Segger: 'NoneType' object has no attribute 'matrix'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22635
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\Users\\\18810\\\Desktop\\\cryosparc_P86_J910_006_volume_map_sharp.mrc

Opened cryosparc_P86_J910_006_volume_map_sharp.mrc as #1, grid size
288,288,288, pixel 0.69, shown at level 0.113, step 2, values float32  

> volume #1 level 0.07998

> surface dust #1 size 6.9

> open C:/Users/18810/Desktop/UL30-APO-827.pdb

Chain information for UL30-APO-827.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select /A:113

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

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,19.697,0,1,0,-43.098,0,0,1,-59.018

> view matrix models #2,1,0,0,64.506,0,1,0,-20.565,0,0,1,-67.647

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99966,0.025177,-0.0074387,61.986,-0.025168,0.99968,0.0011936,-17.363,0.0074664,-0.001006,0.99997,-68.485

> view matrix models
> #2,0.86559,-0.47852,0.14754,130.16,0.48172,0.87619,0.015609,-68.634,-0.13674,0.057563,0.98893,-56.284

> view matrix models
> #2,0.99827,-0.056362,0.016762,70.463,0.056403,0.99841,-0.0019925,-27.507,-0.016623,0.0029345,0.99986,-65.852

> view matrix models
> #2,0.93562,0.33924,-0.097623,38.072,-0.33771,0.9407,0.032313,28.011,0.1028,0.0027357,0.9947,-80.873

> view matrix models
> #2,0.44779,0.86363,-0.23156,46.122,-0.8505,0.49132,0.18776,138.36,0.27593,0.11286,0.95453,-113.89

> view matrix models
> #2,0.30508,0.94447,-0.12207,38.429,-0.74081,0.31591,0.59279,93.333,0.59844,-0.090417,0.79605,-105.77

> view matrix models
> #2,0.15334,0.96852,-0.19609,65.173,0.70063,0.033379,0.71274,-73.069,0.69686,-0.24667,-0.67346,104.97

> view matrix models
> #2,-0.9276,-0.0052821,0.37354,268.39,0.36193,0.23502,0.90209,-83.056,-0.092557,0.97198,-0.2161,-27.127

> view matrix models
> #2,-0.80004,0.2199,0.55819,194.17,-0.50221,0.26353,-0.82361,263.5,-0.32821,-0.93925,-0.1004,260.29

> view matrix models
> #2,0.51177,-0.59253,0.62209,128.02,-0.80676,-0.082508,0.58509,159.83,-0.29536,-0.80131,-0.52025,293.87

> view matrix models
> #2,0.30245,-0.87587,0.37599,229.73,0.8908,0.40008,0.21542,-82.202,-0.33911,0.26978,0.90123,-47.781

> view matrix models
> #2,0.64221,-0.51872,0.56436,108.21,0.32391,0.85093,0.41352,-98.769,-0.69473,-0.082763,0.71449,74.951

> view matrix models
> #2,0.52867,-0.33832,0.77849,68.146,-0.044487,0.90483,0.42344,-59.196,-0.84766,-0.25849,0.46331,154.6

> view matrix models
> #2,0.84565,0.3925,0.36168,-20.614,-0.45057,0.88824,0.08955,42.525,-0.28611,-0.23869,0.92799,13.971

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.84565,0.3925,0.36168,-117.32,-0.45057,0.88824,0.08955,20.738,-0.28611,-0.23869,0.92799,44.597

> transparency sel 50

> select clear

> select #1

2 models selected  

> transparency #1.1 80

> transparency #1.1 50

> select clear

> select /A

7946 atoms, 8140 bonds, 2 pseudobonds, 1044 residues, 2 models selected  

> view matrix models
> #2,0.84565,0.3925,0.36168,-117.68,-0.45057,0.88824,0.08955,16.888,-0.28611,-0.23869,0.92799,43.994

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.86189,0.356,0.36113,-114.55,-0.38529,0.92274,0.0099067,14.28,-0.32971,-0.14768,0.93246,36.172

> view matrix models
> #2,0.76431,0.55593,0.32677,-125.43,-0.55182,0.82605,-0.11463,67.1,-0.33365,-0.0927,0.93813,28.086

> select clear

> select #1

2 models selected  

> transparency #1.1 30

> set bgColor white

> select clear

> volume #1 level 0.06204

> surface dust #1 size 6.9

> select /A

7946 atoms, 8140 bonds, 2 pseudobonds, 1044 residues, 2 models selected  

> view matrix models
> #2,0.64079,0.71657,-0.27552,-49.44,-0.76088,0.54498,-0.35223,167.29,-0.10225,0.43534,0.89444,-71.659

> view matrix models
> #2,0.71461,0.65059,0.25703,-122.8,-0.58837,0.75776,-0.28218,104.62,-0.37835,0.050418,0.92429,15.498

> view matrix models
> #2,0.75026,0.65916,-0.051067,-86.482,-0.64092,0.70619,-0.30086,121.46,-0.16225,0.25845,0.9523,-46.482

> view matrix models
> #2,0.76731,0.6406,0.029287,-97.105,-0.5896,0.72271,-0.36063,120.53,-0.25219,0.25945,0.93225,-32.008

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.76731,0.6406,0.029287,-29.051,-0.5896,0.72271,-0.36063,150.55,-0.25219,0.25945,0.93225,-2.1909

> view matrix models
> #2,0.76731,0.6406,0.029287,-30.738,-0.5896,0.72271,-0.36063,136.21,-0.25219,0.25945,0.93225,12.062

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.78171,0.46751,0.41276,-60.561,-0.28574,0.85678,-0.42928,86.439,-0.55433,0.21763,0.80334,75.559

> view matrix models
> #2,0.75101,0.49881,0.43264,-63.694,-0.25009,0.82129,-0.51278,98.238,-0.6111,0.27691,0.74154,83.081

> view matrix models
> #2,0.9119,0.24413,0.32992,-34.569,-0.027629,0.83855,-0.54412,70.723,-0.40949,0.48707,0.77142,22.452

> view matrix models
> #2,0.73911,0.17563,-0.65029,132.37,-0.67329,0.16417,-0.72092,276.2,-0.019856,0.97067,0.23959,-24.916

> view matrix models
> #2,0.51768,0.46387,-0.71891,129.95,-0.84623,0.15373,-0.51017,271.61,-0.12613,0.87246,0.47212,-28.788

> view matrix models
> #2,0.57501,0.40028,-0.71354,130.7,-0.81096,0.16355,-0.56177,272.63,-0.10817,0.90168,0.41866,-27.989

> view matrix models
> #2,0.34497,0.62465,-0.70057,127.33,-0.92595,0.10431,-0.36294,268.98,-0.15363,0.7739,0.61439,-30.628

> view matrix models
> #2,0.92329,0.37935,-0.060188,-1.8458,-0.33854,0.72971,-0.59406,134.09,-0.18144,0.56887,0.80217,-23.504

> view matrix models
> #2,-0.83369,0.1087,-0.54143,334.51,-0.54012,0.0438,0.84045,61.7,0.11508,0.99311,0.022197,-16.11

> view matrix models
> #2,-0.061892,0.30537,-0.95022,260.71,-0.90901,0.3759,0.18001,153.63,0.41215,0.8749,0.25432,-70.299

> view matrix models
> #2,0.046834,0.63232,-0.77329,175.54,0.23361,0.74574,0.62394,-110.67,0.9712,-0.20987,-0.11279,60.753

> view matrix models
> #2,0.10193,0.55277,-0.82708,186.98,0.26599,0.78599,0.55809,-111.65,0.95857,-0.27688,-0.066917,65.675

> view matrix models
> #2,0.17839,0.1855,-0.96632,248.28,0.18068,0.95919,0.21749,-78.363,0.96723,-0.2134,0.13759,27.452

> view matrix models
> #2,0.6713,0.52945,-0.51868,72.887,-0.1652,0.78908,0.59166,-59.798,0.72254,-0.3115,0.61718,7.9576

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.6713,0.52945,-0.51868,-2.3676,-0.1652,0.78908,0.59166,-82.068,0.72254,-0.3115,0.61718,-45.065

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.81595,0.50807,-0.27584,-51.702,-0.23261,0.72533,0.64791,-71.806,0.52926,-0.4645,0.71002,-10.501

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.81595,0.50807,-0.27584,-41.324,-0.23261,0.72533,0.64791,-73.974,0.52926,-0.4645,0.71002,-17.794

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.80472,0.54784,-0.22869,-51.971,-0.19352,0.60625,0.77137,-79.1,0.56123,-0.57648,0.59388,9.8575

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.80472,0.54784,-0.22869,-51.534,-0.19352,0.60625,0.77137,-74.987,0.56123,-0.57648,0.59388,17.149

> select clear

[Repeated 1 time(s)]

> select /A:115

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

> view matrix models
> #2,0.80472,0.54784,-0.22869,-56.955,-0.19352,0.60625,0.77137,-77.537,0.56123,-0.57648,0.59388,20.741

> hide #!2 models

> volume #1 level 0.03593

> surface dust #1 size 6.9

[Repeated 1 time(s)]

> volume #1 level 0.04735

> surface dust #1 size 6.9

> volume #1 level 0.05388

> ui tool show "Segment Map"

Segmenting cryosparc_P86_J910_006_volume_map_sharp.mrc, density threshold
0.053878  
Only showing 20 of 2281 regions.  
Showing 20 of 2281 region surfaces  
4837 watershed regions, grouped to 2281 regions  
Showing cryosparc_P86_J910_006_volume_map_sharp.seg - 2281 regions, 20
surfaces  

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #3.1

1 model selected  
Drag select of 5665, 22048 of 30428 triangles, 5597, 5176 of 29200 triangles  
Grouped 2 regions  
Drag select of 5701, 18521 of 55800 triangles, 5562, 4970 of 28756 triangles  
Grouped 2 regions  

> select #3.3

1 model selected  

> select add #3.7

2 models selected  

> select add #3.9

3 models selected  

> select add #3.11

4 models selected  

> select add #3.2

5 models selected  

> select add #3.5

6 models selected  

> select add #3.17

7 models selected  

> select add #3.10

8 models selected  

> select add #3.6

9 models selected  
Grouped 9 regions  
Drag select of 5488, 34315 of 97824 triangles, 5693, 8397 of 64728 triangles,
5554, 19174 of 43108 triangles, 6111, 2997 of 30368 triangles, 5946, 6086 of
30824 triangles, 5699, 2412 of 25492 triangles, 6140, 160935 of 575960
triangles  
Grouped 6 regions  

> select add #3.2

2 models selected  

> select subtract #3.3

1 model selected  

> select subtract #3.2

Nothing selected  

> select add #3.2

1 model selected  

> select add #3.3

2 models selected  

> select subtract #3.3

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  

> select clear

> select #3.2

1 model selected  

> transparency #3.2 60

> select clear

> show #!2 models

> select clear

> select /A

7946 atoms, 8140 bonds, 2 pseudobonds, 1044 residues, 2 models selected  

> view matrix models
> #2,0.80472,0.54784,-0.22869,-55.642,-0.19352,0.60625,0.77137,-76.078,0.56123,-0.57648,0.59388,16.159

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.84428,0.51676,-0.14194,-68.329,-0.083677,0.38873,0.91754,-79.634,0.52933,-0.76279,0.37144,77.398

> view matrix models
> #2,0.845,0.53242,-0.050131,-83.24,-0.088728,0.23203,0.96865,-63.658,0.52736,-0.81406,0.2433,102.53

> view matrix models
> #2,0.82315,0.56711,-0.028233,-88.302,-0.032417,0.096577,0.9948,-55.383,0.56689,-0.81796,0.097882,117.8

> view matrix models
> #2,0.86752,0.4949,-0.049941,-80.894,0.0089375,0.084877,0.99635,-59.386,0.49733,-0.8648,0.069209,137.58

> view matrix models
> #2,0.85114,0.52441,-0.023679,-86.537,0.055012,-0.044245,0.9975,-47.235,0.52206,-0.85031,-0.066508,150.87

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.85114,0.52441,-0.023679,-86.432,0.055012,-0.044245,0.9975,-45.997,0.52206,-0.85031,-0.066508,148.74

> select #3.2

1 model selected  
Ungrouped to 2 regions  

> select #3.4

1 model selected  
Ungrouped to 6 regions  

> select clear

> select #3.6

1 model selected  

> select add #3.7

2 models selected  

> select add #3.3

3 models selected  

> select add #3.5

4 models selected  
Grouped 4 regions  

> select clear

> select add #3.2

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  

> select add #3.9

2 models selected  

> select clear

> select add #3.9

1 model selected  

> select add #3.16

2 models selected  
Grouped 2 regions  

> select clear

> select #3.2

1 model selected  

> transparency #3.2 50

> select clear

> select add #3.3

1 model selected  

> select subtract #3.3

Nothing selected  

> select #3.3

1 model selected  

> select add #3.8

2 models selected  

> select add #3.2

3 models selected  
Grouped 3 regions  

> undo

[Repeated 1 time(s)]Ungrouped to 3 regions  

> select clear

> select #3.4

1 model selected  

> select add #3.5

2 models selected  
Grouped 2 regions  

> color #3.2 cyan

> transparency #3.2 50

> select clear

> select #3.2

1 model selected  

> select #3.3

1 model selected  

> select #3.2

1 model selected  

> select #3.13

1 model selected  

> select #3.2

1 model selected  

> color #3.2 hot pink

> select clear

> select /A

7946 atoms, 8140 bonds, 2 pseudobonds, 1044 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.79367,0.59844,0.10937,-107.63,-0.060191,-0.10166,0.993,-22.002,0.60537,-0.79469,-0.044661,126.83

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.79367,0.59844,0.10937,-108.76,-0.060191,-0.10166,0.993,-19.076,0.60537,-0.79469,-0.044661,124.36

> view matrix models
> #2,0.79367,0.59844,0.10937,-108,-0.060191,-0.10166,0.993,-19.224,0.60537,-0.79469,-0.044661,124.59

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.87724,0.45982,0.13793,-103.2,-0.11106,-0.085124,0.99016,-14.477,0.46704,-0.88392,-0.023604,152.66

> select clear

> open C:/Users/18810/Desktop/8oj6.cif

8oj6.cif title:  
HSV-1 DNA polymerase-processivity factor complex in pre-translocation state
[more info...]  
  
Chain information for 8oj6.cif #4  
---  
Chain | Description | UniProt  
A | DNA polymerase catalytic subunit | DPOL_HHV11  
B | DNA polymerase processivity factor | PAP_HHV11  
C | DNA (22-MER) |  
D | DNA (48-MER) |  
  
Non-standard residues in 8oj6.cif #4  
---  
MG — magnesium ion  
  

> hide #!2 models

> select #4/A:175

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

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.86641,0.20358,-0.45595,67.512,-0.21299,0.97655,0.031312,31.865,0.45164,0.069983,0.88945,-63.157

> view matrix models
> #4,0.8599,0.1833,-0.47643,74.972,-0.22089,0.97501,-0.023563,42.546,0.4602,0.1255,0.8789,-70.942

> view matrix models
> #4,0.6775,0.68004,-0.28025,-2.5055,-0.64692,0.73224,0.21287,106.07,0.34998,0.037079,0.93602,-50.045

> view matrix models
> #4,0.93453,-0.34403,-0.09104,76.443,0.32759,0.93158,-0.15759,-15.217,0.13903,0.11745,0.9833,-36.519

> view matrix models
> #4,0.76893,-0.44831,-0.45582,179.21,0.42126,0.89157,-0.16627,-22.651,0.48093,-0.064171,0.87441,-45.441

> view matrix models
> #4,0.095762,0.95964,-0.26444,45.449,-0.98472,0.13014,0.11569,264.7,0.14543,0.24932,0.95744,-52.675

> view matrix models
> #4,-0.94753,0.0043445,0.31963,253.46,0.23262,-0.67646,0.69878,93.719,0.21925,0.73647,0.63996,-83.058

> view matrix models
> #4,0.99073,-0.10906,-0.081026,31.17,0.13297,0.65587,0.74307,-94.81,-0.027901,-0.74696,0.66429,171.08

> view matrix models
> #4,0.99089,-0.066441,-0.11712,30.902,0.13181,0.6565,0.74273,-94.661,0.027544,-0.7514,0.65927,163.82

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.99089,-0.066441,-0.11712,26.894,0.13181,0.6565,0.74273,-138.71,0.027544,-0.7514,0.65927,101.67

> view matrix models
> #4,0.99089,-0.066441,-0.11712,-10.778,0.13181,0.6565,0.74273,-126.71,0.027544,-0.7514,0.65927,115.63

> view matrix models
> #4,0.99089,-0.066441,-0.11712,-15.275,0.13181,0.6565,0.74273,-137.78,0.027544,-0.7514,0.65927,99.397

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.95341,0.051141,-0.29731,3.4989,0.15265,0.76827,0.62166,-137.28,0.26021,-0.63808,0.72467,34.924

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.95341,0.051141,-0.29731,-5.0058,0.15265,0.76827,0.62166,-142.58,0.26021,-0.63808,0.72467,37.936

> view matrix models
> #4,0.95341,0.051141,-0.29731,-6.4097,0.15265,0.76827,0.62166,-141.59,0.26021,-0.63808,0.72467,34.76

> select #4/C

455 atoms, 511 bonds, 22 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #4/D

590 atoms, 659 bonds, 29 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3.1

1 model selected  

> transparency #3.1 50

> select clear

> select #4/A:228

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

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.94545,0.032896,-0.3241,1.9987,0.23035,0.63599,0.73651,-153.19,0.23036,-0.77099,0.59372,80.929

> view matrix models
> #4,0.94055,-0.091326,-0.32716,21.615,0.32368,0.533,0.78176,-159.84,0.10298,-0.84117,0.53087,121.33

> view matrix models
> #4,0.95224,-0.018538,-0.30479,5.3192,0.26075,0.56878,0.78006,-155.22,0.1589,-0.82228,0.54645,107.37

> select clear

> select #4/A

8556 atoms, 8751 bonds, 7 pseudobonds, 1091 residues, 3 models selected  

> view matrix models
> #4,0.93896,-0.088526,-0.33243,22.327,0.33021,0.50288,0.79879,-159.25,0.096461,-0.85981,0.50142,130.02

> view matrix models
> #4,0.94582,-0.05001,-0.32083,13.642,0.29992,0.51315,0.80419,-157.04,0.12442,-0.85684,0.50035,125.48

> view matrix models
> #4,0.94019,-0.048487,-0.33717,17.019,0.3186,0.47546,0.82002,-156.98,0.12055,-0.8784,0.46247,135.61

> view matrix models
> #4,0.94809,-0.22311,-0.22658,23.059,0.31688,0.72234,0.61466,-158.75,0.026532,-0.65456,0.75555,67.762

> view matrix models
> #4,0.91584,-0.18599,-0.35587,44.194,0.36177,0.76675,0.53031,-158.03,0.17423,-0.61442,0.7695,36.896

> view matrix models
> #4,0.93157,0.14769,-0.3322,-11.481,0.071085,0.82213,0.56485,-127.54,0.35653,-0.54981,0.75537,1.8317

> view matrix models
> #4,0.92509,0.22632,-0.30494,-26.678,-0.014499,0.82347,0.56718,-115.03,0.37948,-0.52027,0.76506,-7.6682

> view matrix models
> #4,0.97427,0.18578,-0.12759,-57.961,-0.070861,0.78993,0.60909,-108.48,0.21395,-0.58438,0.78277,24.157

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.97427,0.18578,-0.12759,-56.019,-0.070861,0.78993,0.60909,-107.37,0.21395,-0.58438,0.78277,25.998

> view matrix models
> #4,0.97427,0.18578,-0.12759,-52.992,-0.070861,0.78993,0.60909,-107.12,0.21395,-0.58438,0.78277,26.337

> view matrix models
> #4,0.97427,0.18578,-0.12759,-52.871,-0.070861,0.78993,0.60909,-104.44,0.21395,-0.58438,0.78277,25.688

> view matrix models
> #4,0.97427,0.18578,-0.12759,-9.235,-0.070861,0.78993,0.60909,-28.802,0.21395,-0.58438,0.78277,-9.0395

> view matrix models
> #4,0.97427,0.18578,-0.12759,-21.212,-0.070861,0.78993,0.60909,3.4308,0.21395,-0.58438,0.78277,-5.9357

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.30164,-0.95333,0.01366,226.29,0.80706,0.24768,-0.53601,141.32,0.50761,0.1727,0.8441,-173

> view matrix models
> #4,-0.12428,-0.86476,0.48656,199.03,0.5985,-0.45645,-0.65837,297.78,0.79143,0.20939,0.57428,-176.58

> view matrix models
> #4,-0.20841,-0.75236,0.62492,172.09,0.46771,-0.63782,-0.61191,336.79,0.85896,0.16475,0.48481,-165.31

> view matrix models
> #4,-0.77999,-0.62519,0.027347,340.98,0.6073,-0.76677,-0.20798,266.74,0.151,-0.14561,0.97775,-93.837

> view matrix models
> #4,-0.79911,-0.60015,0.035101,338.91,0.59541,-0.79816,-0.091777,253.7,0.083097,-0.05244,0.99516,-100.14

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.79911,-0.60015,0.035101,320.76,0.59541,-0.79816,-0.091777,148.15,0.083097,-0.05244,0.99516,-60.911

> view matrix models
> #4,-0.79911,-0.60015,0.035101,320.33,0.59541,-0.79816,-0.091777,143.62,0.083097,-0.05244,0.99516,-60.527

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.89055,-0.44842,0.076445,304.96,0.45025,-0.89287,0.0075968,163.15,0.064849,0.041184,0.99704,-71.884

> view matrix models
> #4,-0.88105,-0.46944,0.058129,309.68,0.473,-0.87313,0.118,138.23,-0.0046392,0.13146,0.99131,-73.63

> view matrix models
> #4,-0.91623,-0.38465,-0.11208,331.09,0.36709,-0.91805,0.1498,155.74,-0.16052,0.096108,0.98234,-43.056

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.91623,-0.38465,-0.11208,319.49,0.36709,-0.91805,0.1498,157.66,-0.16052,0.096108,0.98234,-44.004

> view matrix models
> #4,-0.91623,-0.38465,-0.11208,316.51,0.36709,-0.91805,0.1498,153.36,-0.16052,0.096108,0.98234,-42.831

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.95128,-0.28348,-0.12127,308.47,0.27217,-0.95686,0.10174,181.67,-0.14488,0.063781,0.98739,-41.294

> select clear

> select #3.2

1 model selected  

> select add #3.1

2 models selected  

> ui tool show "Fit to Segments"

Simulating map res 4.000, grid 2.000  

> molmap #4 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 8oj6.cif map 4 as #5, grid size 47,64,83, pixel 2, shown at level
0.105, step 1, values float32  
Opened cryosparc_P86_J910_006_volume_map_sharp_masked as #6, grid size
288,288,288, pixel 0.69, shown at step 1, values float32  
Top score: 0.44907, z-score: 1.85006 (avg: 0.3997, stdev: 0.0267)  

QWindowsWindow::setGeometry: Unable to set geometry 2560x1476+2560+29 (frame:
2578x1523+2551-9) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 2560x1351+2560+29 (frame:
2578x1398+2551-9) margins: 9, 38, 9, 9 minimum size: 630x1181
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=0, y=0), mintrack=POINT(x=806, y=1523)))  

> select clear

> hide #!3 models

> show #!3 models

> select #3.2

1 model selected  

> select clear

> select #3.2

1 model selected  

> color #3.2 hot pink

> select clear

> lighting soft

> lighting full

> lighting simple

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> select clear

> select #4/A:232

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

> select clear

> select #3.2

1 model selected  

> select subtract #3.3

3 models selected  

> select subtract #3.2

2 models selected  

> select clear

> select add #3.2

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  
Ungrouped to 2 regions  

> select clear

> select #3.4

1 model selected  
Ungrouped to 2 regions  

> select #3.5

1 model selected  

> select #3.3

1 model selected  
Grouped 1 regions  

> select #3.5

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  

> select #3.2

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  

> select clear

> select #3.2

1 model selected  

> transparency #3.2 50

> select clear

> select #3.2

1 model selected  

> select clear

> select #3.2

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 4 regions  
Ungrouped to 38 regions, but did not show all surfaces, see Options  
Ungrouped to 30 regions, but did not show all surfaces, see Options  
Ungrouped to 12 regions, but did not show their surfaces, see Options  
Ungrouped to 1841 regions, but did not show their surfaces, see Options  

> undo

[Repeated 2 time(s)]

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> show #!5 models

> hide #!5 models

> show #!3 models

> close #5

> select add #3

25 models selected  

> select clear

Deleted 24 regions  

> select #1

2 models selected  

> volume #1 level 0.0464

> volume #1 level 0.05089

> surface dust #1 size 6.9

> ui tool show "Fit in Map"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit  
self.Fit()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit  
func()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit  
self.Fit()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit  
func()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit  
self.Fit()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit  
func()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  

> select clear

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit  
self.Fit()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit  
func()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Segmenting cryosparc_P86_J910_006_volume_map_sharp.mrc, density threshold
0.050889  
Only showing 30 of 2597 regions.  
Showing 30 of 2597 region surfaces  
5606 watershed regions, grouped to 2597 regions  
Showing cryosparc_P86_J910_006_volume_map_sharp.seg - 2597 regions, 30
surfaces  

> select #3.5

1 model selected  

> select add #3.2

2 models selected  

> select add #3.4

3 models selected  

> select add #3.6

4 models selected  
Grouped 4 regions  

> select add #3.8

2 models selected  

> select subtract #3.8

1 model selected  

> select add #3.17

2 models selected  

> select add #3.8

3 models selected  
Grouped 3 regions  

> select add #3.10

2 models selected  

> select add #3.15

3 models selected  

> select add #3.3

4 models selected  

> select add #3.7

5 models selected  
Grouped 5 regions  

> select add #3.18

2 models selected  

> select add #3.9

3 models selected  

> select clear

> select #3.9

1 model selected  
Ungrouped to 10 regions  

> select #3.6

1 model selected  
Ungrouped to 8 regions, but did not show all surfaces, see Options  

> select clear

> select add #3.18

1 model selected  

> select add #3.2

2 models selected  

> select add #3.15

3 models selected  
Grouped 3 regions  

> select clear

> select add #3.14

1 model selected  

> select add #3.2

2 models selected  
Grouped 2 regions  

> select add #3.12

2 models selected  
Grouped 2 regions  
Ungrouped to 2 regions  

> select #3.12

1 model selected  

> select add #3.6

2 models selected  
Grouped 2 regions  

> select #3.1

1 model selected  

> select add #3.2

2 models selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit  
self.Fit()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit  
func()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  

> select clear

> select add #3.2

1 model selected  

> select add #3.1

2 models selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit  
self.Fit()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit  
func()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  

> ui tool show "Fit to Segments"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit  
self.Fit()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit  
func()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 289, in _fit  
self.Fit()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 1335, in Fit  
func()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\segger\fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 551.52
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: LENOVO
Model: 82JQ
OS: Microsoft Windows 11 专业版 (Build 22635)
Memory: 17,024,741,376
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics         
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

[pett]

Duplicate of #14384