'ArrayGridData' object has no attribute 'dicom_data'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.4-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/avenka/Downloads/cryosparc_P1_J65_005_volume_map.mrc

Opened cryosparc_P1_J65_005_volume_map.mrc as #1, grid size 256,256,256, pixel
1.66, shown at level 0.0456, step 1, values float32  

> volume #1 level 0.195

> volume #1 level 0.1972

> volume #1 level 0.2565

> volume flip #1

Opened cryosparc_P1_J65_005_volume_map.mrc z flip as #2, grid size
256,256,256, pixel 1.66, shown at step 1, values float32  

> open /Users/avenka/Downloads/8dnx.pdb

Summary of feedback from opening /Users/avenka/Downloads/8dnx.pdb  
---  
warnings | CONECT record for nonexistent atom: 4208  
Cannot find LINK/SSBOND residue T09 (1 )  
Cannot find LINK/SSBOND residue T09 (1 )  
Cannot find LINK/SSBOND residue MLE (2 )  
Cannot find LINK/SSBOND residue LEU (3 )  
Cannot find LINK/SSBOND residue SZF (4 )  
2 messages similar to the above omitted  
  
8dnx.pdb title:  
Cryo-em structure of the human SEC61 complex inhibited by cotransin [more
info...]  
  
Chain information for 8dnx.pdb #3  
---  
Chain | Description | UniProt  
A | SEC61 α-1 | S61A1_HUMAN 1-476  
B | protein transport protein SEC61 subunit γ | SC61G_HUMAN 1-68  
C | protein transport protein SEC61 subunit β | SC61B_HUMAN 1-96  
  

> ui mousemode right select

> select add #3

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 3 models selected  

> ui mousemode right "move picked models"

Drag select of 7 residues  

> select add #3

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 3 models selected  

> view matrix models #3,1,0,0,-12.633,0,1,0,121.01,0,0,1,35.488

> view matrix models #3,1,0,0,83.038,0,1,0,103.58,0,0,1,109.31

> view matrix models #3,1,0,0,78.961,0,1,0,86.57,0,0,1,105.37

> select subtract #3

Nothing selected  

> ui tool show "Fit in Map"

> fitmap #3 inMap #2

Fit molecule 8dnx.pdb (#3) to map cryosparc_P1_J65_005_volume_map.mrc z flip
(#2) using 4204 atoms  
average map value = 0.1759, steps = 96  
shifted from previous position = 7.44  
rotated from previous position = 16.9 degrees  
atoms outside contour = 3046, contour level = 0.25653  
  
Position of 8dnx.pdb (#3) relative to cryosparc_P1_J65_005_volume_map.mrc z
flip (#2) coordinates:  
Matrix rotation and translation  
0.95878961 -0.00567822 -0.28406028 120.88555094  
0.02370171 0.99791378 0.06005268 83.14585506  
0.28312668 -0.06431060 0.95692394 85.09174448  
Axis -0.21390172 -0.97554728 0.05053274  
Axis point -260.14147838 0.00000000 385.99096719  
Rotation angle (degrees) 16.89998447  
Shift along axis -102.67042073  
  

> volume #2 color #b2b2b280

> set bgColor white

> select add #3

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 3 models selected  

> view matrix models #2,1,0,0,0.20067,0,1,0,6.1812,0,0,1,-1.2102

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.95879,-0.0056782,-0.28406,128.97,0.023702,0.99791,0.060053,173.94,0.28313,-0.064311,0.95692,57.532

> select subtract #3

Nothing selected  

> ui mousemode right "rotate selected models"

> select add #3

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 3 models selected  

> view matrix models
> #3,0.67365,0.66857,-0.31497,82.613,-0.66414,0.36069,-0.65484,430.23,-0.3242,0.65032,0.687,76.115

> view matrix models
> #3,0.16754,0.55521,-0.81466,222.09,-0.39445,-0.71957,-0.57152,525.01,-0.90352,0.41709,0.098446,251.1

> view matrix models
> #3,-0.78682,0.60917,0.099076,232.64,-0.073368,0.067071,-0.99505,430.92,-0.6128,-0.7902,-0.0080796,381.85

> view matrix models
> #3,-0.87558,-0.48286,0.014308,395.53,-0.35808,0.62886,-0.69015,359.66,0.32425,-0.60941,-0.72352,319.91

> view matrix models
> #3,-0.88007,0.47174,-0.054231,280.61,0.37425,0.75938,0.53224,103.58,0.29226,0.44811,-0.84486,201.46

> view matrix models
> #3,-0.52877,0.65982,0.53389,141.33,0.61988,-0.12946,0.77394,158.14,0.57978,0.74019,-0.34056,66.889

> view matrix models
> #3,-0.31367,0.4974,0.80883,101.96,0.53555,-0.61073,0.58326,253.83,0.78409,0.61612,-0.074817,25.051

> view matrix models
> #3,-0.40929,0.66342,0.62638,114.39,0.60713,-0.31444,0.72974,188.93,0.68109,0.67897,-0.27408,53.767

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.40929,0.66342,0.62638,114.06,0.60713,-0.31444,0.72974,203.95,0.68109,0.67897,-0.27408,77.8

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.091609,0.59676,0.79717,37.158,0.74097,-0.57567,0.34579,265.32,0.66526,0.559,-0.49492,121.31

> view matrix models
> #3,0.25691,0.61231,0.74771,19.339,0.57044,-0.7206,0.39412,300.7,0.78013,0.32527,-0.53442,141.18

> view matrix models
> #3,-0.17232,0.52831,0.83138,76.507,0.42934,-0.71934,0.5461,301.15,0.88655,0.45105,-0.10286,60.344

> view matrix models
> #3,-0.36756,0.35939,0.85775,120.8,0.86153,-0.21577,0.45959,189.62,0.35024,0.9079,-0.23031,86.286

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.36756,0.35939,0.85775,162.48,0.86153,-0.21577,0.45959,206.38,0.35024,0.9079,-0.23031,141.87

> view matrix models
> #3,-0.36756,0.35939,0.85775,155.54,0.86153,-0.21577,0.45959,181.72,0.35024,0.9079,-0.23031,118.63

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.18279,0.63813,0.74792,108.2,0.85339,-0.27475,0.44299,192.37,0.48818,0.71924,-0.49435,156

> hide #!2 models

> show #!1 models

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.18279,0.63813,0.74792,155.21,0.85339,-0.27475,0.44299,19.023,0.48818,0.71924,-0.49435,101.21

> view matrix models
> #3,-0.18279,0.63813,0.74792,154.61,0.85339,-0.27475,0.44299,19.061,0.48818,0.71924,-0.49435,102.25

> select clear

> select add #3

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 3 models selected  

> view matrix models
> #3,-0.18279,0.63813,0.74792,132.38,0.85339,-0.27475,0.44299,34.085,0.48818,0.71924,-0.49435,53.477

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.95428,-0.29,-0.072428,449.63,-0.28692,0.95665,-0.050081,81.65,0.083811,-0.027011,-0.99612,261.81

> view matrix models
> #3,-0.077798,-0.95902,0.27245,381.16,-0.74123,-0.12712,-0.65911,352.78,0.66673,-0.25323,-0.70096,180.24

> view matrix models
> #3,-0.13614,0.76594,0.62833,123.78,-0.94941,-0.28203,0.13809,306.49,0.28298,-0.57775,0.76559,100.31

> view matrix models
> #3,0.33819,0.56621,0.75169,73.141,-0.77601,-0.28409,0.56312,234.21,0.53239,-0.77376,0.3433,142.63

> view matrix models
> #3,0.75363,0.64477,-0.1277,111.86,0.59824,-0.59236,0.53965,97.205,0.27231,-0.48309,-0.83215,276.95

> view matrix models
> #3,0.99682,0.030914,0.073476,135.91,0.034303,-0.99838,-0.04532,292.13,0.071956,0.047696,-0.99627,253.7

> view matrix models
> #3,0.99134,0.019555,-0.12985,161.95,-0.12273,-0.21385,-0.96913,319.53,-0.046721,0.97667,-0.2096,56.672

> view matrix models
> #3,0.75829,0.14528,0.63552,86.331,0.18115,0.88951,-0.41948,72.498,-0.62624,0.43321,0.64819,102.11

> view matrix models
> #3,0.50405,-0.79383,0.34025,275.76,0.54143,0.59737,0.59161,-55.446,-0.67289,-0.11398,0.73091,169.32

> view matrix models
> #3,-0.37273,-0.79668,-0.4758,486.52,0.79576,-0.53817,0.27774,95.105,-0.47733,-0.2751,0.83455,152.44

> view matrix models
> #3,-0.8055,-0.11668,-0.581,467.43,0.46899,-0.72482,-0.50465,253.8,-0.36224,-0.67898,0.63857,212.67

> view matrix models
> #3,-0.92094,0.24259,-0.30499,403.64,0.019257,-0.75333,-0.65736,334.2,-0.38923,-0.61126,0.6891,201.5

> view matrix models
> #3,-0.97647,-0.0085897,0.21547,382.33,-0.0074381,-0.99727,-0.073463,300.74,0.21552,-0.073337,0.97374,19.419

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.97647,-0.0085897,0.21547,311.58,-0.0074381,-0.99727,-0.073463,320.93,0.21552,-0.073337,0.97374,59.384

> view matrix models
> #3,-0.97647,-0.0085897,0.21547,331.18,-0.0074381,-0.99727,-0.073463,344.41,0.21552,-0.073337,0.97374,48.734

> view matrix models
> #3,-0.97647,-0.0085897,0.21547,318.01,-0.0074381,-0.99727,-0.073463,352.08,0.21552,-0.073337,0.97374,55.863

> color #1 #b2b2b281 models

> color #1 #b2b2b282 models

> view matrix models
> #3,-0.97647,-0.0085897,0.21547,323.01,-0.0074381,-0.99727,-0.073463,353.94,0.21552,-0.073337,0.97374,55.512

> view matrix models
> #3,-0.97647,-0.0085897,0.21547,323.11,-0.0074381,-0.99727,-0.073463,354.06,0.21552,-0.073337,0.97374,56.559

> fitmap #3 inMap #2

Fit molecule 8dnx.pdb (#3) to map cryosparc_P1_J65_005_volume_map.mrc z flip
(#2) using 4204 atoms  
average map value = 0.1751, steps = 72  
shifted from previous position = 3.82  
rotated from previous position = 12.7 degrees  
atoms outside contour = 3146, contour level = 0.25653  
  
Position of 8dnx.pdb (#3) relative to cryosparc_P1_J65_005_volume_map.mrc z
flip (#2) coordinates:  
Matrix rotation and translation  
-0.97409200 0.18591848 0.12875985 309.95728682  
-0.19933507 -0.97476079 -0.10053328 375.47606944  
0.10681906 -0.12359502 0.98656676 75.67159164  
Axis -0.05965790 0.05675816 -0.99660396  
Axis point 171.29383286 174.93336134 0.00000000  
Rotation angle (degrees) 168.85555142  
Shift along axis -72.59468007  
  

> fitmap #3 inMap #1

Fit molecule 8dnx.pdb (#3) to map cryosparc_P1_J65_005_volume_map.mrc (#1)
using 4204 atoms  
average map value = 0.2862, steps = 80  
shifted from previous position = 8.69  
rotated from previous position = 13.4 degrees  
atoms outside contour = 1749, contour level = 0.25653  
  
Position of 8dnx.pdb (#3) relative to cryosparc_P1_J65_005_volume_map.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.96970606 -0.01423505 0.24385964 315.98860673  
-0.01003106 -0.99513798 -0.09797855 362.12037501  
0.24406872 -0.09745656 0.96484853 61.27441513  
Axis 0.12306852 -0.04929382 0.99117317  
Axis point 153.99439537 182.74750136 0.00000000  
Rotation angle (degrees) 179.87849191  
Shift along axis 81.77150845  
  

> select subtract #3

Nothing selected  

> select clear

Alignment identifier is 3/B  
Alignment identifier is 3/C  
Alignment identifier is 3/A  

> select
> /A:6-14,27-46,62-70,81-97,108-134,139-172,177-197,211-223,225-236,241-260,288-312,315-321,340-345,350-384,386-398,408-439,442-468

2526 atoms, 2562 bonds, 327 residues, 1 model selected  

> select clear

> select
> /A:6-14,27-46,62-70,81-97,108-134,139-172,177-197,211-223,225-236,241-260,288-312,315-321,340-345,350-384,386-398,408-439,442-468

2526 atoms, 2562 bonds, 327 residues, 1 model selected  

> select clear

> select
> /A:6-14,27-46,62-70,81-97,108-134,139-172,177-197,211-223,225-236,241-260,288-312,315-321,340-345,350-384,386-398,408-439,442-468

2526 atoms, 2562 bonds, 327 residues, 1 model selected  

> select clear

> select:300.A

Unknown command: select:300.A  

> select :300.A

Expected an objects specifier or a keyword  

> select 300.A

Expected an objects specifier or a keyword  

> select /A:300

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> volume #1 level 0.2433

> volume #1 level 0.2631

> volume #1 level 0.3491

> volume #1 level 0.4417

> volume #1 level 0.2852

> view matrix models
> #3,-0.96971,-0.014235,0.24386,316.05,-0.010031,-0.99514,-0.097979,362.05,0.24407,-0.097457,0.96485,61.325

> volume #1 level 0.2587

> view matrix models
> #3,-0.96971,-0.014235,0.24386,316.25,-0.010031,-0.99514,-0.097979,362.12,0.24407,-0.097457,0.96485,61.167

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 3 time(s)]

> open /Users/avenka/Downloads/cryosparc_P1_J65_005_volume_map_sharp.mrc

Opened cryosparc_P1_J65_005_volume_map_sharp.mrc as #4, grid size 256,256,256,
pixel 1.66, shown at level 0.0678, step 1, values float32  

> view matrix models
> #3,-0.96971,-0.014235,0.24386,335.7,-0.010031,-0.99514,-0.097979,354.75,0.24407,-0.097457,0.96485,61.527

> view matrix models
> #3,-0.96971,-0.014235,0.24386,334.35,-0.010031,-0.99514,-0.097979,355.24,0.24407,-0.097457,0.96485,62.059

> view matrix models
> #3,-0.96971,-0.014235,0.24386,335.41,-0.010031,-0.99514,-0.097979,353.73,0.24407,-0.097457,0.96485,59.663

> volume #4 level 0.3034

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> hide #!4 models

> show #!3 models

> fitmap #3 inMap #4

Fit molecule 8dnx.pdb (#3) to map cryosparc_P1_J65_005_volume_map_sharp.mrc
(#4) using 4204 atoms  
average map value = 0.3209, steps = 112  
shifted from previous position = 21.2  
rotated from previous position = 0.114 degrees  
atoms outside contour = 1945, contour level = 0.30338  
  
Position of 8dnx.pdb (#3) relative to
cryosparc_P1_J65_005_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.96970057 -0.01245535 0.24397884 315.71735270  
-0.01154192 -0.99524840 -0.09668206 362.16741403  
0.24402375 -0.09656863 0.96494918 61.19225895  
Axis 0.12308391 -0.04874112 0.99119860  
Axis point 154.01679272 182.62375887 0.00000000  
Rotation angle (degrees) 179.97359986  
Shift along axis 81.86096020  
  

> show #!4 models

> hide #!1 models

> color #4 #b2ffffd5 models

> color #4 #b2ffff90 models

> color #4 #b2ffff8f models

> view matrix models
> #3,-0.9697,-0.012455,0.24398,316.45,-0.011542,-0.99525,-0.096682,361.55,0.24402,-0.096569,0.96495,61.017

Average map value = 0.3055 for 4204 atoms, 2093 outside contour  

> fitmap #3 inMap #4

Fit molecule 8dnx.pdb (#3) to map cryosparc_P1_J65_005_volume_map_sharp.mrc
(#4) using 4204 atoms  
average map value = 0.3209, steps = 48  
shifted from previous position = 0.973  
rotated from previous position = 0.0424 degrees  
atoms outside contour = 1945, contour level = 0.30338  
  
Position of 8dnx.pdb (#3) relative to
cryosparc_P1_J65_005_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.96976535 -0.01250442 0.24371872 315.76003056  
-0.01130156 -0.99531374 -0.09603564 362.07011896  
0.24377746 -0.09588644 0.96507945 61.10414941  
Axis 0.12295212 -0.04840455 0.99123144  
Axis point 154.03432925 182.57378118 0.00000000  
Rotation angle (degrees) 179.96523586  
Shift along axis 81.86587935  
  

> volume #4 level 0.2863

> volume #4 level 0.2658

> color #4 #b2ffffb0 models

> color #4 #b2ffffff models

> color #4 #b2ffff93 models

> color #4 #b2ffffff models

> color #4 #b2ffffc4 models

> view matrix models
> #3,-0.96977,-0.012504,0.24372,316.56,-0.011302,-0.99531,-0.096036,361.65,0.24378,-0.095886,0.96508,61.334

> fitmap #3 inMap #4

Fit molecule 8dnx.pdb (#3) to map cryosparc_P1_J65_005_volume_map_sharp.mrc
(#4) using 4204 atoms  
average map value = 0.3209, steps = 64  
shifted from previous position = 0.915  
rotated from previous position = 0.0474 degrees  
atoms outside contour = 1630, contour level = 0.26583  
  
Position of 8dnx.pdb (#3) relative to
cryosparc_P1_J65_005_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.96966881 -0.01253465 0.24410099 315.71751992  
-0.01148664 -0.99524383 -0.09673567 362.16051748  
0.24415255 -0.09660546 0.96491291 61.19629598  
Axis 0.12314835 -0.04876445 0.99118944  
Axis point 154.00833120 182.62637736 0.00000000  
Rotation angle (degrees) 179.96970978  
Shift along axis 81.87665349  
  

> view matrix models
> #3,-0.96967,-0.012535,0.2441,315.26,-0.011487,-0.99524,-0.096736,362.68,0.24415,-0.096605,0.96491,62.006

> fitmap #3 inMap #4

Fit molecule 8dnx.pdb (#3) to map cryosparc_P1_J65_005_volume_map_sharp.mrc
(#4) using 4204 atoms  
average map value = 0.3209, steps = 48  
shifted from previous position = 1.06  
rotated from previous position = 0.0305 degrees  
atoms outside contour = 1629, contour level = 0.26583  
  
Position of 8dnx.pdb (#3) relative to
cryosparc_P1_J65_005_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.96955956 -0.01259322 0.24453154 315.66097557  
-0.01154233 -0.99521571 -0.09701795 362.19423477  
0.24458340 -0.09688715 0.96477555 61.20505802  
Axis 0.12336992 -0.04890841 0.99115480  
Axis point 153.97239722 182.64805303 0.00000000  
Rotation angle (degrees) 179.96962578  
Shift along axis 81.89241385  
  

> ui mousemode right zoom

> ui tool show "Selection Inspector"

> open /Users/avenka/Downloads/cryosparc_P1_J64_005_volume_map_sharp.mrc

Opened cryosparc_P1_J64_005_volume_map_sharp.mrc as #5, grid size 256,256,256,
pixel 1.66, shown at level 0.0662, step 1, values float32  

> hide #!4 models

> volume #5 level 0.2629

> volume #5 level 0.3202

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.96956,-0.012593,0.24453,308.25,-0.011542,-0.99522,-0.097018,335.53,0.24458,-0.096887,0.96478,66.988

> fitmap #3 inMap #5

Fit molecule 8dnx.pdb (#3) to map cryosparc_P1_J64_005_volume_map_sharp.mrc
(#5) using 4204 atoms  
average map value = 0.1846, steps = 96  
shifted from previous position = 10.2  
rotated from previous position = 24.7 degrees  
atoms outside contour = 3396, contour level = 0.32023  
  
Position of 8dnx.pdb (#3) relative to
cryosparc_P1_J64_005_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.96411571 -0.23862288 -0.11636164 386.99850349  
0.24776675 -0.96617484 -0.07153898 301.70804014  
-0.09535485 -0.09780240 0.99062715 105.11155001  
Axis -0.05386805 -0.04308635 0.99761806  
Axis point 177.43387326 177.36470693 0.00000000  
Rotation angle (degrees) 165.89052063  
Shift along axis 71.01482901  
  

> view matrix models
> #3,-0.96412,-0.23862,-0.11636,362.31,0.24777,-0.96617,-0.071539,259.6,-0.095355,-0.097802,0.99063,127.76

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.79133,0.50808,0.34008,189.52,-0.51466,-0.2533,-0.81913,354.74,-0.33004,-0.82322,0.46193,314.37

> view matrix models
> #3,-0.75777,0.47582,0.44652,176.81,-0.56362,-0.13245,-0.81535,345.05,-0.32882,-0.86951,0.36855,331.16

> view matrix models
> #3,-0.74848,0.4653,0.47252,173.91,-0.5755,-0.10172,-0.81145,342.17,-0.3295,-0.87929,0.34392,335.4

> view matrix models
> #3,-0.62362,0.27277,0.73259,151.99,-0.69013,0.24808,-0.67984,296.44,-0.36718,-0.92954,0.033532,383.26

> view matrix models
> #3,-0.46682,-0.051435,0.88286,155.81,-0.75148,0.54937,-0.36534,228.56,-0.46622,-0.834,-0.29511,422.41

> view matrix models
> #3,-0.45267,-0.084798,0.88764,157.72,-0.7529,0.56969,-0.32953,221.91,-0.47773,-0.81748,-0.32172,424.9

> view matrix models
> #3,0.07302,0.87651,0.4758,12.908,0.71175,-0.37999,0.59078,45.348,0.69863,0.29552,-0.65161,165.77

> view matrix models
> #3,0.85287,-0.10243,-0.51198,153.57,-0.086598,0.93924,-0.33217,87.287,0.51489,0.32763,0.79218,16.206

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.85287,-0.10243,-0.51198,164.97,-0.086598,0.93924,-0.33217,118.82,0.51489,0.32763,0.79218,-13.524

> view matrix models
> #3,0.85287,-0.10243,-0.51198,172.52,-0.086598,0.93924,-0.33217,121.05,0.51489,0.32763,0.79218,1.1476

> view matrix models
> #3,0.85287,-0.10243,-0.51198,173.9,-0.086598,0.93924,-0.33217,136.11,0.51489,0.32763,0.79218,-0.59395

> color #5 #b2b2ffaf models

> color #5 #b2b2ffa9 models

> color #5 #b2b2ffa8 models

> fitmap #3 inMap #5

Fit molecule 8dnx.pdb (#3) to map cryosparc_P1_J64_005_volume_map_sharp.mrc
(#5) using 4204 atoms  
average map value = 0.2886, steps = 92  
shifted from previous position = 8.43  
rotated from previous position = 23.6 degrees  
atoms outside contour = 2337, contour level = 0.32023  
  
Position of 8dnx.pdb (#3) relative to
cryosparc_P1_J64_005_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.78298018 0.18610800 -0.59355359 157.60514812  
-0.18855331 0.98031026 0.05864690 96.28012355  
0.59278132 0.06599713 0.80265478 14.57501743  
Axis 0.00590802 -0.95355928 -0.30114748  
Axis point 100.31367918 0.00000000 229.79884857  
Rotation angle (degrees) 38.46644432  
Shift along axis -95.26690097  
  

> volume #5 level 0.3448

> view matrix models
> #3,0.78298,0.18611,-0.59355,156.73,-0.18855,0.98031,0.058647,95.319,0.59278,0.065997,0.80265,15.336

> fitmap #3 inMap #5

Fit molecule 8dnx.pdb (#3) to map cryosparc_P1_J64_005_volume_map_sharp.mrc
(#5) using 4204 atoms  
average map value = 0.2886, steps = 44  
shifted from previous position = 1.5  
rotated from previous position = 0.0177 degrees  
atoms outside contour = 2537, contour level = 0.34481  
  
Position of 8dnx.pdb (#3) relative to
cryosparc_P1_J64_005_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.78303221 0.18580770 -0.59357903 157.64222907  
-0.18828992 0.98036978 0.05849798 96.24763657  
0.59279631 0.06595914 0.80264683 14.58018124  
Axis 0.00599780 -0.95369175 -0.30072592  
Axis point 100.25157327 0.00000000 229.89699918  
Rotation angle (degrees) 38.46167256  
Shift along axis -95.22970841  
  

> volume #5 level 0.2711

> hide #!5 models

> show #!1 models

> hide #!3 models

> view matrix models
> #3,0.78303,0.18581,-0.59358,157.74,-0.18829,0.98037,0.058498,97.315,0.5928,0.065959,0.80265,14.568

> ui mousemode right zoom

> volume #2 level 0.2588

> volume #5 level 0.3038

> hide #!5 models

> hide #!2 models

> volume #2 level 0.2565

> hide #!2 models

> volume #1 level 0.227

> volume #1 level 0.3677

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 3 time(s)]

> show #!5 models

> hide #!1 models

> volume #5 level 0.2916

> show #!3 models

> volume #5 level 0.312

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 23 time(s)]

> close session

> open /Users/avenka/Downloads/cryosparc_P3_J40_class_00_final_volume.mrc

Opened cryosparc_P3_J40_class_00_final_volume.mrc as #1, grid size
200,200,200, pixel 3.3, shown at level 0.277, step 1, values float32  

> open /Users/avenka/Downloads/emd_2644.map

Opened emd_2644.map as #2, grid size 420,420,420, pixel 1.34, shown at level
0.0838, step 2, values float32  

> lighting soft

> volume #!1 showOutlineBox true

> set bgColor black

> select add #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.90967,0.057336,0.41135,-112.63,0.039036,-0.99784,0.052759,609.27,0.41349,-0.031936,-0.90995,450.06

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.90967,0.057336,0.41135,-111.76,0.039036,-0.99784,0.052759,596.8,0.41349,-0.031936,-0.90995,490.22

> view matrix models
> #2,0.90967,0.057336,0.41135,-114.46,0.039036,-0.99784,0.052759,575.1,0.41349,-0.031936,-0.90995,485.97

> volume #1 level 0.2957

> view matrix models
> #2,0.90967,0.057336,0.41135,-103.5,0.039036,-0.99784,0.052759,542.66,0.41349,-0.031936,-0.90995,478.84

> view matrix models
> #2,0.90967,0.057336,0.41135,-119.79,0.039036,-0.99784,0.052759,578.75,0.41349,-0.031936,-0.90995,486.99

> select clear

> ui mousemode right zoom

> ui mousemode right translate

> vop resample #2 onGrid #1

Opened emd_2644.map resampled as #3, grid size 200,200,200, pixel 3.3, shown
at step 1, values float32  

> save /Users/avenka/Desktop/emd_2644_resampled.mrc models #3

> ui mousemode right "map eraser"

> volume erase #1 center -200.71,371.08,340.49 radius 571.58

Opened cryosparc_P3_J40_class_00_final_volume.mrc copy as #5, grid size
200,200,200, pixel 3.3, shown at step 1, values float32  

> vop max #1,2 onGrid #1

Opened volume maximum as #6, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> volume #6 level 0.3583

> close #6

> vop max #5,2 onGrid #1

Opened volume maximum as #6, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> close #6

> vop max #5,3 onGrid #1

Opened volume maximum as #6, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> close #6

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> vop max #5,3 scaleFactors 0.5,1 onGrid #1

Opened volume maximum as #6, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> volume #6 level 0.1509

> vop max #5,3 scaleFactors 0.8,1 onGrid #1

Opened volume maximum as #7, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> hide #!6 models

> vop max #5,3 scaleFactors 0.3,1 onGrid #1

Opened volume maximum as #8, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> hide #!7 models

> hide #!8 models

> vop max #5,3 scaleFactors 0.3,1 onGrid #1

Opened volume maximum as #9, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> volume #9 level 0.06936

> volume #9 level 0.09141

> volume #9 level 0.07894

> volume #8 level 0.09429

> vop max #5,3 scaleFactors 0.4,1 onGrid #1

Opened volume maximum as #10, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> volume #10 level 0.195

> vop max #5,3 scaleFactors 0.6,1 onGrid #1

Opened volume maximum as #11, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> volume #11 level 0.1758

> vop max #5,3 scaleFactors 0.5,1 onGrid #1

Opened volume maximum as #12, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> volume #12 level 0.1528

> save /Users/avenka/Downloads/ribosec_vopmax.mrc models #12

> vop max #1,3 scaleFactors 0.5,1 onGrid #1

Opened volume maximum as #13, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> hide #!12 models

> volume #13 level 0.1661

> vop max #1,3 scaleFactors 0.7,1 onGrid #1

Opened volume maximum as #14, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> hide #!13 models

> volume #14 level 0.2533

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> vop max #1,3 scaleFactors 0.3,1 onGrid #1

Opened volume maximum as #15, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> hide #!14 models

> volume #15 level 0.1096

> vop max #1,3 scaleFactors 0.4,1 onGrid #1

Opened volume maximum as #16, grid size 200,200,200, pixel 3.3, shown at step
1, values float32  

> hide #!15 models

[Repeated 1 time(s)]

> volume #16 level 0.1624

> volume #15 level 0.1394

> save /Users/avenka/Downloads/ribosec_vopmax1.mrc models #15

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 11 time(s)]

> volume #15 level 0.1259

> show #4 models

> hide #4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!15 models

> open /Users/avenka/Downloads/emd_0075.map

Opened emd_0075.map as #17, grid size 120,120,120, pixel 5.24, shown at level
0.437, step 1, values float32  

> select add #17

2 models selected  

> volume #17 level 0.2812

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.70552,0.43682,-0.55806,124.97,-0.63595,0.042715,-0.77055,732.8,-0.31275,0.89853,0.30793,26.869

> view matrix models
> #17,0.074764,-0.16944,-0.9827,642.33,-0.99702,-0.031552,-0.070413,659.8,-0.019075,0.98504,-0.17129,50.927

> view matrix models
> #17,-0.22996,-0.081163,-0.96981,707.56,-0.86934,0.46507,0.16722,392.61,0.43745,0.88155,-0.17751,-59.729

> view matrix models
> #17,-0.11098,-0.08959,-0.98978,678.45,-0.67204,0.74047,0.0083314,291.81,0.73215,0.66609,-0.14239,-96.499

> view matrix models
> #17,-0.12734,-0.069798,-0.9894,677.35,-0.58221,0.81284,0.017591,237.91,0.803,0.57828,-0.14415,-91.018

> view matrix models
> #17,-0.1601,0.018473,-0.98693,659.42,0.054936,0.99844,0.009776,-19.887,0.98557,-0.052653,-0.16087,53.193

> view matrix models
> #17,0.032556,-0.2626,-0.96435,679.31,-0.94832,0.29661,-0.11278,554.59,0.31565,0.91818,-0.23937,-13.902

> view matrix models
> #17,-0.28296,-0.016417,-0.95899,700.89,-0.25563,0.96498,0.058905,74.319,0.92444,0.26182,-0.27724,9.3812

> view matrix models
> #17,0.025446,0.06284,-0.9977,589.93,-0.93662,-0.34734,-0.045766,731.87,-0.34942,0.93563,0.050019,104.56

> ui mousemode right zoom

> select clear

[Repeated 1 time(s)]

> ui mousemode right translate

> ui mousemode right "translate selected models"

> select add #17

2 models selected  

> view matrix models
> #17,0.025446,0.06284,-0.9977,628.63,-0.93662,-0.34734,-0.045766,729.16,-0.34942,0.93563,0.050019,123.75

> view matrix models
> #17,0.025446,0.06284,-0.9977,624.84,-0.93662,-0.34734,-0.045766,728.96,-0.34942,0.93563,0.050019,108.69

> view matrix models
> #17,0.025446,0.06284,-0.9977,623.17,-0.93662,-0.34734,-0.045766,760.11,-0.34942,0.93563,0.050019,105.84

> view matrix models
> #17,0.025446,0.06284,-0.9977,626,-0.93662,-0.34734,-0.045766,750.62,-0.34942,0.93563,0.050019,106.39

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.022735,0.094344,-0.99528,616.29,-0.97301,-0.22659,-0.043705,723.82,-0.22964,0.96941,0.086646,46.81

> view matrix models
> #17,0.018378,0.13595,-0.99054,603.25,-0.99549,-0.089681,-0.030779,684.3,-0.093017,0.98665,0.13369,-16.089

> view matrix models
> #17,0.02002,0.093581,-0.99541,617.43,-0.98866,-0.14638,-0.033645,700.7,-0.14886,0.98479,0.089589,15.485

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #17,-0.014489,0.085421,-0.99624,631.18,-0.98767,-0.15653,0.00094316,693.15,-0.15586,0.98397,0.086636,18.851

> view matrix models
> #17,0.016514,0.08656,-0.99611,620.94,-0.99568,0.092508,-0.0084684,620.72,0.091416,0.99194,0.087714,-62.422

> view matrix models
> #17,-0.0083567,0.048258,-0.9988,641.61,-0.98249,-0.18633,-0.00078262,701.33,-0.18615,0.9813,0.04897,40.635

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.0046354,-0.0012978,-0.99999,653.33,-0.98252,-0.18613,-0.0043128,702.34,-0.18612,0.98253,-0.0021379,55.629

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.0046354,-0.0012978,-0.99999,654.5,-0.98252,-0.18613,-0.0043128,698.79,-0.18612,0.98253,-0.0021379,55.671

> vop resample #17 onGrid #1

Opened emd_0075.map resampled as #18, grid size 200,200,200, pixel 3.3, shown
at step 1, values float32  

> select add #18

4 models selected  

> select subtract #17

2 models selected  

> hide #!1 models

> save /Users/avenka/Downloads/emdb_0075_resampled.mrc models #18

> open /Users/avenka/Downloads/cryosparc_P3_J54_003_volume_map.mrc

Opened cryosparc_P3_J54_003_volume_map.mrc as #19, grid size 200,200,200,
pixel 3.3, shown at level 0.318, step 1, values float32  

> volume #19 level 0.1768

> volume #19 level 0.1942

> volume #19 level 0.2399

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 7 time(s)]

> hide #!19 models

> select subtract #18

Nothing selected  

> open /Users/avenka/Downloads/cryosparc_P1_J66_008_volume_map.mrc

Opened cryosparc_P1_J66_008_volume_map.mrc as #20, grid size 512,512,512,
pixel 0.828, shown at level 0.0157, step 2, values float32  

> ui mousemode right zoom

> select add #20

2 models selected  

> select subtract #20

Nothing selected  

> show #!20 target m

[Repeated 3 time(s)]

> close session

> open /Users/avenka/Downloads/cryosparc_P1_J66_008_volume_map.mrc

Opened cryosparc_P1_J66_008_volume_map.mrc as #1, grid size 512,512,512, pixel
0.828, shown at level 0.0157, step 2, values float32  

> volume #1 level 0.0962

> open /Users/avenka/Downloads/8dnx.pdb

Summary of feedback from opening /Users/avenka/Downloads/8dnx.pdb  
---  
warnings | CONECT record for nonexistent atom: 4208  
Cannot find LINK/SSBOND residue T09 (1 )  
Cannot find LINK/SSBOND residue T09 (1 )  
Cannot find LINK/SSBOND residue MLE (2 )  
Cannot find LINK/SSBOND residue LEU (3 )  
Cannot find LINK/SSBOND residue SZF (4 )  
2 messages similar to the above omitted  
  
8dnx.pdb title:  
Cryo-em structure of the human SEC61 complex inhibited by cotransin [more
info...]  
  
Chain information for 8dnx.pdb #2  
---  
Chain | Description | UniProt  
A | SEC61 α-1 | S61A1_HUMAN 1-476  
B | protein transport protein SEC61 subunit γ | SC61G_HUMAN 1-68  
C | protein transport protein SEC61 subunit β | SC61B_HUMAN 1-96  
  

> ui mousemode right "translate selected models"

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 3 models selected  

> view matrix models #2,1,0,0,42.729,0,1,0,17.882,0,0,1,97.972

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.57232,0.75171,-0.32769,39.805,-0.76488,0.34527,-0.54383,266.43,-0.29566,0.56188,0.77257,90.592

> view matrix models
> #2,-0.45327,0.54342,-0.70658,245.3,-0.38961,-0.83373,-0.39127,352.06,-0.80172,0.09794,0.58962,238.26

> view matrix models
> #2,-0.15993,-0.8954,-0.41556,359.02,0.96553,-0.22947,0.12285,36.362,-0.20536,-0.38159,0.90123,185.8

> view matrix models
> #2,0.42514,-0.87022,0.24893,201.3,0.84562,0.2838,-0.45208,53.077,0.32276,0.4027,0.85654,20.492

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.42514,-0.87022,0.24893,233.45,0.84562,0.2838,-0.45208,6.0241,0.32276,0.4027,0.85654,-2.3525

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.84859,-0.079033,0.52311,265.39,-0.23257,-0.83239,-0.50303,297.42,0.47519,-0.54852,0.68798,120.61

> view matrix models
> #2,-0.02093,0.89139,0.45276,39.853,-0.89667,0.18356,-0.40284,240.99,-0.4422,-0.41441,0.79544,210.58

> view matrix models
> #2,0.61755,0.57511,0.53655,-12.515,-0.57161,0.79675,-0.19612,94.877,-0.54028,-0.18558,0.82076,190.81

> view matrix models
> #2,0.74782,0.19894,-0.6334,156.44,-0.66317,0.26872,-0.69856,234.15,0.03124,0.94245,0.33288,27.354

> view matrix models
> #2,-0.042198,-0.42545,-0.904,372.28,-0.9944,0.10564,-0.0033,216.97,0.096901,0.89879,-0.42753,113.66

> view matrix models
> #2,-0.28382,0.052115,-0.95746,348.33,-0.69813,0.67326,0.24359,75.799,0.65731,0.73757,-0.1547,29.241

> view matrix models
> #2,0.55693,-0.66507,-0.49751,277.27,-0.76863,-0.18574,-0.61214,296.61,0.3147,0.72332,-0.61463,129.85

> view matrix models
> #2,0.089111,-0.58521,-0.80597,364.29,-0.92622,0.24889,-0.28313,222.35,0.36629,0.77174,-0.51986,105.72

> view matrix models
> #2,-0.46156,0.42563,-0.77834,302.21,-0.34941,0.71924,0.60051,-17.626,0.8154,0.54912,-0.18325,36.313

> view matrix models
> #2,-0.43342,0.5692,-0.69868,270.6,-0.21185,0.68921,0.6929,-42.564,0.87594,0.44834,-0.17813,40.843

> view matrix models
> #2,-0.45437,0.69532,-0.55684,240.37,-0.091721,0.58525,0.80565,-58.045,0.88608,0.41714,-0.20215,46.373

> view matrix models
> #2,-0.47606,0.3666,-0.79936,314.21,-0.40593,0.71473,0.56954,-6.0193,0.78012,0.59562,-0.19145,35.87

> view matrix models
> #2,-0.40318,0.74383,-0.53307,224.61,-0.0014264,0.582,0.81319,-70.314,0.91512,0.32862,-0.23359,57.722

> view matrix models
> #2,-0.2256,0.84697,-0.48141,181.98,0.042154,0.50217,0.86374,-71.612,0.97331,0.17456,-0.14899,60.126

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.2256,0.84697,-0.48141,221.68,0.042154,0.50217,0.86374,14.444,0.97331,0.17456,-0.14899,61.399

> view matrix models
> #2,-0.2256,0.84697,-0.48141,181.91,0.042154,0.50217,0.86374,41.478,0.97331,0.17456,-0.14899,95.16

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 8dnx.pdb (#2) to map cryosparc_P1_J66_008_volume_map.mrc (#1)
using 4204 atoms  
average map value = 0.05955, steps = 124  
shifted from previous position = 4.68  
rotated from previous position = 12.6 degrees  
atoms outside contour = 3371, contour level = 0.096203  
  
Position of 8dnx.pdb (#2) relative to cryosparc_P1_J66_008_volume_map.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.12486889 0.84893081 -0.51354089 175.21265821  
0.22815281 0.52828986 0.81783624 22.66357092  
0.96558482 -0.01504349 -0.25965292 135.84870817  
Axis -0.46080436 -0.81835054 -0.34345560  
Axis point 48.08164980 0.00000000 104.91025365  
Rotation angle (degrees) 115.34805459  
Shift along axis -145.94350067  
  

> volume #1 color #b2b2b264

> volume #1 color #b2b2b263

> view matrix models
> #2,-0.12487,0.84893,-0.51354,175.41,0.22815,0.52829,0.81784,24.56,0.96558,-0.015043,-0.25965,131.87

> ui mousemode right "translate selected models"

> ui mousemode right select

> select clear

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 3 models selected  

> view matrix models
> #2,-0.12487,0.84893,-0.51354,279.51,0.22815,0.52829,0.81784,31.5,0.96558,-0.015043,-0.25965,98.581

> set bgColor white

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.11232,0.93019,-0.34946,248.1,0.28552,0.36707,0.88529,36.95,0.95177,-0.00033902,-0.30682,104.02

> view matrix models
> #2,-0.39074,0.30448,-0.86868,426.41,-0.18355,0.89898,0.39766,86.653,0.90202,0.31483,-0.29538,68.39

> view matrix models
> #2,-0.54273,0.36433,-0.75677,425.4,-0.14039,0.84899,0.50941,74.368,0.82809,0.38272,-0.40963,82.676

> view matrix models
> #2,-0.53476,0.44201,-0.72018,410.01,-0.07106,0.82574,0.55956,62.429,0.84201,0.35041,-0.41016,85.1

> select up

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 3 models selected  

> select up

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 3 models selected  

> volume flip #1

Opened cryosparc_P1_J66_008_volume_map.mrc z flip as #3, grid size
512,512,512, pixel 0.828, shown at step 1, values float32  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.53476,0.44201,-0.72018,413.74,-0.07106,0.82574,0.55956,17.409,0.84201,0.35041,-0.41016,126.64

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.83235,0.32288,-0.4505,436.41,0.014461,0.82517,0.5647,5.6988,0.55406,0.46351,-0.6915,182.66

> view matrix models
> #2,-0.78138,-0.028654,-0.62339,495.54,-0.49639,0.63394,0.59306,93.906,0.3782,0.77285,-0.50957,144.26

> view matrix models
> #2,-0.57266,0.13383,0.8088,279.15,0.80871,0.25392,0.53058,-20.197,-0.13436,0.95792,-0.25364,157.29

> view matrix models
> #2,-0.18226,0.8706,0.45698,174.04,0.12555,0.48157,-0.86737,203.7,-0.9752,-0.10071,-0.19708,397.59

> view matrix models
> #2,-0.0033808,0.21032,0.97763,175.02,-0.4549,0.8703,-0.1888,149.64,-0.89054,-0.44536,0.092729,397.11

> view matrix models
> #2,0.88646,-0.23136,0.40084,183.54,0.29594,0.94924,-0.1066,31.62,-0.35583,0.21312,0.90993,146.09

> view matrix models
> #2,0.90434,0.37218,0.20893,125.61,-0.2201,0.82607,-0.51881,163.4,-0.36568,0.4232,0.82896,129.69

> view matrix models
> #2,0.88399,0.41286,0.21932,121.78,-0.32225,0.87801,-0.35391,150.68,-0.33868,0.24217,0.9092,140.17

> view matrix models
> #2,0.59704,0.79718,-0.089688,145.82,-0.77775,0.54781,-0.30824,247.6,-0.19659,0.25379,0.94707,115.65

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.59704,0.79718,-0.089688,41.736,-0.77775,0.54781,-0.30824,310.81,-0.19659,0.25379,0.94707,79.858

> view matrix models
> #2,0.59704,0.79718,-0.089688,24.711,-0.77775,0.54781,-0.30824,283.93,-0.19659,0.25379,0.94707,70.266

> view matrix models
> #2,0.59704,0.79718,-0.089688,28.697,-0.77775,0.54781,-0.30824,278.88,-0.19659,0.25379,0.94707,69.843

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.60671,0.79298,-0.055521,23.967,-0.76553,0.56403,-0.30956,275.33,-0.21416,0.23032,0.94926,74.921

> view matrix models
> #2,0.88724,0.44221,-0.13138,41.593,-0.46109,0.84123,-0.28236,196.47,-0.014345,0.3111,0.95027,38.225

> fitmap #2 inMap #3

Fit molecule 8dnx.pdb (#2) to map cryosparc_P1_J66_008_volume_map.mrc z flip
(#3) using 4204 atoms  
average map value = 0.1104, steps = 128  
shifted from previous position = 4.4  
rotated from previous position = 20.5 degrees  
atoms outside contour = 1748, contour level = 0.096203  
  
Position of 8dnx.pdb (#2) relative to cryosparc_P1_J66_008_volume_map.mrc z
flip (#3) coordinates:  
Matrix rotation and translation  
0.78427958 0.62040040 -0.00298102 19.68310187  
-0.62038186 0.78419430 -0.01287065 191.79694846  
-0.00564726 0.01194356 0.99991273 73.23193997  
Axis 0.01999480 0.00214840 -0.99979778  
Axis point 286.59356845 65.59171965 0.00000000  
Rotation angle (degrees) 38.35386993  
Shift along axis -72.41151500  
  

> select subtract #2

Nothing selected  

> set bgColor black

> volume #3 color #b2b2b2b3

> set bgColor white

> select clear

> ui mousemode right select

> ui mousemode right zoom

> volume #3 color #b2b2b2cd

> volume #3 color #b2b2b2cc

> volume #3 color #b2b2b29c

> volume #3 color #b2b2b2a3

> volume #3 color #b2b2b2b5

> color #3 #b2b2b2ff models

> color #3 #b2b2b2f0 models

> color #3 #b2b2b2ef models

> color #3 #b2b2b2f0 models

> color #3 #cbcbcbf0 models

> color #3 #adadadf0 models

> color #3 #adadadac models

> color #3 #adadada5 models

> color #3 #adadada4 models

> color #3 #adadada1 models

> color #3 #adadad9b models

[Repeated 1 time(s)]

> color #3 #6a6a6a9b models

> color #3 #6c6c6c9b models

> color #3 #3939399b models

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 3 time(s)]

> open /Users/avenka/Downloads/cryosparc_P1_J104_007_volume_map_sharp.mrc

Opened cryosparc_P1_J104_007_volume_map_sharp.mrc as #4, grid size
512,512,512, pixel 0.828, shown at level 0.0207, step 2, values float32  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> volume flip #4

Opened cryosparc_P1_J104_007_volume_map_sharp.mrc z flip as #5, grid size
512,512,512, pixel 0.828, shown at step 1, values float32  

> volume #5 level 0.08765

> show #!4 models

> volume #4 level 0.1282

> hide #!5 models

> hide #!3 models

> close #5

> volume #4 level 0.1134

> volume #4 color #b2fffffb

> volume #4 color #b2fffffc

> volume #4 color #b2ffff

> volume #4 level 0.1067

> show #!3 models

> volume #4 color #b2ffffc7

> volume #4 color #b2ffffb8

> volume #4 level 0.09324

> hide #!2 models

> show #!2 models

> hide #!3 models

> volume #4 color #ff5ae3b8

> show #!3 models

> hide #!4 models

> volume #3 color #2424249b

> volume #3 color #2424249c

> volume #3 color #2121219c

> volume #3 level 0.0997

> volume #3 color #212121c8

> volume #3 color #212121cc

> save /Users/avenka/Desktop/image1.png supersample 3

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

Alignment identifier is 2/B  
Alignment identifier is 2/C  
Alignment identifier is 2/A  

> select
> /A:6-14,27-46,62-70,81-97,108-134,139-172,177-197,211-223,225-236,241-260,288-312,315-321,340-345,350-384,386-398,408-439,442-468

2526 atoms, 2562 bonds, 327 residues, 1 model selected  

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 3 models selected  

> select subtract #2

Nothing selected  

> label delete

> select /A:300

8 atoms, 7 bonds, 1 residue, 1 model selected  

> save /Users/avenka/Desktop/image3.png supersample 3

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select /A:300

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select
> /A:6-14,27-46,62-70,81-97,108-134,139-172,177-197,211-223,225-236,241-260,288-312,315-321,340-345,350-384,386-398,408-439,442-468

2526 atoms, 2562 bonds, 327 residues, 1 model selected  

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> select subtract #2

Nothing selected  
Destroying pre-existing alignment with identifier 2/B  
Alignment identifier is 2/B  
Destroying pre-existing alignment with identifier 2/C  
Alignment identifier is 2/C  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  
Destroying pre-existing alignment with identifier 2/B  
Alignment identifier is 2/B  
Destroying pre-existing alignment with identifier 2/C  
Alignment identifier is 2/C  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  

> select /A:300

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> select subtract #2

Nothing selected  

> hide #!2 models

> show #!2 models

> select /A:300

8 atoms, 7 bonds, 1 residue, 1 model selected  

> save /Users/avenka/Desktop/image4.png supersample 3

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select /A:300

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> select subtract #2

Nothing selected  

> hide #!2 models

> show #!2 models

> select /A:300

8 atoms, 7 bonds, 1 residue, 1 model selected  

> save /Users/avenka/Desktop/image5.png supersample 3

> hide #!2 models

> volume #3 level 0.1102

> save /Users/avenka/Desktop/image6.png supersample 3

> volume #3 level 0.04724

> save /Users/avenka/Desktop/image7.png supersample 3

> volume #3 level 0.1498

> volume #3 level 0.1044

> show #!2 models

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> select subtract #2

Nothing selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> select /A:300

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #3 color #212121e7

> volume #3 color #3b3b3be7

> volume #3 color #282828e7

[Repeated 1 time(s)]

> volume #3 color #282828e8

> save /Users/avenka/Desktop/image8.png supersample 3

> volume #3 color #9c9c9ce8

> hide #!2 models

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> select subtract #2

Nothing selected  

> volume #3 color #919191e8

> volume #3 color #949494e8

> volume #3 color #419094e8

> volume #3 color #71948de8

> volume #3 color #619294e8

> volume #3 color #2c7c94e8

> volume #3 color #618794e8

> volume #3 color #45616ae8

> volume #3 color #47646de8

> volume #3 color #606d6be8

> volume #3 color #91a5a3e8

> volume #3 color #00fdff

> volume #3 color #73fdff

> volume #3 color #76d6ff

> volume #3 color #7a81ff

> volume #3 color #0433ff

> volume #3 color #7a81ff

> volume #3 color #d6d6d6

[Repeated 1 time(s)]

> volume #3 color silver

> save /Users/avenka/Desktop/image9.png supersample 3

> show #!2 models

> volume #3 color silver

> volume #3 color #c0c0c0f5

> volume #3 color #c0c0c0ec

> volume #3 color #c0c0c0b2

> volume #3 color silver

> volume #3 color #c0c0c0cc

> volume #3 color #929292

> volume #3 color #929292cb

> volume #3 color #929292cc

> volume #3 color #929292e6

> volume #3 color #929292d9

> save /Users/avenka/Desktop/image10.png supersample 3

> select /A:300

8 atoms, 7 bonds, 1 residue, 1 model selected  

> save /Users/avenka/Desktop/image11.png supersample 3

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> select subtract #2

Nothing selected  

> save /Users/avenka/Desktop/image12.png supersample 3

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 15 time(s)]

Unsupported scale factor (0.000000) detected on Display0  

[Repeated 5 time(s)]

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 3 time(s)]

> open /Users/avenka/Downloads/cryosparc_P1_J133_006_volume_map_sharp.mrc

Opened cryosparc_P1_J133_006_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 1.66, shown at level 0.0642, step 1, values float32  

> volume #4 level 0.1765

> hide #!4 models

> volume #5 level 0.4481

> volume flip #5

Opened cryosparc_P1_J133_006_volume_map_sharp.mrc z flip as #6, grid size
256,256,256, pixel 1.66, shown at step 1, values float32  

> hide #!3 models

> volume #6 level 0.3053

> show #!3 models

> hide #!6 models

> show #!6 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> volume #6 color #ffb2fff5

> volume #6 color #ffb2ffb1

> volume #6 color #ffb2ffb4

> volume #6 color #d783ff

> volume #6 color #d783ffdf

> volume #6 color #7a81ff

> volume #6 color #7a81ffca

> volume #6 color darkgrey

> volume #6 color #a9a9a9cc

> volume #6 color #00fdff

> volume #6 color #00fdffcc

> volume #6 color #ff8ad8

> volume #6 color #ff9300

> volume #6 color #ff930074

> volume #6 color #ff930080

> volume #6 color #531b93

> volume #6 color #531b93bd

> volume #6 color #ff85ff

> volume #6 color #ff85ff00

> volume #6 color #ff85ff99

> volume #6 color #797979

> volume #6 color #797979ac

> volume #6 color #797979ad

> volume #6 color #797979b4

> volume #6 color #797979b5

> show #!3 models

> hide #!6 models

> show #!6 models

> hide #!3 models

> hide #!2 models

> hide #!6 models

> open /Users/avenka/Downloads/cryosparc_P1_J136_00032_volume_series.cs

Unrecognized file suffix '.cs'  

> open /Users/avenka/Downloads/cryosparc_P1_J136_class_00_00032_volume.mrc
> /Users/avenka/Downloads/cryosparc_P1_J136_class_01_00032_volume.mrc
> /Users/avenka/Downloads/cryosparc_P1_J136_class_02_00032_volume.mrc
> /Users/avenka/Downloads/cryosparc_P1_J136_class_04_00032_volume.mrc
> /Users/avenka/Downloads/cryosparc_P1_J136_class_03_00032_volume.mrc
> /Users/avenka/Downloads/cryosparc_P1_J136_class_05_00032_volume.mrc

Opened cryosparc_P1_J136_class_00_00032_volume.mrc as #7.1, grid size
112,112,112, pixel 3.79, shown at level 0.117, step 1, values float32  
Opened cryosparc_P1_J136_class_01_00032_volume.mrc as #7.2, grid size
112,112,112, pixel 3.79, shown at level 0.122, step 1, values float32  
Opened cryosparc_P1_J136_class_02_00032_volume.mrc as #7.3, grid size
112,112,112, pixel 3.79, shown at level 0.113, step 1, values float32  
Opened cryosparc_P1_J136_class_04_00032_volume.mrc as #7.4, grid size
112,112,112, pixel 3.79, shown at level 0.113, step 1, values float32  
Opened cryosparc_P1_J136_class_03_00032_volume.mrc as #7.5, grid size
112,112,112, pixel 3.79, shown at level 0.104, step 1, values float32  
Opened cryosparc_P1_J136_class_05_00032_volume.mrc as #7.6, grid size
112,112,112, pixel 3.79, shown at level 0.119, step 1, values float32  
Drag select of 7.1 cryosparc_P1_J136_class_00_00032_volume.mrc , 7.2
cryosparc_P1_J136_class_01_00032_volume.mrc , 7.3
cryosparc_P1_J136_class_02_00032_volume.mrc , 7.4
cryosparc_P1_J136_class_04_00032_volume.mrc , 7.5
cryosparc_P1_J136_class_03_00032_volume.mrc , 7.6
cryosparc_P1_J136_class_05_00032_volume.mrc  

> select add #7

13 models selected  

> select subtract #7

Nothing selected  

> select clear

[Repeated 1 time(s)]

> morph

Missing or invalid "structures" argument: empty atom specifier  

> morph #7

Require at least 2 structures for morph  

> morph #7.1-7.6

Require at least 2 structures for morph  

> morph #7.1-6

Require at least 2 structures for morph  

> morph #7.1,7.2

Require at least 2 structures for morph  

> morph #7.1,#7.2

Missing or invalid "structures" argument: only initial part "#7.1" of atom
specifier valid  

> volume morph #7

Opened morph as #8, grid size 112,112,112, pixel 3.79, shown at step 1, values
float32  

> volume #8 level 0.7008

> color #7 grey

[Repeated 1 time(s)]

> color #8 grey

> volume #8 level 0.844

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!8 models

> show #!8 models

> hide #!6 models

> volume flip #8

Opened morph z flip as #9, grid size 112,112,112, pixel 3.79, shown at step 1,
values float32  

> show #!6 models

> hide #!6 models

> show #!2 models

> show #!6 models

> hide #!9 models

> hide #!7 models

> hide #!6 models

> show #!3 models

> hide #!3 models

> show #!9 models

> show #!3 models

> hide #!3 models

> volume #9 level 0.7861

> hide #!9 models

Unsupported scale factor (0.000000) detected on Display1  

[Repeated 3 time(s)]

> hide #!2 models

> open /Users/avenka/Downloads/cryosparc_P1_J140_component_000.cs

Unrecognized file suffix '.cs'  

> show #!5 models

> volume #5 level 0.2217

> volume guassian #5 sDev 2

Expected a density maps specifier or a keyword  

> volume gaussian #5 sDev 2

Opened cryosparc_P1_J133_006_volume_map_sharp.mrc gaussian as #10, grid size
256,256,256, pixel 1.66, shown at step 1, values float32  

> ui tool show "Segment Map"

Segmenting cryosparc_P1_J133_006_volume_map_sharp.mrc gaussian, density
threshold 0.036952  
Showing 16 region surfaces  
361 watershed regions, grouped to 16 regions  
Showing cryosparc_P1_J133_006_volume_map_sharp gaussian.seg - 16 regions, 16
surfaces  

> hide #!10 models

> hide #11.1 models

> show #11.1 models

> hide #11.1 models

> show #11.1 models

> hide #11.1 models

> show #11.1 models

> hide #11.2 models

> show #11.2 models

> hide #11.10 models

> hide #11.11 models

> show #11.11 models

> hide #11.16 models

> hide #11.8 models

> hide #11.11 models

> show #11.11 models

> hide #11.5 models

> hide #11.4 models

> hide #11.1 models

> hide #11.2 models

> hide #11.6 models

> hide #11.15 models

> show #!2 models

> volume #10 color #ffb2ffb1

> volume #10 color #ffb2ff80

> volume #10 color #ffb2ff

> transparency #2#11.3,7,9,11-14#!11 50

> hide #!2 models

> transparency #11.3,7,9,11-14#!11 0

Please select one ore more regions to save to .mrc file  
[Repeated 1 time(s)]

> select clear

> select add #11

17 models selected  

> select subtract #11.1

16 models selected  

> select subtract #11.2

15 models selected  

> select subtract #11.4

14 models selected  

> select subtract #11.5

13 models selected  

> select subtract #11.6

12 models selected  

> select subtract #11.8

11 models selected  

> select subtract #11.10

10 models selected  

> select subtract #11.15

9 models selected  

> select subtract #11.16

8 models selected  
Saving 7 regions to mrc file...  
Opened cryosparc_P1_J133_006_volume_map_sharp_7_regions.mrc as #12, grid size
53,74,85, pixel 1.66, shown at step 1, values float32  
Wrote cryosparc_P1_J133_006_volume_map_sharp_7_regions.mrc  

> hide #!11 models

> select add #11

17 models selected  

> select subtract #11

Nothing selected  

> select add #12

2 models selected  

> volume #12 level 0.1425

> select subtract #12

Nothing selected  

> volume #12 level 0.06865

> volume resample #12 onGrid #5

Opened cryosparc_P1_J133_006_volume_map_sharp_7_regions.mrc resampled as #13,
grid size 256,256,256, pixel 1.66, shown at step 1, values float32  

> save /Users/avenka/Downloads/mask_256_J133.mrc models #13

> show #!5 models

> color #5 #ffb2ffaa models

> color #5 #ffb2ffac models

> color #5 #ffb2ff86 models

> color #5 #ffb2ff87 models

> hide #!5 models

> volume #13 level 0.1503

> show #!2 models

> select add #2

4204 atoms, 4294 bonds, 2 pseudobonds, 543 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.78428,0.6204,-0.002981,-33.688,-0.62038,0.78419,-0.012871,182.97,-0.0056473,0.011944,0.99991,112.91

> ui mousemode right "rotate selected models"

> select subtract #2

Nothing selected  

> hide #!2 models

> show #!5 models

> volume #4 level 0.1887

> volume #5 level 0.378

> hide #!4 models

> volume #6 level 0.4081

> hide #!6 models

> volume #5 level 0.6415

> volume #5 level 0.378

> hide #!13 models

> show #!11 models

> show #11.1 models

> show #11.2 models

> show #11.4 models

> show #11.5 models

> show #11.6 models

> show #11.8 models

> show #11.10 models

> show #11.15 models

> show #11.16 models

> show #!12 models

> color #11 #b2b2b262

> color #11 #b2b2b280

> hide #!12 models

> hide #!5 models

> show #!2 models

> hide #!2 models

> show #!6 models

> color #6 #797979c3 models

> color #6 #797979c2 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> color #11 #b2b2b2ff

> hide #!6 models

> show #!2 models

> color #11 #b2b2b280

> show #!5 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!10 models

> hide #11.1 models

> hide #11.2 models

> hide #11.3 models

> hide #11.4 models

> hide #11.5 models

> hide #11.6 models

> hide #11.7 models

> hide #11.8 models

> hide #11.9 models

> hide #11.10 models

> hide #11.11 models

> hide #11.12 models

> hide #11.13 models

> hide #11.14 models

> hide #11.15 models

> hide #11.16 models

> hide #!5 models

> volume #10 level 0.03186

> volume #10 level 0.0325

> hide #!2 models

> ui tool show "Segment Map"

Segmenting cryosparc_P1_J133_006_volume_map_sharp.mrc gaussian, density
threshold 0.032500  
Showing 16 region surfaces  
361 watershed regions, grouped to 16 regions  
Showing cryosparc_P1_J133_006_volume_map_sharp gaussian.seg - 16 regions, 16
surfaces  

> hide #!10 models

> hide #11.5 models

> hide #11.8 models

> hide #11.10 models

> hide #11.9 models

> show #11.9 models

> hide #11.15 models

> hide #11.16 models

> hide #11.6 models

> hide #11.4 models

> hide #11.2 models

> close #11

> show #!10 models

> ui tool show Segmentations

> ui view fourup

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 742, in
_onSliderMoved  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 742, in
_onSliderMoved  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,8
      Model Number: Z1FF000KKKS/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 48 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4 (24E248)
      Kernel Version: Darwin 24.4.0
      Time since boot: 14 days, 1 hour

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        P27h-20:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13