![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7671 closed defect (can't reproduce)
Crash during color drop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x0000000110199600 (most recent call first):
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 1400000,
"procLaunch" : "2022-09-22 20:38:58.4011 +0900",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"procStartAbsTime" : 1178634348437196,
"coalitionID" : 46291,
"osVersion" : {
"train" : "macOS 12.1",
"build" : "21C52",
"releaseType" : "User"
},
"captureTime" : "2022-09-26 15:44:19.4958 +0900",
"incident" : "5359164C-0274-4BD6-BB04-2365D0BF169A",
"bug_type" : "309",
"pid" : 1776,
"procExitAbsTime" : 1441341105839818,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7A5A9E8A-7F5A-57F7-918F-A4C6A8216CD8","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F6173C33-7833-68D1-A4A7-E6B615A19B58",
"wakeTime" : 13723,
"bridgeVersion" : {"build":"19P647","train":"6.1"},
"sleepWakeUUID" : "AB5FA8DF-A567-4B45-A4B4-F47FB7015788",
"sip" : "enabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"asi" : {"libsystem_c.dylib":["Assertion failed: (backingScaleFactor > 0.f), function drawnFocusRingBitmapForTime, file NSAutomaticFocusRing.m, line 346."]},
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"faultingThread" : 0,
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"path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
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===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/kunwoong/Desktop/hBEST1_KKW/Analysis/hB_1uM_BRIL_Close_J869.pdb
Chain information for hB_1uM_BRIL_Close_J869.pdb #1
---
Chain | Description
A B C D E | No description available
> lighting soft
> set bgColor white
> style stick
Changed 15460 atom styles
> style sphere
Changed 15460 atom styles
> style ball
Changed 15460 atom styles
> style sphere
Changed 15460 atom styles
> show cartoons
> hide cartoons
> show cartoons
> show atoms
> hide atoms
> hide cartoons
> show cartoons
> show atoms
> hide atoms
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> color byhetero
> color bychain
> show atoms
> color byhetero
> color bychain
> color bypolymer
> color bychain
> rainbow
> color bychain
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for hB_1uM_BRIL_Close_J869.pdb_A SES surface #1.1: minimum,
-18.17, mean -1.05, maximum 12.92
Coulombic values for hB_1uM_BRIL_Close_J869.pdb_B SES surface #1.2: minimum,
-17.96, mean -1.03, maximum 12.99
Coulombic values for hB_1uM_BRIL_Close_J869.pdb_C SES surface #1.3: minimum,
-18.22, mean -1.03, maximum 13.48
Coulombic values for hB_1uM_BRIL_Close_J869.pdb_D SES surface #1.4: minimum,
-17.73, mean -1.03, maximum 13.38
Coulombic values for hB_1uM_BRIL_Close_J869.pdb_E SES surface #1.5: minimum,
-18.21, mean -1.02, maximum 13.00
To also show corresponding color key, enter the above coulombic command and
add key true
> color bypolymer
> coulombic
Coulombic values for hB_1uM_BRIL_Close_J869.pdb_A SES surface #1.1: minimum,
-18.17, mean -1.05, maximum 12.92
Coulombic values for hB_1uM_BRIL_Close_J869.pdb_B SES surface #1.2: minimum,
-17.96, mean -1.03, maximum 12.99
Coulombic values for hB_1uM_BRIL_Close_J869.pdb_C SES surface #1.3: minimum,
-18.22, mean -1.03, maximum 13.48
Coulombic values for hB_1uM_BRIL_Close_J869.pdb_D SES surface #1.4: minimum,
-17.73, mean -1.03, maximum 13.38
Coulombic values for hB_1uM_BRIL_Close_J869.pdb_E SES surface #1.5: minimum,
-18.21, mean -1.02, maximum 13.00
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of hB_1uM_BRIL_Close_J869.pdb_A SES surface, 5700 of 414034
triangles, hB_1uM_BRIL_Close_J869.pdb_B SES surface, 4238 of 413800 triangles,
hB_1uM_BRIL_Close_J869.pdb_E SES surface, 135 of 415282 triangles, 27 atoms,
14 residues
> mlp sel
Map values for surface "hB_1uM_BRIL_Close_J869.pdb_A SES surface": minimum
-28.94, mean -1.652, maximum 23.9
Map values for surface "hB_1uM_BRIL_Close_J869.pdb_B SES surface": minimum
-28.56, mean -1.689, maximum 24.25
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> mlp
Map values for surface "hB_1uM_BRIL_Close_J869.pdb_A SES surface": minimum
-28.94, mean -1.652, maximum 23.9
Map values for surface "hB_1uM_BRIL_Close_J869.pdb_B SES surface": minimum
-28.56, mean -1.689, maximum 24.25
Map values for surface "hB_1uM_BRIL_Close_J869.pdb_C SES surface": minimum
-28.83, mean -1.673, maximum 24.11
Map values for surface "hB_1uM_BRIL_Close_J869.pdb_D SES surface": minimum
-28.85, mean -1.655, maximum 24.16
Map values for surface "hB_1uM_BRIL_Close_J869.pdb_E SES surface": minimum
-30.12, mean -1.648, maximum 24.54
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor
15460 atoms, 1870 residues, 5 surfaces, atom bfactor range 30 to 117
> color bynucleotide
> lighting soft
> color byhetero
> interfaces ~solvent
10 buried areas: D E 5222, A E 5212, A B 5203, C D 5196, B C 5192, A D 730, B
E 725, B D 724, A C 719, C E 718
> color bychain
> color byhetero
> color bychain
> style stick
Changed 15460 atom styles
> hide atoms
> show cartoons
> hide atoms
> show atoms
> hide atoms
> hide cartoons
> style stick
Changed 15460 atom styles
> style stick
Changed 15460 atom styles
> style stick
Changed 15460 atom styles
> style sphere
Changed 15460 atom styles
> style ball
Changed 15460 atom styles
> close #1
> open
> "/Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hBEST1_1uM_Ca2+_2_84_3_Rifined_add
> 365-376-more-5-coot-0.pdb"
Chain information for hBEST1_1uM_Ca2+_2_84_3_Rifined_add
365-376-more-5-coot-0.pdb #1
---
Chain | Description
A | No description available
B C D E | No description available
> color byhetero
> color bychain
> lighting soft
> show atoms
> hide cartoons
> show cartoons
> hide atoms
> open
> /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
Opened hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc as
#2, grid size 256,256,256, pixel 0.855, shown at level 0.666, step 1, values
float32
Drag select of 13 residues, 2
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
> select clear
Drag select of 2
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
> select clear
> ui tool show "Hide Dust"
> surface dust #2 size 4.12
> toolshed show
> help help:user/preferences.html#startup
> surface dust #2 size 8.55
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1616, steps = 72
shifted from previous position = 0.366
rotated from previous position = 5.82 degrees
atoms outside contour = 11856, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.99485217 -0.10132814 -0.00132629 11.81503200
0.10132736 0.99485293 -0.00064249 -10.44701308
0.00138457 0.00050479 0.99999891 0.15827496
Axis 0.00566060 -0.01337527 0.99989452
Axis point 108.69485305 111.05922478 0.00000000
Rotation angle (degrees) 5.81624885
Shift along axis 0.36487008
> volume show
> volume hide
> volume show
> volume hide
> volume show
> transparency 50
> volume style image
> volume style mesh
> volume step 2
> volume step 1
> volume style surface
> volume step 1
> volume step 2
> volume step 1
> volume step 2
> volume step 1
> volume style surface
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1615, steps = 28
shifted from previous position = 0.0142
rotated from previous position = 0.0126 degrees
atoms outside contour = 11849, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.99486629 -0.10119103 -0.00120322 11.78944005
0.10119016 0.99486681 -0.00076096 -10.40674069
0.00127404 0.00063530 0.99999899 0.15475061
Axis 0.00689847 -0.01223934 0.99990130
Axis point 108.42931063 110.98106554 0.00000000
Rotation angle (degrees) 5.80830946
Shift along axis 0.36343612
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select add #1
15585 atoms, 16043 bonds, 1887 residues, 4 models selected
> select subtract #1
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select clear
> select /E:369
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right select
> ui mousemode right translate
> hide #!2 models
> show #!2 models
Drag select of 1 residues
> select clear
> volume show
> ui tool show "Color Zone"
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1616, steps = 40
shifted from previous position = 0.0187
rotated from previous position = 0.0128 degrees
atoms outside contour = 11860, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.99485745 -0.10127572 -0.00136974 11.81284953
0.10127492 0.99485827 -0.00063925 -10.44672821
0.00142744 0.00049724 0.99999886 0.15456740
Axis 0.00561027 -0.01380825 0.99988892
Axis point 108.74286941 111.09855465 0.00000000
Rotation angle (degrees) 5.81326182
Shift along axis 0.36507454
> volume style surface
> volume style mesh
> volume style surface
> transparency 0
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1616, steps = 44
shifted from previous position = 0.00164
rotated from previous position = 0.00177 degrees
atoms outside contour = 11859, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.99485583 -0.10129133 -0.00139519 11.81600456
0.10129050 0.99485668 -0.00064735 -10.44728670
0.00145358 0.00050270 0.99999882 0.15106904
Axis 0.00567627 -0.01406071 0.99988503
Axis point 108.73313571 111.11110157 0.00000000
Rotation angle (degrees) 5.81418271
Shift along axis 0.36501880
> volume showOutlineBox true
> volume showOutlineBox false
> transparency 50
> volume showOutlineBox true
> volume showOutlineBox false
> volume showOutlineBox true
> volume showOutlineBox false
> volume showOutlineBox true
> volume showOutlineBox false
> volume showOutlineBox true
> transparency 0
> volume style image
> volume showOutlineBox false
> volume style mesh
> volume style image
> volume style mesh
> transparency 50
> transparency 0
> transparency 50
> transparency 0
> volume style mesh
> volume style surface
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1616, steps = 44
shifted from previous position = 0.0122
rotated from previous position = 0.00751 degrees
atoms outside contour = 11852, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.99486096 -0.10124137 -0.00136096 11.81476790
0.10124040 0.99486170 -0.00076347 -10.42056744
0.00143126 0.00062176 0.99999878 0.14108959
Axis 0.00684044 -0.01378833 0.99988154
Axis point 108.52119988 111.16574517 0.00000000
Rotation angle (degrees) 5.81132155
Shift along axis 0.36557337
> lighting flat
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> graphics silhouettes false
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting flat
> lighting soft
> view #1 clip false
> log metadata #1
The model has no metadata
> log chains #1
Chain information for hBEST1_1uM_Ca2+_2_84_3_Rifined_add
365-376-more-5-coot-0.pdb #1
---
Chain | Description
A | No description available
B C D E | No description available
> toolshed show
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,-0.9663,0,1,0,-0.40548,0,0,1,-0.27405
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,-0.56269,0,1,0,-1.1395,0,0,1,-0.28211
> view matrix models #2,1,0,0,-0.44695,0,1,0,-2.3303,0,0,1,-0.29952
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,-10.933,0,1,0,-11.918,0,0,1,-0.77204
> view matrix models #2,1,0,0,-16.965,0,1,0,-20.242,0,0,1,0.17308
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> turn z models #2
> view matrix models
> #2,-0.98209,0.013321,0.18796,192.5,0.013321,-0.99009,0.13977,200.42,0.18796,0.13977,0.97218,-35.429
> turn z models #2
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1541, steps = 264
shifted from previous position = 1.44
rotated from previous position = 7.98 degrees
atoms outside contour = 11800, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.00277062 0.99930394 0.03720674 -8.20892403
-0.99710842 -0.00006494 0.07599458 211.74042453
0.07594406 -0.03730965 0.99641431 -0.21328296
Axis -0.05665211 -0.01936866 -0.99820609
Axis point 101.88221282 110.07940750 0.00000000
Rotation angle (degrees) 90.02521039
Shift along axis -3.42317485
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1541, steps = 40
shifted from previous position = 0.00918
rotated from previous position = 0.0212 degrees
atoms outside contour = 11799, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.00277185 0.99930923 0.03706424 -8.19015256
-0.99708243 -0.00006557 0.07633482 211.69106841
0.07628448 -0.03716763 0.99639362 -0.26767757
Axis -0.05675122 -0.01961012 -0.99819574
Axis point 101.86810172 110.04595197 0.00000000
Rotation angle (degrees) 90.02578605
Shift along axis -3.41929166
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1542, steps = 28
shifted from previous position = 0.0209
rotated from previous position = 0.0203 degrees
atoms outside contour = 11792, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.00276122 0.99930950 0.03705764 -8.18898023
-0.99705534 -0.00008884 0.07668785 211.64333090
0.07663815 -0.03716022 0.99636675 -0.32379426
Axis -0.05692403 -0.01979025 -0.99818235
Axis point 101.84450432 110.02172645 0.00000000
Rotation angle (degrees) 90.02752702
Shift along axis -3.39911987
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1541, steps = 28
shifted from previous position = 0.0227
rotated from previous position = 0.0199 degrees
atoms outside contour = 11797, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.00274432 0.99931173 0.03699886 -8.17786900
-0.99708155 -0.00008847 0.07634625 211.68978144
0.07629694 -0.03710034 0.99639517 -0.27422570
Axis -0.05672329 -0.01964904 -0.99819657
Axis point 101.87101298 110.03914825 0.00000000
Rotation angle (degrees) 90.02718605
Shift along axis -3.42189440
> transparency 50
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1541, steps = 28
shifted from previous position = 0.00414
rotated from previous position = 0.00305 degrees
atoms outside contour = 11800, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.00277538 0.99931138 0.03700588 -8.18348868
-0.99708472 -0.00005647 0.07630485 211.69359395
0.07625436 -0.03710972 0.99639808 -0.26569602
Axis -0.05670728 -0.01962424 -0.99819796
Axis point 101.87322551 110.04397532 0.00000000
Rotation angle (degrees) 90.02529618
Shift along axis -3.42504471
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1542, steps = 40
shifted from previous position = 0.0129
rotated from previous position = 0.0111 degrees
atoms outside contour = 11799, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.00270160 0.99930510 0.03718067 -8.19578682
-0.99708216 -0.00014468 0.07633816 211.70188390
0.07629045 -0.03727836 0.99638902 -0.26276099
Axis -0.05680826 -0.01955489 -0.99819358
Axis point 101.86280727 110.05369919 0.00000000
Rotation angle (degrees) 90.03019643
Shift along axis -3.41193255
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1542, steps = 44
shifted from previous position = 0.0102
rotated from previous position = 0.00553 degrees
atoms outside contour = 11787, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.00276758 0.99930241 0.03724794 -8.21475666
-0.99708359 -0.00008329 0.07631965 211.69617522
0.07626948 -0.03735048 0.99638793 -0.26156908
Axis -0.05683506 -0.01951076 -0.99819292
Axis point 101.85736242 110.06036678 0.00000000
Rotation angle (degrees) 90.02657905
Shift along axis -3.40237161
> view matrix models
> #1,0.99604,0.0028939,0.088817,-10.607,-0.0040597,0.99991,0.012949,-0.50458,-0.088772,-0.013258,0.99596,9.7526
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 2.323, steps = 116
shifted from previous position = 3.27
rotated from previous position = 13.4 degrees
atoms outside contour = 1151, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.21412230 0.97680705 -0.00005397 25.97424766
-0.97680705 -0.21412230 0.00005753 239.77396814
0.00004459 0.00006509 1.00000049 0.30676796
Axis 0.00000387 -0.00005045 -1.00000000
Axis point 109.44071440 109.43834532 0.00000000
Rotation angle (degrees) 102.36402352
Shift along axis -0.31876368
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 2.324, steps = 44
shifted from previous position = 0.0171
rotated from previous position = 0.00412 degrees
atoms outside contour = 1160, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.21415744 0.97679934 -0.00011503 25.99021348
-0.97679935 -0.21415743 0.00006929 239.76962632
0.00004299 0.00012725 1.00000049 0.28468522
Axis 0.00002967 -0.00008089 -1.00000000
Axis point 109.44339968 109.43012990 0.00000000
Rotation angle (degrees) 102.36608434
Shift along axis -0.30330872
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 2.324, steps = 40
shifted from previous position = 0.014
rotated from previous position = 0.00651 degrees
atoms outside contour = 1152, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.21404976 0.97682294 -0.00011968 25.97380748
-0.97682295 -0.21404975 0.00004238 239.76481986
0.00001572 0.00012602 1.00000049 0.30147511
Axis 0.00004282 -0.00006931 -1.00000000
Axis point 109.44415118 109.43314614 0.00000000
Rotation angle (degrees) 102.35976839
Shift along axis -0.31698015
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 2.324, steps = 40
shifted from previous position = 0.0156
rotated from previous position = 0.00689 degrees
atoms outside contour = 1163, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.21416027 0.97679872 -0.00016018 25.99459578
-0.97679873 -0.21416026 0.00004470 239.77329215
0.00000930 0.00016609 1.00000048 0.28224211
Axis 0.00006214 -0.00008675 -0.99999999
Axis point 109.44678264 109.43022645 0.00000000
Rotation angle (degrees) 102.36625080
Shift along axis -0.30142808
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 2.324, steps = 40
shifted from previous position = 0.0118
rotated from previous position = 0.0149 degrees
atoms outside contour = 1157, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.21411422 0.97680882 0.00009257 25.96085653
-0.97680882 -0.21411421 0.00000978 239.77341081
0.00002932 -0.00008828 1.00000049 0.31958252
Axis -0.00005019 0.00003237 -1.00000000
Axis point 109.43461385 109.44338472 0.00000000
Rotation angle (degrees) 102.36354932
Shift along axis -0.31312302
> reset
Unknown command: reset
> ui mousemode right "move picked models"
> ui mousemode right rotate
> ui mousemode right select
> volume zone #2 nearAtoms #1 range 5.13
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #2 orthoplanes xyz positionPlanes 128,128,128 style image region all
> mousemode rightMode "move planes"
> volume #2 orthoplanes xyz positionPlanes 128,128,128 style image region all
> mousemode rightMode "move planes"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 109.4 tiltedSlabSpacing 0.855 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #2 orthoplanes xyz positionPlanes 128,128,128 style image region all
> mousemode rightMode "move planes"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume zone #2 nearAtoms #1 range 5.13
> volume style surface
> volume zone #2 nearAtoms #1 range 5.13
> surface dust #2 size 8.55
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume style surface
> volume hide
> volume show
> surface dust #2 size 8.55
> volume style surface
> transparency 0
> transparency 50
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 109.4 tiltedSlabSpacing 0.855 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 109.4 tiltedSlabSpacing 0.855 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #2 orthoplanes xyz positionPlanes 128,128,128 style image region all
> mousemode rightMode "move planes"
> volume #2 orthoplanes xyz positionPlanes 128,128,128 style image region all
> mousemode rightMode "move planes"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume zone #2 nearAtoms #1 range 5.13
> volume #2 region 0,0,1,255,255,255
> volume #2 region 0,0,64,255,255,255
> volume style surface
> volume #2 region 0,0,126,255,255,255
> close #1#2
> open
> /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
> "/Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hBEST1_1uM_Ca2+_2_84_3_Rifined_add
> 365-376-more-5-coot-0.pdb"
Opened hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc as
#1, grid size 256,256,256, pixel 0.855, shown at level 0.666, step 1, values
float32
Chain information for hBEST1_1uM_Ca2+_2_84_3_Rifined_add
365-376-more-5-coot-0.pdb #2
---
Chain | Description
A | No description available
B C D E | No description available
> surface dust #1 size 8.55
> lighting soft
> color bychain
> volume #1 region 0,0,0,255,255,255
> volume #1 region 0,0,24,255,255,255
> volume #1 region 0,0,16,255,255,255
> select clear
> volume #1 region 0,0,16,255,255,255
> volume #1 region 0,0,59,255,255,255
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 15578 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> close session
> open
> /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
> format mrc
Opened hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc as
#1, grid size 256,256,256, pixel 0.855, shown at level 0.666, step 1, values
float32
> ui tool show "Color Actions"
> set bgColor white
> close session
> open
> "/Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hBEST1_1uM_Ca2+_2_84_3_Rifined_add
> 365-376-more-5-coot-0.pdb"
> /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
Chain information for hBEST1_1uM_Ca2+_2_84_3_Rifined_add
365-376-more-5-coot-0.pdb #1
---
Chain | Description
A | No description available
B C D E | No description available
Opened hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc as
#2, grid size 256,256,256, pixel 0.855, shown at level 0.666, step 1, values
float32
> surface dust #2 size 8.55
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1616, steps = 72
shifted from previous position = 0.366
rotated from previous position = 5.82 degrees
atoms outside contour = 11856, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.99485217 -0.10132814 -0.00132629 11.81503200
0.10132736 0.99485293 -0.00064249 -10.44701308
0.00138457 0.00050479 0.99999891 0.15827496
Axis 0.00566060 -0.01337527 0.99989452
Axis point 108.69485305 111.05922478 0.00000000
Rotation angle (degrees) 5.81624885
Shift along axis 0.36487008
> color byhetero
> color bychain
> graphics silhouettes true
> rainbow
> color bypolymer
> color bychain
> hide cartoons
> show atoms
> hide atoms
> show cartoons
> volume #2 region 0,0,85,255,255,255
> volume #2 region 0,0,172,255,255,255
> volume #2 region 0,0,0,255,255,255
> transparency 50
> ui mousemode right "translate selected models"
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,1.7761,0,1,0,0.93388,0,0,1,0.19071
> view matrix models #2,1,0,0,0.00032648,0,1,0,-2.987,0,0,1,1.3749
> view matrix models #2,1,0,0,0.91576,0,1,0,-0.91704,0,0,1,1.5981
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,1.7393,0,1,0,1.1656,0,0,1,1.4784
> view matrix models #2,1,0,0,1.7088,0,1,0,-2.6028,0,0,1,1.22
> view matrix models #2,1,0,0,3.5404,0,1,0,-7.3298,0,0,1,1.2143
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1373, steps = 120
shifted from previous position = 2.44
rotated from previous position = 4.19 degrees
atoms outside contour = 12139, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.99313810 -0.10779553 0.04535248 3.96071680
0.10524710 0.99290942 0.05526248 -11.94811310
-0.05098796 -0.05011006 0.99744133 11.51926146
Axis -0.41087231 0.37565403 0.83070331
Axis point 128.66082497 41.71562623 0.00000000
Rotation angle (degrees) 7.36733852
Shift along axis 3.45338291
> view matrix models #2,1,0,0,0.086309,0,1,0,-2.8764,0,0,1,1.1026
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1615, steps = 68
shifted from previous position = 0.653
rotated from previous position = 4.19 degrees
atoms outside contour = 11850, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
0.99486445 -0.10120975 -0.00114681 11.78399238
0.10120889 0.99486489 -0.00078731 -10.40320970
0.00122061 0.00066720 0.99999903 0.15667417
Axis 0.00718497 -0.01169456 0.99990580
Axis point 108.37469673 110.90651497 0.00000000
Rotation angle (degrees) 5.80936170
Shift along axis 0.36298801
> turn z models #2
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1228, steps = 76
shifted from previous position = 2.96
rotated from previous position = 0.888 degrees
atoms outside contour = 12115, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.08873665 -0.99008412 -0.10889999 236.34273135
0.99243426 -0.07857025 -0.09434470 23.72648838
0.08485289 -0.11644791 0.98956549 7.49165273
Axis -0.01109551 -0.09726129 0.99519703
Axis point 107.19597112 120.86101346 0.00000000
Rotation angle (degrees) 95.09864272
Shift along axis 2.52565913
> turn z models #2
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1279, steps = 96
shifted from previous position = 2.94
rotated from previous position = 2.81 degrees
atoms outside contour = 12304, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.99858661 0.04773022 -0.02337864 207.24390802
-0.04164017 -0.97596023 -0.21393381 248.63994883
-0.03302773 -0.21265795 0.97656836 32.68438574
Axis 0.01419213 0.10733273 -0.99412186
Axis point 106.67072921 123.74011059 0.00000000
Rotation angle (degrees) 177.42372036
Shift along axis -2.86382565
> view matrix models
> #2,-0.99966,0.002547,-0.025814,223.54,0.002547,-0.98072,-0.1954,236.74,-0.025814,-0.1954,0.98038,30.285
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1586, steps = 68
shifted from previous position = 1.68
rotated from previous position = 5.05 degrees
atoms outside contour = 11717, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.99782829 -0.03196519 -0.05759231 228.77280239
0.04264137 -0.97989000 -0.19492882 235.09076777
-0.05020319 -0.19696132 0.97912506 29.57757493
Axis -0.02710021 -0.09852276 0.99476572
Axis point 112.57290594 121.16686199 0.00000000
Rotation angle (degrees) 177.85092936
Shift along axis 0.06117521
> view matrix models
> #2,-0.99966,0.002547,-0.025814,220.3,0.002547,-0.98072,-0.1954,236.61,-0.025814,-0.1954,0.98038,30.194
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1171, steps = 64
shifted from previous position = 1.27
rotated from previous position = 3.52 degrees
atoms outside contour = 12116, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.99769166 0.01962392 -0.06500925 219.74760688
-0.00417607 -0.97325259 -0.22969960 242.53414363
-0.06777802 -0.22889790 0.97108799 35.90746425
Axis 0.03344054 0.11549116 -0.99274545
Axis point 111.21082277 122.69233005 0.00000000
Rotation angle (degrees) 179.31318150
Shift along axis -0.28794250
> view matrix models
> #2,-0.99966,0.002547,-0.025814,223.92,0.002547,-0.98072,-0.1954,236.92,-0.025814,-0.1954,0.98038,28.94
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 0.1449, steps = 84
shifted from previous position = 1.81
rotated from previous position = 3.23 degrees
atoms outside contour = 11867, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.99420632 -0.01896635 -0.10580182 231.69210513
0.04282517 -0.97270654 -0.22805250 236.75776086
-0.09858879 -0.23126222 0.96788327 39.53681246
Axis -0.05152556 -0.11579029 0.99193635
Axis point 115.01402666 122.50565444 0.00000000
Rotation angle (degrees) 178.21512428
Shift along axis -0.13431315
> view matrix models
> #2,-0.99966,0.002547,-0.025814,221.85,0.002547,-0.98072,-0.1954,232.97,-0.025814,-0.1954,0.98038,28.661
> fitmap #1 inMap #2
Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
(#2) using 15585 atoms
average map value = 2.323, steps = 156
shifted from previous position = 5.39
rotated from previous position = 16.3 degrees
atoms outside contour = 1166, contour level = 0.66583
Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1)
relative to
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.99516389 0.09822817 0.00002831 207.59840355
-0.09822818 -0.99516389 -0.00007824 229.10798570
0.00002049 -0.00008064 0.99999999 0.32145125
Axis -0.00001221 0.00003979 -1.00000000
Axis point 109.43905253 109.44363903 0.00000000
Rotation angle (degrees) 174.36284979
Shift along axis -0.31487072
> ui mousemode right rotate
> ui mousemode right zoom
> ui mousemode right pivot
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right zoom
> lighting flat
> lighting soft
> view
> view orient
> ui tool show "Side View"
> view
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color byhetero
> color bychain
> hide atoms
> show cartoons
> ui mousemode right windowing
> toolshed show
> ui mousemode right translate
> ui mousemode right zoom
> ui windowfill toggle
> help help:user
> open
> /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/RealSpaceRefine_4/hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb
Chain information for hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb #3
---
Chain | Description
A B C D E | No description available
> close session
> open
> /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/RealSpaceRefine_4/hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb
Chain information for hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb #1
---
Chain | Description
A B C D E | No description available
> open
> /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc
Opened hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc as
#2, grid size 256,256,256, pixel 0.855, shown at level 0.666, step 1, values
float32
> lighting soft
> hide atoms
> hide cartoons
> show cartoons
> surface dust #2 size 8.55
> fitmap #1 inMap #2
Fit molecule hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb (#1) to map
hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
using 15460 atoms
average map value = 2.301, steps = 44
shifted from previous position = 0.0101
rotated from previous position = 0.00636 degrees
atoms outside contour = 1090, contour level = 0.66583
Position of hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb (#1) relative
to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
1.00000000 0.00002600 -0.00006674 0.01063972
-0.00002601 1.00000000 -0.00008476 0.02061419
0.00006673 0.00008476 0.99999999 -0.01849326
Axis 0.76381772 -0.60138485 -0.23434749
Axis point 0.00000000 218.02504749 243.65302120
Rotation angle (degrees) 0.00635797
Shift along axis 0.00006360
> transparency 50
> volume style surface
> volume style image
> volume style surface
> volume hide
> volume show
> transparency 0
> transparency 50
> lighting soft
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> view orient
> ui tool show "Side View"
> view
> view orient
> color bychain
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> ui tool show "Selection Inspector"
> view
> view orient
> ui tool show "Side View"
> view
> set bgColor gray
> set bgColor #80808000
> set bgColor gray
> set bgColor white
> set bgColor #ffffff00
> volume hide
> hide atoms
> show atoms
> lighting soft
> lighting full
> lighting soft
> hide atoms
> volume show
> ui tool show "Side View"
> view orient
> ui tool show "Side View"
> view orient
> volume #2 color #f9fff780
> volume #2 color #90938f80
> volume #2 color #bec2bc80
> volume #2 color #c5c9c380
> volume #2 color #b8b8b880
> volume #2 color #b4b4b480
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.7.101
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i9
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0)
OS Loader Version: 540.60.2~89
Software:
System Software Overview:
System Version: macOS 12.1 (21C52)
Kernel Version: Darwin 21.2.0
Time since boot: 25 days 25 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
2476 IPS:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 202024760068
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: DVI or HDMI
Adapter Firmware Version: 3.0d
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash during color drop |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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*Probably* while trying to color volume.