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Opened 4 weeks ago
Last modified 4 weeks ago
#19088 assigned defect
ffmpeg: Permission Denied
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.7-x86_64-i386-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/lemmona/Desktop/cryosparc_P6_J15_0061_volumes/*.mrc
No such file/path: /Users/lemmona/Desktop/cryosparc_P6_J15_0061_volumes/*.mrc
> open /Users/lemmona/Desktop/cryosparc_P6_J115_00612_volumes/*.mrc
No such file/path:
/Users/lemmona/Desktop/cryosparc_P6_J115_00612_volumes/*.mrc
> open /Users/lemmona/Desktop/cryosparc_P6_J115_00162_volumes/*.mrc
Opened J115_class_00_00162_volume.mrc as #1.1, grid size 128,128,128, pixel
2.18, shown at level 0.192, step 1, values float32
Opened J115_class_01_00162_volume.mrc as #1.2, grid size 128,128,128, pixel
2.18, shown at level 0.174, step 1, values float32
Opened J115_class_02_00162_volume.mrc as #1.3, grid size 128,128,128, pixel
2.18, shown at level 0.179, step 1, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J116_00162_volumes/*.mrc
Opened J116_class_00_00162_volume.mrc as #2.1, grid size 128,128,128, pixel
2.18, shown at level 0.184, step 1, values float32
Opened J116_class_01_00162_volume.mrc as #2.2, grid size 128,128,128, pixel
2.18, shown at level 0.177, step 1, values float32
Opened J116_class_02_00162_volume.mrc as #2.3, grid size 128,128,128, pixel
2.18, shown at level 0.212, step 1, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J117_00162_volumes/*.mrc
Opened J117_class_00_00162_volume.mrc as #3.1, grid size 128,128,128, pixel
2.18, shown at level 0.237, step 1, values float32
Opened J117_class_01_00162_volume.mrc as #3.2, grid size 128,128,128, pixel
2.18, shown at level 0.202, step 1, values float32
Opened J117_class_02_00162_volume.mrc as #3.3, grid size 128,128,128, pixel
2.18, shown at level 0.228, step 1, values float32
Opened J117_class_03_00162_volume.mrc as #3.4, grid size 128,128,128, pixel
2.18, shown at level 0.209, step 1, values float32
Opened J117_class_04_00162_volume.mrc as #3.5, grid size 128,128,128, pixel
2.18, shown at level 0.25, step 1, values float32
Opened J117_class_05_00162_volume.mrc as #3.6, grid size 128,128,128, pixel
2.18, shown at level 0.212, step 1, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J119_006_volume_map.mrc
Opened cryosparc_P6_J119_006_volume_map.mrc as #4, grid size 384,384,384,
pixel 0.725, shown at level 0.0417, step 2, values float32
> volume flip #1
Opened J115_class_00_00162_volume.mrc z flip as #5, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
Opened J115_class_01_00162_volume.mrc z flip as #6, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
Opened J115_class_02_00162_volume.mrc z flip as #7, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
> close #1
> volume flip #2
Opened J116_class_00_00162_volume.mrc z flip as #1, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
Opened J116_class_01_00162_volume.mrc z flip as #8, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
Opened J116_class_02_00162_volume.mrc z flip as #9, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
> close #2
> volume flip #3
Opened J117_class_00_00162_volume.mrc z flip as #2, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
Opened J117_class_01_00162_volume.mrc z flip as #10, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
Opened J117_class_02_00162_volume.mrc z flip as #11, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
Opened J117_class_03_00162_volume.mrc z flip as #12, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
Opened J117_class_04_00162_volume.mrc z flip as #13, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
Opened J117_class_05_00162_volume.mrc z flip as #14, grid size 128,128,128,
pixel 2.18, shown at step 1, values float32
> close #3
> volume flip #4
Opened cryosparc_P6_J119_006_volume_map.mrc z flip as #3, grid size
384,384,384, pixel 0.725, shown at step 1, values float32
> close #4
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> ui tool show "Fit in Map"
> fitmap #6 inMap #5
Fit map J115_class_01_00162_volume.mrc z flip in map
J115_class_00_00162_volume.mrc z flip using 20967 points
correlation = 0.9779, correlation about mean = 0.4587, overlap = 916.9
steps = 72, shift = 0.921, angle = 0.808 degrees
Position of J115_class_01_00162_volume.mrc z flip (#6) relative to
J115_class_00_00162_volume.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.99992429 0.01029808 0.00673568 -2.73619864
-0.01034426 0.99992299 0.00685689 0.95665009
-0.00666455 -0.00692605 0.99995381 2.61808681
Axis -0.48863317 0.47506560 -0.73181302
Axis point 96.17072228 272.31331801 0.00000000
Rotation angle (degrees) 0.80810154
Shift along axis -0.12448106
> fitmap #7 inMap #5
Fit map J115_class_02_00162_volume.mrc z flip in map
J115_class_00_00162_volume.mrc z flip using 20961 points
correlation = 0.9774, correlation about mean = 0.4155, overlap = 927.9
steps = 48, shift = 0.948, angle = 0.924 degrees
Position of J115_class_02_00162_volume.mrc z flip (#7) relative to
J115_class_00_00162_volume.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.99987998 0.01479364 0.00460253 -2.99383067
-0.01481397 0.99988052 0.00441534 2.05541998
-0.00453666 -0.00448299 0.99997966 2.01291063
Axis -0.27601629 0.28348749 -0.91839526
Axis point 145.45351803 211.75514310 0.00000000
Rotation angle (degrees) 0.92360283
Shift along axis -0.43961568
> volume #5 level 0.1357
> volume #6 level 0.1025
> volume #7 level 0.1061
> show #!3 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> volume #3 level 0.02818
> fitmap #5 inMap #3
Fit map J115_class_00_00162_volume.mrc z flip in map
cryosparc_P6_J119_006_volume_map.mrc z flip using 54556 points
correlation = 0.8726, correlation about mean = 0.3567, overlap = 355.5
steps = 80, shift = 0.802, angle = 1.95 degrees
Position of J115_class_00_00162_volume.mrc z flip (#5) relative to
cryosparc_P6_J119_006_volume_map.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99946079 0.00093052 -0.03282165 5.20038963
-0.00123385 0.99995671 -0.00922297 1.36714641
0.03281165 0.00925850 0.99941867 -6.24404528
Axis 0.27090952 -0.96208184 -0.03172627
Axis point 192.72610573 0.00000000 152.87058067
Rotation angle (degrees) 1.95474056
Shift along axis 0.29162859
> fitmap #6 inMap #3
Fit map J115_class_01_00162_volume.mrc z flip in map
cryosparc_P6_J119_006_volume_map.mrc z flip using 64913 points
correlation = 0.8508, correlation about mean = 0.3115, overlap = 341.9
steps = 76, shift = 0.306, angle = 0.812 degrees
Position of J115_class_01_00162_volume.mrc z flip (#6) relative to
cryosparc_P6_J119_006_volume_map.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99984071 0.01734348 -0.00421401 -1.96110110
-0.01733831 0.99984889 0.00125864 2.67588234
0.00423520 -0.00118538 0.99999033 0.47996689
Axis -0.06830754 -0.23614499 -0.96931400
Axis point 140.18538746 118.15528377 0.00000000
Rotation angle (degrees) 1.02506838
Shift along axis -0.96317684
> fitmap #7 inMap #3
Fit map J115_class_02_00162_volume.mrc z flip in map
cryosparc_P6_J119_006_volume_map.mrc z flip using 63573 points
correlation = 0.8553, correlation about mean = 0.3363, overlap = 344.1
steps = 48, shift = 0.553, angle = 0.428 degrees
Position of J115_class_02_00162_volume.mrc z flip (#7) relative to
cryosparc_P6_J119_006_volume_map.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99981281 0.01933970 -0.00057363 -2.69818630
-0.01933882 0.99981186 0.00150104 3.11273799
0.00060255 -0.00148966 0.99999871 1.38401940
Axis -0.07705649 -0.03030469 -0.99656607
Axis point 157.55343567 146.08336284 0.00000000
Rotation angle (degrees) 1.11194596
Shift along axis -1.26568457
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!14 models
> show #!13 models
> show #!12 models
> show #!11 models
> show #!10 models
> show #!9 models
> show #!8 models
> show #!7 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> hide #!8 models
> hide #!9 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> volume #10 level 0.1215
> show #!11 models
> hide #!10 models
> volume #11 level 0.1326
> show #!12 models
> volume #12 level 0.1523
> hide #!11 models
> show #!11 models
> show #!13 models
> hide #!12 models
> hide #!11 models
> volume #13 level 0.07761
> fitmap #14 inMap #13
Fit map J117_class_05_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 20964 points
correlation = 0.9614, correlation about mean = 0.6118, overlap = 1865
steps = 52, shift = 0.172, angle = 1.03 degrees
Position of J117_class_05_00162_volume.mrc z flip (#14) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99996330 0.00715723 0.00470943 -1.46821772
-0.00723041 0.99985043 0.01571097 -1.08940655
-0.00459628 -0.01574445 0.99986548 2.83189224
Axis -0.87816216 0.25979390 -0.40166945
Axis point 0.00000000 175.93143379 68.84630210
Rotation angle (degrees) 1.02621096
Shift along axis -0.13117254
> show #!14 models
> show #!12 models
> fitmap #12 inMap #13
Fit map J117_class_03_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 39011 points
correlation = 0.9622, correlation about mean = 0.7323, overlap = 2614
steps = 40, shift = 0.147, angle = 1.07 degrees
Position of J117_class_03_00162_volume.mrc z flip (#12) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99986717 0.01628560 -0.00064964 -2.01872652
-0.01627907 0.99982662 0.00904017 1.02329258
0.00079676 -0.00902840 0.99995893 1.15089221
Axis -0.48480717 -0.03880914 -0.87375961
Axis point 61.35391036 126.44148544 0.00000000
Rotation angle (degrees) 1.06775707
Shift along axis -0.06662314
> show #!11 models
> fitmap #11 inMap #13
Fit map J117_class_02_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 50623 points
correlation = 0.9731, correlation about mean = 0.8414, overlap = 3199
steps = 44, shift = 0.216, angle = 1.19 degrees
Position of J117_class_02_00162_volume.mrc z flip (#11) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99985526 0.01427098 -0.00926290 -0.51810375
-0.01415980 0.99982822 0.01195926 0.42906032
0.00943198 -0.01182637 0.99988558 0.34267110
Axis -0.57292914 -0.45030720 -0.68481795
Axis point 25.62660066 41.82538358 -0.00000000
Rotation angle (degrees) 1.18942642
Shift along axis -0.13103954
> show #!10 models
> fitmap #10 inMap #13
Fit map J117_class_01_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 54776 points
correlation = 0.9341, correlation about mean = 0.6839, overlap = 2653
steps = 48, shift = 0.26, angle = 0.59 degrees
Position of J117_class_01_00162_volume.mrc z flip (#10) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99998116 0.00257996 -0.00556965 0.64070080
-0.00253387 0.99996263 0.00826579 -0.70501732
0.00559076 -0.00825152 0.99995033 0.28898254
Axis -0.80259867 -0.54229984 -0.24848794
Axis point 0.00000000 28.29269428 98.78589906
Rotation angle (degrees) 0.58957763
Shift along axis -0.20370351
> show #!9 models
> fitmap #9 inMap #13
Fit map J116_class_02_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 20962 points
correlation = 0.8459, correlation about mean = 0.2907, overlap = 1327
steps = 104, shift = 0.95, angle = 1.38 degrees
Position of J116_class_02_00162_volume.mrc z flip (#9) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99995490 0.00135466 -0.00939979 0.91458155
-0.00114671 0.99975527 0.02209277 -3.80161265
0.00942742 -0.02208099 0.99971174 2.29087564
Axis -0.91868475 -0.39155091 -0.05202131
Axis point 0.00000000 102.85651703 163.83644822
Rotation angle (degrees) 1.37762913
Shift along axis 0.52913843
> show #!8 models
> fitmap #8 inMap #13
Fit map J116_class_01_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 20970 points
correlation = 0.8503, correlation about mean = 0.1311, overlap = 1051
steps = 60, shift = 0.359, angle = 0.678 degrees
Position of J116_class_01_00162_volume.mrc z flip (#8) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99999145 0.00144070 -0.00387713 0.63500053
-0.00139759 0.99993744 0.01109816 -1.40305969
0.00389287 -0.01109264 0.99993090 1.19878064
Axis -0.93701295 -0.32809037 -0.11984756
Axis point 0.00000000 104.22008374 135.23884537
Rotation angle (degrees) 0.67846931
Shift along axis -0.27834428
> show #!7 models
> fitmap #7 inMap #13
Fit map J115_class_02_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 63573 points
correlation = 0.8483, correlation about mean = 0.3082, overlap = 2051
steps = 52, shift = 1.22, angle = 0.792 degrees
Position of J115_class_02_00162_volume.mrc z flip (#7) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99993017 0.01181653 0.00014398 -1.39205305
-0.01181741 0.99984473 0.01307189 -0.09597843
0.00001051 -0.01307268 0.99991455 2.09557325
Axis -0.74182222 0.00378697 -0.67058590
Axis point 0.00000000 141.11136393 8.91049637
Rotation angle (degrees) 1.00971038
Shift along axis -0.37296945
> fitmap #6 inMap #13
Fit map J115_class_01_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 64913 points
correlation = 0.8512, correlation about mean = 0.3079, overlap = 2041
steps = 48, shift = 0.956, angle = 0.798 degrees
Position of J115_class_01_00162_volume.mrc z flip (#6) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99986775 0.01613674 -0.00202264 -1.72587824
-0.01610473 0.99975857 0.01494817 0.33748414
0.00226336 -0.01491362 0.99988622 1.87648324
Axis -0.67630430 -0.09706850 -0.73019873
Axis point 17.78096953 116.97940745 0.00000000
Rotation angle (degrees) 1.26503250
Shift along axis -0.23574589
> fitmap #5 inMap #13
Fit map J115_class_00_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 54556 points
correlation = 0.8702, correlation about mean = 0.3862, overlap = 2041
steps = 52, shift = 0.369, angle = 1.88 degrees
Position of J115_class_00_00162_volume.mrc z flip (#5) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99997221 0.00586419 -0.00460249 0.38157940
-0.00583277 0.99995980 0.00681054 -0.60046519
0.00464224 -0.00678350 0.99996622 -0.01444172
Axis -0.67376393 -0.45819834 -0.57973826
Axis point 0.00000000 -0.30209710 86.38849176
Rotation angle (degrees) 0.57801716
Shift along axis 0.02641014
> fitmap #3 inMap #13
Fit map cryosparc_P6_J119_006_volume_map.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 1209187 points
correlation = 0.8263, correlation about mean = 0.289, overlap = 1.067e+04
steps = 92, shift = 1.13, angle = 1.14 degrees
Position of cryosparc_P6_J119_006_volume_map.mrc z flip (#3) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99998929 0.00238808 -0.00396341 0.07835773
-0.00231103 0.99981045 0.01933207 -2.87050699
0.00400882 -0.01932270 0.99980526 1.26379298
Axis -0.97251883 -0.20057398 -0.11822526
Axis point 0.00000000 66.08047316 145.49945209
Rotation angle (degrees) 1.13874451
Shift along axis 0.35013241
> fitmap #2 inMap #13
Fit map J117_class_00_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 20957 points
correlation = 0.9858, correlation about mean = 0.8235, overlap = 2577
steps = 52, shift = 0.236, angle = 1.1 degrees
Position of J117_class_00_00162_volume.mrc z flip (#2) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99987453 0.01574453 0.00174349 -2.16084705
-0.01576246 0.99981747 0.01079673 0.66808897
-0.00157318 -0.01082286 0.99994019 1.67705622
Axis -0.56367239 0.08647335 -0.82145955
Axis point 41.30826387 141.21993062 0.00000000
Rotation angle (degrees) 1.09885388
Shift along axis -0.10185214
> fitmap #1 inMap #13
Fit map J116_class_00_00162_volume.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 20955 points
correlation = 0.8799, correlation about mean = 0.2223, overlap = 1155
steps = 60, shift = 0.484, angle = 0.985 degrees
Position of J116_class_00_00162_volume.mrc z flip (#1) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99995427 0.00143961 -0.00945434 1.33012044
-0.00130444 0.99989707 0.01428778 -2.22153293
0.00947394 -0.01427479 0.99985323 0.59781524
Axis -0.83091478 -0.55064351 -0.07982700
Axis point 0.00000000 40.69857341 153.06740800
Rotation angle (degrees) 0.98481524
Shift along axis 0.07033415
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> show #!1 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!5 models
> show #!6 models
> show #!7 models
> hide #!6 models
> hide #!5 models
> volume #7 level 0.1093
> hide #!7 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!14 models
> show #!13 models
> volume #13 level 0.1832
> show #!12 models
> show #!11 models
> hide #!3 models
> show #!3 models
> show #!10 models
> show #!9 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> show #!5 models
> show #!6 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> hide #!5 models
> show #!6 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!5 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!6 models
> show #!7 models
> hide #!7 models
> volume #5 level 0.1412
> hide #!6 models
> volume #5 level 0.06048
> volume #6 level 0.07044
> volume #7 level 0.08467
> show #!3 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> volume #3 level 0.02261
> volume #3 level 0.02851
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> save /Users/lemmona/Desktop/J119.tif width 1333 height 1186 supersample 3
> transparentBackground true
> show #!5 models
> show #!6 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> save /Users/lemmona/Desktop/J115-00.tif width 1333 height 1186 supersample 3
> transparentBackground true
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> volume #6 level 0.07846
> save /Users/lemmona/Desktop/J115-01.tif width 1333 height 1186 supersample 3
> transparentBackground true
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!1 models
> show #!8 models
> show #!9 models
> volume #1 level 0.1191
> volume #8 level 0.1402
> volume #9 level 0.2034
> hide #!9 models
> hide #!8 models
> volume #1 level 0.1482
> save /Users/lemmona/Desktop/J116-00.tif width 1333 height 1186 supersample 3
> transparentBackground true
> show #!6 models
> hide #!6 models
> show #!8 models
> hide #!1 models
> volume #8 level 0.141
> save /Users/lemmona/Desktop/J116-01.tif width 1333 height 1186 supersample 3
> transparentBackground true
> show #!9 models
> hide #!8 models
> volume #9 level 0.1407
> save /Users/lemmona/Desktop/J116-002_low.tif width 1333 height 1186
> supersample 3 transparentBackground true
> volume #9 level 0.08038
> save /Users/lemmona/Desktop/J116-02_high.tif width 1333 height 1186
> supersample 3 transparentBackground true
> show #!10 models
> hide #!9 models
> show #!11 models
> show #!12 models
> show #!13 models
> show #!14 models
> show #!2 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> volume #2 level 0.1959
> volume #2 level 0.08748
> volume #2 level 0.07252
> save /Users/lemmona/Desktop/J117-00_high.tif width 1333 height 1186
> supersample 3 transparentBackground true
> volume #2 level 0.1922
> save /Users/lemmona/Desktop/J117-00_low.tif width 1333 height 1186
> supersample 3 transparentBackground true
> show #!10 models
> hide #!2 models
> volume #10 level 0.1631
> save /Users/lemmona/Desktop/J117-01.tif width 1333 height 1186 supersample 3
> transparentBackground true
> show #!11 models
> hide #!10 models
> volume #11 level 0.1886
> save /Users/lemmona/Desktop/J117-02_low.tif width 1333 height 1186
> supersample 3 transparentBackground true
> volume #11 level 0.1128
> save /Users/lemmona/Desktop/J117-02_high.tif width 1333 height 1186
> supersample 3 transparentBackground true
> show #!12 models
> hide #!11 models
> volume #12 level 0.1357
> save /Users/lemmona/Desktop/J117-03.tif width 1333 height 1186 supersample 3
> transparentBackground true
> show #!13 models
> hide #!12 models
> volume #13 level 0.2177
> save /Users/lemmona/Desktop/J117-04_low.tif width 1333 height 1186
> supersample 3 transparentBackground true
> volume #13 level 0.08912
> save /Users/lemmona/Desktop/J117-04_high.tif width 1333 height 1186
> supersample 3 transparentBackground true
> show #!14 models
> hide #!13 models
> volume #14 level 0.1995
> save /Users/lemmona/Desktop/J117-05_low.tif width 1333 height 1186
> supersample 3 transparentBackground true
> volume #14 level 0.1098
> save /Users/lemmona/Desktop/J117-05_high.tif width 1333 height 1186
> supersample 3 transparentBackground true
> show #!12 models
> show #!13 models
> hide #!13 models
> hide #!14 models
> color #12 #cc9f99ff models
> color #12 #cc9999ff models
> show #!13 models
> hide #!12 models
> color #13 #b28e8fff models
> color #13 #8eb290ff models
> color #13 #8e95b2ff models
> color #13 #a5a7b2ff models
> color #13 #a6a8b3ff models
> color #13 #9599b3ff models
> color #13 #95a4b3ff models
> color #13 #95b3b3ff models
> show #!14 models
> hide #!13 models
> color #14 #b2ffd6ff models
> color #14 #b2ffd9ff models
> color #14 #b2ffd3ff models
> color #14 #b2ffd2ff models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> hide #!13 models
> show #!12 models
> save /Users/lemmona/Desktop/J117-03.tif width 1333 height 1186 supersample 3
> transparentBackground true
> show #!13 models
> hide #!12 models
> save /Users/lemmona/Desktop/J117-002_high.tif width 1333 height 1186
> supersample 3 transparentBackground true
> volume #13 level 0.187
> save /Users/lemmona/Desktop/J117-00_low.tif width 1333 height 1186
> supersample 3 transparentBackground true
> save /Users/lemmona/Desktop/J117-04_low.tif width 1333 height 1186
> supersample 3 transparentBackground true
> volume #13 level 0.09104
> save /Users/lemmona/Desktop/J117-04_high.tif width 1333 height 1186
> supersample 3 transparentBackground true
> show #!11 models
> hide #!11 models
> hide #!13 models
> show #!2 models
> save /Users/lemmona/Desktop/J117-00_low.tif width 1333 height 1186
> supersample 3 transparentBackground true
> show #!14 models
> hide #!2 models
> save /Users/lemmona/Desktop/J117-05_high.tif width 1333 height 1186
> supersample 3 transparentBackground true
> volume #14 level 0.1895
> save /Users/lemmona/Desktop/J117-05_low.tif width 1333 height 1186
> supersample 3 transparentBackground true
> show #!7 models
> hide #!14 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!11 models
> show #!12 models
> show #!13 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!7 models
> hide #!5 models
> show #!1 models
> hide #!14 models
> hide #!1 models
> show #!5 models
> show #!6 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!11 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!6 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> volume #7 level 0.0966
> save /Users/lemmona/Desktop/J115-02.tif width 1333 height 1186 supersample 3
> transparentBackground true
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!1 models
> show #!9 models
> hide #!8 models
> hide #!1 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!11 models
> hide #!11 models
> hide #!9 models
> hide #!3 models
> show #!9 models
> show #!10 models
> hide #!9 models
> show #!2 models
> volume #2 level 0.1323
> volume #10 level 0.1202
> show #!11 models
> volume #11 level 0.1111
> show #!12 models
> show #!13 models
> show #!14 models
> volume #13 level 0.1064
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> show #!10 models
> show #!11 models
> hide #!11 models
> hide #!14 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> volume #2 level 0.09309
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!2 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!12 models
> hide #!11 models
> volume #12 level 0.1371
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!12 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!12 models
> volume #11 level 0.1045
> show #!12 models
> show #!13 models
> hide #!12 models
> hide #!11 models
> open /Users/lemmona/Desktop/cryosparc_P6_J170_volume_map.mrc
Opened cryosparc_P6_J170_volume_map.mrc as #4, grid size 384,384,384, pixel
0.725, shown at level 0.0441, step 2, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J169_volume_map.mrc
Opened cryosparc_P6_J169_volume_map.mrc as #15, grid size 384,384,384, pixel
0.725, shown at level 0.0491, step 2, values float32
> hide #!13 models
> hide #!4 models
> show #!4 models
> hide #!15 models
> show #!15 models
> hide #!4 models
> show #!4 models
> hide #!15 models
> hide #!4 models
> show #!15 models
> volume #4 step 1
> volume #15 step 1
> show #!4 models
> hide #!4 models
> show #!4 models
> open /Users/lemmona/Desktop/cryosparc_P6_J162_map.mrc
Opened cryosparc_P6_J162_map.mrc as #16, grid size 384,384,384, pixel 0.725,
shown at level 0.000311, step 2, values float32
> volume #15 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #15 style surface
> volume #16 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #16 style surface region 0,0,0,383,383,383 step 1
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> hide #!4 models
> show #!4 models
> hide #!15 models
> show #!15 models
> open /Users/lemmona/Desktop/cryosparc_P6_J162_mask.mrc
Opened cryosparc_P6_J162_mask.mrc as #17, grid size 384,384,384, pixel 0.725,
shown at level 0.0192, step 2, values float32
> fitmap #15 inMap #16
Fit map cryosparc_P6_J169_volume_map.mrc in map cryosparc_P6_J162_map.mrc
using 566101 points
correlation = 0.3558, correlation about mean = 0.02188, overlap = 23.31
steps = 180, shift = 0.0853, angle = 0.0572 degrees
Position of cryosparc_P6_J169_volume_map.mrc (#15) relative to
cryosparc_P6_J162_map.mrc (#16) coordinates:
Matrix rotation and translation
0.99999980 -0.00011319 0.00061627 0.00797141
0.00011271 0.99999969 0.00077822 -0.12974171
-0.00061636 -0.00077816 0.99999951 0.18004665
Axis -0.77889992 0.61687447 0.11305221
Axis point 0.00000000 240.87622471 114.58283557
Rotation angle (degrees) 0.05724355
Shift along axis -0.06588861
> fitmap #4 inMap #16
Fit map cryosparc_P6_J170_volume_map.mrc in map cryosparc_P6_J162_map.mrc
using 565443 points
correlation = 0.3614, correlation about mean = 0.03592, overlap = 19.75
steps = 140, shift = 0.0591, angle = 0.0549 degrees
Position of cryosparc_P6_J170_volume_map.mrc (#4) relative to
cryosparc_P6_J162_map.mrc (#16) coordinates:
Matrix rotation and translation
0.99999966 0.00054681 0.00061367 -0.13196386
-0.00054712 0.99999973 0.00049087 -0.06882588
-0.00061341 -0.00049121 0.99999969 0.13686234
Axis -0.51286044 0.64080127 -0.57126869
Axis point 172.12907292 0.00000000 260.77232602
Rotation angle (degrees) 0.05485827
Shift along axis -0.05460984
> volume #15 change image level -0.003578,0 level 0.04908,0.8 level 0.2509,1
> volume #16 change image level -4.22e-07,0 level 0.0003099,0.8 level
> 0.01268,1
> close #17
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> show #!15 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> open /Users/lemmona/Desktop/J132-001-008_resampled-J147.mrc
Opened J132-001-008_resampled-J147.mrc as #17, grid size 384,384,384, pixel
0.725, shown at level 0.0466, step 2, values float32
> close #17
> open /Users/lemmona/Desktop/cryosparc_P6_J120-FUN-mask_251009_125227.mrc
Opened cryosparc_P6_J120-FUN-mask_251009_125227.mrc as #17, grid size
384,384,384, pixel 0.725, shown at level 0.0193, step 2, values float32
> volume #17 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #17 style surface region 0,0,0,383,383,383 step 1
> fitmap #17 inMap #16
Fit map cryosparc_P6_J120-FUN-mask_251009_125227.mrc in map
cryosparc_P6_J162_map.mrc using 566228 points
correlation = 0.8673, correlation about mean = 0.8415, overlap = 26.63
steps = 336, shift = 40.9, angle = 0.0212 degrees
Position of cryosparc_P6_J120-FUN-mask_251009_125227.mrc (#17) relative to
cryosparc_P6_J162_map.mrc (#16) coordinates:
Matrix rotation and translation
0.99999998 0.00012209 -0.00016523 -37.47736118
-0.00012214 0.99999995 -0.00030746 -15.72970494
0.00016520 0.00030748 0.99999994 4.45838409
Axis 0.83146706 -0.44678087 -0.33022626
Axis point 0.00000000 12982.68338682 -88371.03949864
Rotation angle (degrees) 0.02118754
Shift along axis -25.60573552
> volume resample #17 onGrid #16
Opened cryosparc_P6_J120-FUN-mask_251009_125227.mrc resampled as #18, grid
size 384,384,384, pixel 0.725, shown at step 1, values float32
> save J120-FUN-mask-resample.mrc #18
> close #15-18
> close #4
> show #!1 models
> show #!14 models
> show #!13 models
> hide #!14 models
> hide #!1 models
> open /Users/lemmona/Desktop/cryosparc_P6_J120_005_volume_map.mrc
Opened cryosparc_P6_J120_005_volume_map.mrc as #4, grid size 384,384,384,
pixel 0.725, shown at level 0.0494, step 2, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J120-FUN-mask_251009_125227.mrc
Opened cryosparc_P6_J120-FUN-mask_251009_125227.mrc as #15, grid size
384,384,384, pixel 0.725, shown at level 0.0193, step 2, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J121_004_volume_map.mrc
Opened cryosparc_P6_J121_004_volume_map.mrc as #16, grid size 384,384,384,
pixel 0.725, shown at level 0.0466, step 2, values float32
> close #15
> open /Users/lemmona/Desktop/cryosparc_P6_J123_006_volume_map.mrc
Opened cryosparc_P6_J123_006_volume_map.mrc as #15, grid size 384,384,384,
pixel 0.725, shown at level 0.0439, step 2, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J124_006_volume_map.mrc
Opened cryosparc_P6_J124_006_volume_map.mrc as #17, grid size 384,384,384,
pixel 0.725, shown at level 0.0394, step 2, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J125_007_volume_map.mrc
Opened cryosparc_P6_J125_007_volume_map.mrc as #18, grid size 384,384,384,
pixel 0.725, shown at level 0.0391, step 2, values float32
> volume flip #4
Opened cryosparc_P6_J120_005_volume_map.mrc z flip as #19, grid size
384,384,384, pixel 0.725, shown at step 1, values float32
> volume flip #15
Opened cryosparc_P6_J123_006_volume_map.mrc z flip as #20, grid size
384,384,384, pixel 0.725, shown at step 1, values float32
> volume flip #16
Opened cryosparc_P6_J121_004_volume_map.mrc z flip as #21, grid size
384,384,384, pixel 0.725, shown at step 1, values float32
> volume flip #17
Opened cryosparc_P6_J124_006_volume_map.mrc z flip as #22, grid size
384,384,384, pixel 0.725, shown at step 1, values float32
> volume flip #18
Opened cryosparc_P6_J125_007_volume_map.mrc z flip as #23, grid size
384,384,384, pixel 0.725, shown at step 1, values float32
> close #4
> show #!3 models
> fitmap #3 inMap #13
Fit map cryosparc_P6_J119_006_volume_map.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 1187955 points
correlation = 0.8266, correlation about mean = 0.2872, overlap = 1.059e+04
steps = 76, shift = 0.0341, angle = 0.0238 degrees
Position of cryosparc_P6_J119_006_volume_map.mrc z flip (#3) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99998990 0.00257493 -0.00368295 0.03673619
-0.00250236 0.99980526 0.01957487 -2.88831196
0.00373264 -0.01956545 0.99980161 1.35820873
Axis -0.97463709 -0.18465640 -0.12643002
Axis point 0.00000000 70.05211092 145.17537861
Rotation angle (degrees) 1.15054400
Shift along axis 0.32582248
> fitmap #3 inMap #13
Fit map cryosparc_P6_J119_006_volume_map.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 1187955 points
correlation = 0.8267, correlation about mean = 0.2872, overlap = 1.059e+04
steps = 28, shift = 0.0482, angle = 0.0274 degrees
Position of cryosparc_P6_J119_006_volume_map.mrc z flip (#3) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99998961 0.00222835 -0.00397764 0.09418908
-0.00215069 0.99980902 0.01942426 -2.91890801
0.00402016 -0.01941551 0.99980342 1.26233336
Axis -0.97353224 -0.20046755 -0.10976217
Axis point 0.00000000 65.53216193 147.25288340
Rotation angle (degrees) 1.14300401
Shift along axis 0.35489379
> fitmap #19 inMap #13
Fit map cryosparc_P6_J120_005_volume_map.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 566553 points
correlation = 0.9715, correlation about mean = 0.7128, overlap = 1.522e+04
steps = 64, shift = 1.4, angle = 0.0728 degrees
Position of cryosparc_P6_J120_005_volume_map.mrc z flip (#19) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99999958 -0.00087265 -0.00027500 0.23158024
0.00087289 0.99999923 0.00088032 -0.23021670
0.00027424 -0.00088056 0.99999957 -1.31244321
Axis -0.69338779 -0.21627482 0.68734167
Axis point 0.00000000 -700.07955302 509.74399890
Rotation angle (degrees) 0.07275250
Shift along axis -1.01288175
> fitmap #19 inMap #13
Fit map cryosparc_P6_J120_005_volume_map.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 566553 points
correlation = 0.9715, correlation about mean = 0.713, overlap = 1.523e+04
steps = 40, shift = 0.00778, angle = 0.00925 degrees
Position of cryosparc_P6_J120_005_volume_map.mrc z flip (#19) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99999956 -0.00090435 -0.00025661 0.22734403
0.00090453 0.99999933 0.00072313 -0.21477420
0.00025595 -0.00072336 0.99999971 -1.33638700
Axis -0.60977910 -0.21607469 0.76254913
Axis point 502.53673021 -498.16679105 0.00000000
Rotation angle (degrees) 0.06795699
Shift along axis -1.11128312
> fitmap #20 inMap #13
Fit map cryosparc_P6_J123_006_volume_map.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 566553 points
correlation = 0.9828, correlation about mean = 0.7835, overlap = 1.155e+04
steps = 48, shift = 1.38, angle = 1.14 degrees
Position of cryosparc_P6_J123_006_volume_map.mrc z flip (#20) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99985650 0.01349442 -0.01024095 -0.19974956
-0.01338527 0.99985366 0.01065299 0.54337649
0.01038321 -0.01051438 0.99989081 -1.22474943
Axis -0.52985846 -0.51626093 -0.67284817
Axis point 65.75077573 -9.99655125 0.00000000
Rotation angle (degrees) 1.14453371
Shift along axis 0.64938536
> fitmap #21 inMap #13
Fit map cryosparc_P6_J121_004_volume_map.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 565200 points
correlation = 0.9697, correlation about mean = 0.6891, overlap = 1.383e+04
steps = 64, shift = 1.46, angle = 0.973 degrees
Position of cryosparc_P6_J121_004_volume_map.mrc z flip (#21) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99990614 0.01365290 0.00114050 -1.77443762
-0.01366364 0.99985653 0.01001122 0.47797605
-0.00100365 -0.01002586 0.99994924 0.08187559
Axis -0.59027770 0.06316515 -0.80472505
Axis point 29.39707667 86.42883849 0.00000000
Rotation angle (degrees) 0.97250430
Shift along axis 1.01171505
> fitmap #22 inMap #13
Fit map cryosparc_P6_J124_006_volume_map.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 565841 points
correlation = 0.9683, correlation about mean = 0.6415, overlap = 9042
steps = 64, shift = 1.48, angle = 0.887 degrees
Position of cryosparc_P6_J124_006_volume_map.mrc z flip (#22) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99990807 0.01355624 0.00027786 -1.58788438
-0.01355794 0.99988007 0.00748497 0.86004101
-0.00017636 -0.00748805 0.99997195 -0.38072132
Axis -0.48335903 0.01466336 -0.87529940
Axis point 61.54170397 77.85215612 0.00000000
Rotation angle (degrees) 0.88746192
Shift along axis 1.11337449
> fitmap #23 inMap #13
Fit map cryosparc_P6_J125_007_volume_map.mrc z flip in map
J117_class_04_00162_volume.mrc z flip using 565536 points
correlation = 0.9499, correlation about mean = 0.5148, overlap = 7915
steps = 64, shift = 1.44, angle = 0.937 degrees
Position of cryosparc_P6_J125_007_volume_map.mrc z flip (#23) relative to
J117_class_04_00162_volume.mrc z flip (#13) coordinates:
Matrix rotation and translation
0.99996030 0.00670220 0.00587236 -1.26280219
-0.00678215 0.99988311 0.01370256 -0.84524544
-0.00577983 -0.01374185 0.99988887 1.39525129
Axis -0.83868781 0.35608525 -0.41207530
Axis point 0.00000000 106.48101841 67.35347841
Rotation angle (degrees) 0.93748765
Shift along axis 0.18316878
> hide #!13 models
> volume #19 level 0.03409
> hide #!23 models
> hide #!22 models
> hide #!21 models
> hide #!20 models
> hide #!19 models
> volume #3 level 0.0249
> volume #3 level 0.03362
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> save /Users/lemmona/Desktop/J119_low.tif width 1274 height 1186 supersample
> 3 transparentBackground true
> volume #3 level 0.02009
> close #15-18
> close #1-2
> close #5-14
> save /Users/lemmona/Desktop/J119_high.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> show #!19 models
> hide #!3 models
> volume #19 level 0.04132
> save /Users/lemmona/Desktop/J120_low.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> show #!20 models
> hide #!19 models
> show #!19 models
> volume #20 level 0.03355
> hide #!19 models
> volume #20 level 0.0354
> show #!19 models
> hide #!20 models
> volume #19 level 0.02292
> save /Users/lemmona/Desktop/J120_high.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> show #!20 models
> hide #!19 models
> volume #20 level 0.03725
> save /Users/lemmona/Desktop/J123_low.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> volume #20 level 0.02431
> save /Users/lemmona/Desktop/J123_high.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> show #!21 models
> hide #!20 models
> volume #21 level 0.0489
> save /Users/lemmona/Desktop/J121_low.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> volume #21 level 0.02758
> save /Users/lemmona/Desktop/J121_high.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> show #!22 models
> hide #!21 models
> volume #22 level 0.03359
> save /Users/lemmona/Desktop/J124_low.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> volume #22 level 0.01661
> save /Users/lemmona/Desktop/J124_high.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> show #!23 models
> hide #!22 models
> volume #23 level 0.0345
> save /Users/lemmona/Desktop/J125_low.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> volume #23 level 0.01573
> save /Users/lemmona/Desktop/J125_high.tif width 1436 height 1186 supersample
> 3 transparentBackground true
> open /Users/lemmona/Desktop/cryosparc_P6_J164_mask.mrc
Opened cryosparc_P6_J164_mask.mrc as #1, grid size 384,384,384, pixel 0.725,
shown at level 0.977, step 2, values float32
> hide #!23 models
> open /Users/lemmona/Desktop/cryosparc_P6_J170_volume_map.mrc
Opened cryosparc_P6_J170_volume_map.mrc as #2, grid size 384,384,384, pixel
0.725, shown at level 0.0441, step 2, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J120-FUN-mask-resample.mrc
Opened cryosparc_P6_J120-FUN-mask-resample.mrc as #4, grid size 384,384,384,
pixel 0.725, shown at level 0.0192, step 2, values float32
> fitmap #2 inMap #4
Fit map cryosparc_P6_J170_volume_map.mrc in map cryosparc_P6_J120-FUN-mask-
resample.mrc using 70705 points
correlation = 0.3699, correlation about mean = -0.08179, overlap = 34.34
steps = 192, shift = 0.259, angle = 0.217 degrees
Position of cryosparc_P6_J170_volume_map.mrc (#2) relative to
cryosparc_P6_J120-FUN-mask-resample.mrc (#4) coordinates:
Matrix rotation and translation
0.99999357 0.00010821 0.00358454 -0.32906633
-0.00011251 0.99999928 0.00119888 -0.28330165
-0.00358441 -0.00119928 0.99999286 0.61206061
Axis -0.31710579 0.94794100 -0.02918526
Axis point 169.05827047 0.00000000 108.21137106
Rotation angle (degrees) 0.21665460
Shift along axis -0.18206756
> fitmap #2 inMap #4
Fit map cryosparc_P6_J170_volume_map.mrc in map cryosparc_P6_J120-FUN-mask-
resample.mrc using 70705 points
correlation = 0.3699, correlation about mean = -0.08179, overlap = 34.34
steps = 72, shift = 0.0042, angle = 0.0063 degrees
Position of cryosparc_P6_J170_volume_map.mrc (#2) relative to
cryosparc_P6_J120-FUN-mask-resample.mrc (#4) coordinates:
Matrix rotation and translation
0.99999319 0.00009407 0.00368841 -0.33959697
-0.00009861 0.99999924 0.00123239 -0.28852115
-0.00368829 -0.00123275 0.99999244 0.62954268
Axis -0.31685297 0.94815128 -0.02476573
Axis point 169.24651381 0.00000000 107.97988332
Rotation angle (degrees) 0.22288352
Shift along axis -0.18155048
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> show #!1 models
> fitmap #1 inMap #2
Fit map cryosparc_P6_J164_mask.mrc in map cryosparc_P6_J170_volume_map.mrc
using 61082 points
correlation = 0.7835, correlation about mean = 0.4065, overlap = 3123
steps = 360, shift = 40.9, angle = 0.225 degrees
Position of cryosparc_P6_J164_mask.mrc (#1) relative to
cryosparc_P6_J170_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99999954 0.00095899 0.00000084 -37.69194843
-0.00095899 0.99999946 -0.00038801 -15.74471342
-0.00000122 0.00038801 0.99999992 4.52124783
Axis 0.37506666 0.00099471 -0.92699731
Axis point -16416.85910112 32121.42291431 0.00000000
Rotation angle (degrees) 0.05927340
Shift along axis -18.34383908
> volume #1 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #1 style surface region 0,0,0,383,383,383 step 1
> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #2 style surface region 0,0,0,383,383,383 step 1
> volume #4 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #4 style surface region 0,0,0,383,383,383 step 1
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> volume #4 change image level 0,0 level 0.01915,0.8 level 0.07816,1
> volume #2 change image level -0.003086,0 level 0.04409,0.8 level 0.2217,1
> volume #1 change image level 0,0 level 0.9769,0.8 level 1,1
> volume resample #1 onGrid #4
Opened cryosparc_P6_J164_mask.mrc resampled as #5, grid size 384,384,384,
pixel 0.725, shown at step 1, values float32
> save J120-p97-mask-resample.mrc #5
> close #4-5
> close #1-2
> show #!3 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!3 models
> open /Users/lemmona/Desktop/cryosparc_P6_J120-FUN-mask-resample.mrc
Opened cryosparc_P6_J120-FUN-mask-resample.mrc as #1, grid size 384,384,384,
pixel 0.725, shown at level 0.0192, step 2, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J120_005_volume_map.mrc
Opened cryosparc_P6_J120_005_volume_map.mrc as #2, grid size 384,384,384,
pixel 0.725, shown at level 0.0494, step 2, values float32
> hide #!19 models
> select add #2
2 models selected
> volume #1 region 0,46,0,383,383,383
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99184,-0.073092,-0.10446,25.209,0.10756,0.91961,0.37782,-55.246,0.068451,-0.38597,0.91997,53.703
> view matrix models
> #2,0.99184,-0.073092,-0.10446,-6.0313,0.10756,0.91961,0.37782,-64.12,0.068451,-0.38597,0.91997,54.543
> fitmap #2 inMap #1
Fit map cryosparc_P6_J120_005_volume_map.mrc in map cryosparc_P6_J120-FUN-
mask-resample.mrc using 70728 points
correlation = 0.4384, correlation about mean = 0.1397, overlap = 38.09
steps = 376, shift = 27.8, angle = 24.5 degrees
Position of cryosparc_P6_J120_005_volume_map.mrc (#2) relative to
cryosparc_P6_J120-FUN-mask-resample.mrc (#1) coordinates:
Matrix rotation and translation
0.93977843 0.00361536 -0.34176516 49.65986875
0.01766040 0.99809462 0.05912054 -25.31969630
0.34132771 -0.06159592 0.93792395 -35.94587021
Axis -0.17398825 -0.98453964 0.02024307
Axis point 129.93733539 0.00000000 130.32971864
Rotation angle (degrees) 20.29842011
Shift along axis 15.56035641
> view matrix models
> #2,0.95691,-0.018252,-0.28982,43.208,-0.05851,0.96544,-0.25398,32.254,0.28444,0.26,0.92277,-69.871
> view matrix models
> #2,0.92327,0.085618,-0.37449,45.136,-0.18003,0.9576,-0.22492,47.947,0.33935,0.27508,0.89954,-77.225
> view matrix models
> #2,0.90006,0.13894,-0.41301,46.375,-0.27117,0.92051,-0.2813,74.4,0.3411,0.36519,0.86619,-85.562
> view matrix models
> #2,0.96829,-0.019223,-0.24909,36.217,-0.069626,0.93677,-0.34296,49.702,0.23993,0.34942,0.90573,-73.248
> view matrix models
> #2,0.96258,0.0025053,-0.27097,36.972,-0.097806,0.93577,-0.33878,53.568,0.25272,0.35261,0.901,-75.007
> view matrix models
> #2,0.90974,0.12789,-0.39499,44.049,-0.29136,0.87443,-0.38793,97.978,0.29578,0.468,0.83276,-88.5
> view matrix models
> #2,0.98955,-0.14039,-0.03298,21.154,0.12728,0.95775,-0.25791,5.6207,0.067794,0.25101,0.96561,-41.397
> view matrix models
> #2,0.99318,-0.053315,-0.10372,17.906,0.016579,0.9449,-0.32694,33.36,0.11544,0.32299,0.93934,-55.129
> view matrix models
> #2,0.99318,-0.053315,-0.10372,-8.2535,0.016579,0.9449,-0.32694,30.277,0.11544,0.32299,0.93934,-55.882
> view matrix models
> #2,0.97608,0.041802,-0.21334,-4.3198,-0.026828,0.997,0.072609,-23.281,0.21573,-0.065149,0.97428,-21.946
> view matrix models
> #2,0.97608,0.041802,-0.21334,-5.6485,-0.026828,0.997,0.072609,-23.676,0.21573,-0.065149,0.97428,-22.056
> view matrix models
> #2,0.97608,0.041802,-0.21334,-7.146,-0.026828,0.997,0.072609,-24.333,0.21573,-0.065149,0.97428,-22.704
> view matrix models
> #2,0.97608,0.041802,-0.21334,-1.573,-0.026828,0.997,0.072609,-21.23,0.21573,-0.065149,0.97428,-18.666
> view matrix models
> #2,0.96905,0.094434,-0.22808,-5.8476,-0.078577,0.99388,0.077652,-13.606,0.23401,-0.057328,0.97054,-22.031
> view matrix models
> #2,0.97591,-0.010751,-0.21789,6.3395,0.040494,0.99035,0.1325,-38.469,0.21436,-0.13814,0.96694,-7.369
> view matrix models
> #2,0.97407,0.031787,-0.22399,1.531,-0.0040271,0.99236,0.12332,-30.768,0.22619,-0.11922,0.96676,-11.765
> view matrix models
> #2,0.97407,0.031787,-0.22399,0.38702,-0.0040271,0.99236,0.12332,-31.451,0.22619,-0.11922,0.96676,-12.708
> view matrix models
> #2,0.97407,0.031787,-0.22399,-1.5768,-0.0040271,0.99236,0.12332,-31.959,0.22619,-0.11922,0.96676,-12.681
> view matrix models
> #2,0.98683,0.0503,-0.15375,-15.384,-0.02764,0.98888,0.14611,-30.91,0.15939,-0.13993,0.97725,-1.0535
> view matrix models
> #2,0.9897,0.055696,-0.13185,-19.47,-0.035226,0.98763,0.15277,-30.467,0.13873,-0.14655,0.97943,2.7139
> view matrix models
> #2,0.99211,0.06101,-0.10956,-23.525,-0.043055,0.98628,0.15935,-29.962,0.11777,-0.15337,0.98112,6.6165
> view matrix models
> #2,0.99263,-0.015596,-0.12017,-11.581,0.035076,0.98621,0.16174,-42.136,0.11599,-0.16476,0.97949,8.6832
> view matrix models
> #2,0.9901,-0.025972,-0.13793,-7.4054,0.037065,0.99623,0.078475,-32.796,0.13537,-0.082811,0.98733,-6.6584
> view matrix models
> #2,0.99784,0.058691,-0.029499,-34.68,-0.05725,0.99723,0.047531,-14.51,0.032206,-0.04574,0.99843,2.4014
> view matrix models
> #2,0.99784,0.058691,-0.029499,-35.239,-0.05725,0.99723,0.047531,-14.533,0.032206,-0.04574,0.99843,4.0378
> view matrix models
> #2,0.99728,0.062694,-0.038641,-34.498,-0.059353,0.99484,0.082268,-18.485,0.0436,-0.079751,0.99586,7.3623
> fitmap #2 inMap #1
Fit map cryosparc_P6_J120_005_volume_map.mrc in map cryosparc_P6_J120-FUN-
mask-resample.mrc using 70728 points
correlation = 0.3523, correlation about mean = -0.1208, overlap = 38.89
steps = 156, shift = 6.65, angle = 6.25 degrees
Position of cryosparc_P6_J120_005_volume_map.mrc (#2) relative to
cryosparc_P6_J120-FUN-mask-resample.mrc (#1) coordinates:
Matrix rotation and translation
0.99999767 -0.00075611 0.00202516 -37.38652920
0.00075139 0.99999700 0.00233238 -16.31179875
-0.00202692 -0.00233085 0.99999523 5.28920344
Axis -0.73332086 0.63721401 0.23706289
Axis point 0.00000000 385.88260544 11987.23062795
Rotation angle (degrees) 0.18217376
Shift along axis 18.27608899
> volume resample #2 onGrid #1
Opened cryosparc_P6_J120_005_volume_map.mrc resampled as #4, grid size
384,384,384, pixel 0.725, shown at step 1, values float32
> save J120-resample.mrc #4
> close #4
> close #1-2
> show #!3 models
> show #!19 models
> hide #!3 models
> open
> /Users/lemmona/Desktop/cryosparc_P6_J132_component_000_2/J132_component_000_frame_000.mrc
Opened J132_component_000_frame_000.mrc as #1, grid size 384,384,384, pixel
0.725, shown at level 0.0463, step 2, values float32
> ui tool show Log
> open /Users/lemmona/Desktop/cryosparc_P6_J132_component_000_2/*.mrc vseries
> true
Opened map series J132_component_000_frame_000.mrc as #2, 10 images, grid size
384,384,384, pixel 0.725, shown at level 0.0463, step 2, values float32
> close #1
> hide #!19 models
> close #3,19-23
> open /Users/lemmona/Desktop/cryosparc_P6_J132_component_001_2/*.mrc vseries
> true
Opened map series J132_component_001_frame_000.mrc as #1, 10 images, grid size
384,384,384, pixel 0.725, shown at level 0.0461, step 2, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J132_component_002_2/*.mrc vseries
> true
Opened map series J132_component_002_frame_000.mrc as #3, 10 images, grid size
384,384,384, pixel 0.725, shown at level 0.0472, step 2, values float32
> volume #2.1 step 1
> volume #1.1 step 1
> volume #3.1 step 1
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> volume #2.10 level 0.03183
> show #!1 models
> hide #!2 models
> volume #1.10 level 0.02507
> show #!3 models
> hide #!1 models
> volume #3.10 level 0.02606
> show #!2 models
> show #!1 models
> open /Users/lemmona/Desktop/cryosparc_P6_J181_volume_map.mrc
Opened cryosparc_P6_J181_volume_map.mrc as #4, grid size 384,384,384, pixel
0.725, shown at level 0.0425, step 2, values float32
> open /Users/lemmona/Desktop/cryosparc_P6_J182_volume_map.mrc
Opened cryosparc_P6_J182_volume_map.mrc as #5, grid size 384,384,384, pixel
0.725, shown at level 0.0204, step 2, values float32
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #!5 models
> volume #4 step 1
> volume #5 step 1
> volume #4 level 0.06135
> show #!5 models
> hide #!4 models
> volume #5 level 0.01967
> close #5
> close #4
> open /Users/lemmona/Desktop/J120-resample.mrc
Opened J120-resample.mrc as #4, grid size 384,384,384, pixel 0.725, shown at
level 0.0489, step 2, values float32
> volume gaussian #4 sDev 2
Opened J120-resample.mrc gaussian as #5, grid size 384,384,384, pixel 0.725,
shown at step 1, values float32
> volume #5 level 0.006609
> ui tool show "Segment Map"
Segmenting J120-resample.mrc gaussian, density threshold 0.006609
Showing 214 region surfaces
857 watershed regions, grouped to 214 regions
Showing J120-resample gaussian.seg - 214 regions, 214 surfaces
Saving 214 regions to mrc file...
Opened mask.mrc as #7, grid size 263,258,257, pixel 0.725, shown at step 1,
values float32
Wrote mask.mrc
> volume resample #7 onGrid #4
Opened mask.mrc resampled as #8, grid size 384,384,384, pixel 0.725, shown at
step 1, values float32
> hide #!6 models
> select add #6
215 models selected
> hide #!5 models
> select up
226 models selected
> save J120-mask.mrc #8
> close #5-8
> close #4
> select add #1
23 models selected
> select add #2
43 models selected
> select add #3
63 models selected
> select subtract #3
42 models selected
> select subtract #2
21 models selected
> select subtract #1
Nothing selected
> show #!1 models
> volume #1.10 level 0.02117
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> show #!2 models
> hide #!1 models
> volume #2.10 level 0.0269
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1.10 level 0.02624
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> movie record
> movie encode /Users/lemmona/Desktop/movie1.mp4 framerate 25.0
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/slider.py", line 164, in next_value_cb
self.stop()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/slider.py", line 148, in stop
self.record_cb()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/slider.py", line 211, in record_cb
run(ses, f'movie encode %s framerate %.1f'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode
encode_op(session, output[-1], format, quality, qscale, bitrate,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding
self.encoder.run(Status_Reporter())
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
Error processing trigger "new frame":
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
See log for complete Python traceback.
OpenGL version: 4.1 ATI-7.0.24
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3.3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2092.0.0.0.0 (iBridge: 23.16.10350.0.0,0)
OS Loader Version: 583~2317
Software:
System Software Overview:
System Version: macOS 15.7 (24G222)
Kernel Version: Darwin 24.6.0
Time since boot: 12 days, 20 hours, 51 minutes
Graphics/Displays:
AMD Radeon Pro 5300:
Chipset Model: AMD Radeon Pro 5300
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0047
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XL-012
Option ROM Version: 113-D322A1XL-012
EFI Driver Version: 01.01.231
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (1)
comment:1 by , 4 weeks ago
| Component: | Unassigned → Build System |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ffmpeg: Permission Denied |
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