
atoms outside contour = 1228, contour level = 0.057074
Position of MZB127AF.pdb (#9) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.91728694 -0.10564300 -0.38395863 146.85128507
0.38969120 0.03956895 0.92009515 100.20746465
-0.08200878 -0.99361656 0.07746423 205.24567931
Axis -0.95699676 -0.15099716 0.24770357
Axis point 0.00000000 161.41019895 76.77956534
Rotation angle (degrees) 89.01675268
Shift along axis -104.82715830
> view matrix models
> #9,0.98911,-0.13795,0.051244,109.59,0.13278,0.98674,0.093391,185.02,-0.063448,-0.08557,0.99431,65.047
> view matrix models
> #9,0.98911,-0.13795,0.051244,108.64,0.13278,0.98674,0.093391,181.01,-0.063448,-0.08557,0.99431,71.339
Alignment identifier is 9/A
> select #9/A:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:47-48
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/A:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:48-52
38 atoms, 38 bonds, 5 residues, 1 model selected
> color sel orange
> color sel white
> view matrix models
> #9,0.98911,-0.13795,0.051244,116.87,0.13278,0.98674,0.093391,182.46,-0.063448,-0.08557,0.99431,71.969
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.44527,-0.66421,-0.60047,129.76,-0.67474,0.68975,-0.26263,189.93,0.58861,0.28822,-0.75529,25.516
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.44527,-0.66421,-0.60047,108.75,-0.67474,0.68975,-0.26263,188.26,0.58861,0.28822,-0.75529,83.321
> view matrix models
> #9,-0.44527,-0.66421,-0.60047,126.47,-0.67474,0.68975,-0.26263,189.13,0.58861,0.28822,-0.75529,88.449
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.33521,-0.94124,0.04115,140.22,-0.21651,0.034451,-0.97567,176.26,0.91693,-0.33597,-0.21534,101
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.33521,-0.94124,0.04115,138.73,-0.21651,0.034451,-0.97567,164.44,0.91693,-0.33597,-0.21534,91.529
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.15495,-0.98651,-0.052776,134.94,-0.17985,0.080697,-0.98038,163.35,0.97141,-0.14242,-0.18993,89.182
> view matrix models
> #9,0.2784,-0.95968,0.038869,130.46,-0.32271,-0.13158,-0.93731,168.43,0.90463,0.2484,-0.34633,82.895
Fit molecule MZB127AF.pdb (#9) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip (#8) using 1461 atoms
average map value = 0.1098, steps = 200
shifted from previous position = 7.24
rotated from previous position = 39.8 degrees
atoms outside contour = 889, contour level = 0.057074
Position of MZB127AF.pdb (#9) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.23056391 -0.89991252 0.37013203 186.62224072
0.47003051 -0.23005860 -0.85214104 159.56955141
0.85200445 0.37044631 0.36994314 135.88636489
Axis 0.64403239 -0.25383990 0.72165615
Axis point -69.70627639 139.76995173 0.00000000
Rotation angle (degrees) 108.34727840
Shift along axis 177.74887867
Fit molecule MZB127AF.pdb (#9) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip (#8) using 1461 atoms
average map value = 0.1098, steps = 44
shifted from previous position = 0.00375
rotated from previous position = 0.0119 degrees
atoms outside contour = 889, contour level = 0.057074
Position of MZB127AF.pdb (#9) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.23062733 -0.89985034 0.37024368 186.62191292
0.46992106 -0.23018585 -0.85216704 159.56919596
0.85204766 0.37051832 0.36977148 135.87966694
Axis 0.64411051 -0.25381428 0.72159542
Axis point -69.70938273 139.75764622 0.00000000
Rotation angle (degrees) 108.35438581
Shift along axis 177.75434087
Average map value = 0.1098 for 1461 atoms, 889 outside contour
Average map value = 0.1098 for 1461 atoms, 889 outside contour
Opened MZB127AF.pdb map 5 as #10, grid size 49,55,45, pixel 1.67, shown at
level 0.0846, step 1, values float32
Opened MZB127AF.pdb map 5 as #11, grid size 49,55,45, pixel 1.67, shown at
level 0.0846, step 1, values float32
Correlation = 0.5152, Correlation about mean = 0.1644, Overlap = 203.2
QWindowsWindow::setGeometry: Unable to set geometry 1920x1060+0+29 (frame:
1938x1107-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x991+0+29 (frame: 1938x1038-9-9) margins: 9, 38, 9, 9
minimum size: 558x1060 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=576,1107
maxtrack=0,0)
Fit map MZB127AF.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip using 5822 points
correlation = 0.5185, correlation about mean = 0.1744, overlap = 205.9
steps = 84, shift = 0.549, angle = 8.24 degrees
Position of MZB127AF.pdb map 5 (#10) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.20239528 -0.87316478 0.44341786 187.96960027
0.58382989 -0.25594175 -0.77047808 159.50407144
0.78624347 0.41482173 0.45797831 138.08171275
Axis 0.62081423 -0.17955880 0.76311750
Axis point -55.79568147 128.71639971 0.00000000
Rotation angle (degrees) 107.32455828
Shift along axis 193.42641453
Average map value = 0.1063 for 1461 atoms, 886 outside contour
Fit map MZB127AF.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip using 5822 points
correlation = 0.5185, correlation about mean = 0.1744, overlap = 205.9
steps = 68, shift = 0.00189, angle = 0.0132 degrees
Position of MZB127AF.pdb map 5 (#10) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.20238858 -0.87312455 0.44350012 187.97137858
0.58401226 -0.25592154 -0.77034657 159.50506120
0.78610974 0.41491886 0.45811986 138.08623077
Axis 0.62078050 -0.17944113 0.76317262
Axis point -55.78234305 128.70272427 0.00000000
Rotation angle (degrees) 107.31990517
Shift along axis 193.45082886
Average map value = 0.1063 for 1461 atoms, 886 outside contour
> view matrix models
> #9,-0.048639,-0.99749,0.051527,134.76,-0.81433,0.0097305,-0.58032,179.34,0.57836,-0.070186,-0.81276,91.202
Fit map MZB127AF.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip using 5822 points
correlation = 0.6678, correlation about mean = 0.4466, overlap = 285.3
steps = 100, shift = 4.12, angle = 23 degrees
Position of MZB127AF.pdb map 5 (#10) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.28454406 -0.94496863 0.16145878 189.66684189
0.65685881 -0.31485244 -0.68513096 158.21398447
0.69826296 -0.08889432 0.71030038 146.44428745
Axis 0.33281235 -0.29963784 0.89412142
Axis point -2.52195809 152.48932715 0.00000000
Rotation angle (degrees) 116.39442772
Shift along axis 146.65554360
Average map value = 0.1647 for 1461 atoms, 650 outside contour
Fit map MZB127AF.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip using 5822 points
correlation = 0.6678, correlation about mean = 0.4466, overlap = 285.3
steps = 40, shift = 0.00472, angle = 0.00743 degrees
Position of MZB127AF.pdb map 5 (#10) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.28466149 -0.94494106 0.16141315 189.67242030
0.65683411 -0.31490282 -0.68513148 158.21553462
0.69823833 -0.08900889 0.71031025 146.44619359
Axis 0.33276325 -0.29966267 0.89413137
Axis point -2.50841768 152.49226428 0.00000000
Rotation angle (degrees) 116.39947919
Shift along axis 146.64685606
Average map value = 0.1647 for 1461 atoms, 652 outside contour
> close #10
> close #11
> open C:/Users/mbegl/Downloads/AF/MZB127/MZB127AF.pdb
Chain information for MZB127AF.pdb #10
---
Chain | Description
A | No description available
> select #9
1461 atoms, 1487 bonds, 182 residues, 1 model selected
> ~select #9
Nothing selected
> select #10
1461 atoms, 1487 bonds, 182 residues, 1 model selected
Alignment identifier is 10/A
> select #10/A:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:48-52
38 atoms, 38 bonds, 5 residues, 1 model selected
> color sel white
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,48.843,0,1,0,51.879,0,0,1,-35.763
> view matrix models #10,1,0,0,49.451,0,1,0,85.392,0,0,1,78.34
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.95836,-0.071694,0.27643,56.085,-0.086624,0.84939,0.52062,98.166,-0.27212,-0.52288,0.8078,84.031
> view matrix models
> #10,0.93747,-0.3027,0.17181,56.858,0.050384,0.60645,0.79352,104.13,-0.3444,-0.73525,0.58378,83.024
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.93747,-0.3027,0.17181,61.783,0.050384,0.60645,0.79352,108.02,-0.3444,-0.73525,0.58378,65.864
> view matrix models
> #10,0.93747,-0.3027,0.17181,66.497,0.050384,0.60645,0.79352,114,-0.3444,-0.73525,0.58378,80.898
> view matrix models
> #10,0.93747,-0.3027,0.17181,68.716,0.050384,0.60645,0.79352,118.77,-0.3444,-0.73525,0.58378,74.024
> ui tool show "Fit in Map"
Fit molecule MZB127AF.pdb (#10) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc
z flip (#8) using 1461 atoms
average map value = 0.03397, steps = 136
shifted from previous position = 8.07
rotated from previous position = 12.8 degrees
atoms outside contour = 1189, contour level = 0.057074
Position of MZB127AF.pdb (#10) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.99648835 0.05074696 0.06660117 147.54145689
-0.02544274 -0.57428977 0.81825664 119.76826234
0.07977241 -0.81707773 -0.57098193 188.86335819
Axis -0.99888414 -0.00804517 -0.04653769
Axis point 0.00000000 106.53998835 60.15311515
Rotation angle (degrees) 125.05704178
Shift along axis -157.12964105
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.86289,0.47636,0.16882,65.31,-0.47407,0.87869,-0.05626,114.33,-0.17514,-0.031485,0.98404,76.13
Fit molecule MZB127AF.pdb (#10) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc
z flip (#8) using 1461 atoms
average map value = 0.03607, steps = 136
shifted from previous position = 7.75
rotated from previous position = 27.7 degrees
atoms outside contour = 1125, contour level = 0.057074
Position of MZB127AF.pdb (#10) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.64532988 0.46978277 -0.60237322 141.93772075
0.54713781 0.26604227 0.79363829 105.08647698
0.53309433 -0.84173967 -0.08535089 188.61731862
Axis -0.82080043 -0.56989411 0.03882470
Axis point 0.00000000 112.23572847 92.78847677
Rotation angle (degrees) 94.99043144
Shift along axis -169.06769629
Fit molecule MZB127AF.pdb (#10) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc
z flip (#8) using 1461 atoms
average map value = 0.03606, steps = 48
shifted from previous position = 0.0268
rotated from previous position = 0.0281 degrees
atoms outside contour = 1126, contour level = 0.057074
Position of MZB127AF.pdb (#10) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.64570388 0.46960126 -0.60211390 141.93109510
0.54689047 0.26589360 0.79385856 105.06825838
0.53289521 -0.84188792 -0.08513193 188.62694639
Axis -0.82096943 -0.56965293 0.03879090
Axis point 0.00000000 112.26381042 92.77328764
Rotation angle (degrees) 94.97765503
Shift along axis -169.05652189
Fit molecule MZB127AF.pdb (#10) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc
z flip (#8) using 1461 atoms
average map value = 0.03606, steps = 48
shifted from previous position = 0.023
rotated from previous position = 0.0265 degrees
atoms outside contour = 1125, contour level = 0.057074
Position of MZB127AF.pdb (#10) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.64536295 0.46968239 -0.60241606 141.93811161
0.54714769 0.26609008 0.79361544 105.08142267
0.53304414 -0.84178057 -0.08526096 188.62605568
Axis -0.82080335 -0.56988615 0.03887974
Axis point 0.00000000 112.25269662 92.79491013
Rotation angle (degrees) 94.98551913
Shift along axis -169.05399233
> view matrix models
> #10,0.71416,0.58675,-0.38171,62.785,-0.48592,0.80808,0.33301,126.58,0.50384,-0.052341,0.86221,63.529
> undo
> select #10
1461 atoms, 1487 bonds, 182 residues, 1 model selected
> ~select #10
Nothing selected
> show #2 models
> select #2
4858 atoms, 4939 bonds, 617 residues, 1 model selected
> ui tool show "Fit in Map"
Fit molecule AP3D1.pdb (#2) to map cryosparc_P123_J67_map_sharp_CHAOS.mrc z
flip (#8) using 4858 atoms
average map value = 0.09894, steps = 100
shifted from previous position = 1.98
rotated from previous position = 3.92 degrees
atoms outside contour = 2664, contour level = 0.057074
Position of AP3D1.pdb (#2) relative to cryosparc_P123_J67_map_sharp_CHAOS.mrc
z flip (#8) coordinates:
Matrix rotation and translation
0.19007645 -0.87042191 0.45413285 179.45800323
0.66471057 -0.22632129 -0.71199616 165.15738083
0.72251699 0.43720061 0.53556030 210.57583108
Axis 0.59349687 -0.13860564 0.79281142
Axis point -86.70087224 116.00208830 0.00000000
Rotation angle (degrees) 104.49776706
Shift along axis 250.56294220
Average map value = 0.09894 for 4858 atoms, 2664 outside contour
Opened AP3D1.pdb map 5 as #11, grid size 94,59,67, pixel 1.67, shown at level
0.0923, step 1, values float32
Opened AP3D1.pdb map 5 as #12, grid size 94,59,67, pixel 1.67, shown at level
0.0923, step 1, values float32
Correlation = 0.6102, Correlation about mean = 0.3196, Overlap = 621.2
Fit map AP3D1.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip
using 19096 points
correlation = 0.6109, correlation about mean = 0.3203, overlap = 623.7
steps = 100, shift = 0.565, angle = 0.56 degrees
Position of AP3D1.pdb map 5 (#11) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.18277692 -0.87000999 0.45790306 179.18026082
0.66230801 -0.23525059 -0.71134047 164.78975679
0.72659528 0.43328949 0.53321621 210.21441287
Axis 0.59263740 -0.13911662 0.79336466
Axis point -85.35275391 115.80221232 0.00000000
Rotation angle (degrees) 105.04803331
Shift along axis 250.04061450
Average map value = 0.09854 for 4858 atoms, 2702 outside contour
Fit map AP3D1.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip
using 19096 points
correlation = 0.611, correlation about mean = 0.3202, overlap = 623.7
steps = 76, shift = 0.0207, angle = 0.014 degrees
Position of AP3D1.pdb map 5 (#11) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.18273738 -0.86999602 0.45794539 179.19755077
0.66214690 -0.23540498 -0.71143938 164.78957041
0.72675205 0.43323369 0.53304788 210.20324057
Axis 0.59268962 -0.13918290 0.79331402
Axis point -85.34647942 115.81427978 0.00000000
Rotation angle (degrees) 105.05878015
Shift along axis 250.02981669
Average map value = 0.09853 for 4858 atoms, 2704 outside contour
> ~select #2
Nothing selected
> show #1 models
> hide #2 models
> select #1
5051 atoms, 5133 bonds, 633 residues, 1 model selected
Opened AP3B1.pdb map 5 as #13, grid size 89,74,61, pixel 1.67, shown at level
0.0869, step 1, values float32
Opened AP3B1.pdb map 5 as #14, grid size 89,74,61, pixel 1.67, shown at level
0.0869, step 1, values float32
Fit map AP3B1.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip
using 20121 points
correlation = 0.6157, correlation about mean = 0.4066, overlap = 1108
steps = 72, shift = 1.11, angle = 2.76 degrees
Position of AP3B1.pdb map 5 (#14) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.22772815 0.88945737 -0.39623917 153.04512318
-0.38836986 -0.45613155 -0.80069524 186.38293039
-0.89292147 -0.02845349 0.44931243 204.01956169
Axis 0.49078054 0.31565505 -0.81209381
Axis point 196.99598060 82.33742598 0.00000000
Rotation angle (degrees) 128.11731275
Shift along axis -31.73874035
Average map value = 0.1796 for 5051 atoms, 2435 outside contour
Fit map AP3B1.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip
using 20121 points
correlation = 0.6157, correlation about mean = 0.4066, overlap = 1108
steps = 48, shift = 0.00391, angle = 0.00594 degrees
Position of AP3B1.pdb map 5 (#13) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.22764362 0.88946495 -0.39627073 153.04291129
-0.38832731 -0.45612032 -0.80072227 186.38149884
-0.89296153 -0.02839657 0.44923641 204.02267985
Axis 0.49082907 0.31565735 -0.81206359
Axis point 197.00598606 82.33805940 0.00000000
Rotation angle (degrees) 128.11659408
Shift along axis -31.72879030
Average map value = 0.1796 for 5051 atoms, 2434 outside contour
> ~select #1
Nothing selected
> hide #1 models
> show #3 models
> select #3
1133 atoms, 1163 bonds, 140 residues, 1 model selected
Opened AP3M1.pdb map 5 as #15, grid size 40,36,49, pixel 1.67, shown at level
0.0932, step 1, values float32
Opened AP3M1.pdb map 5 as #16, grid size 40,36,49, pixel 1.67, shown at level
0.0932, step 1, values float32
Fit map AP3M1.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip
using 4425 points
correlation = 0.7174, correlation about mean = 0.5628, overlap = 308
steps = 60, shift = 3.1, angle = 2.61 degrees
Position of AP3M1.pdb map 5 (#16) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.04076859 -0.93861948 -0.34253671 138.57724673
-0.93693839 0.15500815 -0.31323943 170.63279961
0.34710861 0.30816546 -0.88574808 194.86027144
Axis 0.66939447 -0.74290495 0.00181092
Axis point 113.87257182 0.00000000 124.32591504
Rotation angle (degrees) 152.34448460
Shift along axis -33.64823175
Average map value = 0.2497 for 1133 atoms, 383 outside contour
> hide #3 models
> ~select #3
Nothing selected
> show #6 models
> select #6
1525 atoms, 1551 bonds, 193 residues, 1 model selected
Opened AP3S1.pdb map 5 as #17, grid size 60,54,44, pixel 1.67, shown at level
0.0822, step 1, values float32
Opened AP3S1.pdb map 5 as #18, grid size 60,54,44, pixel 1.67, shown at level
0.0822, step 1, values float32
Fit map AP3S1.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip
using 6193 points
correlation = 0.6033, correlation about mean = 0.3822, overlap = 247.3
steps = 88, shift = 2.1, angle = 11.7 degrees
Position of AP3S1.pdb map 5 (#18) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.56479386 0.27344864 -0.77861013 177.53818835
-0.56256379 -0.81787540 0.12083797 146.16506135
-0.60376310 0.50626641 0.61576331 192.85178167
Axis 0.41132564 -0.18659513 -0.89218466
Axis point 150.31551235 20.92261717 0.00000000
Rotation angle (degrees) 152.06174120
Shift along axis -126.30708098
Average map value = 0.133 for 1525 atoms, 835 outside contour
> hide #5 models
Alignment identifier is 6/A
> select #6/A:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:114-115
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/A:106
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:106-114
77 atoms, 78 bonds, 9 residues, 1 model selected
> select #6/A:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:159-167
63 atoms, 62 bonds, 9 residues, 1 model selected
> select #6/A:134
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:134-167
245 atoms, 245 bonds, 34 residues, 1 model selected
> select #6/A:134
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:134-155
166 atoms, 165 bonds, 22 residues, 1 model selected
> select #6/A:155
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:124-155
236 atoms, 235 bonds, 32 residues, 1 model selected
Fit map AP3S1.pdb map 5 in map cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip
using 6193 points
correlation = 0.6033, correlation about mean = 0.3822, overlap = 247.3
steps = 48, shift = 0.0149, angle = 0.0229 degrees
Position of AP3S1.pdb map 5 (#17) relative to
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.56468751 0.27344908 -0.77868711 177.54440478
-0.56237460 -0.81804785 0.12055096 146.17001059
-0.60403877 0.50598748 0.61572222 192.84302210
Axis 0.41142301 -0.18642330 -0.89217569
Axis point 150.32867660 20.95235698 0.00000000
Rotation angle (degrees) 152.06829584
Shift along axis -126.25349975
Average map value = 0.1328 for 1525 atoms, 833 outside contour
Opened AP3S1.pdb map 5 as #17, grid size 60,54,44, pixel 1.67, shown at level
0.082, step 1, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1141+0+29 (frame:
1938x1188-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x991+0+29 (frame: 1938x1038-9-9) margins: 9, 38, 9, 9
minimum size: 535x1141 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=553,1188
maxtrack=0,0)
> view matrix models
> #6,-0.8006,-0.072853,-0.59476,115.46,0.489,-0.65308,-0.57824,126.17,-0.3463,-0.75377,0.55848,90.24
> undo
> ui mousemode right select
> select clear
> show #5 models
> hide #!8 models
> hide #5 models
> show #!8 models
> show #1 models
> show #2 models
> show #3 models
> save "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Oct
> 2023/WTF.cxs" includeMaps true
> save C:/Users/mbegl/OneDrive/transfer/HAILMARY.cxs includeMaps true
——— End of log from Sat Nov 25 18:56:35 2023 ———
opened ChimeraX session
> open C:/ProgramData/ChimeraX/Hail_mary_redock_spin.mp4
Unrecognized file suffix '.mp4'
> movie record
> turn y 2 180
> wait 180
> movie encode C:\ProgramData\ChimeraX\movie13.mp4
Movie saved to C:\ProgramData\ChimeraX\movie13.mp4
> volume #8 level -0.01123
> volume #8 level 0.01913
> select #1
5051 atoms, 5133 bonds, 633 residues, 1 model selected
Alignment identifier is 1/A
> select #1/A:391
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:391-410
160 atoms, 160 bonds, 20 residues, 1 model selected
> color sel magenta
> open "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Oct
> 2023/cryosparc_P123_J94_map_sharp_not as clean.mrc"
Opened cryosparc_P123_J94_map_sharp_not as clean.mrc as #18, grid size
300,300,300, pixel 1.06, shown at level 0.0168, step 2, values float32
> close #11
> close #12
> show #!4 models
> hide #!4 models
> close #15
> close #14
> close #13
> close #16
> close #17
> select #18
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #18,-0.73154,-0.67469,-0.098223,390.01,-0.08198,-0.055977,0.99506,22.235,-0.67685,0.73598,-0.014361,148.77
> volume flip #18
Opened cryosparc_P123_J94_map_sharp_not as clean.mrc z flip as #11, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> close #18
> select #11
2 models selected
> view matrix models
> #11,-0.90076,-0.36299,0.2385,313.82,-0.099767,-0.36151,-0.92702,377.87,0.42271,-0.85881,0.28942,180.93
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.90076,-0.36299,0.2385,256.49,-0.099767,-0.36151,-0.92702,384.54,0.42271,-0.85881,0.28942,122.26
> ui tool show "Fit in Map"
Fit map cryosparc_P123_J94_map_sharp_not as clean.mrc z flip in map
cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip using 268895 points
correlation = 0.8622, correlation about mean = 0.7733, overlap = 1.473e+04
steps = 272, shift = 11.3, angle = 11.1 degrees
Position of cryosparc_P123_J94_map_sharp_not as clean.mrc z flip (#11)
relative to cryosparc_P123_J67_map_sharp_CHAOS.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.99979082 -0.00090136 0.02043344 314.09272856
0.00146277 -0.99962141 0.02747593 313.51008275
0.02040095 0.02750008 0.99941363 -6.35204435
Axis 0.01021372 0.01374459 0.99985337
Axis point 156.98613825 156.89154415 0.00000000
Rotation angle (degrees) 179.93226271
Shift along axis 1.16601095
> transparency #11.1 70
> surface dust #11 size 10.6
> hide #!8 models
> open 1o3Y
1o3y title:
Crystal structure of mouse ARF1 (delta17-Q71L), GTP form [more info...]
Chain information for 1o3y #12
---
Chain | Description
A B | ADP-ribosylation factor 1
Non-standard residues in 1o3y #12
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
1o3y mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select #12
3043 atoms, 2778 bonds, 12 pseudobonds, 649 residues, 2 models selected
> view matrix models #12,1,0,0,199.98,0,1,0,158.81,0,0,1,49.163
> select #12/B
1490 atoms, 1389 bonds, 6 pseudobonds, 293 residues, 2 models selected
> delete atoms (#!12 & sel)
> delete bonds (#!12 & sel)
> select #12/A
1553 atoms, 1389 bonds, 6 pseudobonds, 356 residues, 2 models selected
Alignment identifier is 12/A
> select #12/A:63
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:45-63
153 atoms, 156 bonds, 19 residues, 1 model selected
> select #12/A:51
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:50-51
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #12/A:53
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/A:46-53
60 atoms, 61 bonds, 8 residues, 1 model selected
> color sel white
> select #12/A:16
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #12/A:16-17
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #12
1553 atoms, 1389 bonds, 6 pseudobonds, 356 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.14327,0.97897,-0.14521,213.95,-0.98679,-0.15251,-0.05463,168.58,-0.075628,0.13546,0.98789,50.168
> view matrix models
> #12,-0.098859,0.56005,0.82254,200.33,-0.99318,-0.10691,-0.046575,168.57,0.061854,-0.82153,0.5668,53.77
> view matrix models
> #12,-0.45573,0.87222,0.17761,212.69,-0.81445,-0.3281,-0.47856,172.4,-0.35914,-0.36275,0.8599,54.362
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.45573,0.87222,0.17761,189.96,-0.81445,-0.3281,-0.47856,224.66,-0.35914,-0.36275,0.8599,77.916
> view matrix models
> #12,-0.45573,0.87222,0.17761,139.54,-0.81445,-0.3281,-0.47856,189.49,-0.35914,-0.36275,0.8599,76.763
> view matrix models
> #12,-0.45573,0.87222,0.17761,143.6,-0.81445,-0.3281,-0.47856,193.09,-0.35914,-0.36275,0.8599,96.19
> ui tool show "Fit in Map"
Fit molecule 1o3y (#12) to map cryosparc_P123_J94_map_sharp_not as clean.mrc z
flip (#11) using 1553 atoms
average map value = 0.125, steps = 124
shifted from previous position = 9.11
rotated from previous position = 32.9 degrees
atoms outside contour = 786, contour level = 0.016842
Position of 1o3y (#12) relative to cryosparc_P123_J94_map_sharp_not as
clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
-0.20648274 -0.92713103 0.31271856 128.73331565
0.87321099 -0.31880252 -0.36860207 132.85659666
0.44143788 0.19695933 0.87540824 126.28530786
Axis 0.29900623 -0.06805252 0.95182148
Axis point -9.10403261 102.43462624 0.00000000
Rotation angle (degrees) 108.96184999
Shift along axis 149.65190587
> hide #9 models
Average map value = 0.125 for 1553 atoms, 786 outside contour
Average map value = 0.125 for 1553 atoms, 786 outside contour
Opened 1o3y map 5 as #13, grid size 44,42,48, pixel 1.67, shown at level
0.101, step 1, values float32
Opened 1o3y map 5 as #14, grid size 44,42,48, pixel 1.67, shown at level
0.101, step 1, values float32
Correlation = 0.4781, Correlation about mean = 0.08459, Overlap = 253.8
Fit map 1o3y map 5 in map cryosparc_P123_J94_map_sharp_not as clean.mrc z flip
using 6265 points
correlation = 0.4806, correlation about mean = 0.09169, overlap = 257.1
steps = 68, shift = 3.46, angle = 11.9 degrees
Position of 1o3y map 5 (#13) relative to cryosparc_P123_J94_map_sharp_not as
clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
-0.20909155 -0.95828710 0.19485002 132.22233686
0.94149349 -0.25113091 -0.22477374 129.54556262
0.26433064 0.13645174 0.95473043 123.70712220
Axis 0.18667354 -0.03590609 0.98176563
Axis point 1.39704990 108.65445907 0.00000000
Rotation angle (degrees) 104.64006702
Shift along axis 141.48233712
Average map value = 0.1214 for 1553 atoms, 782 outside contour
> close #13
> close #14
> mmaker #12 to #9
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 MZB127AF.pdb, chain A (#9) with 1o3y, chain A (#12), sequence
alignment score = 839.9
RMSD between 135 pruned atom pairs is 0.587 angstroms; (across all 166 pairs:
2.069)
Opened 1o3y map 5 as #13, grid size 44,42,48, pixel 1.67, shown at level
0.101, step 1, values float32
Fit map 1o3y map 5 in map cryosparc_P123_J94_map_sharp_not as clean.mrc z flip
using 6265 points
correlation = 0.7078, correlation about mean = 0.5761, overlap = 400.2
steps = 60, shift = 0.0595, angle = 0.693 degrees
Position of 1o3y map 5 (#13) relative to cryosparc_P123_J94_map_sharp_not as
clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
-0.52036119 -0.68256301 -0.51315879 147.28945667
0.51718911 0.22627313 -0.82541860 143.77453814
0.67951425 -0.69491595 0.23527041 136.18624587
Axis 0.07691405 -0.70292296 0.70709514
Axis point 8.03427830 197.15348319 0.00000000
Rotation angle (degrees) 121.96552059
Shift along axis 6.56283715
Average map value = 0.2211 for 1553 atoms, 463 outside contour
Fit map 1o3y map 5 in map cryosparc_P123_J94_map_sharp_not as clean.mrc z flip
using 6265 points
correlation = 0.7078, correlation about mean = 0.5762, overlap = 400.2
steps = 48, shift = 0.00271, angle = 0.0421 degrees
Position of 1o3y map 5 (#13) relative to cryosparc_P123_J94_map_sharp_not as
clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
-0.52067104 -0.68202859 -0.51355491 147.29982983
0.51730885 0.22650008 -0.82528131 143.77320558
0.67918568 -0.69536658 0.23488740 136.19650017
Axis 0.07658067 -0.70308329 0.70697192
Axis point 8.10058231 197.18388031 0.00000000
Rotation angle (degrees) 121.98125484
Shift along axis 6.48288260
Average map value = 0.2211 for 1553 atoms, 464 outside contour
> close #13
> show #9 models
Opened MZB127AF.pdb map 5 as #13, grid size 49,55,45, pixel 1.67, shown at
level 0.0846, step 1, values float32
Opened MZB127AF.pdb map 5 as #14, grid size 49,55,45, pixel 1.67, shown at
level 0.0846, step 1, values float32
Fit map MZB127AF.pdb map 5 in map cryosparc_P123_J94_map_sharp_not as
clean.mrc z flip using 5822 points
correlation = 0.6166, correlation about mean = 0.2491, overlap = 81.82
steps = 104, shift = 1.17, angle = 8.31 degrees
Position of MZB127AF.pdb map 5 (#14) relative to
cryosparc_P123_J94_map_sharp_not as clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
-0.57398920 -0.53998168 0.61559414 174.87383946
-0.61815547 -0.20731168 -0.75822533 215.84225772
0.53704765 -0.81574605 -0.21479797 184.83564621
Axis -0.46069196 0.62909051 -0.62610546
Axis point 170.11842968 0.00000000 196.17638108
Rotation angle (degrees) 176.42077649
Shift along axis -60.50526415
Average map value = 0.04293 for 1461 atoms, 664 outside contour
Fit map MZB127AF.pdb map 5 in map cryosparc_P123_J94_map_sharp_not as
clean.mrc z flip using 5822 points
correlation = 0.6167, correlation about mean = 0.2491, overlap = 81.82
steps = 40, shift = 0.00479, angle = 0.0246 degrees
Position of MZB127AF.pdb map 5 (#13) relative to
cryosparc_P123_J94_map_sharp_not as clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
-0.57364540 -0.54019987 0.61572317 174.86691897
-0.61828713 -0.20748595 -0.75807030 215.84775284
0.53726339 -0.81555726 -0.21497526 184.83174303
Axis -0.46088034 0.62902211 -0.62603554
Axis point 170.15426106 0.00000000 196.18083865
Rotation angle (degrees) 176.42434370
Shift along axis -60.53095457
Average map value = 0.04293 for 1461 atoms, 664 outside contour
Fit molecule MZB127AF.pdb (#10) to map cryosparc_P123_J94_map_sharp_not as
clean.mrc z flip (#11) using 1461 atoms
average map value = 0.04331, steps = 64
shifted from previous position = 0.408
rotated from previous position = 0.691 degrees
atoms outside contour = 664, contour level = 0.016842
Position of MZB127AF.pdb (#10) relative to cryosparc_P123_J94_map_sharp_not as
clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
-0.57138112 -0.53597034 0.62149769 174.89860056
-0.62712295 -0.20334044 -0.75191053 216.26923803
0.52937737 -0.81938295 -0.21993441 185.24963966
Axis -0.46179902 0.63049575 -0.62387241
Axis point 170.93903052 -0.00000000 195.35391233
Rotation angle (degrees) 175.81058887
Shift along axis -59.98330647
Fit molecule MZB127AF.pdb (#10) to map cryosparc_P123_J94_map_sharp_not as
clean.mrc z flip (#11) using 1461 atoms
average map value = 0.04331, steps = 40
shifted from previous position = 0.0179
rotated from previous position = 0.0144 degrees
atoms outside contour = 664, contour level = 0.016842
Position of MZB127AF.pdb (#10) relative to cryosparc_P123_J94_map_sharp_not as
clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
-0.57155670 -0.53588468 0.62141011 174.90387640
-0.62710264 -0.20314662 -0.75197985 216.28445494
0.52921185 -0.81948705 -0.21994489 185.25611505
Axis -0.46170217 0.63057177 -0.62386726
Axis point 170.92455904 -0.00000000 195.34748051
Rotation angle (degrees) 175.80754470
Shift along axis -59.94585266
> close #13
> close #14
> save "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Oct
> 2023/WTF_HighestRes.cxs" includeMaps true
——— End of log from Sun Nov 26 15:48:41 2023 ———
opened ChimeraX session
> open "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Oct
> 2023/cryosparc_P123_J243_map_sharp.mrc"
MRC file is truncated. Failed reading 1 values, type int32
> open "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Oct
> 2023/cryosparc_P123_J243_map_sharp(1).mrc"
Opened cryosparc_P123_J243_map_sharp(1).mrc as #13, grid size 400,400,400,
pixel 1.06, shown at level 0.00178, step 2, values float32
> hide #!12 models
> select add #13
1553 atoms, 1389 bonds, 6 pseudobonds, 356 residues, 4 models selected
> select subtract #12
2 models selected
> surface dust #13 size 10.6
> ui mousemode right "translate selected models"
> view matrix models #13,1,0,0,-70.899,0,1,0,16.597,0,0,1,79.36
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.69386,0.68187,0.23156,-195.97,-0.40209,0.63361,-0.66096,309.6,-0.5974,0.3655,0.71381,185
> view matrix models
> #13,0.11119,0.061389,0.9919,-93.593,0.9919,-0.06847,-0.10695,53.947,0.06135,0.99576,-0.068505,68.902
> view matrix models
> #13,0.34137,0.18261,0.92202,-153.71,0.9139,-0.29374,-0.28019,152.19,0.21967,0.93828,-0.26716,87.108
> view matrix models
> #13,0.48642,0.22697,0.84373,-178.04,0.82463,-0.4384,-0.35748,216.79,0.28876,0.86965,-0.40041,113.46
> view matrix models
> #13,0.61045,0.40993,0.67772,-209.72,0.74686,-0.58281,-0.32021,256.16,0.26372,0.70163,-0.66194,206.03
> view matrix models
> #13,-0.22419,0.15386,0.96232,-36.578,0.32622,-0.91864,0.22287,307.63,0.91832,0.3639,0.15576,-23.012
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.22419,0.15386,0.96232,-55.296,0.32622,-0.91864,0.22287,279.09,0.91832,0.3639,0.15576,-197.05
> view matrix models
> #13,-0.22419,0.15386,0.96232,-82.122,0.32622,-0.91864,0.22287,272.17,0.91832,0.3639,0.15576,-199.65
> view matrix models
> #13,-0.22419,0.15386,0.96232,-72.493,0.32622,-0.91864,0.22287,266.05,0.91832,0.3639,0.15576,-195.7
> view matrix models
> #13,-0.22419,0.15386,0.96232,-79.12,0.32622,-0.91864,0.22287,254.46,0.91832,0.3639,0.15576,-192.93
> volume #13 level 0.01205
> view matrix models
> #13,-0.22419,0.15386,0.96232,-75.399,0.32622,-0.91864,0.22287,254.55,0.91832,0.3639,0.15576,-198.56
> ui tool show "Fit in Map"
> fitmap #13 inMap #11
Fit map cryosparc_P123_J243_map_sharp(1).mrc in map
cryosparc_P123_J94_map_sharp_not as clean.mrc z flip using 41059 points
correlation = 0.8702, correlation about mean = 0.7997, overlap = 2081
steps = 320, shift = 10.6, angle = 7.12 degrees
Position of cryosparc_P123_J243_map_sharp(1).mrc (#13) relative to
cryosparc_P123_J94_map_sharp_not as clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
0.58608247 -0.09552290 -0.80460095 222.31292745
-0.80682314 -0.16005459 -0.56869933 475.90103249
-0.07445627 0.98247538 -0.17087527 -4.16211314
Axis 0.83570568 -0.39337030 -0.38321773
Axis point 0.00000000 291.92868791 241.45935564
Rotation angle (degrees) 111.86517113
Shift along axis 0.17783960
> hide #!11 models
> transparency #13.1 70
> open
> C:/Users/mbegl/Downloads/AF/LAMPI/sequences_0_model_5_multimer_v3_0_unrelaxed.pdb
Chain information for sequences_0_model_5_multimer_v3_0_unrelaxed.pdb #14
---
Chain | Description
A | No description available
B | No description available
> select add #14
1959 atoms, 2002 bonds, 248 residues, 3 models selected
> select subtract #13
1959 atoms, 2002 bonds, 248 residues, 1 model selected
> view matrix models #14,1,0,0,31.956,0,1,0,-52.236,0,0,1,123.54
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.21468,0.45053,-0.86657,34.204,-0.24538,0.88368,0.39863,-53.864,0.94536,0.12705,0.30026,126.9
> view matrix models
> #14,0.92432,0.14665,-0.35231,33.108,-0.12688,0.98879,0.078703,-52.634,0.3599,-0.028045,0.93257,124.12
> view matrix models
> #14,0.99639,-0.029946,0.079377,31.676,0.030887,0.99947,-0.010663,-52.169,-0.079015,0.013077,0.99679,123.47
> view matrix models
> #14,0.888,-0.15015,0.43465,30.333,0.17941,0.98341,-0.026817,-51.968,-0.42341,0.10179,0.9002,123.47
> view matrix models
> #14,0.70853,-0.21452,0.67229,29.331,0.29066,0.95683,-0.0010179,-51.948,-0.64305,0.19613,0.74029,123.81
> view matrix models
> #14,0.0041582,-0.83134,0.55574,26.277,0.29078,0.53274,0.79476,-55.146,-0.95678,0.15829,0.24395,124.24
> select subtract #14
Nothing selected
> select add #14
1959 atoms, 2002 bonds, 248 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.0041582,-0.83134,0.55574,45.92,0.29078,0.53274,0.79476,48.1,-0.95678,0.15829,0.24395,199.55
> view matrix models
> #14,0.0041582,-0.83134,0.55574,35.738,0.29078,0.53274,0.79476,58.902,-0.95678,0.15829,0.24395,143.73
> view matrix models
> #14,0.0041582,-0.83134,0.55574,29.986,0.29078,0.53274,0.79476,90.929,-0.95678,0.15829,0.24395,108.07
> view matrix models
> #14,0.0041582,-0.83134,0.55574,53.273,0.29078,0.53274,0.79476,111.95,-0.95678,0.15829,0.24395,144.1
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.30004,-0.428,0.85252,54.558,0.34227,0.88249,0.32258,114.28,-0.89041,0.195,0.41127,143.98
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.30004,-0.428,0.85252,73.709,0.34227,0.88249,0.32258,117.38,-0.89041,0.195,0.41127,128.37
> view matrix models
> #14,0.30004,-0.428,0.85252,71.967,0.34227,0.88249,0.32258,126.01,-0.89041,0.195,0.41127,128.92
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.11882,-0.53584,0.83592,70.976,0.22563,0.80529,0.54827,125.08,-0.96694,0.25375,0.025222,129.82
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.11882,-0.53584,0.83592,77.361,0.22563,0.80529,0.54827,126.85,-0.96694,0.25375,0.025222,133.81
> fitmap #14 inMap #11
Fit molecule sequences_0_model_5_multimer_v3_0_unrelaxed.pdb (#14) to map
cryosparc_P123_J94_map_sharp_not as clean.mrc z flip (#11) using 1959 atoms
average map value = 0.155, steps = 84
shifted from previous position = 3.87
rotated from previous position = 4.4 degrees
atoms outside contour = 582, contour level = 0.016842
Position of sequences_0_model_5_multimer_v3_0_unrelaxed.pdb (#14) relative to
cryosparc_P123_J94_map_sharp_not as clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
-0.32670259 0.63881773 -0.69654671 189.70458625
0.85943939 -0.10583047 -0.50016381 151.60374418
-0.39322938 -0.76204450 -0.51445003 194.63237237
Axis -0.57248441 -0.66306701 0.48229010
Axis point 7.53785159 0.00000000 163.26429794
Rotation angle (degrees) 166.77809983
Shift along axis -115.25709446
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.10962,-0.51402,0.85074,80.321,0.13824,0.8397,0.52516,127.6,-0.98431,0.17517,-0.020991,131.13
> fitmap #14 inMap #11
Fit molecule sequences_0_model_5_multimer_v3_0_unrelaxed.pdb (#14) to map
cryosparc_P123_J94_map_sharp_not as clean.mrc z flip (#11) using 1959 atoms
average map value = 0.1607, steps = 92
shifted from previous position = 1.32
rotated from previous position = 5.11 degrees
atoms outside contour = 558, contour level = 0.016842
Position of sequences_0_model_5_multimer_v3_0_unrelaxed.pdb (#14) relative to
cryosparc_P123_J94_map_sharp_not as clean.mrc z flip (#11) coordinates:
Matrix rotation and translation
-0.39456189 0.56195690 -0.72699750 188.60263388
0.84643726 -0.08561130 -0.52556129 151.76597462
-0.35758199 -0.82272423 -0.44188229 195.18327942
Axis -0.53745858 -0.66813694 0.51452046
Axis point 7.11362990 0.00000000 170.12206275
Rotation angle (degrees) 163.95144057
Shift along axis -102.34076582
> hide #!7 models
> hide #14 models
> select subtract #14
Nothing selected
> show #!7 models
> show #!11 models
> hide #!13 models
> show #!13 models
> hide #!11 models
> open "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Oct
> 2023/Supercomplex.pdb"
Supercomplex.pdb title:
Alphafold monomer V2.0 prediction for ap-3 complex subunit σ-1 (Q92572) [more
info...]
Chain information for Supercomplex.pdb #15
---
Chain | Description | UniProt
A | ap-3 complex subunit σ-1 | AP3S1_HUMAN 1-193
B | No description available |
C | No description available |
D | No description available |
E | No description available |
G H | No description available |
> select add #15
16426 atoms, 16581 bonds, 2181 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,6.9579,0,1,0,267.71,0,0,1,281.77
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.2811,-0.27106,-0.9206,-233.26,-0.8191,0.43209,-0.37732,230.22,0.50006,0.86013,-0.10056,-163.45
> view matrix models
> #15,-0.28066,-0.46487,-0.83972,-176.58,-0.65954,0.72902,-0.18315,253.55,0.69731,0.50243,-0.5112,-252.77
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.28066,-0.46487,-0.83972,-72.473,-0.65954,0.72902,-0.18315,148.17,0.69731,0.50243,-0.5112,-247.75
> view matrix models
> #15,-0.28066,-0.46487,-0.83972,-118.79,-0.65954,0.72902,-0.18315,110.1,0.69731,0.50243,-0.5112,-130.92
> view matrix models
> #15,-0.28066,-0.46487,-0.83972,-112.34,-0.65954,0.72902,-0.18315,95.928,0.69731,0.50243,-0.5112,-129.82
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.13638,-0.53604,-0.8331,-104.74,-0.63241,0.69442,-0.34328,50.068,0.76253,0.48005,-0.43371,-104.55
> view matrix models
> #15,-0.18091,-0.5875,-0.78874,-84.465,-0.486,0.75062,-0.44763,9.0014,0.85503,0.30234,-0.42132,-82.193
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.18091,-0.5875,-0.78874,-87.084,-0.486,0.75062,-0.44763,11.262,0.85503,0.30234,-0.42132,-76.494
> hide sel atoms
> show sel cartoons
> fitmap #15 inMap #13
Fit molecule Supercomplex.pdb (#15) to map
cryosparc_P123_J243_map_sharp(1).mrc (#13) using 16426 atoms
average map value = 0.0531, steps = 160
shifted from previous position = 4.94
rotated from previous position = 7.53 degrees
atoms outside contour = 9167, contour level = 0.012054
Position of Supercomplex.pdb (#15) relative to
cryosparc_P123_J243_map_sharp(1).mrc (#13) coordinates:
Matrix rotation and translation
0.80500929 0.51446705 -0.29543816 64.74307246
0.57906306 -0.78968244 0.20270080 293.96792106
-0.12901945 -0.33425335 -0.93361056 -41.16137024
Axis -0.94893170 -0.29410331 0.11415725
Axis point 0.00000000 135.14444652 -35.64022071
Rotation angle (degrees) 163.56510823
Shift along axis -152.59256055
> view matrix models
> #15,-0.13552,-0.60757,-0.78262,-81.581,-0.38445,0.76027,-0.52364,-16.846,0.91315,0.22991,-0.33661,-33.599
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.13327,-0.6148,-0.77734,-79.182,-0.40145,0.7506,-0.52482,-15.823,0.90613,0.24212,-0.34685,-37.997
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.13327,-0.6148,-0.77734,-74.735,-0.40145,0.7506,-0.52482,-15.647,0.90613,0.24212,-0.34685,-42.042
> fitmap #15 inMap #13
Fit molecule Supercomplex.pdb (#15) to map
cryosparc_P123_J243_map_sharp(1).mrc (#13) using 16426 atoms
average map value = 0.1048, steps = 96
shifted from previous position = 1.9
rotated from previous position = 5.75 degrees
atoms outside contour = 5993, contour level = 0.012054
Position of Supercomplex.pdb (#15) relative to
cryosparc_P123_J243_map_sharp(1).mrc (#13) coordinates:
Matrix rotation and translation
0.84959100 0.45106204 -0.27338283 76.66100521
0.51069852 -0.83305616 0.21261341 309.11677665
-0.13184141 -0.32025064 -0.93811373 -36.00601794
Axis -0.96088064 -0.25523285 0.10753876
Axis point 0.00000000 142.96527246 -33.52143647
Rotation angle (degrees) 163.90212603
Shift along axis -156.43087314
> fitmap #15 inMap #13
Fit molecule Supercomplex.pdb (#15) to map
cryosparc_P123_J243_map_sharp(1).mrc (#13) using 16426 atoms
average map value = 0.1048, steps = 80
shifted from previous position = 0.00904
rotated from previous position = 0.0148 degrees
atoms outside contour = 5996, contour level = 0.012054
Position of Supercomplex.pdb (#15) relative to
cryosparc_P123_J243_map_sharp(1).mrc (#13) coordinates:
Matrix rotation and translation
0.84963561 0.45094905 -0.27343057 76.65385383
0.51057845 -0.83317555 0.21243388 309.07197138
-0.13201882 -0.32009915 -0.93814048 -36.02347629
Axis -0.96089352 -0.25516097 0.10759429
Axis point 0.00000000 142.94684692 -33.51326147
Rotation angle (degrees) 163.91261931
Shift along axis -156.39521523
> select subtract #15
Nothing selected
> hide #!13 models
> show #!11 models
> hide #!11 models
> show #!13 models
> select #15/C
1133 atoms, 1163 bonds, 140 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #33cc33ff
> ui mousemode right select
> select clear
> select #15/D
1241 atoms, 1261 bonds, 155 residues, 1 model selected
> color sel #cc3333ff
> select clear
> select #15/E
2110 atoms, 2020 bonds, 383 residues, 1 model selected
> color sel #33cc33ff
> select clear
> select #15/G
1327 atoms, 1350 bonds, 165 residues, 1 model selected
> color sel white
> select clear
> select #15/H
1327 atoms, 1350 bonds, 165 residues, 1 model selected
> color sel white
> select clear
> select #15/H
1327 atoms, 1350 bonds, 165 residues, 1 model selected
> select clear
> select #15/A
4685 atoms, 4759 bonds, 588 residues, 1 model selected
> color sel #1d76bbff
> select clear
> close #4
> close #5
> close #8
> close #12
> select add #14
1959 atoms, 2002 bonds, 248 residues, 1 model selected
> select subtract #14
Nothing selected
> select add #14
1959 atoms, 2002 bonds, 248 residues, 1 model selected
> select subtract #14
Nothing selected
> close #14
Drag select of 13 cryosparc_P123_J243_map_sharp(1).mrc , 10 residues
> select clear
Drag select of 4 residues
Alignment identifier is 15/B
> select #15/B
4601 atoms, 4678 bonds, 583 residues, 1 model selected
> color sel #90298dff
> select clear
> color #1 #1d76bbff
> select add #1
5051 atoms, 5133 bonds, 633 residues, 1 model selected
Alignment identifier is 1/A
> select #1/A:677
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:654-677
192 atoms, 196 bonds, 24 residues, 1 model selected
> select #1/A:677
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:653-677
199 atoms, 203 bonds, 25 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #9
1461 atoms, 1487 bonds, 182 residues, 1 model selected
Alignment identifier is 9/A
> select #9/A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/A:1-16
126 atoms, 128 bonds, 16 residues, 1 model selected
> select #9/A:17
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:1-17
134 atoms, 136 bonds, 17 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #10
1461 atoms, 1487 bonds, 182 residues, 1 model selected
Alignment identifier is 10/A
> select #10/A:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #10/A:1-17
134 atoms, 136 bonds, 17 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save "D:/Back-up/Baker Lab/Structures/Data Processing/NCCAT Oct
> 2023/Colored_sandwich.cxs" includeMaps true
——— End of log from Fri Dec 1 15:07:38 2023 ———
opened ChimeraX session
> volume #13 level 0.08178
> volume #13 level -0.001227
> volume #13 level 0.01537
> open 1o3y
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\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\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\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\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\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\ChimeraX\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\ChimeraX\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\ChimeraX\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\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\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\ChimeraX\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.
> hide #15 models
> show #15 models
> open 1o3y
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\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\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\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\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\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\ChimeraX\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\ChimeraX\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\ChimeraX\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\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\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\ChimeraX\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: 3.3.0 Core Profile Context 22.20.44.56.230407
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: LENOVO
Model: 82KU
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 6,297,477,120
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5500U with Radeon Graphics
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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