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

> 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.  
  

> view matrix models
> #8,0.94441,-0.29171,0.15167,47.079,-0.32147,-0.91605,0.23982,148.9,0.068974,-0.27525,-0.9589,236.29

> view matrix models
> #8,0.41778,-0.73652,0.53197,107.68,-0.73986,-0.61563,-0.2713,215.88,0.52732,-0.28024,-0.80212,172.24

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
> #8,0.81392,-0.47974,0.32769,61.476,-0.40662,-0.87326,-0.26848,208.21,0.41496,0.085274,-0.90584,156.48

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 "translate 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
> #8,0.81392,-0.47974,0.32769,12.009,-0.40662,-0.87326,-0.26848,256.94,0.41496,0.085274,-0.90584,149.41

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
> #8,0.81392,-0.47974,0.32769,29.712,-0.40662,-0.87326,-0.26848,269.97,0.41496,0.085274,-0.90584,141.59

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.  
  

> fitmap #2 inMap #8 resolution 5

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.  
  
Fit map 5n69 (2).pdb map 5 in map denmod_map.ccp4 using 63070 points  
correlation = 0.04127, correlation about mean = 0.02531, overlap = 412.8  
steps = 144, shift = 2.58, angle = 6.04 degrees  
  
Position of 5n69 (2).pdb map 5 (#4) relative to denmod_map.ccp4 (#8)
coordinates:  
Matrix rotation and translation  
-0.70554676 0.10520671 -0.70081047 127.31285922  
0.17087527 -0.93448394 -0.31231621 114.76209484  
-0.68775389 -0.34010487 0.64134489 72.42371495  
Axis -0.38333582 -0.18011147 0.90587721  
Axis point 77.83866147 65.83998106 0.00000000  
Rotation angle (degrees) 177.92281119  
Shift along axis -3.86655562  
  
Average map value = 0.04856 for 9000 atoms, 14541 outside contour  

> hide #!7 models

> fitmap #2 inMap #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.  
  
Fit molecule 5n69 (2).pdb (#2) to map denmod_map.ccp4 (#8) using 15954 atoms  
average map value = 0.05027, steps = 112  
shifted from previous position = 0.357  
rotated from previous position = 1.47 degrees  
atoms outside contour = 14567, contour level = 0.42085  
  
Position of 5n69 (2).pdb (#2) relative to denmod_map.ccp4 (#8) coordinates:  
Matrix rotation and translation  
-0.70584098 0.12642461 -0.69699737 127.26899420  
0.16568832 -0.92718553 -0.33596781 115.68975331  
-0.68872048 -0.35262418 0.63349846 72.46450256  
Axis -0.38337822 -0.19050860 0.90372983  
Axis point 78.31568215 66.23530523 0.00000000  
Rotation angle (degrees) 178.75525755  
Shift along axis -5.34372096  
  

> volume #8 level 0.248

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.  
  

> surface dust #8 size 8.2

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.  
  

> transparency sel 50

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.  
  

> volume sel style mesh

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
> #8,0.81392,-0.47974,0.32769,35.165,-0.40662,-0.87326,-0.26848,275.42,0.41496,0.085274,-0.90584,140.1

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
> #8,0.81392,-0.47974,0.32769,26.958,-0.40662,-0.87326,-0.26848,273.53,0.41496,0.085274,-0.90584,142.33

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.  
  

> fitmap #2 inMap #8 resolution 5

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.  
  
Fit map 5n69 (2).pdb map 5 in map denmod_map.ccp4 using 63070 points  
correlation = 0.2061, correlation about mean = 0.2848, overlap = 2181  
steps = 408, shift = 13.2, angle = 34 degrees  
  
Position of 5n69 (2).pdb map 5 (#4) relative to denmod_map.ccp4 (#8)
coordinates:  
Matrix rotation and translation  
-0.65214489 -0.39069660 -0.64966392 125.75729277  
0.34058885 -0.91661024 0.20934397 93.33292591  
-0.67727858 -0.08474569 0.73082959 72.75454824  
Axis -0.37288438 0.03501339 0.92721697  
Axis point 67.25773700 60.21341323 0.00000000  
Rotation angle (degrees) 156.77491387  
Shift along axis 23.83422367  
  
Average map value = 0.3872 for 8559 atoms, 12197 outside contour  

> 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 ::name="ADP"

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.  
  
54 atoms, 58 bonds, 2 residues, 1 model selected  

> show sel atoms

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 select

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 clear

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.  
  
Drag select of 26 atoms, 28 bonds  

> hide sel atoms

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.  
  
Drag select of 4 residues, 8 denmod_map.ccp4  

> select clear

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 #2

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.  
  
15954 atoms, 15376 bonds, 25 pseudobonds, 2720 residues, 3 models selected  

> select subtract #2

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.  
  
Nothing selected  

> ui mousemode right translate

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.  
  

> volume #8 level 0.225

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.  
  

> save /Users/ruchigautamsharma/Desktop/pdbs/S1E525K/S1E525K.ccp4 models #8

> save /Users/ruchigautamsharma/Desktop/pdbs/S1E525K/S1E525k.cxs

> 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

Movie saved to /Users/ruchigautamsharma/Desktop/movie1.mp4  
  

> volume #8 level 0.6628

> save /Users/ruchigautamsharma/Desktop/image2.png supersample 3




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, 33 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