No space left on device saving command history

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-142-generic-x86_64-with-glibc2.23
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /media/bunt16/DATA/Honza/Projects/Tv20S/J178_map_sharp.mrc

Opened J178_map_sharp.mrc as #1, grid size 440,440,440, pixel 0.7, shown at
level 0.0569, step 2, values float32  

> lighting soft

> set bgColor white

> open /media/bunt16/DATA/Honza/Projects/Tv20S/7zyj.pdb

7zyj.pdb title:  
Leishmania tarentolae proteasome 20S subunit In complex with compound 2 [more
info...]  
  
Chain information for 7zyj.pdb #2  
---  
Chain | Description  
A a | proteasome subunit α type  
B b | proteasome subunit α type  
C c | proteasome subunit α type  
D d | proteasome subunit α type  
E e | proteasome α 5 subunit, putative  
F f | proteasome α 1 subunit, putative  
G g | proteasome α 7 subunit, putative  
H h | proteasome subunit β  
I i | proteasome subunit β  
J j | proteasome subunit β  
K k | proteasome subunit β  
L l | proteasome subunit β  
M m | proteasome β 6 subunit, putative  
N n | proteasome subunit β  
  
Non-standard residues in 7zyj.pdb #2  
---  
KFC — ~{N}-cyclopentyl-6-methyl-4-phenylazanyl-quinoline-2-carboxamide  
  

> select #2

49234 atoms, 50172 bonds, 6364 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.63178,0.68956,0.35406,76.776,0.53638,0.71866,-0.44252,23.215,-0.5596,-0.089666,-0.8239,315.33

> view matrix models
> #2,-0.54864,0.66298,0.50936,49.757,0.48207,0.74862,-0.45516,27.966,-0.68308,-0.0041758,-0.73033,308.37

> view matrix models
> #2,-0.54864,0.66298,0.50936,69.699,0.48207,0.74862,-0.45516,57.565,-0.68308,-0.0041758,-0.73033,310.21

> view matrix models
> #2,-0.54864,0.66298,0.50936,72.801,0.48207,0.74862,-0.45516,51.434,-0.68308,-0.0041758,-0.73033,309.7

> view matrix models
> #2,-0.54864,0.66298,0.50936,66.822,0.48207,0.74862,-0.45516,59.451,-0.68308,-0.0041758,-0.73033,310.4

> view matrix models
> #2,-0.54864,0.66298,0.50936,81.402,0.48207,0.74862,-0.45516,57.596,-0.68308,-0.0041758,-0.73033,332.97

> fitmap #2 inMap #1

Fit molecule 7zyj.pdb (#2) to map J178_map_sharp.mrc (#1) using 49234 atoms  
average map value = 0.02809, steps = 92  
shifted from previous position = 3.77  
rotated from previous position = 3.16 degrees  
atoms outside contour = 38693, contour level = 0.056872  
  
Position of 7zyj.pdb (#2) relative to J178_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.56834804 0.67027427 0.47719275 84.49849585  
0.51384280 0.74211324 -0.43038765 48.67562876  
-0.64260882 0.00059208 -0.76619420 332.78425778  
Axis 0.35617309 0.92543376 -0.12927912  
Axis point 94.19926706 0.00000000 156.49662793  
Rotation angle (degrees) 142.77011910  
Shift along axis 32.12010356  
  

> hide sel cartoons

> show sel cartoons

> hide sel surfaces

> hide sel atoms

> fitmap #2 inMap #1

Fit molecule 7zyj.pdb (#2) to map J178_map_sharp.mrc (#1) using 49234 atoms  
average map value = 0.02809, steps = 48  
shifted from previous position = 0.00249  
rotated from previous position = 0.00379 degrees  
atoms outside contour = 38691, contour level = 0.056872  
  
Position of 7zyj.pdb (#2) relative to J178_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.56837358 0.67022665 0.47722920 84.50508284  
0.51379890 0.74215625 -0.43036589 48.67240435  
-0.64262132 0.00059124 -0.76618372 332.78621177  
Axis 0.35614359 0.92544609 -0.12927212  
Axis point 94.20590889 0.00000000 156.49541939  
Rotation angle (degrees) 142.76879601  
Shift along axis 32.11965199  
  

> view matrix models
> #2,-0.56837,0.67023,0.47723,78.462,0.5138,0.74216,-0.43037,56.521,-0.64262,0.00059124,-0.76618,335.95

> view matrix models
> #2,-0.62643,0.77606,-0.072918,141.95,0.76448,0.62995,0.13691,-37.139,0.15218,0.030019,-0.9879,260.39

> view matrix models
> #2,-0.18721,0.77537,0.60312,-1.0552,0.26611,0.63105,-0.72867,137.67,-0.94559,0.02408,-0.32447,318.01

> view matrix models
> #2,0.54958,0.80723,-0.21526,4.3711,-0.76397,0.58987,0.26155,149.33,0.33811,0.020713,0.94088,-8.9522

> fitmap #2 inMap #1

Fit molecule 7zyj.pdb (#2) to map J178_map_sharp.mrc (#1) using 49234 atoms  
average map value = 0.03529, steps = 212  
shifted from previous position = 8.19  
rotated from previous position = 14.3 degrees  
atoms outside contour = 36201, contour level = 0.056872  
  
Position of 7zyj.pdb (#2) relative to J178_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.55456754 0.83031618 -0.05504439 -17.21081921  
-0.82614543 0.55729225 0.08312085 178.03874355  
0.09969240 -0.00062145 0.99501811 13.37154882  
Axis -0.05027214 -0.09289152 -0.99440629  
Axis point 155.49863745 105.90102526 0.00000000  
Rotation angle (degrees) 56.39673932  
Shift along axis -28.96981705  
  

> select up

49234 atoms, 50172 bonds, 6364 residues, 3 models selected  

> vop zflip #1

> volume zflip #1

Expected a density maps specifier or a keyword  

> ~select #1

49234 atoms, 50172 bonds, 6364 residues, 1 model selected  

> ~select #2

Nothing selected  

> volume flip #1

Opened J178_map_sharp.mrc z flip as #3, grid size 440,440,440, pixel 0.7,
shown at step 1, values float32  

> fitmap #2 inMap #1

Fit molecule 7zyj.pdb (#2) to map J178_map_sharp.mrc (#1) using 49234 atoms  
average map value = 0.03529, steps = 44  
shifted from previous position = 0.00513  
rotated from previous position = 0.00371 degrees  
atoms outside contour = 36195, contour level = 0.056872  
  
Position of 7zyj.pdb (#2) relative to J178_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.55453852 0.83033483 -0.05505545 -17.20551618  
-0.82616934 0.55726451 0.08306922 178.05323149  
0.09965572 -0.00057996 0.99502181 13.36614893  
Axis -0.05021517 -0.09287417 -0.99441079  
Axis point 155.50933974 105.90109804 0.00000000  
Rotation angle (degrees) 56.39856457  
Shift along axis -28.96401112  
  

> fitmap #2 inMap #3

Fit molecule 7zyj.pdb (#2) to map J178_map_sharp.mrc z flip (#3) using 49234
atoms  
average map value = 0.03131, steps = 128  
shifted from previous position = 2.5  
rotated from previous position = 5.66 degrees  
atoms outside contour = 37399, contour level = 0.056872  
  
Position of 7zyj.pdb (#2) relative to J178_map_sharp.mrc z flip (#3)
coordinates:  
Matrix rotation and translation  
0.52018413 0.84520939 -0.12259512 -6.07784012  
-0.83282846 0.53380638 0.14644971 173.18177953  
0.18922273 0.02591989 0.98159204 -2.30605306  
Axis -0.07044351 -0.18224155 -0.98072714  
Axis point 148.92837339 94.14214351 0.00000000  
Rotation angle (degrees) 58.81578955  
Shift along axis -28.87116340  
  

> volume #1 step 1

> volume #1 level 0.06584

> volume #1 level 0.09074

> volume #1 level 0.09473

> hide #!1 models

> select #2

49234 atoms, 50172 bonds, 6364 residues, 1 model selected  

> view matrix models
> #2,0.50638,0.86116,-0.044484,-16.34,-0.85533,0.50817,0.10089,185.22,0.10949,-0.01304,0.9939,11.436

> view matrix models
> #2,0.56787,0.81864,0.085746,-35.435,-0.79576,0.57265,-0.19709,207.3,-0.21044,0.043687,0.97663,47.609

> view matrix models
> #2,0.44792,0.8911,0.072824,-27.655,-0.85796,0.45132,-0.24537,237.16,-0.25152,0.047428,0.96669,53.697

> fitmap #2 inMap #3

Fit molecule 7zyj.pdb (#2) to map J178_map_sharp.mrc z flip (#3) using 49234
atoms  
average map value = 0.04612, steps = 196  
shifted from previous position = 1.08  
rotated from previous position = 13.6 degrees  
atoms outside contour = 32643, contour level = 0.056872  
  
Position of 7zyj.pdb (#2) relative to J178_map_sharp.mrc z flip (#3)
coordinates:  
Matrix rotation and translation  
0.49229017 0.83223387 0.25502389 -49.60310613  
-0.75532364 0.55405241 -0.35001732 224.90650826  
-0.43259286 -0.02031549 0.90136047 94.87333203  
Axis 0.18720194 0.39042303 -0.90140185  
Axis point 196.38382034 177.83392616 0.00000000  
Rotation angle (degrees) 61.71540057  
Shift along axis -6.99611477  
  

> volume #1 level 0.1057

> volume #1 level 0.1137

> hide #!1 models

> close #1

> volume #3 level 0.07532

> volume #3 level 0.06853

> save /home/bunt16/Documents/Tv20S_7Zyj_fit.cxs

> hide #2 models

> open
> /media/bunt16/DATA/Honza/Projects/Tv20S/AlphaFold_Tv20S/TVAG_A1_AF-A2F568-F1-model_v4.pdb

TVAG_A1_AF-A2F568-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for family T1, proteasome α subunit,
threonine peptidase (A2F568) [more info...]  
  
Chain information for TVAG_A1_AF-A2F568-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | family T1, proteasome α subunit, threonine peptidase | A2F568_TRIVA  
  

> select #3

2 models selected  

> view matrix models #3,1,0,0,-29.446,0,1,0,-30.683,0,0,1,20.899

> select #2

49234 atoms, 50172 bonds, 6364 residues, 1 model selected  

> select #1

1860 atoms, 1892 bonds, 241 residues, 1 model selected  

> view matrix models #1,1,0,0,18.868,0,1,0,156.21,0,0,1,116.89

> view matrix models #1,1,0,0,86.969,0,1,0,89.382,0,0,1,129.03

> view matrix models #1,1,0,0,78.763,0,1,0,91.273,0,0,1,146.86

> view matrix models #1,1,0,0,79.237,0,1,0,90.977,0,0,1,146.59

> fitmap #1 inMap #3

Fit molecule TVAG_A1_AF-A2F568-F1-model_v4.pdb (#1) to map J178_map_sharp.mrc
z flip (#3) using 1860 atoms  
average map value = 0.04128, steps = 112  
shifted from previous position = 2.09  
rotated from previous position = 6.12 degrees  
atoms outside contour = 1364, contour level = 0.068526  
  
Position of TVAG_A1_AF-A2F568-F1-model_v4.pdb (#1) relative to
J178_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.99433599 -0.10268571 -0.02741492 107.74588989  
0.10291382 0.99466536 0.00703992 120.67379217  
0.02654577 -0.00982142 0.99959935 124.09589432  
Axis -0.07907565 -0.25306278 0.96421277  
Axis point -1309.40540547 1183.56887897 0.00000000  
Rotation angle (degrees) 6.12023477  
Shift along axis 80.59672470  
  

> fitmap #1 inMap #3

Fit molecule TVAG_A1_AF-A2F568-F1-model_v4.pdb (#1) to map J178_map_sharp.mrc
z flip (#3) using 1860 atoms  
average map value = 0.04128, steps = 60  
shifted from previous position = 0.0122  
rotated from previous position = 0.0264 degrees  
atoms outside contour = 1365, contour level = 0.068526  
  
Position of TVAG_A1_AF-A2F568-F1-model_v4.pdb (#1) relative to
J178_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.99430489 -0.10288650 -0.02778753 107.73580135  
0.10311332 0.99464601 0.00685318 120.67444952  
0.02693365 -0.00967942 0.99959036 124.08903521  
Axis -0.07733313 -0.25596463 0.96358793  
Axis point -1308.50131953 1179.95682974 0.00000000  
Rotation angle (degrees) 6.13618808  
Shift along axis 80.35075810  
  

> view matrix models
> #1,0.9943,-0.10289,-0.027788,79.051,0.10311,0.99465,0.0068532,97.313,0.026934,-0.0096794,0.99959,185.14

> view matrix models
> #1,-0.33934,-0.2084,0.91729,81.401,-0.69895,0.70848,-0.097609,100.3,-0.62953,-0.67426,-0.38608,164.38

> fitmap #1 inMap #3

Fit molecule TVAG_A1_AF-A2F568-F1-model_v4.pdb (#1) to map J178_map_sharp.mrc
z flip (#3) using 1860 atoms  
average map value = 0.02528, steps = 128  
shifted from previous position = 4  
rotated from previous position = 16.9 degrees  
atoms outside contour = 1537, contour level = 0.068526  
  
Position of TVAG_A1_AF-A2F568-F1-model_v4.pdb (#1) relative to
J178_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.17232947 -0.44285774 0.87987475 109.16540210  
-0.79905585 0.58519631 0.13803992 134.57599396  
-0.57603151 -0.67928072 -0.45471464 143.45172510  
Axis -0.47874746 0.85280045 -0.20864387  
Axis point 141.79716723 0.00000000 47.13525641  
Rotation angle (degrees) 121.39424540  
Shift along axis 32.57348730  
  

> fitmap #1 inMap #3

Fit molecule TVAG_A1_AF-A2F568-F1-model_v4.pdb (#1) to map J178_map_sharp.mrc
z flip (#3) using 1860 atoms  
average map value = 0.02528, steps = 44  
shifted from previous position = 0.00189  
rotated from previous position = 0.00598 degrees  
atoms outside contour = 1538, contour level = 0.068526  
  
Position of TVAG_A1_AF-A2F568-F1-model_v4.pdb (#1) relative to
J178_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.17224645 -0.44280963 0.87991522 109.16720131  
-0.79905739 0.58518669 0.13807182 134.57627731  
-0.57605420 -0.67932038 -0.45462664 143.45115783  
Axis -0.47876175 0.85278826 -0.20866091  
Axis point 141.80557100 0.00000000 47.13167731  
Rotation angle (degrees) 121.38882883  
Shift along axis 32.56733903  
  

> view matrix models
> #1,-0.17225,-0.44281,0.87992,58.058,-0.79906,0.58519,0.13807,111.71,-0.57605,-0.67932,-0.45463,130.51

Drag select of 8 residues  

> view matrix models
> #1,-0.17225,-0.44281,0.87992,62.337,-0.79906,0.58519,0.13807,144.72,-0.57605,-0.67932,-0.45463,139.12

> hide #1 models

> select #1

1860 atoms, 1892 bonds, 241 residues, 1 model selected  

> show #1 models

> ~select #1

Nothing selected  

> close #1

> open
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_B7_AF-A2F3X4-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_B6_AF-A2F716-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_B5_AF-A2DD57-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_B4_AF-A2F8W4-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_B3_AF-A2F3H9-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_B2_AF-A2F2T6-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_B1_AF-A2E7Z2-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_A7_AF-A2D8G5-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_A6_AF-A2E1I9-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_A5_AF-A2FCM7-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_A4_AF-A2DTN3-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_A3_AF-A2FT79-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_A2_AF-A2FJV7-F1-model_v4.pdb
> /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_A1_AF-A2F568-F1-model_v4.pdb

Chain information for TVAG_B7_AF-A2F3X4-F1-model_v4.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_B6_AF-A2F716-F1-model_v4.pdb #4  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_B5_AF-A2DD57-F1-model_v4.pdb #5  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_B4_AF-A2F8W4-F1-model_v4.pdb #6  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_B3_AF-A2F3H9-F1-model_v4.pdb #7  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_B2_AF-A2F2T6-F1-model_v4.pdb #8  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_B1_AF-A2E7Z2-F1-model_v4.pdb #9  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_A7_AF-A2D8G5-F1-model_v4.pdb #10  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_A6_AF-A2E1I9-F1-model_v4.pdb #11  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_A5_AF-A2FCM7-F1-model_v4.pdb #12  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_A4_AF-A2DTN3-F1-model_v4.pdb #13  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_A3_AF-A2FT79-F1-model_v4.pdb #14  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_A2_AF-A2FJV7-F1-model_v4.pdb #15  
---  
Chain | Description  
A | No description available  
  
Chain information for TVAG_A1_AF-A2F568-F1-model_v4.pdb #16  
---  
Chain | Description  
A | No description available  
  

> select #3

2 models selected  

> view matrix models #3,1,0,0,-19.703,0,1,0,-37.546,0,0,1,15.15

> view matrix models #3,1,0,0,-120.79,0,1,0,-123.92,0,0,1,4.862

> view matrix models #3,1,0,0,-129.27,0,1,0,9.7439,0,0,1,38.211

> view matrix models
> #3,0.18593,-0.20498,0.96094,-129.99,0.9814,0.086287,-0.17148,37.035,-0.047767,0.97495,0.21721,25.622

> view matrix models
> #3,0.32901,-0.58495,-0.74134,184.57,0.75788,0.6319,-0.16225,-14.074,0.56336,-0.50846,0.65122,89.054

> view matrix models
> #3,0.32901,-0.58495,-0.74134,196.79,0.75788,0.6319,-0.16225,-96.382,0.56336,-0.50846,0.65122,79.488

> view matrix models
> #3,0.32901,-0.58495,-0.74134,274.61,0.75788,0.6319,-0.16225,-55.743,0.56336,-0.50846,0.65122,12.571

> view matrix models
> #3,0.32901,-0.58495,-0.74134,282.4,0.75788,0.6319,-0.16225,-64.076,0.56336,-0.50846,0.65122,10.848

> view matrix models
> #3,0.13251,-0.26572,-0.9549,298.38,0.85713,0.51453,-0.02424,-82.672,0.49777,-0.81526,0.29594,127.89

> view matrix models
> #3,0.095841,-0.208,-0.97342,296.87,0.84525,0.53349,-0.030773,-81.474,0.52571,-0.81983,0.22694,135.98

> save /media/bunt16/DATA/Honza/Projects/Tv20S/Tv20S_model_2_map.cxs

> fitmap #1,#4,#5,#6,#7,#8,#9,#10,#11,#12,#13,#14,#15,#16 inMap #3

Missing or invalid "atomsOrMap" argument: only initial part "#1" of atom
specifier valid  

> fitmap #1, inMap #3

Missing or invalid "atomsOrMap" argument: only initial part "#1" of atom
specifier valid  

> fitmap #1 inMap #3

Fit molecule TVAG_B7_AF-A2F3X4-F1-model_v4.pdb (#1) to map J178_map_sharp.mrc
z flip (#3) using 1650 atoms  
average map value = 0.04344, steps = 80  
shifted from previous position = 0.864  
rotated from previous position = 4.77 degrees  
atoms outside contour = 1184, contour level = 0.068526  
  
Position of TVAG_B7_AF-A2F3X4-F1-model_v4.pdb (#1) relative to
J178_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.16296471 0.85759550 0.48782422 -37.29535570  
-0.18327486 0.51214138 -0.83911950 218.96980640  
-0.96946007 0.04734095 0.24063666 244.37450616  
Axis 0.44362408 0.72928961 -0.52089763  
Axis point 80.80807220 -0.00000000 229.52410928  
Rotation angle (degrees) 92.41450677  
Shift along axis 15.85318538  
  

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #10 models

> hide #9 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> hide #15 models

> hide #16 models

> hide #1 models

> show #1 models

> show #4 models

> show #5 models

> show #6 models

> show #7 models

> show #8 models

> show #9 models

> show #10 models

> show #11 models

> show #12 models

> show #13 models

> show #14 models

> show #15 models

> show #16 models

> open /media/bunt16/cryo3/processing/Tv20S/CS-
> tv20s/J183/J183_005_volume_map_sharp.mrc

Opened J183_005_volume_map_sharp.mrc as #17, grid size 440,440,440, pixel 0.7,
shown at level 0.0993, step 2, values float32  

> volume #17 step 1

> volume #17 level 0.1619

> volume #17 level 0.1477

> hide #1 models

> close #4-16

> close #1

> hide #!3 models

> ~select #3

Nothing selected  

> open /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_20S_alphafold.pdb

Chain information for TVAG_20S_alphafold.pdb #1  
---  
Chain | Description  
A | No description available  
  

> hide #!17 models

> show #!17 models

> close #1

OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 845, in resizeEvent  
self.session.ui.settings.last_window_size = wh  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/settings.py", line 187, in __setattr__  
ConfigFile.__setattr__(self, name, value)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/configfile.py", line 375, in __setattr__  
ConfigFile.save(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/configfile.py", line 325, in save  
self._config.write(f)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
OSError: [Errno 28] No space left on device  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  
OSError: [Errno 28] No space left on device  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 845, in resizeEvent  
self.session.ui.settings.last_window_size = wh  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/settings.py", line 187, in __setattr__  
ConfigFile.__setattr__(self, name, value)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/configfile.py", line 375, in __setattr__  
ConfigFile.save(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/configfile.py", line 325, in save  
self._config.write(f)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/safesave.py", line 85, in __exit__  
self._f.close()  
OSError: [Errno 28] No space left on device  
  
OSError: [Errno 28] No space left on device  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/safesave.py", line 85, in __exit__  
self._f.close()  
  
See log for complete Python traceback.  
  

> open /media/bunt16/DATA/Honza/Projects/Tv20S/TVAG_20S_alphafold.pdb

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 325, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 423, in add  
self._history.enqueue((item, typed))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.9/json/__init__.py", line 180, in
dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Chain information for TVAG_20S_alphafold.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
  

> fitmap #17 inMap #3

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 325, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 423, in add  
self._history.enqueue((item, typed))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.9/json/__init__.py", line 180, in
dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  
Fit map J183_005_volume_map_sharp.mrc in map J178_map_sharp.mrc z flip using
510391 points  
correlation = 0.3035, correlation about mean = 0.03807, overlap = 2432  
steps = 224, shift = 18.6, angle = 4.31 degrees  
  
Position of J183_005_volume_map_sharp.mrc (#17) relative to J178_map_sharp.mrc
z flip (#3) coordinates:  
Matrix rotation and translation  
0.10295868 0.87747665 0.46843808 -41.05725787  
-0.17931741 0.47959881 -0.85897046 240.16929886  
-0.97838887 0.00443936 0.20672570 253.33429119  
Axis 0.43412109 0.72746230 -0.53135438  
Axis point 71.77847967 0.00000000 245.74803790  
Rotation angle (degrees) 96.04781628  
Shift along axis 22.28000452  
  

> select #17

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 325, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 423, in add  
self._history.enqueue((item, typed))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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
> #17,0.99955,-0.019978,0.022326,-14.897,0.021469,0.99741,-0.06867,45.775,-0.020896,0.069118,0.99739,7.2655

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 325, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 423, in add  
self._history.enqueue((item, typed))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/history.py", line 109, in save  
json.dump(obj, f, ensure_ascii=False)  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.9/json/__init__.py", line 180, in
dump  
fp.write(chunk)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.56
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: MSI
Model: MS-7918
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-4790K CPU @ 4.00GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            31G        4.2G         18G        161M        8.6G         26G
	Swap:          8.9G        6.1G        2.8G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GV104 [GeForce GTX 1180] [10de:1e87] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:8665]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0