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Opened 6 years ago
Closed 6 years ago
#3102 closed defect (fixed)
volume subregion: 'NoneType' object has no attribute 'size'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/shirinmortazavi/Downloads/cryosparc_P22_J2141_007_volume_map_sharp_local.mrc
Opened cryosparc_P22_J2141_007_volume_map_sharp_local.mrc, grid size
256,256,256, pixel 1.23, shown at level 0.124, step 1, values float32
> ui mousemode rightMode zoom
> volume #1 level 0.8104
> volume #1 level 0.4071
> volume #1 level 0.3283
> volume #1 level 0.4395
> open2
> "/Users/shirinmortazavi/Downloads/cryosparc_P22_J2130_006_volume_map_sharp
> (1).mrc"
Opened cryosparc_P22_J2130_006_volume_map_sharp (1).mrc, grid size
384,384,384, pixel 0.818, shown at level 0.126, step 2, values float32
> volume #2 level 0.3427
> volume #2 step 1
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2051_006_volume_map_sharp.mrc
Opened cryosparc_P22_J2051_006_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.23, shown at level 0.17, step 1, values float32
> volume #3 level 0.5534
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2130_006_volume_map_sharp (1).mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 133933 points
correlation = 0.9509, correlation about mean = 0.6857, overlap = 6.739e+04
steps = 56, shift = 0.773, angle = 1.56 degrees
Position of cryosparc_P22_J2130_006_volume_map_sharp (1).mrc (#2) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99963010 0.02718969 -0.00061710 -4.14343340
-0.02719067 0.99962892 -0.00163723 4.76353371
0.00057235 0.00165340 0.99999847 0.40024337
Axis 0.06038652 -0.02182770 -0.99793638
Axis point 172.49617079 153.06286590 0.00000000
Rotation angle (degrees) 1.56129734
Shift along axis -0.75360192
> set bgColor white
> graphics silhouettes true
> set bgColor gray
> set bgColor gray
> set bgColor black
> set bgColor white
> volume #3 level 0.7846
> volume #2 level 0.5238
> volume #2 level 0.3751
> volume #2 level 0.346
> volume #2 level 0.2716
> volume #3 level 0.4855
> volume #2 level 0.2135
> volume #2 level 0.2846
> volume #3 level 0.3699
> toolshed show "Side View"
> volume #3 level 0.3087
> volume #3 level 0.2815
> open2 "/Users/shirinmortazavi/Documents/cryo-EM/CH's
> data/cryosparc_P22_J2136_006_volume_map_sharp_local.mrc"
Opened cryosparc_P22_J2136_006_volume_map_sharp_local.mrc, grid size
292,292,292, pixel 1.03, shown at level 0.276, step 2, values float32
> volume #4 step 1
> volume #4 level 0.3658
> select #4
3 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2018_008_volume_map_sharp_local.mrc
Opened cryosparc_P22_J2018_008_volume_map_sharp_local.mrc, grid size
256,256,256, pixel 1.23, shown at level 0.422, step 1, values float32
> volume #5 level 0.6006
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2136_006_volume_map_sharp_local.mrc in map
cryosparc_P22_J2018_008_volume_map_sharp_local.mrc using 101160 points
correlation = 0.9751, correlation about mean = 0.6829, overlap = 3.926e+04
steps = 88, shift = 8.34, angle = 8.25 degrees
Position of cryosparc_P22_J2136_006_volume_map_sharp_local.mrc (#4) relative
to cryosparc_P22_J2018_008_volume_map_sharp_local.mrc (#5) coordinates:
Matrix rotation and translation
0.03854178 0.84419391 -0.53465053 105.27755894
-0.00374780 -0.53492219 -0.84489303 365.72350600
-0.99924997 0.03456744 -0.01745298 306.48365519
Axis 0.67287311 0.35546393 -0.64875818
Axis point 0.00000000 69.98187886 304.88314994
Rotation angle (degrees) 139.19312916
Shift along axis 2.00617405
> ui mousemode rightMode zoom
> volume #4 level 0.4017
> volume #4 level 0.2889
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2117_map_sharp.mrc
Opened cryosparc_P22_J2117_map_sharp.mrc, grid size 256,256,256, pixel 1.23,
shown at level 0.422, step 1, values float32
> volume #6 level 0.5641
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2117_map_sharp.mrc in map
cryosparc_P22_J2018_008_volume_map_sharp_local.mrc using 62757 points
correlation = 0.99, correlation about mean = 0.8551, overlap = 4.367e+04
steps = 40, shift = 0.00576, angle = 0.00669 degrees
Position of cryosparc_P22_J2117_map_sharp.mrc (#6) relative to
cryosparc_P22_J2018_008_volume_map_sharp_local.mrc (#5) coordinates:
Matrix rotation and translation
1.00000000 0.00007639 -0.00003823 -0.00915817
-0.00007639 0.99999999 -0.00007964 0.02138608
0.00003822 0.00007964 1.00000000 -0.01711682
Axis 0.68194223 -0.32731382 -0.65407986
Axis point 0.00000000 231.76332473 260.09197916
Rotation angle (degrees) 0.00669139
Shift along axis -0.00204954
Fit map cryosparc_P22_J2117_map_sharp.mrc in map
cryosparc_P22_J2018_008_volume_map_sharp_local.mrc using 62757 points
correlation = 0.9901, correlation about mean = 0.8556, overlap = 4.363e+04
steps = 28, shift = 0.0267, angle = 0.0175 degrees
Position of cryosparc_P22_J2117_map_sharp.mrc (#6) relative to
cryosparc_P22_J2018_008_volume_map_sharp_local.mrc (#5) coordinates:
Matrix rotation and translation
0.99999996 0.00027314 -0.00002887 -0.03943950
-0.00027313 0.99999995 0.00015375 0.03888397
0.00002892 -0.00015375 0.99999999 0.02047535
Axis -0.48845621 -0.09179728 -0.86774639
Axis point 141.63904340 148.11936421 0.00000000
Rotation angle (degrees) 0.01803472
Shift along axis -0.00207238
> volume #4 level 0.3684
> open2 "/Users/shirinmortazavi/Documents/cryo-EM/CH's
> data/cryosparc_P22_J2143_map_sharp.mrc"
Opened cryosparc_P22_J2143_map_sharp.mrc, grid size 292,292,292, pixel 1.03,
shown at level 0.259, step 2, values float32
> volume #7 step 1
> volume #7 level 0.3239
> select #7
3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> undo
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2143_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 99714 points
correlation = 0.9679, correlation about mean = 0.6508, overlap = 3.283e+04
steps = 92, shift = 5.24, angle = 11.3 degrees
Position of cryosparc_P22_J2143_map_sharp.mrc (#7) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.00409633 0.53514700 0.84474902 -50.48993157
0.03590078 0.84429024 -0.53468227 106.09127097
-0.99934697 0.02813691 -0.02267069 308.30509650
Axis 0.28258824 0.92590989 -0.25066863
Axis point 111.32199244 0.00000000 194.32495755
Rotation angle (degrees) 95.23485495
Shift along axis 6.68067977
Fit map cryosparc_P22_J2143_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 99714 points
correlation = 0.9679, correlation about mean = 0.6509, overlap = 3.283e+04
steps = 36, shift = 0.00517, angle = 0.0114 degrees
Position of cryosparc_P22_J2143_map_sharp.mrc (#7) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.00414088 0.53498756 0.84484979 -50.47195303
0.03585622 0.84439318 -0.53452268 106.06187693
-0.99934839 0.02807972 -0.02267916 308.31550848
Axis 0.28247875 0.92595907 -0.25061037
Axis point 111.34375734 -0.00000000 194.31269548
Rotation angle (degrees) 95.23341877
Shift along axis 6.68463831
> ui mousemode rightMode zoom
> volume #7 level 0.3347
> volume #6 level 0.5866
> volume #6 level 0.8001
> volume #6 color salmon
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> volume #7 color dodger blue
> volume #7 color sky blue
> volume #7 color deep sky blue
Expected a keyword
> volume #7 color dodger blue
> volume #7 color royal blue
> volume #7 color cornflower blue
> volume #7 color dodger blue
> ui mousemode rightMode "move planes"
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting full
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> volume #7 color royal blue
Expected a keyword
> volume #7 color steel blue
> volume #7 color royal blue
> volume #7 color cornflower blue
> volume #7 color dodger blue
> volume #7 color deep sky blue
> volume #7 color royal blue
> volume #7 color cornflower blue
> volume #7 color royal blue
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> ~select #7
Nothing selected
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting full
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting simple
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> lighting shadows true
> lighting shadows false
> show #!6 models
> hide #!6 models
> volume #7 level 0.3024
> show #!6 models
> hide #!6 models
> volume #7 level 0.3588
> volume #6 region 0,0,0,255,255,255
> volume #6 region 0,0,0,255,255,255
> ui mousemode rightMode zoom
> volume #7 level 0.4488
> volume #6 level 0.8263
> volume #7 level 0.4166
> volume #6 level 0.8525
> volume #7 level 0.3373
> volume #7 level 0.3548
> volume #7 level 0.3481
> volume #6 level 0.7209
> ui mousemode rightMode "rotate selected models"
> select #7
4 models selected
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2143_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 79394 points
correlation = 0.9761, correlation about mean = 0.6534, overlap = 2.928e+04
steps = 60, shift = 3.31, angle = 2.84 degrees
Position of cryosparc_P22_J2143_map_sharp.mrc (#7) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.03888261 0.84437801 -0.53433503 105.14478637
-0.00396457 -0.53460484 -0.84509287 365.74979344
-0.99923593 0.03497782 -0.01743924 306.46005063
Axis 0.67293951 0.35548301 -0.64867884
Axis point 0.00000000 69.98414577 304.87538260
Rotation angle (degrees) 139.16368307
Shift along axis 1.97976845
Fit map cryosparc_P22_J2143_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 79394 points
correlation = 0.9761, correlation about mean = 0.6535, overlap = 2.928e+04
steps = 28, shift = 0.021, angle = 0.0208 degrees
Position of cryosparc_P22_J2143_map_sharp.mrc (#7) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.03900481 0.84442765 -0.53424767 105.10287351
-0.00363417 -0.53453112 -0.84514099 365.68150390
-0.99923242 0.03490611 -0.01778049 306.52202599
Axis 0.67300801 0.35559286 -0.64854756
Axis point 0.00000000 69.96229298 304.82488286
Rotation angle (degrees) 139.17005056
Shift along axis 1.97469435
> ui mousemode rightMode zoom
> volume #6 level 0.5794
> volume #6 level 0.594
> volume #6 level 0.6916
> volume #6 level 0.7257
> volume #7 level 0.3376
> volume #7 level 0.3271
> volume #7 level 0.2974
> lighting simple
> lighting shadows true
> lighting shadows false
> save /Users/shirinmortazavi/Desktop/image9.png supersample 3
> ~select #7
Nothing selected
> save /Users/shirinmortazavi/Desktop/image9.png supersample 3
> save /Users/shirinmortazavi/Desktop/image10.png supersample 3
> show #!7 models
> volume #7 transparency 0.5
> volume #7 transparency 0.7
> save /Users/shirinmortazavi/Desktop/image11.png supersample 3
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0084_Ca2+andNS309/Cryosparc/cryosparc_P22_J1330_006_volume_map_sharp_local.mrc
Opened cryosparc_P22_J1330_006_volume_map_sharp_local.mrc, grid size
300,300,300, pixel 1.03, shown at level 0.466, step 2, values float32
> volume #8 step 1
> select #8
2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> volume #8 level 0.5862
> ui mousemode rightMode "rotate selected models"
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0084_Ca2+andNS309/cryosparc_P22_J2120_map_sharp.mrc
Opened cryosparc_P22_J2120_map_sharp.mrc, grid size 320,320,320, pixel 1.03,
shown at level 0.443, step 2, values float32
> volume #9 step 1
> volume #9 level 0.7195
> select #9
2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2120_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 68076 points
correlation = 0.9882, correlation about mean = 0.7825, overlap = 5.963e+04
steps = 76, shift = 4.02, angle = 7.38 degrees
Position of cryosparc_P22_J2120_map_sharp.mrc (#9) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.98624556 -0.16528567 -0.00060842 21.01183521
-0.16528590 -0.98622159 -0.00689565 349.12692320
0.00053972 0.00690137 -0.99997604 323.21520745
Axis 0.99655541 -0.08292963 -0.00001721
Axis point 0.00000000 174.87643246 162.21292102
Rotation angle (degrees) 179.60337512
Shift along axis -8.01906961
Fit map cryosparc_P22_J2120_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 68076 points
correlation = 0.9882, correlation about mean = 0.7825, overlap = 5.963e+04
steps = 24, shift = 0.01, angle = 0.0137 degrees
Position of cryosparc_P22_J2120_map_sharp.mrc (#9) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.98626016 -0.16519817 -0.00069209 21.01481988
-0.16519889 -0.98623471 -0.00710133 349.15314058
0.00049056 0.00711809 -0.99997455 323.18808085
Axis 0.99655907 -0.08288560 -0.00005053
Axis point 0.00000000 174.87206643 162.21827999
Rotation angle (degrees) 179.59123347
Shift along axis -8.01358969
> select #9
3 models selected
> ~select #9
Nothing selected
> ui mousemode rightMode zoom
> volume #9 level 0.6832
> hide #!6 models
> hide #!6.1 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!6 models
> volume #9 level 0.5971
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
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, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
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, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
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, fuchsia
, gainsboro
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, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
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, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
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, light pink
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, mediumspringgreen
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, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
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, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
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, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
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, saddle brown
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, salmon
, sandy brown
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, seashell
, sienna
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, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
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> volume #9 color #8f8ed4
> volume #9 color #9190d4
> volume #9 color #9391d4
> volume #9 color #9591d4
> volume #9 color #9692d4
> volume #9 color #9792d4
> volume #9 color #9793d4
> volume #9 color #9893d4
> volume #9 color #9793d4
> volume #9 color #9693d4
> volume #9 color #9694d4
> volume #9 color #9695d4
> volume #9 color #9696d4
> volume #9 color #9797d4
> volume #9 color #9798d4
> volume #9 color #989ad4
> volume #9 color #989bd4
> volume #9 color #989cd4
> volume #9 color #979bd4
> volume #9 color #979ad4
> volume #9 color #979bd4
> volume #9 color #969ad4
> volume #9 color #9699d4
> volume #9 color #9599d4
> volume #9 color #9498d4
> volume #9 color #9397d4
> volume #9 color #9396d4
> volume #9 color #9295d4
> volume #9 color #9395d4
> volume #9 color #9293d4
> volume #9 color #8e8ed4
> volume #9 color #8f8fd4
> volume #9 color #8f90d4
> volume #9 color #9091d4
> volume #9 color #9192d4
> volume #9 color #9293d4
> volume #9 color #9294d4
> volume #9 color #9395d4
> volume #9 color #9396d4
> volume #9 color #9497d4
> volume #9 color #9598d4
> volume #9 color #9599d4
> volume #9 color #9499d4
> volume #9 color #9399d4
> volume #6 level 0.5648
> volume #6 level 0.5892
> volume #9 level 0.6561
> volume #9 level 0.6243
> volume #6 level 0.4867
> volume #6 level 0.5599
> volume #6 level 0.5989
> volume #6 level 0.716
> volume #6 level 0.716
> volume #6 level 0.7257
> volume #7 level 0.3096
> volume #9 level 0.8419
> volume #9 level 0.7059
> volume #9 level 0.7512
> volume #9 level 0.6878
> volume #6 level 0.6965
> save /Users/shirinmortazavi/Desktop/image9.png supersample 3
> volume #7 transparency 0
> save /Users/shirinmortazavi/Desktop/image9.png supersample 3
> volume #6 level 0.7989
> volume #6 level 0.7745
> save /Users/shirinmortazavi/Desktop/image9.png supersample 3
> save /Users/shirinmortazavi/Desktop/image10.png supersample 3
> save /Users/shirinmortazavi/Desktop/image11.png supersample 3
> volume #9 level 0.647
> save /Users/shirinmortazavi/Desktop/image12.png supersample 3
> volume #7 transparency 0.7
> volume #9 transparency 0.7
> volume #9 transparency 0
> volume #7 transparency 0
> volume #6 transparency 0.7
> save /Users/shirinmortazavi/Desktop/image13.png supersample 3
> save /Users/shirinmortazavi/Desktop/image14.png supersample 3
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> lighting shadows false
> graphics silhouettes true
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> save /Users/shirinmortazavi/Desktop/image15.png supersample 3
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/Kv1.2-KCa31-TRAM-34_Wulff.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0120_TRAM34/Kv1.2-KCa31-TRAM-34_Wulff.pdb" mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 6114
END
Chain information for Kv1.2-KCa31-TRAM-34_Wulff.pdb #10
---
Chain | Description
A B C D | No description available
> set bgColor black
> toolshed show "Side View"
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/TRAM34_dockingposition_in_Kv1.2.pdb
> close #10
> set bgColor white
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2051_006_volume_map_sharp.mrc
Opened cryosparc_P22_J2051_006_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.23, shown at level 0.17, step 1, values float32
> volume #2 level 0.4986
> volume #10 level 0.5825
> hide #!7 models
> close #8
> close #2
> close #4
> close #1
> close #7
> close #3
> ui mousemode rightMode pivot
> ui mousemode rightMode zoom
> toolshed show "Map Coordinates"
> molmap #11 4
> volume #1 color #ffff66
> volume #1 color #ffff0a
> volume #1 color #21ff06
> volume #1 color #66ff66
> volume #1 level 0.01452
> volume #10 level -0.9451
> volume #1 level 0
> volume #10 level 0.1614
> volume #10 level 0.2377
> select #1
4 models selected
> ui mousemode rightMode translate
> select #11
42 atoms, 45 bonds, 1 model selected
> select #1
4 models selected
> ui mousemode rightMode translate
> ui mousemode rightMode "translate selected models"
> volume #1 level 0.2952
> volume #1 level 0.3048
> ui mousemode rightMode zoom
> ui mousemode rightMode "translate selected models"
> volume #10 level 1.276
> ui mousemode rightMode zoom
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode translate
> ui mousemode rightMode rotate
> ui mousemode rightMode zoom
> volume #10 level 1.016
> select #11
42 atoms, 45 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> volume #10 level 0.6269
> ui mousemode rightMode zoom
> ui mousemode rightMode "translate selected models"
> ~select #11
Nothing selected
> ui mousemode rightMode zoom
> open 6cnn
6cnn title:
Cryo-EM structure of the human SK4/calmodulin channel complex in the Ca2+
bound state I [more info...]
Chain information for 6cnn #1
---
Chain | Description
A B C D | Intermediate conductance calcium-activated potassium channel protein
4
E F G H | Calmodulin-1
Non-standard residues in 6cnn #1
---
CA — calcium ion
K — potassium ion
LMT — dodecyl-β-D-maltoside
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)
> show cartoons
> hide atoms
> select #1
15740 atoms, 16004 bonds, 120 pseudobonds, 3 models selected
> ui mousemode rightMode rotate
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode translate
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode zoom
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> toolshed show "Fit in Map"
Fit molecule 6cnn (#1) to map cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) using 15740 atoms
average map value = 0.5517, steps = 92
shifted from previous position = 7.34
rotated from previous position = 11.4 degrees
atoms outside contour = 8931, contour level = 0.62692
Position of 6cnn (#1) relative to cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) coordinates:
Matrix rotation and translation
-0.00260445 0.99998876 -0.00395907 3.19825843
0.99998910 0.00258908 -0.00388288 2.99397884
-0.00387259 -0.00396914 -0.99998462 313.41629416
Axis -0.70618940 -0.70801730 0.00283433
Axis point 0.09924564 0.00000000 156.71415563
Rotation angle (degrees) 179.99650077
Shift along axis -3.49004125
Fit molecule 6cnn (#1) to map cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) using 15740 atoms
average map value = 0.5517, steps = 40
shifted from previous position = 0.00841
rotated from previous position = 0.0177 degrees
atoms outside contour = 8936, contour level = 0.62692
Position of 6cnn (#1) relative to cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) coordinates:
Matrix rotation and translation
-0.00251755 0.99998929 -0.00387866 3.16791249
0.99999039 0.00250360 -0.00359674 2.96305596
-0.00358699 -0.00388767 -0.99998600 313.35416659
Axis -0.70621733 -0.70799012 0.00266116
Axis point 0.08334543 0.00000000 156.68270257
Rotation angle (degrees) 179.98819803
Shift along axis -3.50116329
Fit molecule 6cnn (#1) to map cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) using 15740 atoms
average map value = 0.5517, steps = 48
shifted from previous position = 0.0205
rotated from previous position = 0.0206 degrees
atoms outside contour = 8932, contour level = 0.62692
Position of 6cnn (#1) relative to cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) coordinates:
Matrix rotation and translation
-0.00248954 0.99998806 -0.00420148 3.22549746
0.99998989 0.00247378 -0.00375197 2.99865854
-0.00374153 -0.00421078 -0.99998413 313.41794072
Axis -0.70622679 -0.70798005 0.00282340
Axis point 0.08118154 0.00000000 156.71503480
Rotation angle (degrees) 179.98138875
Shift along axis -3.51601737
Missing or invalid "atoms" argument: invalid atoms specifier
> molmap #1 6
> ui mousemode rightMode zoom
> undo
> undo
> volume #2 level 0.4495
> hide #11 models
> show #11 models
> hide #11 models
> select #11
42 atoms, 45 bonds, 1 model selected
> show #11 models
> hide #!1 models
> hide #11 models
> show #11 models
> show #11 target m
> set bgColor black
> set bgColor white
> molmap #11 5
> volume #2 level 0.3272
> ~select #11
Nothing selected
> show #11 atoms
> color #11 byhetero
> color #11 byhetero
> molmap #11 6
> molmap #11 5
> molmap #11 6
> volume #2 level 0.07118
> toolshed show "Map Coordinates"
> volume #2 level 0.4781
> volume #2 level 0.3061
> volume #2 level 0.4288
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting full
> lighting shadows false
> lighting simple
> graphics silhouettes false
> volume #2 level 0.2036
> volume #10 level 0.3507
> volume #10 level 0.3238
> volume #10 level 0.189
> volume #10 level 0.4383
> open2 /Users/shirinmortazavi/Documents/cryo-EM/SM0120_TRAM34/O1_T34.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-EM/SM0120_TRAM34/O1_T34.pdb"
mode="rt" encoding="utf-8">
---
warnings | Ignored bad PDB record found on line 32467
Transform_accept_ratio 0.594
Ignored bad PDB record found on line 32468
if_X_angle_constraint 0
Ignored bad PDB record found on line 32469
if_X_atom_pair_constraint 0
Ignored bad PDB record found on line 32470
if_X_chainbreak 0
Ignored bad PDB record found on line 32471
if_X_coordinate_constraint 0
31 messages similar to the above omitted
Chain information for O1_T34.pdb #3
---
Chain | Description
A B C D | No description available
E F G H | No description available
> hide #11#!3 atoms
> show #11#!3 cartoons
> select #3
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ~select #3
Nothing selected
> ui mousemode rightMode zoom
> toolshed show "Fit in Map"
Fit molecule O1_T34.pdb (#3) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 108
shifted from previous position = 10.1
rotated from previous position = 9.43 degrees
atoms outside contour = 18863, contour level = 0.43829
Position of O1_T34.pdb (#3) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00373250 0.99998421 -0.00419925 3.41400431
0.99998707 0.00371795 -0.00346681 2.75398645
-0.00345114 -0.00421214 -0.99998516 313.33347555
Axis -0.70579006 -0.70841590 0.00270441
Axis point 0.27672610 0.00000000 156.67216864
Rotation angle (degrees) 179.96974718
Shift along axis -3.51315529
Fit molecule O1_T34.pdb (#3) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 48
shifted from previous position = 0.0197
rotated from previous position = 0.0145 degrees
atoms outside contour = 18865, contour level = 0.43829
Position of O1_T34.pdb (#3) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00396554 0.99998326 -0.00421307 3.45078661
0.99998582 0.00395052 -0.00356712 2.73240630
-0.00355042 -0.00422716 -0.99998475 313.37072137
Axis -0.70570805 -0.70849744 0.00274409
Axis point 0.31285671 0.00000000 156.69081268
Rotation angle (degrees) 179.97320569
Shift along axis -3.51123383
Fit molecule O1_T34.pdb (#3) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 60
shifted from previous position = 0.0214
rotated from previous position = 0.0156 degrees
atoms outside contour = 18863, contour level = 0.43829
Position of O1_T34.pdb (#3) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00374264 0.99998418 -0.00419816 3.41437367
0.99998612 0.00372702 -0.00372077 2.78351849
-0.00370507 -0.00421203 -0.99998426 313.37143815
Axis -0.70578864 -0.70841697 0.00279115
Axis point 0.28210254 0.00000000 156.69131793
Rotation angle (degrees) 179.98005970
Shift along axis -3.50705021
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> volume #10 transparency 0.5
> volume #10 transparency 0.7
> volume #10 transparency 0.6
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/O1_T34_HB278.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-EM/SM0120_TRAM34/O1_T34_HB278.pdb"
mode="rt" encoding="utf-8">
---
warnings | Ignored bad PDB record found on line 32467
Transform_accept_ratio 0.614
Ignored bad PDB record found on line 32468
if_X_angle_constraint 0
Ignored bad PDB record found on line 32469
if_X_atom_pair_constraint 0
Ignored bad PDB record found on line 32470
if_X_chainbreak 0
Ignored bad PDB record found on line 32471
if_X_coordinate_constraint 0
31 messages similar to the above omitted
Chain information for O1_T34_HB278.pdb #4
---
Chain | Description
A B C D | No description available
E F G H | No description available
> hide #11#!3-4 atoms
> show #11#!3-4 cartoons
> select #4
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
Fit molecule O1_T34_HB278.pdb (#4) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 120
shifted from previous position = 4.79
rotated from previous position = 5.96 degrees
atoms outside contour = 18853, contour level = 0.43829
Position of O1_T34_HB278.pdb (#4) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00399729 0.99998322 -0.00418927 3.44809573
0.99998556 0.00398220 -0.00360470 2.72823848
-0.00358795 -0.00420362 -0.99998472 313.37368798
Axis -0.70569115 -0.70851421 0.00275976
Axis point 0.31843990 0.00000000 156.69230373
Rotation angle (degrees) 179.97568632
Shift along axis -3.50145123
Fit molecule O1_T34_HB278.pdb (#4) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 44
shifted from previous position = 0.012
rotated from previous position = 0.0213 degrees
atoms outside contour = 18850, contour level = 0.43829
Position of O1_T34_HB278.pdb (#4) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00379538 0.99998450 -0.00406891 3.40128458
0.99998527 0.00377955 -0.00389148 2.81201680
-0.00387605 -0.00408362 -0.99998414 313.39927313
Axis -0.70576068 -0.70844468 0.00282860
Axis point 0.28490638 0.00000000 156.70529483
Rotation angle (degrees) 179.99220103
Shift along axis -3.50617144
> hide #!3 models
> ~select #4
Nothing selected
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> hide #!10 models
> show #!10 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/O1_T34_hb278_1to296_alignedto_6cnn_1to296.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0120_TRAM34/O1_T34_hb278_1to296_alignedto_6cnn_1to296.pdb" mode="rt"
encoding="utf-8">
---
warnings | Start residue of secondary structure not found: HELIX 51 51 GLU E 6
LEU E 18 1 13
Start residue of secondary structure not found: HELIX 52 52 THR E 29 SER E 38
1 10
Start residue of secondary structure not found: HELIX 53 53 GLU E 45 ASN E 53
1 9
Start residue of secondary structure not found: HELIX 54 54 PHE E 65 LYS E 75
1 11
Start residue of secondary structure not found: HELIX 55 55 GLU E 83 PHE E 92
1 10
35 messages similar to the above omitted
Chain information for O1_T34_hb278_1to296_alignedto_6cnn_1to296.pdb #7
---
Chain | Description
A B C D | No description available
> select #7
23494 atoms, 23733 bonds, 8 pseudobonds, 2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> close #7
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/Kv1.2-KCa31-TRAM-34_Wulff.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0120_TRAM34/Kv1.2-KCa31-TRAM-34_Wulff.pdb" mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 6114
END
Chain information for Kv1.2-KCa31-TRAM-34_Wulff.pdb #7
---
Chain | Description
A B C D | No description available
> select #7
6055 atoms, 6126 bonds, 1 model selected
> ~select #7
Nothing selected
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> hide #7 models
> show #7 models
> select #7
6055 atoms, 6126 bonds, 1 model selected
> ~select #7
Nothing selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode zoom
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode zoom
> hide #!10 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> toolshed show "Fit to Segments"
> select #4
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
Density map not found or not selected
Density map not found or not selected
> toolshed show "Fit in Map"
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 108
shifted from previous position = 2.09
rotated from previous position = 15 degrees
atoms outside contour = 3052, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93046748 0.36632247 -0.00617313 131.30923161
0.36635074 0.93046691 -0.00429511 90.96138457
0.00417050 -0.00625799 -0.99997171 318.19472016
Axis -0.18643919 -0.98246283 0.00268546
Axis point 56.59723434 0.00000000 159.36935116
Rotation angle (degrees) 179.69838592
Shift along axis -112.99286627
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 44
shifted from previous position = 0.0131
rotated from previous position = 0.0279 degrees
atoms outside contour = 3050, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93039635 0.36650596 -0.00600036 131.26038688
0.36653476 0.93039246 -0.00470374 91.04709437
0.00385874 -0.00657569 -0.99997093 318.21572653
Axis -0.18653619 -0.98244390 0.00287035
Axis point 56.57993447 0.00000000 159.38154583
Rotation angle (degrees) 179.71250895
Shift along axis -113.02008511
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 64
shifted from previous position = 0.00532
rotated from previous position = 0.00833 degrees
atoms outside contour = 3051, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93040998 0.36646908 -0.00613647 131.28998575
0.36649892 0.93040641 -0.00473683 91.04878307
0.00397351 -0.00665620 -0.99996994 318.21928166
Axis -0.18651707 -0.98244744 0.00289924
Axis point 56.58513543 0.00000000 159.38828566
Rotation angle (degrees) 179.70519468
Shift along axis -113.01587234
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 60
shifted from previous position = 0.00756
rotated from previous position = 0.00592 degrees
atoms outside contour = 3047, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93039214 0.36651306 -0.00621482 131.30163669
0.36654322 0.93038920 -0.00468877 91.04639919
0.00406371 -0.00664040 -0.99996969 318.22396196
Axis -0.18654041 -0.98244306 0.00288300
Axis point 56.58310595 0.00000000 159.39228760
Rotation angle (degrees) 179.70027822
Shift along axis -113.02352313
> hide #7 models
> show #7 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #7 models
> show #7 models
> show #!3 models
> hide #7 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #7 models
> show #!10 models
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select ligand
434 atoms, 443 bonds, 4 models selected
Expected an objects specifier or a keyword
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel byhetero
> color sel bychain
> color sel byhetero
> select #7
6055 atoms, 6126 bonds, 1 model selected
> ~select #7
Nothing selected
> toolshed show "Fit in Map"
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 48
shifted from previous position = 0.0254
rotated from previous position = 0.035 degrees
atoms outside contour = 3050, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93020954 0.36697679 -0.00618308 131.26891174
0.36700529 0.93020875 -0.00433417 90.98490337
0.00416102 -0.00630091 -0.99997148 318.21967005
Axis -0.18678474 -0.98239714 0.00270650
Axis point 56.55815074 0.00000000 159.38274891
Rotation angle (degrees) 179.69835214
Shift along axis -113.04107596
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 48
shifted from previous position = 0.0055
rotated from previous position = 0.0128 degrees
atoms outside contour = 3048, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93025945 0.36685321 -0.00600446 131.24272482
0.36688066 0.93025782 -0.00435225 90.98459548
0.00398906 -0.00625164 -0.99997249 318.21381467
Axis -0.18671912 -0.98240963 0.00269854
Axis point 56.56271840 0.00000000 159.37442290
Rotation angle (degrees) 179.70857936
Shift along axis -113.03095734
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 48
shifted from previous position = 0.0211
rotated from previous position = 0.0431 degrees
atoms outside contour = 3053, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93046360 0.36632774 -0.00643951 131.35197701
0.36635689 0.93046530 -0.00411593 90.93190900
0.00448396 -0.00618888 -0.99997079 318.18812913
Axis -0.18644233 -0.98246241 0.00262228
Axis point 56.59735733 0.00000000 159.37143011
Rotation angle (degrees) 179.68147791
Shift along axis -112.99237162
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 64
shifted from previous position = 0.00401
rotated from previous position = 0.02 degrees
atoms outside contour = 3050, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93045928 0.36634463 -0.00609329 131.29266348
0.36637181 0.93045927 -0.00415164 90.93492084
0.00414862 -0.00609534 -0.99997281 318.17974298
Axis -0.18645053 -0.98246089 0.00260757
Axis point 56.59514496 0.00000000 159.35674730
Rotation angle (degrees) 179.70135157
Shift along axis -112.98991334
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 60
shifted from previous position = 0.00615
rotated from previous position = 0.0159 degrees
atoms outside contour = 3051, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93040874 0.36646904 -0.00632496 131.32392496
0.36649731 0.93041018 -0.00407560 90.93166505
0.00439123 -0.00611005 -0.99997168 318.18057714
Axis -0.18651662 -0.98244839 0.00259200
Axis point 56.58834472 0.00000000 159.36324413
Rotation angle (degrees) 179.68751750
Shift along axis -113.00503936
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 60
shifted from previous position = 0.0216
rotated from previous position = 0.0327 degrees
atoms outside contour = 3043, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93028961 0.36677542 -0.00608370 131.26533458
0.36680385 0.93028754 -0.00447310 91.00548779
0.00401896 -0.00639280 -0.99997148 318.22192595
Axis -0.18667836 -0.98241719 0.00276519
Axis point 56.56947556 0.00000000 159.38318402
Rotation angle (degrees) 179.70539902
Shift along axis -113.02980947
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 64
shifted from previous position = 0.0184
rotated from previous position = 0.0302 degrees
atoms outside contour = 3045, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93047737 0.36629837 -0.00611170 131.30116120
0.36632748 0.93047464 -0.00459518 91.01205272
0.00400358 -0.00651459 -0.99997076 318.21246242
Axis -0.18642671 -0.98246480 0.00282711
Axis point 56.59836325 0.00000000 159.38158235
Rotation angle (degrees) 179.70504507
Shift along axis -112.99455954
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 60
shifted from previous position = 0.0195
rotated from previous position = 0.0196 degrees
atoms outside contour = 3044, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93035431 0.36661183 -0.00605081 131.26846757
0.36664061 0.93035120 -0.00461429 91.02480731
0.00393773 -0.00651140 -0.99997104 318.23176108
Axis -0.18659209 -0.98243340 0.00283125
Axis point 56.57804513 0.00000000 159.38957348
Rotation angle (degrees) 179.70873155
Shift along axis -113.01847385
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 64
shifted from previous position = 0.0208
rotated from previous position = 0.0246 degrees
atoms outside contour = 3051, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93048537 0.36627529 -0.00627451 131.32637108
0.36630532 0.93048353 -0.00456037 91.01062330
0.00416798 -0.00654175 -0.99996991 318.21388540
Axis -0.18641485 -0.98246706 0.00282516
Axis point 56.59817549 0.00000000 159.38690668
Rotation angle (degrees) 179.69550455
Shift along axis -112.99712144
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 76
shifted from previous position = 0.0183
rotated from previous position = 0.0206 degrees
atoms outside contour = 3044, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93036880 0.36657403 -0.00611199 131.28095716
0.36660307 0.93036616 -0.00457966 91.02002078
0.00400760 -0.00650145 -0.99997083 318.22894415
Axis -0.18657223 -0.98243720 0.00281990
Axis point 56.58030013 0.00000000 159.38952011
Rotation angle (degrees) 179.70491130
Shift along axis -113.01746161
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 64
shifted from previous position = 0.018
rotated from previous position = 0.0364 degrees
atoms outside contour = 3050, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93047597 0.36629720 -0.00638787 131.34631555
0.36632593 0.93047759 -0.00409196 90.93075670
0.00444490 -0.00614752 -0.99997122 318.18565209
Axis -0.18642606 -0.98246554 0.00260565
Axis point 56.59916614 0.00000000 159.36811791
Rotation angle (degrees) 179.68412371
Shift along axis -112.99363048
> volume #10 level 0.3086
> volume #10 level 0.2704
> volume #10 transparency 0.4
> volume #10 transparency 0.3
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> set bgColor black
> select #11
42 atoms, 45 bonds, 1 model selected
> show #11 models
> hide #7 models
> hide #!10 models
> show #!10 models
> show #7 models
> close #11
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/TRAM34_dockingposition_in_Kv1.2.pdb
> hide #7 models
> show #7 models
> set bgColor white
> set bgColor black
> volume #10 level 0.5528
> ui mousemode rightMode "translate selected models"
> select #8
42 atoms, 45 bonds, 1 model selected
> ui mousemode rightMode zoom
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode zoom
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select H
35792 atoms, 4 models selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select #8
42 atoms, 45 bonds, 1 model selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select #8
42 atoms, 45 bonds, 1 model selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select #8
42 atoms, 45 bonds, 1 model selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select H
35792 atoms, 4 models selected
> hide sel target a
> select #8
42 atoms, 45 bonds, 1 model selected
> hide #8 models
> ~select #8
Nothing selected
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> select #7 /a,b,c,d:250
56 atoms, 52 bonds, 1 model selected
> color sel byhetero
> ~select #7 /a,b,c,d:250
Nothing selected
> volume #10 level 0.3849
Missing or invalid "filename" argument: Expected a file name
No help found for 'help:user/commands/open.htmlpubchem'
> open 679 pubchem
Missing filename suffix 679
> open 75151 pubchem
Missing filename suffix 75151
> open 75151 fromDatabase pubchem
Summary of feedback from opening 75151 fetched from pubchem
---
note | Fetching compressed PubChem 75151 from
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/75151/SDF?record_type=3d
PubChem entry 75151
> hide #7 models
> ui mousemode rightMode "translate selected models"
> select #11
10 atoms, 9 bonds, 1 model selected
> ~select #11
Nothing selected
> ui mousemode rightMode zoom
> select #11
10 atoms, 9 bonds, 1 model selected
> select H
35798 atoms, 5 models selected
> hide sel target a
> show #7 models
> ui mousemode rightMode "translate selected models"
> select #11
10 atoms, 9 bonds, 1 model selected
> ~select #11
Nothing selected
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> toolshed show "Fit in Map"
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 84
shifted from previous position = 0.00235
rotated from previous position = 0.0115 degrees
atoms outside contour = 2832, contour level = 0.38488
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93045997 0.36634087 -0.00621198 131.31556740
0.36636816 0.93046134 -0.00400717 90.91759804
0.00431202 -0.00600439 -0.99997267 318.17455490
Axis -0.18644862 -0.98246141 0.00254766
Axis point 56.59671562 0.00000000 159.35541483
Rotation angle (degrees) 179.69312590
Shift along axis -112.99603633
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 56
shifted from previous position = 0.016
rotated from previous position = 0.019 degrees
atoms outside contour = 2831, contour level = 0.38488
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93036770 0.36657480 -0.00623252 131.30174447
0.36660313 0.93036784 -0.00422077 90.95824108
0.00425131 -0.00621172 -0.99997166 318.20518653
Axis -0.18657245 -0.98243762 0.00265484
Axis point 56.58158442 0.00000000 159.37513908
Rotation angle (degrees) 179.69429005
Shift along axis -113.01330171
> volume #10 level 0.2551
> volume #10 level 0.6138
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2142_006_volume_map_sharp.mrc
Opened cryosparc_P22_J2142_006_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.23, shown at level 0.163, step 1, values float32
> volume #12 level 0.7562
> volume #12 level 0.6661
> volume #10 level 0.6367
> volume #10 level 0.5451
> volume #10 level 0.652
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2142_006_volume_map_sharp.mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 36785 points
correlation = 0.9951, correlation about mean = 0.9464, overlap = 4.432e+04
steps = 44, shift = 0.0238, angle = 0.0617 degrees
Position of cryosparc_P22_J2142_006_volume_map_sharp.mrc (#12) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99999945 0.00104664 -0.00009436 -0.16481899
-0.00104662 0.99999942 0.00023612 0.12215815
0.00009461 -0.00023602 0.99999997 0.04019466
Axis -0.21917592 -0.08772519 -0.97173361
Axis point 115.48470284 160.39383882 0.00000000
Rotation angle (degrees) 0.06171180
Shift along axis -0.01365050
Fit map cryosparc_P22_J2142_006_volume_map_sharp.mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 36785 points
correlation = 0.9951, correlation about mean = 0.9463, overlap = 4.426e+04
steps = 40, shift = 0.0272, angle = 0.0168 degrees
Position of cryosparc_P22_J2142_006_volume_map_sharp.mrc (#12) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99999967 0.00080556 -0.00014088 -0.12152373
-0.00080550 0.99999960 0.00039785 0.08124985
0.00014120 -0.00039774 0.99999991 0.07325534
Axis -0.43742403 -0.15508838 -0.88578090
Axis point 96.10160723 164.10868689 0.00000000
Rotation angle (degrees) 0.05210487
Shift along axis -0.02433169
> hide #7 models
> volume #12 level 0.4107
> volume #12 level 0.7262
> volume #10 level 0.7283
> volume #12 level 0.4858
> volume #10 level 0.6596
> volume #10 level 0.4688
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> set bgColor white
> set bgColor black
> volume #10 level 0.5985
> graphics silhouettes false
> graphics silhouettes true
> volume #10 level 0.4459
> graphics silhouettes false
> volume #10 level 0.4154
> graphics silhouettes true
> volume #10 level 0.4154
> graphics silhouettes false
> volume #10 level 0.4154
> graphics silhouettes true
> graphics silhouettes false
> volume #10 level 0.3925
> graphics silhouettes true
> graphics silhouettes false
> volume #10 level 0.423
> graphics silhouettes true
> volume #10 level 0.4383
> volume #10 level 0.4536
> volume #10 level 0.5451
> volume #10 level 0.5375
> volume #12 level 0.5835
> volume #12 level 0.4708
> volume #12 level 0.4708
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/DockInMap_14/placed_model.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0120_TRAM34/DockInMap_14/placed_model.pdb" mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 6065
Chain information for placed_model.pdb #13
---
Chain | Description
A B C D | No description available
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> preset "overall look" interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting full
> lighting full
> lighting full
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting flat
> lighting full
> set bgColor white
> set bgColor black
> set bgColor white
> set bgColor black
> lighting simple
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> volume #10 level 0.2017
> volume #10 level 0.3391
> show #!4 models
> hide #!4 models
> show #!4 models
> toolshed show "Fit in Map"
Fit molecule O1_T34_HB278.pdb (#4) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 64
shifted from previous position = 0.0229
rotated from previous position = 0.0269 degrees
atoms outside contour = 17053, contour level = 0.33909
Position of O1_T34_HB278.pdb (#4) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00356195 0.99998463 -0.00424610 3.39117534
0.99998749 0.00354700 -0.00352422 2.78838865
-0.00350910 -0.00425860 -0.99998476 313.34803499
Axis -0.70584552 -0.70836046 0.00275051
Axis point 0.24881144 0.00000000 156.67959919
Rotation angle (degrees) 179.97019394
Shift along axis -3.50696172
Fit molecule O1_T34_HB278.pdb (#4) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 48
shifted from previous position = 0.0198
rotated from previous position = 0.0164 degrees
atoms outside contour = 17063, contour level = 0.33909
Position of O1_T34_HB278.pdb (#4) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00380339 0.99998403 -0.00417686 3.41847866
0.99998611 0.00378810 -0.00366193 2.77462426
-0.00364605 -0.00419072 -0.99998456 313.37809900
Axis -0.70575971 -0.70844585 0.00277628
Axis point 0.28575740 0.00000000 156.69461074
Rotation angle (degrees) 179.97853548
Shift along axis -3.50827000
Fit molecule O1_T34.pdb (#3) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 64
shifted from previous position = 0.024
rotated from previous position = 0.000536 degrees
atoms outside contour = 17067, contour level = 0.33909
Position of O1_T34.pdb (#3) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00374769 0.99998419 -0.00419028 3.41326140
0.99998610 0.00373211 -0.00372105 2.77930930
-0.00370536 -0.00420418 -0.99998429 313.39398090
Axis -0.70578695 -0.70841866 0.00278833
Axis point 0.28428441 0.00000000 156.70257368
Rotation angle (degrees) 179.98038984
Shift along axis -3.50410299
Fit molecule O1_T34.pdb (#3) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 64
shifted from previous position = 0.0234
rotated from previous position = 0.0152 degrees
atoms outside contour = 17057, contour level = 0.33909
Position of O1_T34.pdb (#3) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00363636 0.99998506 -0.00407937 3.38068224
0.99998728 0.00362206 -0.00350772 2.77253865
-0.00349290 -0.00409208 -0.99998552 313.32154539
Axis -0.70582527 -0.70838093 0.00267510
Axis point 0.26329833 0.00000000 156.66613950
Rotation angle (degrees) 179.97628231
Shift along axis -3.51201755
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #4
> close #3
> close #9
> close #6
> show #8 models
> hide #8 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> open2 /Users/shirinmortazavi/Documents/cryo-EM/SM0121_TRAM34_2/O1_T34.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-EM/SM0121_TRAM34_2/O1_T34.pdb"
mode="rt" encoding="utf-8">
---
warnings | Ignored bad PDB record found on line 32467
Transform_accept_ratio 0.594
Ignored bad PDB record found on line 32468
if_X_angle_constraint 0
Ignored bad PDB record found on line 32469
if_X_atom_pair_constraint 0
Ignored bad PDB record found on line 32470
if_X_chainbreak 0
Ignored bad PDB record found on line 32471
if_X_coordinate_constraint 0
31 messages similar to the above omitted
Chain information for O1_T34.pdb #2
---
Chain | Description
A B C D | No description available
E F G H | No description available
> show #7,13#!2 cartoons
> hide #7,13#!2 atoms
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select ligand
434 atoms, 443 bonds, 4 models selected
> show sel target ab
> select H
22550 atoms, 5 models selected
> select #8
42 atoms, 45 bonds, 1 model selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select #2
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select H
22550 atoms, 5 models selected
> hide sel target a
> select #2
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #2
Nothing selected
> hide #13 models
> show #13 models
> color #13#!2 byhetero
> select #13
6055 atoms, 6126 bonds, 1 model selected
> color sel byhetero
> select ligand
434 atoms, 443 bonds, 4 models selected
> color sel byhetero
> color sel bychain
> color sel byhetero
> undo
> undo
> select #13
6055 atoms, 6126 bonds, 1 model selected
> ~select #13
Nothing selected
> hide #!2 models
> volume #10 level 1.186
> volume #10 level 0.8351
> volume #10 level 0.6596
> volume #12 level 0.6886
> volume #10 level 0.6291
> close #1
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/DockInMap_15_O1_KCa3.1_TRAM34_rigidbody_in_2051_sharp/placed_model_O1_KCa3.1_T34_rigid_in_2051_sharp.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0121_TRAM34_2/DockInMap_15_O1_KCa3.1_TRAM34_rigidbody_in_2051_sharp/placed_model_O1_KCa3.1_T34_rigid_in_2051_sharp.pdb"
mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 32428
Chain information for placed_model_O1_KCa3.1_T34_rigid_in_2051_sharp.pdb #1
---
Chain | Description
A B C D | No description available
E F G H | No description available
> show #13#!1 cartoons
> hide #13#!1 atoms
> select #13
6055 atoms, 6126 bonds, 1 model selected
> hide #13 models
> close #13
> select #1
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select ligand
126 atoms, 135 bonds, 3 models selected
> show sel atoms
> select H
35798 atoms, 5 models selected
> hide sel target a
> select #1
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #1
Nothing selected
> select #1
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #1
Nothing selected
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/DockInMap_16_O1_KCa3.1_TRAM34_HB278_rigidbody_in_2051_sharp/placed_model_O1_KCa3.1_TRAM34_HB278_rigid_in_2051_sharp.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0121_TRAM34_2/DockInMap_16_O1_KCa3.1_TRAM34_HB278_rigidbody_in_2051_sharp/placed_model_O1_KCa3.1_TRAM34_HB278_rigid_in_2051_sharp.pdb"
mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 32428
Chain information for
placed_model_O1_KCa3.1_TRAM34_HB278_rigid_in_2051_sharp.pdb #3
---
Chain | Description
A B C D | No description available
E F G H | No description available
> hide #!1,3 atoms
> show #!1,3 cartoons
> close #2
> select #3
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select ligand
126 atoms, 135 bonds, 3 models selected
> show sel target ab
> select N
6132 atoms, 4 bonds, 4 models selected
> select H
35798 atoms, 5 models selected
> hide sel target a
> select ligand
126 atoms, 135 bonds, 3 models selected
> color sel byhetero
> color sel byhetero
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> color sel bychain
> undo
> color sel byhetero
> select #3
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> select #3
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select ligand
126 atoms, 135 bonds, 3 models selected
> color sel byhetero
> color sel byhetero
> color sel byhetero
> select #3
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/DockInMap_17_O2_KCa3.1_TRAM34_rigidbody_in_2051_sharp/placed_model_O2_KCa3.1_TRAM34_rigid_in_2051_sharp.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0121_TRAM34_2/DockInMap_17_O2_KCa3.1_TRAM34_rigidbody_in_2051_sharp/placed_model_O2_KCa3.1_TRAM34_rigid_in_2051_sharp.pdb"
mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 32428
Chain information for placed_model_O2_KCa3.1_TRAM34_rigid_in_2051_sharp.pdb #2
---
Chain | Description
A B C D | No description available
E F G H | No description available
> hide #!1-3 atoms
> show #!1-3 cartoons
> volume #10 level 1.14
> select #2
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select ligand
168 atoms, 180 bonds, 4 models selected
> show sel target ab
> select H
52139 atoms, 6 models selected
> hide sel target a
> color sel byhetero
> color sel byhetero
> select #2
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #2
Nothing selected
> volume #10 level 0.8046
> hide #!2 models
> volume #10 level 1.041
> volume #10 level 0.8275
> volume #10 level 0.7054
> volume #10 level 0.5299
> hide #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #10 level 0.3391
> show #11 models
> select #11
10 atoms, 9 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> volume #10 level 0.5604
> hide #!1 models
> hide #!3 models
> ui mousemode rightMode "translate selected atoms"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode zoom
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ~select #11
Nothing selected
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> ui mousemode rightMode "translate selected models"
> select #11
10 atoms, 9 bonds, 1 model selected
> volume #10 level 0.2933
> volume #12 level 0.4558
> volume #10 level 0.5375
> volume #10 level 0.5299
> volume #10 level 0.5451
> volume #10 level 0.5375
> volume #12 level 0.4483
> undo
> ~select #11
Nothing selected
> volume #12 level 0.4633
> volume #12 level 0.4934
> volume #12 level 0.4633
> ui mousemode rightMode zoom
> molmap #11 4
Expected a keyword
> molmap #11 4 cutoffRange 3
> molmap #11 4 cutoffRange 4
> molmap #11 4 cutoffRange 5
> molmap #11 4 cutoffRange 4
> molmap #11 4 cutoffRange 5
> molmap #11 4 cutoffRange 3
> molmap #11 4 cutoffRange 5
> molmap #11 4 onGrid #10
> volume #4 level 0.09668
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2145_map_locres.mrc
Opened cryosparc_P22_J2145_map_locres.mrc, grid size 256,256,256, pixel 1.23,
shown at level 3.75, step 1, values float32
> volume #10 level 1.545
> volume #10 level 0.6062
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2145_map_locres.mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 167735 points
correlation = 0.6639, correlation about mean = -0.0393, overlap = 3.006e+05
steps = 52, shift = 1.16, angle = 2.05 degrees
Position of cryosparc_P22_J2145_map_locres.mrc (#5) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99936584 0.03527935 0.00482592 -6.36493002
-0.03529546 0.99937149 0.00329524 5.19416258
-0.00470663 -0.00346349 0.99998293 2.43291390
Axis -0.09448056 0.13325580 -0.98656795
Axis point 148.02785744 186.03992728 0.00000000
Rotation angle (degrees) 2.04978343
Shift along axis -1.10672042
Fit map cryosparc_P22_J2145_map_locres.mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 167735 points
correlation = 0.6639, correlation about mean = -0.03927, overlap = 3.006e+05
steps = 40, shift = 0.00471, angle = 0.00585 degrees
Position of cryosparc_P22_J2145_map_locres.mrc (#5) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99936549 0.03527564 0.00492368 -6.38291372
-0.03529195 0.99937171 0.00326601 5.20043371
-0.00480537 -0.00343771 0.99998255 2.44716833
Axis -0.09369299 0.13597591 -0.98627186
Axis point 148.30405178 186.55548370 0.00000000
Rotation angle (degrees) 2.05018917
Shift along axis -1.10840525
Fit map cryosparc_P22_J2145_map_locres.mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 167735 points
correlation = 0.664, correlation about mean = -0.03933, overlap = 3.006e+05
steps = 40, shift = 0.011, angle = 0.00374 degrees
Position of cryosparc_P22_J2145_map_locres.mrc (#5) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99936411 0.03532047 0.00488301 -6.37519416
-0.03533676 0.99937005 0.00329035 5.20051206
-0.00476372 -0.00346080 0.99998266 2.43754587
Axis -0.09424828 0.13467147 -0.98639792
Axis point 148.05662576 186.10496414 0.00000000
Rotation angle (degrees) 2.05253217
Shift along axis -1.10317851
> volume #5 level 3.677
> volume #10 level 0.6749
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2051_006_volume_map_sharp.mrc
Opened cryosparc_P22_J2051_006_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.23, shown at level 0.17, step 1, values float32
> volume #6 level 0.5673
> volume #10 level 0.5909
> volume #10 level 0.5757
> volume #6 level 0.552
> volume #10 level 0.5222
> volume #10 level 0.8122
> hide #11 models
> volume #10 level 0.4536
> volume #10 level 0.5299
> volume #10 level 0.7206
> volume #10 level 0.8733
> toolshed show "Measure and Color Blobs"
> toolshed show Shell
Missing or invalid "surfaces" argument: empty atom specifier
Unknown command: local resolution
> color sample #10 map #5 palette rainbow
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> measure blob #!10.1 triangleNumber 42184 color #0000ccff outline true
Surface cryosparc_P22_J2051_006_volume_map_sharp.mrc #10.1 blob:
volume = 5691
area = 6903.5
size = 65.763 49.34 30.353
> measure blob #!10.1 triangleNumber 36022 color #2de170ff outline true
Surface cryosparc_P22_J2051_006_volume_map_sharp.mrc #10.1 blob:
volume = 6038.5
area = 7654.2
size = 53.454 46.664 46.829
> undo
> redo
> ui mousemode rightMode zoom
> hide #!10 models
> show #!10 models
> hide #!5 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> ui mousemode rightMode "pick blobs"
> measure blob #!10.1 triangleNumber 32222 color #0000ccff outline true
Surface cryosparc_P22_J2051_006_volume_map_sharp.mrc #10.1 blob:
volume = 5691
area = 6903.5
size = 65.763 49.34 30.353
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> toolshed show "Measure and Color Blobs"
> color sample #10 map #5 palette rainbow
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> toolshed show "Measure and Color Blobs"
> measure blob #!10.1 triangleNumber 69512 color #0000ccff outline true
Surface cryosparc_P22_J2051_006_volume_map_sharp.mrc #10.1 blob:
volume = 463.47
area = 465.35
size = 22.95 13.622 7.2265
> measure blob #!10.1 triangleNumber 41359 color #0499ccff outline true
Surface cryosparc_P22_J2051_006_volume_map_sharp.mrc #10.1 blob:
volume = 30.687
area = 51.106
size = 4.2121 4.3764 3.6348
> color sample #10 map #5 palette rainbow
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> ui mousemode rightMode distance
> ui mousemode rightMode zoom
> toolshed show ViewDockX
No suitable models found for ViewDockX
> toolshed show "Show Volume Menu"
> toolshed show "Map Coordinates"
> toolshed show "Show Volume Menu"
> toolshed show "Volume Viewer"
> help help:devel
> help help:index.html
> color sample #10 map #5 palette rainbow range full
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> color sample #10 map #5 palette rainbow range full
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
Expected a keyword
Expected a keyword
Expected a keyword
> color sample #10 map #5 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> hide #!10 models
> show #!10 models
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2147_map_locres.mrc
> /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2148_map_locres.mrc
Opened cryosparc_P22_J2147_map_locres.mrc, grid size 256,256,256, pixel 1.23,
shown at level 3.75, step 1, values float32
Opened cryosparc_P22_J2148_map_locres.mrc, grid size 256,256,256, pixel 1.23,
shown at level 3.19, step 1, values float32
> color sample #10 map #5 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> volume #10 level 0.9343
> color sample #10 map #9 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 4.441, maximum 8.05
> volume #9 level 5.914
> color sample #10 map #9 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 4.441, maximum 8.05
> volume #9 level 3.499
> color sample #10 map #9 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 4.441, maximum 8.05
> color sample #10 map #13 palette
> 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 3.458, maximum 6.769
> volume #13 level 2.929
> volume #10 level 0.8351
> volume #10 level 0.8656
> volume #13 level 2.652
> volume #10 level 0.4993
> volume #9 level 3.446
> volume #10 level 0.9801
> open2
> /Users/shirinmortazavi/Downloads/cryosparc_P22_J348_003_volume_map_sharp.mrc
Opened cryosparc_P22_J348_003_volume_map_sharp.mrc, grid size 286,286,286,
pixel 0.72, shown at level 0.0997, step 2, values float32
> volume #6 step 1
> volume #6 level 0.03806
> volume #6 level 0.03009
> volume #6 level 0.01681
> volume #6 level 0.02478
> volume #6 level 0.03965
> volume #6 level 0.03221
> volume #6 level 0.02478
> volume #6 level 0.03434
> volume #6 level 0.04284
> volume #6 level 0.06514
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2153_map_locres.mrc
Opened cryosparc_P22_J2153_map_locres.mrc, grid size 256,256,256, pixel 1.23,
shown at level 51.3, step 1, values float32
> volume #13 level 0.1539
> volume #6 level 46.11
> volume #13 level 3.398
> volume #6 level 48.35
> volume #6 level 51.88
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> volume #6 level 9.433
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> volume #6 level 2.056
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> volume #6 level 0
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> undo
> undo
> undo
> undo
> undo
> undo
> redo
> redo
> undo
> redo
> undo
> redo
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> undo
> undo
> redo
> undo
> redo
> volume #6 level 50.25
> volume #13 level 0
> color sample #10 map #13 palette
> 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 3.451, maximum 5.651
> undo
> redo
> undo
> undo
> redo
> redo
> undo
> redo
> redo
> redo
> undo
> redo
> volume #13 level 4.776
> color sample #10 map #9 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 4.419, maximum 7.997
> color sample #10 map #13 palette
> 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 3.451, maximum 5.651
> volume #13 level 2.733
> color sample #10 map #13 palette
> 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 3.451, maximum 5.651
> undo
> undo
> redo
> undo
> redo
> color sample #10 map #13 palette
> 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 3.451, maximum 5.651
Map values for surface "cap near": minimum 0.438, mean 3.219, maximum 3.855
> set bgColor white
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting full
> lighting full
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting full
> lighting flat
> lighting simple
> lighting full
> lighting shadows false
> lighting simple
> graphics silhouettes false
> lighting full
> lighting simple
> lighting shadows true
> lighting full
> lighting full
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> volume #10 level 0.8759
Expected a keyword
> volume gaussian #10 bfactor -100
> volume #10 level 0.9131
> volume #14 level 1.329
> volume #14 level 1.374
> volume #14 level 1.171
> volume #10 level 0.6674
> volume gaussian #10 bfactor -200
> volume #15 level 14.44
> volume gaussian #10 bfactor -50
> volume #15 level 0.7736
> volume #15 level 0.9198
> volume #15 level 0.7493
> volume #10 level 0.4142
> volume #10 level 0.4366
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
[lots of these deleted]
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Window position QRect(689,1069 100x30) outside any known screen, using primary
screen
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-10.36.19
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → volume subregion: 'NoneType' object has no attribute 'size' |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
A clip cap of one map was colored by volume data value of another map. Then that second map was deleted. When the coloring tried to update it tried to use the deleted volume. Made it detect that and delete the auto coloring callback.