No space left on device

[ruchi.sharma@…]

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!  
  
\-----------------------------  
  




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, 21 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

[Eric Pettersen]

Hi Ruchi,

All these problems you've reported saving sessions and movies is because you have run out of disk space. You need to free up disk space on your machine to get these to work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab