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Opened 2 years ago
Closed 2 years ago
#10043 closed defect (duplicate)
No space left on device
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/ruchigautamsharma/Desktop/pdbs/S1with
> MAva/cryosparc_P20_J808_map_sharp.mrc"
Opened cryosparc_P20_J808_map_sharp.mrc as #1, grid size 256,256,256, pixel
0.82, shown at level 0.00504, step 1, values float32
> surface dust #1 size 8.2
> volume #1 level 0.1131
> open "/Users/ruchigautamsharma/Downloads/5n69 (2).pdb"
5n69 (2).pdb title:
Cardiac muscle myosin S1 fragment In the pre-powerstroke state Co-
crystallized with the activator omecamtiv mecarbil [more info...]
Chain information for 5n69 (2).pdb #2
---
Chain | Description | UniProt
A B | myosin-7 | MYH7_BOVIN 1-828
G H | myosin light chain 3 | MYL3_BOVIN 1-199
Non-standard residues in 5n69 (2).pdb #2
---
2OW — methyl
4-(2-fluoro-3-{[(6-methylpyridin-3-yl)carbamoyl]amino}benzyl)piperazine-1-carboxylate
(omecamtiv mercarbil)
ADP — adenosine-5'-diphosphate
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
TCE — 3,3',3''-phosphanetriyltripropanoic acid
(3-[bis(2-carboxyethyl)phosphanyl]propanoic acid)
VO4 — vanadate ion
> select /G
1279 atoms, 1252 bonds, 2 pseudobonds, 201 residues, 2 models selected
> hide sel cartoons
> select /B
6651 atoms, 6424 bonds, 12 pseudobonds, 1122 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,96.515,0,1,0,231.71,0,0,1,-81.177
> view matrix models #2,1,0,0,88.542,0,1,0,159.51,0,0,1,-15.169
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.56055,-0.09324,-0.82285,116.6,-0.82787,-0.038689,-0.55958,184.74,0.02034,0.99489,-0.098878,15.253
> view matrix models
> #2,-0.6674,0.26235,-0.69695,108.34,-0.25459,0.79912,0.5446,142.09,0.69983,0.54091,-0.46654,31.74
> view matrix models
> #2,-0.64485,0.41835,-0.63965,105.34,-0.10466,0.78068,0.61611,139.98,0.75711,0.46424,-0.45963,32.11
> view matrix models
> #2,-0.85859,0.37923,-0.34499,95.337,0.208,0.87273,0.44168,145.64,0.46858,0.30746,-0.82819,45.368
> view matrix models
> #2,-0.63652,0.69491,-0.33458,93.057,0.45079,0.68721,0.56967,142.89,0.6258,0.21178,-0.75068,43.595
> view matrix models
> #2,-0.54854,0.58905,-0.59341,102.69,0.23896,0.79055,0.56385,142.1,0.80125,0.16749,-0.5744,38.13
> view matrix models
> #2,-0.64145,0.58697,-0.49398,99.217,0.26196,0.77278,0.5781,141.77,0.72106,0.24142,-0.64946,40.066
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.64145,0.58697,-0.49398,153.42,0.26196,0.77278,0.5781,87.138,0.72106,0.24142,-0.64946,113.97
> view matrix models
> #2,-0.64145,0.58697,-0.49398,131.6,0.26196,0.77278,0.5781,86.543,0.72106,0.24142,-0.64946,130.4
> view matrix models
> #2,-0.64145,0.58697,-0.49398,126.93,0.26196,0.77278,0.5781,85.891,0.72106,0.24142,-0.64946,133.51
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.63655,0.65168,-0.41245,123.71,0.35257,0.72153,0.59589,85.755,0.68593,0.2339,-0.68905,134.86
> fitmap #2 inMap #1
Fit molecule 5n69 (2).pdb (#2) to map cryosparc_P20_J808_map_sharp.mrc (#1)
using 15954 atoms
average map value = 0.08012, steps = 236
shifted from previous position = 4.48
rotated from previous position = 16.3 degrees
atoms outside contour = 13103, contour level = 0.1131
Position of 5n69 (2).pdb (#2) relative to cryosparc_P20_J808_map_sharp.mrc
(#1) coordinates:
Matrix rotation and translation
-0.80674793 0.49116947 -0.32849709 114.36434827
0.33036199 0.83584634 0.43843112 91.36410161
0.48991707 0.24518045 -0.83658103 139.65237441
Axis -0.22571846 -0.95591481 -0.18782452
Axis point 33.04906628 0.00000000 70.60106978
Rotation angle (degrees) 154.65428833
Shift along axis -139.38058255
> color #1 #157dbfff models
> set bgColor white
> ui mousemode right translate
> select /A
6648 atoms, 6389 bonds, 11 pseudobonds, 1149 residues, 3 models selected
> hide sel atoms
> select /H
1376 atoms, 1311 bonds, 248 residues, 1 model selected
> hide sel atoms
> select ::name="2OW"
58 atoms, 62 bonds, 2 residues, 1 model selected
> hide sel atoms
> show sel atoms
> select ::name="ADP"
54 atoms, 58 bonds, 2 residues, 1 model selected
> show sel atoms
> ui mousemode right select
Drag select of 56 atoms, 60 bonds
> hide sel atoms
> transparency 50
> save /Users/ruchigautamsharma/Desktop/image7.png supersample 3
> save /Users/ruchigautamsharma/Desktop/image8.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie4.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie4.mp4
> open
> /Users/ruchigautamsharma/Desktop/pdbs/S1E525K/cryosparc_P20_J783_004_volume_map_sharp.mrc
Opened cryosparc_P20_J783_004_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.82, shown at level 0.0488, step 1, values float32
> surface dust #1 size 8.2
> surface dust #3 size 8.2
> ui tool show Matchmaker
No reference and/or match structure/chain chosen
> hide #!2 models
> fitmap #1 inMap #3
Fit map cryosparc_P20_J808_map_sharp.mrc in map
cryosparc_P20_J783_004_volume_map_sharp.mrc using 82564 points
correlation = 0.3565, correlation about mean = 0.04387, overlap = 1639
steps = 76, shift = 3.13, angle = 4.38 degrees
Position of cryosparc_P20_J808_map_sharp.mrc (#1) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99727487 0.07007103 0.02308417 -9.54726539
-0.06959959 0.99736166 -0.02063038 6.97040651
-0.02446885 0.01896751 0.99952064 2.34378507
Axis 0.25920773 0.31128201 -0.91428380
Axis point 106.11990312 131.32323288 0.00000000
Rotation angle (degrees) 4.38066363
Shift along axis -2.44784754
> toolshed show
> ui tool show "Fit in Map"
> ui mousemode right "move picked models"
> view matrix models #3,1,0,0,-46.746,0,1,0,-39.735,0,0,1,-44.734
> view matrix models #3,1,0,0,-48.127,0,1,0,-40.945,0,0,1,-46.348
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.80675,0.49117,-0.3285,114.36,0.33036,0.83585,0.43843,91.364,0.48992,0.24518,-0.83658,139.65
[Repeated 1 time(s)]
> ui mousemode right "move picked models"
> view matrix models #3,1,0,0,-52.468,0,1,0,-45.16,0,0,1,-44.262
> fitmap #1 inMap #3
Fit map cryosparc_P20_J808_map_sharp.mrc in map
cryosparc_P20_J783_004_volume_map_sharp.mrc using 82564 points
correlation = 0.01679, correlation about mean = 0.03716, overlap = 6.405
steps = 80, shift = 1.5, angle = 4.1 degrees
Position of cryosparc_P20_J808_map_sharp.mrc (#1) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99976434 0.01201511 0.01808053 48.66165409
-0.01089201 0.99807941 -0.06098234 50.04677562
-0.01877851 0.06077104 0.99797507 43.24404362
Axis 0.94195262 0.28516224 -0.17722236
Axis point 0.00000000 -844.47013495 602.03376338
Rotation angle (degrees) 3.70550502
Shift along axis 52.44461159
> undo
[Repeated 1 time(s)]
> view matrix models #3,1,0,0,-48.171,0,1,0,-42.416,0,0,1,-56.246
> fitmap #3 inMap #1
Fit map cryosparc_P20_J783_004_volume_map_sharp.mrc in map
cryosparc_P20_J808_map_sharp.mrc using 167626 points
correlation = 0.3275, correlation about mean = 0.1206, overlap = 1489
steps = 464, shift = 61.2, angle = 24.7 degrees
Position of cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) relative to
cryosparc_P20_J808_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.98758453 0.15620503 -0.01663690 -27.58413983
-0.13262718 0.88586741 0.44457729 -25.12926330
0.08418330 -0.43685115 0.89558598 24.57216443
Axis -0.94471641 -0.10805925 -0.30957083
Axis point 0.00000000 55.55929185 65.64215426
Rotation angle (degrees) 27.80761816
Shift along axis 21.16781374
> fitmap #3 inMap #1
Fit map cryosparc_P20_J783_004_volume_map_sharp.mrc in map
cryosparc_P20_J808_map_sharp.mrc using 167626 points
correlation = 0.3275, correlation about mean = 0.1206, overlap = 1489
steps = 44, shift = 0.00768, angle = 0.0187 degrees
Position of cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) relative to
cryosparc_P20_J808_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.98758698 0.15621032 -0.01644052 -27.60699960
-0.13269583 0.88573928 0.44481203 -25.13184097
0.08404624 -0.43710898 0.89547304 24.63270864
Axis -0.94478636 -0.10764969 -0.30950004
Axis point 0.00000000 55.63569034 65.66927088
Rotation angle (degrees) 27.82226714
Shift along axis 21.16432746
> show #!2 models
Opened 5n69 (2).pdb map 5 as #4, grid size 93,110,90, pixel 1.67, shown at
level 0.103, step 1, values float32
> fitmap #2 inMap #3 resolution 5
Fit map 5n69 (2).pdb map 5 in map cryosparc_P20_J783_004_volume_map_sharp.mrc
using 63070 points
correlation = 0.2245, correlation about mean = 0.02025, overlap = 425.3
steps = 388, shift = 13.2, angle = 11.4 degrees
Position of 5n69 (2).pdb map 5 (#4) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.83923607 0.23683689 -0.48948045 121.58156348
-0.06052765 0.85388381 0.51693214 88.01761048
0.54038804 0.46345520 -0.70227491 159.57470873
Axis -0.04982605 -0.95955890 -0.27706333
Axis point 39.96609460 0.00000000 84.50082456
Rotation angle (degrees) 147.54504297
Shift along axis -134.72831027
Average map value = 0.02013 for 15954 atoms, 13471 outside contour
> fitmap #2 inMap #3 resolution 5
Fit map 5n69 (2).pdb map 5 in map cryosparc_P20_J783_004_volume_map_sharp.mrc
using 63070 points
correlation = 0.2245, correlation about mean = 0.02027, overlap = 425.3
steps = 48, shift = 0.0185, angle = 0.0369 degrees
Position of 5n69 (2).pdb map 5 (#4) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.83929548 0.23625851 -0.48965807 121.58873379
-0.06090070 0.85412056 0.51649702 88.02820687
0.54025384 0.46331414 -0.70247121 159.59032156
Axis -0.04955345 -0.95962601 -0.27687971
Axis point 39.97610520 0.00000000 84.52158994
Rotation angle (degrees) 147.54605538
Shift along axis -134.68661975
Average map value = 0.02013 for 15954 atoms, 13466 outside contour
> fitmap #2 inMap #3 resolution 5
Fit map 5n69 (2).pdb map 5 in map cryosparc_P20_J783_004_volume_map_sharp.mrc
using 63070 points
correlation = 0.2245, correlation about mean = 0.02024, overlap = 425.3
steps = 60, shift = 0.0109, angle = 0.00482 degrees
Position of 5n69 (2).pdb map 5 (#4) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.83929153 0.23618608 -0.48969978 121.57850590
-0.06096599 0.85414454 0.51644966 88.02737073
0.54025261 0.46330685 -0.70247696 159.59327762
Axis -0.04951449 -0.95963254 -0.27686405
Axis point 39.97115845 0.00000000 84.52384433
Rotation angle (degrees) 147.54487102
Shift along axis -134.67946814
Average map value = 0.02014 for 15954 atoms, 13468 outside contour
> fitmap #1 inMap #3
Fit map cryosparc_P20_J808_map_sharp.mrc in map
cryosparc_P20_J783_004_volume_map_sharp.mrc using 82564 points
correlation = 0.303, correlation about mean = 0.07867, overlap = 1146
steps = 64, shift = 0.762, angle = 0.779 degrees
Position of cryosparc_P20_J808_map_sharp.mrc (#1) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.98792158 -0.12842022 0.08671334 21.49681323
0.15329617 0.89164261 -0.42599735 36.43238515
-0.02261064 0.43414479 0.90055930 -9.76795573
Axis 0.94346939 0.11991486 0.30900798
Axis point 0.00000000 53.00232724 65.95156972
Rotation angle (degrees) 27.11899319
Shift along axis 21.63199359
> fitmap #1 inMap #3
Fit map cryosparc_P20_J808_map_sharp.mrc in map
cryosparc_P20_J783_004_volume_map_sharp.mrc using 82564 points
correlation = 0.303, correlation about mean = 0.07873, overlap = 1146
steps = 60, shift = 0.0089, angle = 0.00383 degrees
Position of cryosparc_P20_J808_map_sharp.mrc (#1) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.98791969 -0.12841977 0.08673555 21.50311041
0.15330683 0.89161406 -0.42605327 36.43844843
-0.02262097 0.43420357 0.90053071 -9.77234457
Axis 0.94347591 0.11993540 0.30898012
Axis point 0.00000000 53.01206171 65.94825104
Rotation angle (degrees) 27.12270342
Shift along axis 21.63846624
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!3 models
> undo
[Repeated 9 time(s)]
> hide sel atoms
> select add #3
54 atoms, 58 bonds, 2 residues, 3 models selected
> view matrix models #3,1,0,0,68.072,0,1,0,13.843,0,0,1,-4.6654
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.80675,0.49117,-0.3285,114.86,0.33036,0.83585,0.43843,95.066,0.48992,0.24518,-0.83658,149.05,#3,1,0,0,68.569,0,1,0,17.545,0,0,1,4.7344
> undo
> hide #!2 models
> select add #2
15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 5 models selected
> select subtract #2
2 models selected
> view matrix models #3,1,0,0,71.566,0,1,0,17.457,0,0,1,2.7003
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.87975,0.14523,0.45271,22.258,-0.1934,0.97918,0.06173,33.78,-0.43432,-0.14186,0.88952,75.102
> view matrix models
> #3,0.2764,0.1933,0.9414,30.687,-0.48322,0.87469,-0.03773,85.786,-0.83073,-0.44447,0.33517,206.26
> view matrix models
> #3,0.34563,0.51022,0.78754,5.8262,0.93171,-0.086806,-0.35267,69.677,-0.11157,0.85565,-0.50538,79.767
> view matrix models
> #3,0.1409,0.7538,0.64182,16.897,0.5898,-0.5846,0.55712,64.457,0.79516,0.30005,-0.52696,44.449
> view matrix models
> #3,0.89588,0.28548,-0.34044,87.661,0.36026,-0.91521,0.18056,162.52,-0.26003,-0.28441,-0.92277,258.79
> view matrix models
> #3,0.75418,0.02299,-0.65626,162.96,0.18666,-0.96567,0.18068,186.23,-0.62958,-0.25876,-0.73258,275.62
> view matrix models
> #3,0.62873,-0.7478,-0.21329,211.78,-0.76664,-0.55012,-0.33112,296.33,0.13028,0.3717,-0.91916,147.87
> view matrix models
> #3,0.52562,-0.81781,-0.23433,232.26,-0.84695,-0.47713,-0.23459,287.18,0.080045,0.32177,-0.94343,160.97
> view matrix models
> #3,0.82057,-0.50999,-0.25802,170.99,-0.54589,-0.83306,-0.089504,277.8,-0.1693,0.2143,-0.96198,200.64
> view matrix models
> #3,0.80738,-0.46665,-0.36107,178.46,-0.46687,-0.87946,0.09267,255.51,-0.36079,0.093756,-0.92792,230.13
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.80738,-0.46665,-0.36107,129.33,-0.46687,-0.87946,0.09267,213.53,-0.36079,0.093756,-0.92792,225.51
> view matrix models
> #3,0.80738,-0.46665,-0.36107,116.17,-0.46687,-0.87946,0.09267,218.95,-0.36079,0.093756,-0.92792,231.27
> view matrix models
> #3,0.80738,-0.46665,-0.36107,125.42,-0.46687,-0.87946,0.09267,225.01,-0.36079,0.093756,-0.92792,228.3
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.15047,-0.9197,0.36263,168.08,-0.83795,0.075994,0.54043,117.39,-0.52459,-0.38519,-0.75923,278.73
> view matrix models
> #3,0.51461,-0.81886,0.25425,130.05,-0.77048,-0.31152,0.55617,149.47,-0.37622,-0.4821,-0.79122,276.53
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.51461,-0.81886,0.25425,113.1,-0.77048,-0.31152,0.55617,136.4,-0.37622,-0.4821,-0.79122,276.17
> view matrix models
> #3,0.51461,-0.81886,0.25425,102,-0.77048,-0.31152,0.55617,152.66,-0.37622,-0.4821,-0.79122,274.48
> view matrix models
> #3,0.51461,-0.81886,0.25425,106.64,-0.77048,-0.31152,0.55617,155.56,-0.37622,-0.4821,-0.79122,279.34
> fitmap #3 inMap #1
Fit map cryosparc_P20_J783_004_volume_map_sharp.mrc in map
cryosparc_P20_J808_map_sharp.mrc using 167626 points
correlation = 0.5452, correlation about mean = 0.2846, overlap = 3811
steps = 312, shift = 1.87, angle = 30.3 degrees
Position of cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) relative to
cryosparc_P20_J808_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.55048004 -0.78914940 0.27242421 99.35508564
-0.82664598 -0.56086465 0.04568652 244.58672488
0.11673962 -0.25034790 -0.96109198 218.25928508
Axis -0.87955999 0.46256087 -0.11140764
Axis point 0.00000000 158.94130538 91.08607460
Rotation angle (degrees) 170.31184966
Shift along axis 1.43173674
> fitmap #3 inMap #1
Fit map cryosparc_P20_J783_004_volume_map_sharp.mrc in map
cryosparc_P20_J808_map_sharp.mrc using 167626 points
correlation = 0.5452, correlation about mean = 0.2846, overlap = 3811
steps = 24, shift = 0.000477, angle = 0.00109 degrees
Position of cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) relative to
cryosparc_P20_J808_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.55046947 -0.78915997 0.27241494 99.35838244
-0.82665300 -0.56085518 0.04567584 244.58793303
0.11673979 -0.25033578 -0.96109511 218.25865965
Axis -0.87955710 0.46256693 -0.11140529
Axis point 0.00000000 158.94242217 91.08644829
Rotation angle (degrees) 170.31257076
Shift along axis 1.43175050
> show #!2 models
> select subtract #3
Nothing selected
> color #3 #f4fff7ff models
> ui mousemode right select
Drag select of 26 atoms, 28 bonds, 3
cryosparc_P20_J783_004_volume_map_sharp.mrc
> ui mousemode right select
> undo
Drag select of 25 atoms, 27 bonds
Drag select of 27 atoms, 30 bonds
> hide sel atoms
> ui mousemode right translate
> set bgColor black
> set bgColor transparent
> save /Users/ruchigautamsharma/Desktop/image9.png supersample 3
> save /Users/ruchigautamsharma/Desktop/image10.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie6.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie6.mp4
> volume #3 level 0.07985
> volume #3 level 0.09436
> save /Users/ruchigautamsharma/Desktop/image11.png supersample 3
> save /Users/ruchigautamsharma/Desktop/image12.png supersample 3
> save "/Users/ruchigautamsharma/Desktop/pdbs/S1E525K/ComaprisionS1 783mava
> 753E525K.cxs" includeMaps true
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ruchigautamsharma/Desktop/movie7.mp4
Movie saved to /Users/ruchigautamsharma/Desktop/movie7.mp4
> save "/Users/ruchigautamsharma/Desktop/pdbs/S1E525K/S1 comparision.cxs"
> select add #2
15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 3 models selected
> select subtract #2
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
No map chosen to save
[Repeated 1 time(s)]
> select add #1
2 models selected
No map chosen to save
> hide #!1 models
> show #!3 models
> select add #3
4 models selected
> save /Users/ruchigautamsharma/Desktop/pdbs/S1E525K/S1E525K.ccp4 models #3
> hide #!3 models
> show #!1 models
> select subtract #3
2 models selected
> save "/Users/ruchigautamsharma/Desktop/pdbs/S1E525K/S1E525K with Mava.ccp4"
> models #1
> show #!2 models
> show #!3 models
> undo
[Repeated 2 time(s)]
> show #!3 models
> show #!2 models
> fitmap #1 inMap #3
Fit map cryosparc_P20_J808_map_sharp.mrc in map
cryosparc_P20_J783_004_volume_map_sharp.mrc using 82564 points
correlation = 0.562, correlation about mean = 0.1787, overlap = 3335
steps = 40, shift = 0.0514, angle = 0.187 degrees
Position of cryosparc_P20_J808_map_sharp.mrc (#1) relative to
cryosparc_P20_J783_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.54924478 -0.82741454 0.11711261 122.16955178
-0.78908180 -0.55964698 -0.25326897 270.35538897
0.27510015 0.04669523 -0.96028093 171.09163665
Axis 0.87918050 -0.46305379 0.11235139
Axis point 0.00000000 158.99744835 90.98390080
Rotation angle (degrees) 170.17769666
Shift along axis 1.44238212
> select subtract #3
2 models selected
> select subtract #1
Nothing selected
> open "/Users/ruchigautamsharma/Desktop/pdbs/S1with MAva/S1E525K with
> Mava.ccp4"
Opened S1E525K with Mava.ccp4 as #5, grid size 256,256,256, pixel 0.82, shown
at level 0.00504, step 1, values float32
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> select down
Nothing selected
> open /Users/ruchigautamsharma/Desktop/pdbs/S1E525K/S1E525K.ccp4
Opened S1E525K.ccp4 as #6, grid size 256,256,256, pixel 0.82, shown at level
0.0488, step 1, values float32
> select down
Nothing selected
> surface dust #1 size 8.2
> surface dust #3 size 8.2
> surface dust #5 size 8.2
> surface dust #6 size 8.2
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> hide #!6 models
> volume #5 level 0.04614
> show #!6 models
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,7.1533,0,1,0,-34.593,0,0,1,69.124
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.47054,-0.5887,-0.65728,193.21,0.87062,0.43093,0.2373,-91.395,0.14354,-0.68391,0.71531,155.4
> view matrix models
> #6,-0.73408,-0.30039,-0.60901,285.52,0.67857,-0.35872,-0.64099,102.9,-0.025913,-0.88379,0.46716,220.06
> view matrix models
> #6,-0.91848,-0.27382,-0.28532,268.85,0.37514,-0.37504,-0.84771,158.13,0.12511,-0.88564,0.44719,206.31
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.91848,-0.27382,-0.28532,343.92,0.37514,-0.37504,-0.84771,224.64,0.12511,-0.88564,0.44719,163.17
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.62297,-0.65667,0.42507,147.53,-0.76087,-0.38253,0.52416,204.2,-0.1816,-0.64996,-0.73795,293.21
> view matrix models
> #6,0.1657,-0.59772,0.7844,152.68,-0.98262,-0.16758,0.079871,250.92,0.083711,-0.784,-0.6151,266.53
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.1657,-0.59772,0.7844,85.597,-0.98262,-0.16758,0.079871,186.62,0.083711,-0.784,-0.6151,258.19
> view matrix models
> #6,0.1657,-0.59772,0.7844,65.039,-0.98262,-0.16758,0.079871,186.97,0.083711,-0.784,-0.6151,259.54
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.017778,-0.9013,0.43284,149.02,-0.99358,-0.064288,-0.093059,195.09,0.1117,-0.4284,-0.89666,248.16
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.017778,-0.9013,0.43284,136.75,-0.99358,-0.064288,-0.093059,217.13,0.1117,-0.4284,-0.89666,228.28
> view matrix models
> #6,0.017778,-0.9013,0.43284,144.63,-0.99358,-0.064288,-0.093059,226.33,0.1117,-0.4284,-0.89666,225.39
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> fitmap #6 inMap #5
Fit map S1E525K.ccp4 in map S1E525K with Mava.ccp4 using 167626 points
correlation = 0.5453, correlation about mean = 0.2846, overlap = 3811
steps = 412, shift = 7.76, angle = 33.2 degrees
Position of S1E525K.ccp4 (#6) relative to S1E525K with Mava.ccp4 (#5)
coordinates:
Matrix rotation and translation
0.55062249 -0.78913983 0.27216392 99.37988311
-0.82657680 -0.56096015 0.04576573 244.57516164
0.11655755 -0.25016402 -0.96116195 218.25835635
Axis -0.87960151 0.46251381 -0.11127511
Axis point 0.00000000 158.93325034 91.09740254
Rotation angle (degrees) 170.31576956
Shift along axis 1.41797077
> fitmap #6 inMap #5
Fit map S1E525K.ccp4 in map S1E525K with Mava.ccp4 using 167626 points
correlation = 0.5452, correlation about mean = 0.2846, overlap = 3811
steps = 28, shift = 0.0145, angle = 0.0149 degrees
Position of S1E525K.ccp4 (#6) relative to S1E525K with Mava.ccp4 (#5)
coordinates:
Matrix rotation and translation
0.55057899 -0.78910242 0.27236033 99.34939490
-0.82657132 -0.56098127 0.04560550 244.60032987
0.11680163 -0.25023466 -0.96111393 218.24234740
Axis -0.87958960 0.46250586 -0.11140225
Axis point 0.00000000 158.93408122 91.08639757
Rotation angle (degrees) 170.31859735
Shift along axis 1.42970332
> fitmap #6 inMap #5
Fit map S1E525K.ccp4 in map S1E525K with Mava.ccp4 using 167626 points
correlation = 0.5453, correlation about mean = 0.2846, overlap = 3811
steps = 28, shift = 0.0169, angle = 0.0162 degrees
Position of S1E525K.ccp4 (#6) relative to S1E525K with Mava.ccp4 (#5)
coordinates:
Matrix rotation and translation
0.55058932 -0.78915898 0.27217551 99.38552608
-0.82660357 -0.56091789 0.04580025 244.56837066
0.11652443 -0.25019838 -0.96115703 218.26363133
Axis -0.87959157 0.46253382 -0.11127060
Axis point 0.00000000 158.93573151 91.09711377
Rotation angle (degrees) 170.31338315
Shift along axis 1.41614685
> select subtract #6
Nothing selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
[Repeated 1 time(s)]
> transparency #5.1#6.1 50
No map chosen to save
> save "/Users/ruchigautamsharma/Desktop/pdbs/S1E525K/S1 after density
> modification.cxs" includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 630, in save
fserialize(stream, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/safesave.py", line 136, in write
self._f.write(buf)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
See log for complete Python traceback.
Cannot save '/Users/ruchigautamsharma/Desktop/pdbs/S1E525K/S1 after density
modification.cxs': [Errno 28] No space left on device
> open /Users/ruchigautamsharma/Desktop/pdbs/S1E525K/sharpened_map.ccp4
Opened sharpened_map.ccp4 as #7, grid size 256,256,256, pixel 0.82, shown at
level 2.48, step 1, values float32
> surface dust #5 size 8.2
> surface dust #6 size 8.2
> surface dust #7 size 8.2
> hide #!6 models
> hide #!5 models
> show #!6 models
> select add #7
2 models selected
> view matrix models #7,1,0,0,-49.245,0,1,0,12.175,0,0,1,39.721
> view matrix models #7,1,0,0,-84.151,0,1,0,12.153,0,0,1,37.413
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.85124,0.42386,-0.30941,-80.574,0.17653,0.32396,0.92946,-32.169,0.49419,-0.84581,0.20094,155.75
> view matrix models
> #7,0.33163,-0.0523,-0.94196,89.248,0.93614,0.14193,0.3217,-30.734,0.11687,-0.98849,0.096029,221.32
> view matrix models
> #7,0.22461,0.18774,-0.95619,77.051,0.95701,0.1423,0.25274,-25.854,0.18351,-0.97186,-0.1477,237.72
> view matrix models
> #7,-0.049101,0.043916,-0.99783,125.25,0.98667,0.15729,-0.041629,-0.13907,0.15512,-0.98658,-0.051054,232.27
> view matrix models
> #7,-0.6962,-0.6874,0.20684,145.31,-0.36442,0.090193,-0.92686,241.1,0.61846,-0.72066,-0.3133,182.71
> view matrix models
> #7,0.11289,-0.67349,0.73053,4.2397,-0.77446,-0.52024,-0.35994,289.41,0.62247,-0.52513,-0.58032,189.52
> view matrix models
> #7,0.44643,-0.52146,0.72718,-46.491,-0.72449,-0.68759,-0.048287,269.35,0.52518,-0.50528,-0.68475,208.53
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.44643,-0.52146,0.72718,37.912,-0.72449,-0.68759,-0.048287,272.62,0.52518,-0.50528,-0.68475,188.92
> view matrix models
> #7,0.44643,-0.52146,0.72718,37.786,-0.72449,-0.68759,-0.048287,269.6,0.52518,-0.50528,-0.68475,176.45
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.16781,-0.78634,0.59456,108.5,-0.75769,-0.48872,-0.4325,292.11,0.63067,-0.37791,-0.67782,151.33
> view matrix models
> #7,-0.43303,-0.56172,0.70495,137.23,-0.8969,0.34634,-0.27497,203.64,-0.089697,-0.75134,-0.65379,263.85
> view matrix models
> #7,-0.4135,-0.57306,0.70755,136.08,-0.90624,0.33416,-0.25897,204.24,-0.088035,-0.74829,-0.6575,263.74
> view matrix models
> #7,0.11053,-0.83585,0.53772,125.58,-0.98881,-0.14704,-0.025308,238.91,0.10022,-0.52891,-0.84274,240.15
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.11053,-0.83585,0.53772,115.91,-0.98881,-0.14704,-0.025308,228.32,0.10022,-0.52891,-0.84274,234.96
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.51208,-0.75784,0.40429,79.135,-0.84049,-0.53913,0.053996,245.25,0.17704,-0.36745,-0.91304,217.3
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
[Repeated 2 time(s)]
> transparency sel 50
> select subtract #7
Nothing selected
> hide #!6 models
> volume #7 level 5.044
> fitmap #2 inMap #7
Fit molecule 5n69 (2).pdb (#2) to map sharpened_map.ccp4 (#7) using 15954
atoms
average map value = 1.415, steps = 116
shifted from previous position = 5.15
rotated from previous position = 6.4 degrees
atoms outside contour = 13878, contour level = 5.0441
Position of 5n69 (2).pdb (#2) relative to sharpened_map.ccp4 (#7) coordinates:
Matrix rotation and translation
-0.63721752 -0.45841511 -0.61952354 126.41806717
0.33723657 -0.88867085 0.31070182 88.80729194
-0.69298292 -0.01094135 0.72087097 78.07814634
Axis -0.37342043 0.08528467 0.92373357
Axis point 68.44857890 57.77594267 0.00000000
Rotation angle (degrees) 154.48980904
Shift along axis 32.49021630
> ui mousemode right "translate selected models"
> select add #2
15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 3 models selected
> view matrix models
> #2,-0.86205,0.4343,-0.26127,106.77,0.31634,0.86381,0.39212,92.749,0.39598,0.25538,-0.88203,142.12
> fitmap #2 inMap #7 resolution 5
Fit map 5n69 (2).pdb map 5 in map sharpened_map.ccp4 using 63070 points
correlation = 0.4127, correlation about mean = 0.2792, overlap = 4.661e+04
steps = 188, shift = 5.65, angle = 6.52 degrees
Position of 5n69 (2).pdb map 5 (#4) relative to sharpened_map.ccp4 (#7)
coordinates:
Matrix rotation and translation
-0.65233005 -0.38684036 -0.65178220 125.85973072
0.34219738 -0.91762803 0.20213795 93.67856628
-0.67628874 -0.09117750 0.73097210 72.71094218
Axis -0.37307388 0.03117036 0.92727789
Axis point 67.29250877 60.47933400 0.00000000
Rotation angle (degrees) 156.85207290
Shift along axis 23.38826569
Average map value = 3.025 for 15954 atoms, 12104 outside contour
> view matrix models
> #2,-0.8668,0.46046,-0.19143,99.505,0.32727,0.81493,0.47831,91.637,0.37624,0.35195,-0.85707,138.97
> fitmap #2 inMap #7 resolution 5
Fit map 5n69 (2).pdb map 5 in map sharpened_map.ccp4 using 63070 points
correlation = 0.4127, correlation about mean = 0.2792, overlap = 4.661e+04
steps = 140, shift = 2.79, angle = 0.01 degrees
Position of 5n69 (2).pdb map 5 (#4) relative to sharpened_map.ccp4 (#7)
coordinates:
Matrix rotation and translation
-0.65219929 -0.38687121 -0.65189474 125.86894082
0.34222752 -0.91760893 0.20217364 93.67791463
-0.67639960 -0.09123881 0.73086187 72.71536721
Axis -0.37315326 0.03116455 0.92724615
Axis point 67.29996490 60.48225374 0.00000000
Rotation angle (degrees) 156.84918517
Shift along axis 23.37606818
Average map value = 3.025 for 15954 atoms, 12105 outside contour
> select subtract #2
Nothing selected
> volume #7 level 3.194
> set bgColor white
> set bgColor #ffffff00
> volume #7 level 3.811
> volume #!7 style image
> volume #!7 style mesh
> save /Users/ruchigautamsharma/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/movie/movie.py", line 172, in capture_image
i.save(save_path, self.img_fmt)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/Image.py", line 2353, in save
save_handler(self, fp, filename)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/PpmImagePlugin.py", line 324, in _save
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/ImageFile.py", line 505, in _save
_encode_tile(im, fp, tile, bufsize, fh)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/ImageFile.py", line 532, in _encode_tile
s = encoder.encode_to_file(fh, bufsize)
OSError: [Errno 28] No space left on device
Error processing trigger "frame drawn":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/ImageFile.py", line 532, in _encode_tile
s = encoder.encode_to_file(fh, bufsize)
See log for complete Python traceback.
> movie encode /Users/ruchigautamsharma/Desktop/movie1.mp4
/Applications/ChimeraX-1.6.1.app/Contents/bin/ffmpeg -r 25 -i
/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/chimovie_uExP-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 /Users/ruchigautamsharma/Desktop/movie1.mp4
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with Apple clang version 11.0.0 (clang-1100.0.33.16)
configuration: --prefix=/private/var/tmp/chimerax_build/v1.1/chimerax/build
--enable-gpl --enable-version3 --disable-network --disable-doc --disable-
devices --disable-ffplay --disable-ffserver --disable-ffprobe --enable-
libtheora --enable-libvpx --enable-libx264
--yasmexe=/private/var/tmp/chimerax_build/v1.1/chimerax/build/bin/yasm
--optflags=-O --extra-
cflags=-I/private/var/tmp/chimerax_build/v1.1/chimerax/build/include --extra-
ldflags='-O3 -Wall -Wextra
-L/private/var/tmp/chimerax_build/v1.1/chimerax/build/lib' --extra-libs=-ldl
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from
'/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/chimovie_uExP-%05d.ppm':
Duration: 00:00:01.64, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1396x1228, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0x7f8f8380a000] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0x7f8f8380a000] profile High, level 4.0
[libx264 @ 0x7f8f8380a000] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to '/Users/ruchigautamsharma/Desktop/movie1.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1396x1228, q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
av_interleaved_write_frame(): No space left on device
Error writing trailer of /Users/ruchigautamsharma/Desktop/movie1.mp4: No space
left on deviceframe= 41 fps= 31 q=25.0 Lsize= 430kB time=00:00:00.04
bitrate=87991.0kbits/s speed=0.0302x
video:506kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing
overhead: unknown
[libx264 @ 0x7f8f8380a000] frame I:1 Avg QP:11.53 size:142485
[libx264 @ 0x7f8f8380a000] frame P:10 Avg QP:23.38 size:126686
[libx264 @ 0x7f8f8380a000] frame B:30 Avg QP:26.32 size:109070
[libx264 @ 0x7f8f8380a000] consecutive B-frames: 2.4% 0.0% 0.0% 97.6%
[libx264 @ 0x7f8f8380a000] mb I I16..4: 69.1% 17.1% 13.8%
[libx264 @ 0x7f8f8380a000] mb P I16..4: 0.2% 7.0% 9.8% P16..4: 1.5% 1.1% 1.0%
0.0% 0.0% skip:79.3%
[libx264 @ 0x7f8f8380a000] mb B I16..4: 0.1% 1.3% 4.4% B16..8: 4.4% 5.1% 3.7%
direct: 1.4% skip:79.6% L0:21.1% L1:19.9% BI:58.9%
[libx264 @ 0x7f8f8380a000] 8x8 transform intra:28.5% inter:13.8%
[libx264 @ 0x7f8f8380a000] coded y,uvDC,uvAC intra: 77.8% 78.4% 74.4% inter:
9.6% 5.3% 3.5%
[libx264 @ 0x7f8f8380a000] i16 v,h,dc,p: 95% 2% 3% 0%
[libx264 @ 0x7f8f8380a000] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 10% 7% 36% 8% 9% 7%
8% 8% 9%
[libx264 @ 0x7f8f8380a000] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 7% 6% 24% 11% 12%
10% 11% 10% 10%
[libx264 @ 0x7f8f8380a000] i8c dc,h,v,p: 65% 12% 14% 9%
[libx264 @ 0x7f8f8380a000] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0x7f8f8380a000] ref P L0: 64.3% 12.7% 15.2% 7.8%
[libx264 @ 0x7f8f8380a000] ref B L0: 92.0% 6.4% 1.5%
[libx264 @ 0x7f8f8380a000] ref B L1: 97.0% 3.0%
[libx264 @ 0x7f8f8380a000] kb/s:22836.31
Conversion failed!
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 1
Error message:
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with Apple clang version 11.0.0 (clang-1100.0.33.16)
configuration: --prefix=/private/var/tmp/chimerax_build/v1.1/chimerax/build
--enable-gpl --enable-version3 --disable-network --disable-doc --disable-
devices --disable-ffplay --disable-ffserver --disable-ffprobe --enable-
libtheora --enable-libvpx --enable-libx264
--yasmexe=/private/var/tmp/chimerax_build/v1.1/chimerax/build/bin/yasm
--optflags=-O --extra-
cflags=-I/private/var/tmp/chimerax_build/v1.1/chimerax/build/include --extra-
ldflags='-O3 -Wall -Wextra
-L/private/var/tmp/chimerax_build/v1.1/chimerax/build/lib' --extra-libs=-ldl
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from
'/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/chimovie_uExP-%05d.ppm':
Duration: 00:00:01.64, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1396x1228, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0x7f8f8380a000] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0x7f8f8380a000] profile High, level 4.0
[libx264 @ 0x7f8f8380a000] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to '/Users/ruchigautamsharma/Desktop/movie1.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1396x1228, q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
av_interleaved_write_frame(): No space left on device
Error writing trailer of /Users/ruchigautamsharma/Desktop/movie1.mp4: No space
left on deviceframe= 41 fps= 31 q=25.0 Lsize= 430kB time=00:00:00.04
bitrate=87991.0kbits/s speed=0.0302x
video:506kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing
overhead: unknown
[libx264 @ 0x7f8f8380a000] frame I:1 Avg QP:11.53 size:142485
[libx264 @ 0x7f8f8380a000] frame P:10 Avg QP:23.38 size:126686
[libx264 @ 0x7f8f8380a000] frame B:30 Avg QP:26.32 size:109070
[libx264 @ 0x7f8f8380a000] consecutive B-frames: 2.4% 0.0% 0.0% 97.6%
[libx264 @ 0x7f8f8380a000] mb I I16..4: 69.1% 17.1% 13.8%
[libx264 @ 0x7f8f8380a000] mb P I16..4: 0.2% 7.0% 9.8% P16..4: 1.5% 1.1% 1.0%
0.0% 0.0% skip:79.3%
[libx264 @ 0x7f8f8380a000] mb B I16..4: 0.1% 1.3% 4.4% B16..8: 4.4% 5.1% 3.7%
direct: 1.4% skip:79.6% L0:21.1% L1:19.9% BI:58.9%
[libx264 @ 0x7f8f8380a000] 8x8 transform intra:28.5% inter:13.8%
[libx264 @ 0x7f8f8380a000] coded y,uvDC,uvAC intra: 77.8% 78.4% 74.4% inter:
9.6% 5.3% 3.5%
[libx264 @ 0x7f8f8380a000] i16 v,h,dc,p: 95% 2% 3% 0%
[libx264 @ 0x7f8f8380a000] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 10% 7% 36% 8% 9% 7%
8% 8% 9%
[libx264 @ 0x7f8f8380a000] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 7% 6% 24% 11% 12%
10% 11% 10% 10%
[libx264 @ 0x7f8f8380a000] i8c dc,h,v,p: 65% 12% 14% 9%
[libx264 @ 0x7f8f8380a000] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0x7f8f8380a000] ref P L0: 64.3% 12.7% 15.2% 7.8%
[libx264 @ 0x7f8f8380a000] ref B L0: 92.0% 6.4% 1.5%
[libx264 @ 0x7f8f8380a000] ref B L1: 97.0% 3.0%
[libx264 @ 0x7f8f8380a000] kb/s:22836.31
Conversion failed!
\-----------------------------
> movie record
> turn y 2 180
> wait 180
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/movie/movie.py", line 172, in capture_image
i.save(save_path, self.img_fmt)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/Image.py", line 2353, in save
save_handler(self, fp, filename)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/PpmImagePlugin.py", line 324, in _save
ImageFile._save(im, fp, [("raw", (0, 0) + im.size, 0, (rawmode, 0, 1))])
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/ImageFile.py", line 505, in _save
_encode_tile(im, fp, tile, bufsize, fh)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/ImageFile.py", line 532, in _encode_tile
s = encoder.encode_to_file(fh, bufsize)
OSError: [Errno 28] No space left on device
Error processing trigger "frame drawn":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/PIL/ImageFile.py", line 532, in _encode_tile
s = encoder.encode_to_file(fh, bufsize)
See log for complete Python traceback.
> movie encode /Users/ruchigautamsharma/Desktop/movie1.mp4
/Applications/ChimeraX-1.6.1.app/Contents/bin/ffmpeg -r 25 -i
/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/chimovie_uExP-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 /Users/ruchigautamsharma/Desktop/movie1.mp4
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with Apple clang version 11.0.0 (clang-1100.0.33.16)
configuration: --prefix=/private/var/tmp/chimerax_build/v1.1/chimerax/build
--enable-gpl --enable-version3 --disable-network --disable-doc --disable-
devices --disable-ffplay --disable-ffserver --disable-ffprobe --enable-
libtheora --enable-libvpx --enable-libx264
--yasmexe=/private/var/tmp/chimerax_build/v1.1/chimerax/build/bin/yasm
--optflags=-O --extra-
cflags=-I/private/var/tmp/chimerax_build/v1.1/chimerax/build/include --extra-
ldflags='-O3 -Wall -Wextra
-L/private/var/tmp/chimerax_build/v1.1/chimerax/build/lib' --extra-libs=-ldl
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from
'/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/chimovie_uExP-%05d.ppm':
Duration: 00:00:01.64, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1396x1228, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0x7fe570809400] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0x7fe570809400] profile High, level 4.0
[libx264 @ 0x7fe570809400] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to '/Users/ruchigautamsharma/Desktop/movie1.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1396x1228, q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame= 37 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
av_interleaved_write_frame(): No space left on device
Error writing trailer of /Users/ruchigautamsharma/Desktop/movie1.mp4: No space
left on deviceframe= 41 fps= 28 q=25.0 Lsize= 1085kB time=00:00:00.28
bitrate=31726.4kbits/s speed=0.192x
video:1216kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: unknown
[libx264 @ 0x7fe570809400] frame I:1 Avg QP:11.53 size:142485
[libx264 @ 0x7fe570809400] frame P:10 Avg QP:23.38 size:126686
[libx264 @ 0x7fe570809400] frame B:30 Avg QP:26.32 size:109070
[libx264 @ 0x7fe570809400] consecutive B-frames: 2.4% 0.0% 0.0% 97.6%
[libx264 @ 0x7fe570809400] mb I I16..4: 69.1% 17.1% 13.8%
[libx264 @ 0x7fe570809400] mb P I16..4: 0.2% 7.0% 9.8% P16..4: 1.5% 1.1% 1.0%
0.0% 0.0% skip:79.3%
[libx264 @ 0x7fe570809400] mb B I16..4: 0.1% 1.3% 4.4% B16..8: 4.4% 5.1% 3.7%
direct: 1.4% skip:79.6% L0:21.1% L1:19.9% BI:58.9%
[libx264 @ 0x7fe570809400] 8x8 transform intra:28.5% inter:13.8%
[libx264 @ 0x7fe570809400] coded y,uvDC,uvAC intra: 77.8% 78.4% 74.4% inter:
9.6% 5.3% 3.5%
[libx264 @ 0x7fe570809400] i16 v,h,dc,p: 95% 2% 3% 0%
[libx264 @ 0x7fe570809400] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 10% 7% 36% 8% 9% 7%
8% 8% 9%
[libx264 @ 0x7fe570809400] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 7% 6% 24% 11% 12%
10% 11% 10% 10%
[libx264 @ 0x7fe570809400] i8c dc,h,v,p: 65% 12% 14% 9%
[libx264 @ 0x7fe570809400] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0x7fe570809400] ref P L0: 64.3% 12.7% 15.2% 7.8%
[libx264 @ 0x7fe570809400] ref B L0: 92.0% 6.4% 1.5%
[libx264 @ 0x7fe570809400] ref B L1: 97.0% 3.0%
[libx264 @ 0x7fe570809400] kb/s:22836.31
Conversion failed!
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 1
Error message:
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with Apple clang version 11.0.0 (clang-1100.0.33.16)
configuration: --prefix=/private/var/tmp/chimerax_build/v1.1/chimerax/build
--enable-gpl --enable-version3 --disable-network --disable-doc --disable-
devices --disable-ffplay --disable-ffserver --disable-ffprobe --enable-
libtheora --enable-libvpx --enable-libx264
--yasmexe=/private/var/tmp/chimerax_build/v1.1/chimerax/build/bin/yasm
--optflags=-O --extra-
cflags=-I/private/var/tmp/chimerax_build/v1.1/chimerax/build/include --extra-
ldflags='-O3 -Wall -Wextra
-L/private/var/tmp/chimerax_build/v1.1/chimerax/build/lib' --extra-libs=-ldl
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from
'/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/chimovie_uExP-%05d.ppm':
Duration: 00:00:01.64, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1396x1228, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0x7fe570809400] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0x7fe570809400] profile High, level 4.0
[libx264 @ 0x7fe570809400] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to '/Users/ruchigautamsharma/Desktop/movie1.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1396x1228, q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame= 37 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
av_interleaved_write_frame(): No space left on device
Error writing trailer of /Users/ruchigautamsharma/Desktop/movie1.mp4: No space
left on deviceframe= 41 fps= 28 q=25.0 Lsize= 1085kB time=00:00:00.28
bitrate=31726.4kbits/s speed=0.192x
video:1216kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: unknown
[libx264 @ 0x7fe570809400] frame I:1 Avg QP:11.53 size:142485
[libx264 @ 0x7fe570809400] frame P:10 Avg QP:23.38 size:126686
[libx264 @ 0x7fe570809400] frame B:30 Avg QP:26.32 size:109070
[libx264 @ 0x7fe570809400] consecutive B-frames: 2.4% 0.0% 0.0% 97.6%
[libx264 @ 0x7fe570809400] mb I I16..4: 69.1% 17.1% 13.8%
[libx264 @ 0x7fe570809400] mb P I16..4: 0.2% 7.0% 9.8% P16..4: 1.5% 1.1% 1.0%
0.0% 0.0% skip:79.3%
[libx264 @ 0x7fe570809400] mb B I16..4: 0.1% 1.3% 4.4% B16..8: 4.4% 5.1% 3.7%
direct: 1.4% skip:79.6% L0:21.1% L1:19.9% BI:58.9%
[libx264 @ 0x7fe570809400] 8x8 transform intra:28.5% inter:13.8%
[libx264 @ 0x7fe570809400] coded y,uvDC,uvAC intra: 77.8% 78.4% 74.4% inter:
9.6% 5.3% 3.5%
[libx264 @ 0x7fe570809400] i16 v,h,dc,p: 95% 2% 3% 0%
[libx264 @ 0x7fe570809400] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 10% 7% 36% 8% 9% 7%
8% 8% 9%
[libx264 @ 0x7fe570809400] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 7% 6% 24% 11% 12%
10% 11% 10% 10%
[libx264 @ 0x7fe570809400] i8c dc,h,v,p: 65% 12% 14% 9%
[libx264 @ 0x7fe570809400] Weighted P-Frames: Y:0.0% UV:0.0%
[libx264 @ 0x7fe570809400] ref P L0: 64.3% 12.7% 15.2% 7.8%
[libx264 @ 0x7fe570809400] ref B L0: 92.0% 6.4% 1.5%
[libx264 @ 0x7fe570809400] ref B L1: 97.0% 3.0%
[libx264 @ 0x7fe570809400] kb/s:22836.31
Conversion failed!
\-----------------------------
> open /Users/ruchigautamsharma/Desktop/pdbs/S!E525Kdm/denmod_map.ccp4
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
See log for complete Python traceback.
Opened denmod_map.ccp4 as #8, grid size 77,88,125, pixel 0.82, shown at level
1.55, step 1, values float32
> volume #8 level 0.4209
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
See log for complete Python traceback.
> select add #8
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
See log for complete Python traceback.
2 models selected
> view matrix models #8,1,0,0,30.995,0,1,0,-61.833,0,0,1,-6.7322
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
See log for complete Python traceback.
> view matrix models #8,1,0,0,26.86,0,1,0,-61.197,0,0,1,2.4122
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
See log for complete Python traceback.
> ui mousemode right "rotate selected models"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
See log for complete Python traceback.
> view matrix models
> #8,-0.42981,-0.86014,-0.27465,296.07,-0.42681,0.46159,-0.77767,124.22,0.79568,-0.21702,-0.56551,112.08
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
See log for complete Python traceback.
> view matrix models
> #8,0.58563,-0.74837,-0.31142,182.75,-0.73566,-0.65203,0.18348,170.09,-0.34037,0.12165,-0.93239,233.96
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
See log for complete Python traceback.
> view matrix models
> #8,0.96922,0.24084,0.051007,-0.93284,0.1275,-0.66832,0.73287,22.717,0.21059,-0.70381,-0.67846,236.56
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 456, in add
self._history.enqueue((item, typed))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue
self.save()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save
self._history.save(self._queue)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py",
line 180, in dump
fp.write(chunk)
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-20.6.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,4
Processor Name: Quad-Core Intel Core i7
Processor Speed: 1.7 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.0.1.0.0 (iBridge: 21.16.365.0.0,0)
OS Loader Version: 577.140.2~15
Software:
System Software Overview:
System Version: macOS 13.6 (22G120)
Kernel Version: Darwin 22.6.0
Time since boot: 4 days, 12 hours, 24 minutes
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
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: 2021.10.8
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-Clipper: 0.21.0
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-ISOLDE: 1.6.0
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-NIHPresets: 1.1.15
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-OpenCommands: 1.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBImages: 1.2
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-PICKLUSTER: 0.2
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.0
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-StarMap: 1.2.15
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-TugLigands: 1.1
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-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
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
et-xmlfile: 1.1.0
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: 2022.2.22
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
MolecularDynamicsViewer: 1.4
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
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 21.3
pandas: 2.1.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
pyqtgraph: 0.13.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
seaborn: 0.12.2
Send2Trash: 1.8.2
SEQCROW: 1.8.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
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
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 → accepted |
| Summary: | ChimeraX bug report submission → No space left on device |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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