![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 18 months ago
Last modified 18 months ago
#15406 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8rc202406042103 (2024-06-04 21:03:50 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000204f84c00 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 307 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8-rc2024.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.graphics._graphics, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, chimerax.atomic._ribbons (total: 54)
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{
"uptime" : 290000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,7",
"coalitionID" : 22559,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
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"captureTime" : "2024-06-11 08:15:17.9723 +0200",
"codeSigningMonitor" : 1,
"incident" : "087AEA63-7A69-477E-A36E-9651265ED03F",
"pid" : 75066,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-06-10 17:54:54.4182 +0200",
"procStartAbsTime" : 6244628616775,
"procExitAbsTime" : 7172763192219,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.06.04.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"6B78D4E0-27E6-56BC-BF8D-CB872CDB208A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FD67F6DE-C794-B016-DE04-3255D54D996D",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "47156D72-84BF-48AA-AFD2-96F30B07E0E0",
"sip" : "enabled",
"vmRegionInfo" : "0x7b8309cc0638 is not in any region. Bytes after previous region: 30249082160697 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000fb8309cc0638","rawCodes":[1,276540223653432],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000fb8309cc0638 -> 0x00007b8309cc0638 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":75066},
"vmregioninfo" : "0x7b8309cc0638 is not in any region. Bytes after previous region: 30249082160697 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"path" : "\/Applications\/ChimeraX-1.8-rc2024.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bz2.cpython-311-darwin.so",
"name" : "_bz2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4370366464,
"size" : 32768,
"uuid" : "65172ede-2b95-337d-970f-ed6c4a217cb1",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
"name" : "zlib.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4368875520,
"size" : 16384,
"uuid" : "39aa96c6-b691-3e20-9540-292b9dd1c861",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
"name" : "_typing.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4368695296,
"size" : 81920,
"uuid" : "3b2e1e73-f5e1-3fa3-80b3-e46009060893",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
"name" : "_datetime.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4368957440,
"size" : 49152,
"uuid" : "51d31d0d-1dcc-31ad-b6c1-73d57e544a3a",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
"name" : "math.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4385292288,
"CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 3948544,
"uuid" : "88bffd37-99d8-36ab-9b95-9f54b30bd667",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.06.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4366483456,
"CFBundleShortVersionString" : "1.8.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "17982d98-65bc-3327-8526-577ec996453c",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.06.04.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.8.0.0"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6930075648,
"size" : 241660,
"uuid" : "9b8b53f9-e2b6-36df-98e9-28d8fca732f2",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6930317312,
"size" : 53248,
"uuid" : "386b0fc1-7873-3328-8e71-43269fd1b2c7",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6928863232,
"size" : 520184,
"uuid" : "05b44e93-dffc-3bd8-90ab-fd97cb73f171",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6930526208,
"size" : 32744,
"uuid" : "d5bbfc31-d52a-37d6-a41b-48638113ad4c",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6990127104,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 20172800,
"uuid" : "61f710be-9132-3cc2-883d-066365fba1ad",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.60.105"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7022333952,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4853760,
"uuid" : "995bcbdd-5656-3d16-bfa1-0ab357c2a13e",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6928556032,
"size" : 294912,
"uuid" : "502762ee-7aa7-306c-9dbd-88981a86bb78",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6930743296,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5083136,
"uuid" : "84b539d5-22c9-3f8c-84c8-903e9c7b8d29",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2503.1"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7106826240,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2899968,
"uuid" : "7db6c397-563f-3756-908c-e25b019a1848",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6926614528,
"size" : 559640,
"uuid" : "37bbc384-0755-31c7-a808-0ed49e44dd8e",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
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"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
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"arch" : "arm64e",
"base" : 6929383424,
"size" : 577528,
"uuid" : "ec33cd83-7098-3ad6-82c8-bc03ac81e87b",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
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"sharedCache" : {
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"size" : 4220698624,
"uuid" : "3406ad1b-2469-30eb-9863-5dce861e6dea"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=6.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG image 1664K 64 \nColorSync 624K 31 \nCoreAnimation 3232K 189 \nCoreGraphics 64K 4 \nCoreUI image data 5712K 65 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 5.6G 230 \nMALLOC guard page 192K 12 \nMach message 96K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 704K 44 \nStack 173.6M 45 \nStack Guard 56.0M 1 \nVM_ALLOCATE 260.2M 459 \nVM_ALLOCATE (reserved) 288.0M 5 reserved VM address space (unallocated)\n__AUTH 2199K 404 \n__AUTH_CONST 31.8M 623 \n__CTF 824 1 \n__DATA 22.7M 793 \n__DATA_CONST 42.9M 804 \n__DATA_DIRTY 2024K 232 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 567.7M 176 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2199K 1 \n__TEXT 956.4M 821 \ndyld private memory 592K 6 \nmapped file 557.4M 83 \nshared memory 3280K 28 \n=========== ======= ======= \nTOTAL 8.6G 5141 \nTOTAL, minus reserved VM space 8.3G 5141 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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},
"logWritingSignature" : "96145996747e38012c2c7e9ecab35aacc1406c7c",
"trialInfo" : {
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202406042103 (2024-06-04)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/floriansestak/Code/chimerax_scripts/volumes/*.mrc format mrc
> vseries true
Opened map series volume_001.mrc as #1, 1000 images, grid size 84,84,84, pixel
0.2, shown at level 0.0145, step 1, values float32
> volume #0 planes z 50
Expected a keyword
> volume #0 planes z50
Invalid "planes" argument: Planes argument first field must be x, y, or z, got
"z50"
> volume #0 planes z
No volumes specified
> volume #1 planes z 50
Expected a keyword
> volume #1 planes z
> volume #1 color colormap heatmap
Invalid "color" argument: Invalid color name or specifier
> volume #1.285 level 0
> volume #1.285 level 0.1141
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> volume #1 planes z50
Invalid "planes" argument: Planes argument first field must be x, y, or z, got
"z50"
> volume #1 planes z 50
Expected a keyword
> volume #1 planes z
> ui mousemode right "clip rotate"
> clip off
> ui mousemode right select
> volume #1 color colormap heatmap
Invalid "color" argument: Invalid color name or specifier
> volume #1 colormapSize viridis
Invalid "colormapSize" argument: Expected an integer
> volume #1 colormapSize ^
Invalid "colormapSize" argument: Expected an integer
> volume #1 colormapSize 1
> volume #1 region all planes z,50
> volume #1 region all planes z,30
> volume #1 region all planes z,20
> volume #1 region all planes z,60
> volume #1 region all planes z,45
> volume #1 region all planes z,41
> volume #1 colormapSize viridis
Invalid "colormapSize" argument: Expected an integer
> volume #1 colormapSize 3
> volume #1 colormapSize 5
> volume #1 colormapSize vidris
Invalid "colormapSize" argument: Expected an integer
> color byattribute #1 attribute volume step 100 palette redblue
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> volume #1 color colormap heat
Invalid "color" argument: Invalid color name or specifier
> volume #1 color colormap 5
Invalid "color" argument: Invalid color name or specifier
> volume #1 color colormap 4
Invalid "color" argument: Invalid color name or specifier
> volume #1 color colormap 3
Invalid "color" argument: Invalid color name or specifier
> volume #1 color colormap 2
Invalid "color" argument: Invalid color name or specifier
> volume #1 color colormap 1
Invalid "color" argument: Invalid color name or specifier
> volume #1 colormapSize 3
> ui tool show "Color Zone"
No atoms chosen for color zoning
> select clear
No atoms chosen for color zoning
> select clear
> ui mousemode right translate
> select add #1
1375 models selected
No atoms selected for color zoning
> ui tool show "Surface Color"
> ui mousemode right "color key"
> ui mousemode right translate
> ui tool show "Color Zone"
> ui tool show "Fit in Map"
> fitmap #1.1 inMap #1.1000
Fit map volume_001.mrc in map volume_999.mrc using 301 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of volume_001.mrc (#1.1) relative to volume_999.mrc (#1.1000)
coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> color radial #1.5.1 palette #ff0000:#ffffff:#0000ff
> color single #1.5.1
No atoms selected for color zoning
> ui tool show "Measure and Color Blobs"
> close #2
> ui tool show "Map Coordinates"
> ui tool show "Surface Zone"
No atoms selected for zoning
> surface unzone #1.1
> ui tool show "Color Zone"
No atoms chosen for color zoning
No atoms selected for color zoning
> ui tool show "Surface Color"
> color radial #1.1.1 palette #ff0000:#ffffff:#0000ff
No surface chosen for coloring
> color single #1.1
No surface chosen for coloring
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> ui mousemode right "pick blobs"
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> ui mousemode right "pick blobs"
No surface chosen for coloring
> ui mousemode right translate
No surface chosen for coloring
> color height #1.2.1 palette #ff0000:#ffffff:#0000ff center
> 14.356,15.151,14.982
> color single #1.2.1
> color height #1.2.1 palette
> 0.0002222,#ff0000:0.0002222,#ffffff:0.0002222,#0000ff center
> 14.356,15.151,14.982
> select subtract #1
Nothing selected
> close #3
> select add #1
1375 models selected
> color height #1.2.1 palette
> 0.0002222,#ff0000:0.0002222,#ffffff:0.0002222,#0000ff center
> 14.356,15.151,14.982
> color single #1.2.1
Surface Color: surface has no bounding box
> color single #1.2.1
> color height #1.2.1 palette
> 0.0002222,#ff0000:0.0002222,#ffffff:0.0002222,#0000ff center
> 14.356,15.151,14.982
> close session
> open /Users/floriansestak/Code/chimerax_scripts/volumes/*.mrc format mrc
> vseries true
Opened map series volume_001.mrc as #1, 1000 images, grid size 84,84,84, pixel
0.2, shown at level 0.0145, step 1, values float32
> ui tool show "Surface Color"
> color radial #1.1.1 palette #ff0000:#ffffff:#0000ff
> color sample #1.1.1 map #1.1 palette 21.3,#ff0000:26.2,#ffffff:31.11,#0000ff
Map values for surface "surface": minimum 0.01451, mean 0.01451, maximum
0.01451
> volume #1 planes z,42
> volume #1 planes z,43
> volume #1 planes z,44
> volume #1 planes z,45
> volume #1 planes z,40
> color sample #1.1.1 map #1.1 palette 0,#ff0000:26.2,#ffffff:31.11,#0000ff
Map values for surface "surface": minimum 0.01451, mean 1.188, maximum 29.97
> volume #1.1 level 0
> volume #1.1 level 0.1108
> color sample #1.1.1 map #1.1 palette 0,#ff0000:15,#ffffff:31,#0000ff
Map values for surface "surface": minimum 0.1108, mean 1.7, maximum 29.97
> color sample #1.1.1 map #1.1 palette 0,#ff0000:15,#ffffff:31,#0000ff
Map values for surface "surface": minimum 0.1108, mean 1.7, maximum 29.97
> color sample #1.1.1 map #1.1 palette 0,#ff0000:15,#ffffff:31,#0000ff
Map values for surface "surface": minimum 0.1108, mean 1.7, maximum 29.97
> key red-white-blue :0 :15 :31 showTool true
> ui mousemode right "color key"
> key red-white-blue :0 :15 :31 white:
> key red:0 white:15 blue:31 white: white:
> key red:0 white:15 blue:31 white: white: white:
> key red:0 white:15 blue:31 white: white:
> key red:0 white:15 blue:31 white:
> key red-white-blue :0 :15 :31
> ui mousemode right translate
> key red-white-blue :0 :15 :31 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> ui tool show "Color Zone"
No atoms chosen for color zoning
No surface chosen for coloring
> select add #1
1070 models selected
No surface chosen for coloring
> close #2
No surface chosen for coloring
> close session
> open /Users/floriansestak/Code/chimerax_scripts/volumes/*.mrc format mrc
> vseries true
Opened map series volume_001.mrc as #1, 1000 images, grid size 84,84,84, pixel
0.2, shown at level 0.0145, step 1, values float32
> volume #1.1 level 0.07441
> ui tool show "Surface Color"
> color radial #1.1.1 palette #ff0000:#ffffff:#0000ff
> color height #1.1.1 palette 21.43,#ff0000:26.21,#ffffff:30.99,#0000ff
> color height #1.1.1 palette 21.43,#ff0000:26.21,#f7ff00:30.99,#01f500
> ui mousemode right clip
> clip off
> color height #1.1.1 palette #ff0000:#f7ff00:#01f500:#00fbec:#2900f7
> color height #1.1.1 palette
> 12.39,#ff0000:13.69,#f7ff00:14.99,#01f500:16.29,#00fbec:17.59,#2900f7
> color height #1.1.1 palette #ff0000:#f7ff00:#01f500:#00fbec:#2900f7
> color height #1.1.1 palette
> 12.39,#ff0000:13.69,#f7ff00:14.99,#01f500:16.29,#00fbec:17.59,#2900f7
> color single #1.1.1
> color height #1.1.1 palette
> 12.39,#ff0000:13.69,#f7ff00:14.99,#01f500:16.29,#00fbec:17.59,#2900f7
> color single #1.1.1
No surface chosen for coloring
> color height #1.1.1 palette
> 12.39,#ff0000:13.69,#f7ff00:14.99,#01f500:16.29,#00fbec:17.59,#2900f7
> close #1
> open /Users/floriansestak/Code/chimerax_scripts/volumes/*.mrc format mrc
> vseries true
Opened map series volume_001.mrc as #1, 1000 images, grid size 84,84,84, pixel
0.2, shown at level 0.0145, step 1, values float32
> ui tool show "Measure Volume and Area"
No surface chosen for coloring
> color height #1.1.1 palette
> 12.39,#ff0000:13.69,#f7ff00:14.99,#01f500:16.29,#00fbec:17.59,#2900f7
> close
> close session
> open /Users/floriansestak/Code/chimerax_scripts/volumes/*.mrc format mrc
> vseries true
Opened map series volume_001.mrc as #1, 1000 images, grid size 84,84,84, pixel
0.2, shown at level 0.0145, step 1, values float32
> ui mousemode right select
> select clear
> ui tool show "Volume Viewer"
> volume #1.1 style image
> volume #1.1 region 0,0,41,83,83,41 step 1 showOutlineBox true
> volume #1.1 region 0,0,0,83,83,83 step 1
> volume #1.1 style surface region 0,0,0,83,83,83 step 1
> volume #1.1 region 0,0,0,83,83,83
> clip off
> volume #1.1
> volume #1.1 style mesh
> volume #1.1 style image colorMode opaque8 imageMode "box faces"
> volume #1.1 colorMode auto8 imageMode "tilted slab" tiltedSlabAxis
> 0.9316,0.07376,0.3558 tiltedSlabOffset 18.54 tiltedSlabSpacing 0.2
> tiltedSlabPlaneCount 16
> volume #1.1
> volume #1.1 style image imageMode "full region"
> volume #1.1 level 0,0 level 0,0.9385 level 41.45,1
> volume #1.1 level 3.125,0.09231 level 0,0.9385 level 41.45,1
> volume #1.1 level 9.971,0 level 0,0.9385 level 41.45,1
> volume #1.1 region 0,0,41,83,83,41 step 1
> ui tool show "Surface Color"
> color radial #1.191.1 palette #ff0000:#ffffff:#0000ff
> ui tool show "Color Zone"
No atoms chosen for color zoning
> volume #1.191 region 0,0,0,83,83,83 step 1
> volume #1.191 style surface region 0,0,0,83,83,83 step 1
> volume #1.268 style image region 0,0,41,83,83,41 step 1
> volume #1.268 level 11.92,0 level 0,0.9385 level 41.45,1
> volume #1.268 level 11.92,0 level 0,1 level 41.45,1
> volume #1.268 level 2.867,0 level 0,1 level 41.45,1
> volume #1.344 region 0,0,0,83,83,83 step 1
> volume #1.344 style mesh region 0,0,0,83,83,83 step 1
> volume #1.344 style image region 0,0,41,83,83,41 step 1
> ui tool show "Surface Zone"
> help help:user/tools/surfacezone.html
> rename #1 volume
> ui tool show "Surface Color"
> volume #1.344 region 0,0,0,83,83,83 step 1
> color gradient #1.344.1 map #1.344 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 0.1587, mean 0.3843, maximum 0.8397
> volume #1.344 level 10.36,0 level 0,1 level 41.45,1
> ui tool show "Color Actions"
> volume #1.344 color #58ffcf color white color white
> volume #1.344 style surface
> volume #1.344 level 0.06934
> color gradient #1.344.1 map #1.344 palette
> 0.1587,#ff0000:0.4992,#ffffff:0.8397,#0000ff
Map values for surface "surface": minimum 0.471, mean 1.342, maximum 2.66
> color single #1.344.1
> color gradient #1.344.1 map #1.344 palette
> 0.1587,#ff0000:0.4992,#ffffff:0.8397,#0000ff
Map values for surface "surface": minimum 0.471, mean 1.342, maximum 2.66
> volume #1.344
> volume #1.344 style mesh
> volume #1.344 style image
> volume #1.344 style surface
> volume #1.344 level 0.06934
> volume #1.344 level 0.1387
> color gradient #1.344.1 map #1.344 palette 0,#ff0000:16,#ffffff:38,#0000ff
Map values for surface "surface": minimum 0.7935, mean 2.311, maximum 4.465
> volume #1.344 level 2.011
> volume #1.344 style image
> volume #1.344 style surface
> volume #1.344 style image region 0,0,41,83,83,41 step 1
> volume #1.344 region 0,0,0,83,83,83 step 1
> volume #1.344 region 0,0,0,83,83,83 step 1 colorMode opaque8 imageMode "box
> faces"
> volume #1.344 style surface
> volume #1.344
> volume #1.344 level 0.9964
> volume #1.344 level 0.9928
> volume #1.344 style mesh
> volume #1.344 style image colorMode auto8 imageMode "full region"
> volume #1.344 style surface
> volume #1.344 level 0.7989
> close
> open /Users/floriansestak/Code/chimerax_scripts/volumes/*.mrc format mrc
> vseries true
Opened map series volume_001.mrc as #1, 1000 images, grid size 84,84,84, pixel
0.2, shown at level 0.0145, step 1, values float32
No surface chosen for coloring
> rename #1 abc
> ui tool show "Show Volume Menu"
> toolshed show
> ui tool show "Fit in Map"
> fitmap #1.1 inMap #1.1000
Fit map volume_001.mrc in map volume_999.mrc using 5889 points
correlation = 0.4618, correlation about mean = 0.4006, overlap = 3.264e+04
steps = 400, shift = 1.21, angle = 73.2 degrees
Position of volume_001.mrc (#1.1) relative to volume_999.mrc (#1.1000)
coordinates:
Matrix rotation and translation
0.28887378 -0.43946869 -0.85054054 28.84517367
0.42505894 0.85492491 -0.29736896 0.14136617
0.85783264 -0.27562776 0.43376549 0.37199731
Axis 0.01135435 -0.89219885 0.45150004
Axis point 14.26865768 0.00000000 21.97915634
Rotation angle (degrees) 73.21494423
Shift along axis 0.36934830
> fitmap #1.1 inMap #1.1000
Fit map volume_001.mrc in map volume_999.mrc using 5889 points
correlation = 0.4609, correlation about mean = 0.3996, overlap = 3.264e+04
steps = 40, shift = 0.00479, angle = 0.213 degrees
Position of volume_001.mrc (#1.1) relative to volume_999.mrc (#1.1000)
coordinates:
Matrix rotation and translation
0.28795546 -0.43656223 -0.85234680 28.84348463
0.42527902 0.85576143 -0.29463559 0.08807643
0.85803229 -0.27764329 0.43208194 0.42117027
Axis 0.00887178 -0.89299852 0.44997215
Axis point 14.22930849 0.00000000 21.94919893
Rotation angle (degrees) 73.26776117
Shift along axis 0.36675568
> fitmap #1.1 inMap #1.1000
Fit map volume_001.mrc in map volume_999.mrc using 5889 points
correlation = 0.4609, correlation about mean = 0.3996, overlap = 3.263e+04
steps = 40, shift = 0.00344, angle = 0.0328 degrees
Position of volume_001.mrc (#1.1) relative to volume_999.mrc (#1.1000)
coordinates:
Matrix rotation and translation
0.28772067 -0.43705444 -0.85217383 28.85397619
0.42545239 0.85550874 -0.29511872 0.09390779
0.85802510 -0.27764764 0.43209340 0.42139503
Axis 0.00912107 -0.89283778 0.45028603
Axis point 14.23531823 0.00000000 21.95688972
Rotation angle (degrees) 73.28200069
Shift along axis 0.36908297
Must specify 6 comma-separated integers, got z,50
Must specify 6 comma-separated integers, got z,50
> volume #1 region all planes z,50
> volume #1 region all planes z,40
> volume #1 region all planes z,50
> close #1
> open /Users/floriansestak/Code/chimerax_scripts/volumes/*.mrc format mrc
> vseries true
Opened map series volume_001.mrc as #1, 1000 images, grid size 84,84,84, pixel
0.2, shown at level 0.0145, step 1, values float32
> volume #1 region all z,50
Expected a keyword
> volume #1 region all
> volume #1.1 level 0.07441
> copy #1
Unknown command: copy #1
Must specify 6 comma-separated integers, got z,50-51
Must specify 6 comma-separated integers, got z,50-51
Must specify 6 comma-separated integers, got z,50
> volume channels #1
Opened multi-channel map volume_ channels as #2, 1000 channels, grid size
84,84,84, pixel 0.2, shown at level 0.0744, step 1, values float32
> close #1
> close #2
> open /Users/floriansestak/Code/chimerax_scripts/volumes/*.mrc format mrc
> vseries true
Opened map series volume_001.mrc as #1, 1000 images, grid size 84,84,84, pixel
0.2, shown at level 0.0145, step 1, values float32
> volume #1.1 level 0.6098
> ui mousemode right "move planes"
> volume #1.1 region 0,0,0,83,83,83
> ui mousemode right "rotate slab"
> volume #1.1 tiltedSlabAxis 0.1588,-0.3335,-0.9293 tiltedSlabOffset -18.86
> volume #1.1 tiltedSlabAxis 0.4322,0.9013,-0.02973 tiltedSlabOffset 19.06
> volume #1.1 tiltedSlabAxis 0.1874,0.975,0.1193 tiltedSlabOffset 18.91
> volume #1.1 tiltedSlabAxis 0.1418,0.6385,-0.7565 tiltedSlabOffset -2.216
> ui mousemode right "crop volume"
> volume #1.1 region 0,0,0,83,83,83
> ui mousemode right "play map series"
> ui mousemode right "contour level"
> volume #1.1 level 1.752
> ui mousemode right "move planes"
> volume #1.1 region 0,0,0,83,83,83
> ui mousemode right "rotate slab"
> volume #1.1 tiltedSlabAxis -0.137,0.989,0.05655 tiltedSlabOffset 14.76
> volume #1.1 tiltedSlabAxis 0.7106,0.6985,-0.0847 tiltedSlabOffset 19.76
> volume #1.1 tiltedSlabAxis 0.1479,0.2016,-0.9682 tiltedSlabOffset -10.68
> ui mousemode right "crop volume"
> volume #1.1 region 0,0,0,83,83,83
> ui mousemode right zone
> ui mousemode right "clip rotate"
> volume #1.1 level 0.07441
> volume #1.1 level 0.1488
> ui mousemode right "color key"
> key blue-white-red :min : :max white:
> key blue:min white: red:max white: white:
Fetching compressed palette custom from
https://www.colourlovers.com/api/palettes?keywords=custom&format=json&numResults=100
Could not find palette custom at COLOURlovers.com using keyword search
> key purples :min : :max : :
> key purples :min : : : :
> key purples :min : : : :max
> ui mousemode right "clip rotate"
> ui mousemode right "color key"
> ui mousemode right "clip rotate"
> ui mousemode right distance
> ui mousemode right select
Drag select of 1.1 volume_001.mrc
> ui tool show "Surface Color"
> color height #1.1.1 palette #ff0000:#ffffff:#0000ff
> color sample #1.1.1 map #1.1 palette
> 12.42,#ff0000:14.99,#ffffff:17.56,#0000ff
Map values for surface "surface": minimum 0.1488, mean 0.1488, maximum 0.1488
Map values for surface "cap front": minimum 0.1214, mean 1.837, maximum 36.48
Drag select of 1.1 volume_001.mrc
> ui mousemode right "clip rotate"
> key red-white-blue :12.4 :15.0 :17.6 showTool true
> ui mousemode right "color key"
> key red-white-blue :12.4 :15.0 :17.6 white:
> key red:12.4 white:15.0 blue:17.6 white: white:
> key purd-5 :12.4 :15.0 :17.6 : :
> ui mousemode right "clip rotate"
> color sample #1.1.1 map #1.1 palette
> 12.42,#ff0000:14.99,#ffffff:17.56,#0000ff
Map values for surface "surface": minimum 0.1488, mean 0.1488, maximum 0.1488
Map values for surface "cap front": minimum 0.1189, mean 1.149, maximum 30.79
> key red-white-blue :12.4 :15.0 :17.6 showTool true
> ui mousemode right "color key"
> key red-white-blue :12.4 :15.0 :17.6 white:
> key red:12.4 white:15.0 blue:17.6 white: white:
Could not find palette custom at COLOURlovers.com using keyword search
> key red-white-blue :12.4 :15.0 :17.6 showTool true
> key bugn-3 :12.4 :15.0 :17.6
> key bugn-3 :12.4 :15.0 :17.6 white:
> key #e5f5f9:12.4 #99d8c9:15.0 #2ca25f:17.6 white: white:
> key white: white: #2ca25f:17.6 #99d8c9:15.0 #e5f5f9:12.4
> key size 0,24000,0,05000
Invalid "size" argument: Need exactly 2 ','-separated 2-tuple of number >= 0s
> key red-white-blue :12.4 :15.0 :17.6 showTool true
> key red-white-blue :12.4 :15.0 :17.6 white:
> key red:12.4 white:15.0 blue:17.6 white: white:
Could not find palette custom at COLOURlovers.com using keyword search
> key red-white-blue :12.4 :15.0 :17.6 showTool true
> key pubugn-3 :12.4 :15.0 :17.6
> key pubugn-3 :12.4 :15.0 :17.6 white:
> key #ece2f0:12.4 #a6bddb:15.0 #1c9099:17.6 white: white:
Could not find palette custom at COLOURlovers.com using keyword search
> key red-white-blue :12.4 :15.0 :17.6 showTool true
> key red-white-blue :12.4 :15.0 :17.6 white:
> key red:12.4 white:15.0 blue:17.6 white: white:
> key purples-5 :12.4 :15.0 :17.6 : :
> key labelColor #bfbfbf
> key labelColor default
> key purples :12.4 :15.0 : : :
> key purples :12.4 :15.0 : : :17.6
> key purples :12.4 : : : :17.6
> key purples :12.4 : : :15.0 :17.6
> ui mousemode right "clip rotate"
> color sample #1.1.1 map #1.1 palette
> 12.42,#ff0000:14.99,#ffffff:17.56,#0000ff
Map values for surface "surface": minimum 0.1488, mean 0.1488, maximum 0.1488
Map values for surface "cap front": minimum 0.1254, mean 1.871, maximum 31.74
> key red-white-blue :12.4 :15.0 :17.6 showTool true
> ui mousemode right "color key"
> ui mousemode right "clip rotate"
> color sample #1.1.1 map #1.1 palette
> 12.42,#ff0000:14.99,#ffffff:17.56,#0000ff
Map values for surface "surface": minimum 0.1488, mean 0.1488, maximum 0.1488
Map values for surface "cap front": minimum 0.1339, mean 1.858, maximum 29.1
> volume #1.1 level 0.07441
> ui mousemode right clip
> color sample #1.1.1 map #1.1 palette
> 12.42,#ff0000:14.99,#ffffff:17.56,#0000ff
Map values for surface "surface": minimum 0.07441, mean 0.07441, maximum
0.07443
Map values for surface "cap front": minimum 0.05945, mean 1.547, maximum 29.79
> vseries play #1
> vseries stop #1
> volume #1.209 level 0.002198
> color sample #1.1.1 map #1.1 palette
> 12.42,#ff0000:14.99,#ffffff:17.56,#0000ff
Map values for surface "surface": minimum 0.002197, mean 0.002198, maximum
0.002198
Map values for surface "cap front": minimum 0.001979, mean 1.077, maximum
25.98
> color sample #1.1.1 map #1.1 palette 0,#ff0000:16,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.002197, mean 0.002198, maximum
0.002198
Map values for surface "cap front": minimum 0.001979, mean 1.077, maximum
25.98
> volume #1.1 level 0.1488
> color sample #1.1.1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.1488, mean 0.1488, maximum 0.1488
Map values for surface "cap front": minimum 0.1314, mean 1.902, maximum 33.03
> color gradient #1.1.1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.4865, mean 2.427, maximum 4.849
Map values for surface "cap front": minimum 0.6094, mean 11.26, maximum 83.51
> volume #1.1 level 6.772e-15
> volume #1.1 level 0.07441
> color gradient #1.1.1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.443, mean 1.41, maximum 2.942
Map values for surface "cap front": minimum 0.7393, mean 9.087, maximum 65.65
> color gradient #1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.443, mean 1.41, maximum 2.942
Map values for surface "cap front": minimum 0.7393, mean 9.087, maximum 65.65
Map values for surface "surface": minimum 0, mean 2.283, maximum 77.81
Map values for surface "surface": minimum 0, mean 1.321, maximum 65.4
Map values for surface "surface": minimum 0, mean 1.988, maximum 76.33
Map values for surface "surface": minimum 0, mean 2.105, maximum 76
Map values for surface "surface": minimum 0, mean 3.127, maximum 86.31
Map values for surface "surface": minimum 0, mean 2.208, maximum 88.61
Map values for surface "surface": minimum 0, mean 2.926, maximum 80.42
Map values for surface "surface": minimum 0, mean 2.654, maximum 85.16
Map values for surface "surface": minimum 0, mean 3.401, maximum 90.64
Map values for surface "surface": minimum 0, mean 2.384, maximum 83.01
Map values for surface "surface": minimum 0, mean 2.361, maximum 80.88
> volume #1.1 level 0.3721
Must specify one map, got 1000
> color gradient #1.1.1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.4987, mean 4.898, maximum 9.04
> color gradient #1.1.1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.4987, mean 4.898, maximum 9.04
Map values for surface "cap front": minimum 1.86, mean 14.15, maximum 68.67
> volume #1.1 level 0.07441
> close #2
> close #1
> open /Users/floriansestak/Code/chimerax_scripts/volumes/*.mrc format mrc
> vseries true
Opened map series volume_001.mrc as #1, 1000 images, grid size 84,84,84, pixel
0.2, shown at level 0.0145, step 1, values float32
> color gradient #1.1.1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.168, mean 0.3804, maximum 0.794
> color gradient #1.1.1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.168, mean 0.3804, maximum 0.794
Map values for surface "cap front": minimum 0.2372, mean 4.935, maximum 65.55
> color gradient #1.1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.168, mean 0.3804, maximum 0.794
Map values for surface "cap front": minimum 0.2462, mean 4.83, maximum 64.88
> color gradient #1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.168, mean 0.3804, maximum 0.794
Map values for surface "cap front": minimum 0.2462, mean 4.83, maximum 64.88
> color gradient #1 map #1.1 palette 0,#ff0000:5,#ffffff:32,#0000ff
Map values for surface "surface": minimum 0.168, mean 0.3804, maximum 0.794
Map values for surface "cap front": minimum 0.2118, mean 5.686, maximum 70.77
Map values for surface "surface": minimum 0, mean 2.213, maximum 73.19
Map values for surface "surface": minimum 0, mean 3.128, maximum 76.5
Map values for surface "surface": minimum 0, mean 2.815, maximum 75.97
Map values for surface "surface": minimum 0, mean 3.524, maximum 88.4
Map values for surface "surface": minimum 0, mean 3.073, maximum 78.86
Map values for surface "surface": minimum 0, mean 3.504, maximum 79.81
> color gradient #1 map #1.1
Map values for surface "surface": minimum 0.168, mean 0.3804, maximum 0.794
Map values for surface "cap front": minimum 0.179, mean 5.49, maximum 59.92
Map values for surface "surface": minimum 0, mean 2.213, maximum 73.19
Map values for surface "surface": minimum 0, mean 3.128, maximum 76.5
Map values for surface "surface": minimum 0, mean 2.815, maximum 75.97
Map values for surface "surface": minimum 0, mean 3.524, maximum 88.4
Map values for surface "surface": minimum 0, mean 3.073, maximum 78.86
Map values for surface "surface": minimum 0, mean 3.504, maximum 79.81
> ui tool show "Surface Color"
> color gradient #1.1.1 map #1.1 palette
> 0.168,#ff0000:0.481,#ffffff:0.794,#0000ff
Map values for surface "surface": minimum 0.168, mean 0.3804, maximum 0.794
Map values for surface "cap front": minimum 0.2404, mean 2.881, maximum 65.47
> color single #1.1.1
> color gradient #1 map #1.1
Map values for surface "surface": minimum 0.168, mean 0.3804, maximum 0.794
Map values for surface "cap front": minimum 0.2404, mean 2.881, maximum 65.47
Map values for surface "surface": minimum 0, mean 2.213, maximum 73.19
Map values for surface "surface": minimum 0, mean 3.128, maximum 76.5
Map values for surface "surface": minimum 0, mean 2.815, maximum 75.97
Map values for surface "surface": minimum 0, mean 3.524, maximum 88.4
Map values for surface "surface": minimum 0, mean 3.073, maximum 78.86
Map values for surface "surface": minimum 0, mean 3.504, maximum 79.81
> color gradient #1.1 map #1.1
Map values for surface "surface": minimum 0.168, mean 0.3804, maximum 0.794
Map values for surface "cap front": minimum 0.2404, mean 2.881, maximum 65.47
> color gradient #1.1.1 map #1.1
Map values for surface "surface": minimum 0.168, mean 0.3804, maximum 0.794
Map values for surface "cap front": minimum 0.2404, mean 2.881, maximum 65.47
> volume #1.1 step 2
> volume #1.1 step 4
> volume #1.39 level 0.04298
> volume #1.39 step 1
> volume #1.39 step 2
> volume #1.39 step 16
> volume #1.39 step 8
> volume #1.39 step 2
> ui mousemode right clip
> volume #1.39 step 1
> volume #1.39 level 1.377
> volume #1.39 step 2
> volume #1.39 step 1
> volume #!1.39 step 2
> volume #!1.39 step 1
> volume #!1.39 step 2
> volume #!1.39 step 1
> view orient
> ui mousemode right select
Drag select of 1.39 volume_039.mrc
> hide #!1 models
> show #!1 models
> select add #1
1011 models selected
> select subtract #1
Nothing selected
Drag select of 1.39 volume_039.mrc
> hide #!1 models
> show #!1 models
> select add #1
1011 models selected
> select subtract #1
Nothing selected
> select clear
> ui mousemode right translate
> ui mousemode right rotate
> volume #1.39 level 1.451
> volume #1.39 level 1.377
> volume #1.39 level 1.303
> volume #1.39 level 1.229
> volume #1.39 level 1.155
> volume #1.39 level 1.08
> volume #1.39 level 1.006
> volume #1.39 level 0.9323
> volume #1.39 level 0.8582
> volume #1.39 level 0.784
> volume #1.39 level 0.7099
> volume #1.39 level 0.6358
> volume #1.39 level 0.5617
> volume #1.39 level 0.4876
> volume #1.39 level 0.4135
> volume #1.39 level 0.3394
> ui mousemode right "contour level"
> volume #1.39 level -3.839
> volume #1.39 level 7.265
> volume #1.39 level 2.147
> ui mousemode right rotate
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right "contour level"
> volume #1.1 level 0.8431
> ui mousemode right clip
> ui mousemode right "move planes"
> volume #1.1 region 0,0,0,83,83,83
> volume #!1.1 projectionMode 2d-xyz
> volume #1.1 region 0,0,0,83,83,83
> volume #1.1 style mesh
> volume #1.1 region 0,0,0,83,83,83
> volume #1.1 style surface
> color gradient #1.1.1 map #1.1
Map values for surface "surface": minimum 1.054, mean 9.009, maximum 16.66
> volume #1.1 region 0,0,0,83,83,83
> ui mousemode right clip
> volume #1.1 level 7.168
> color single #1.1.1
> view orient
> ui mousemode right "clip rotate"
> volume #1.1 level 0.07441
> ui mousemode right "bond rotation"
> ui mousemode right rotate
> surface dust #1.1 size 2
> volume #!1.1 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1.1 region 0,0,42,83,83,42
> volume #1.1 region 0,0,39,83,83,39
> volume #1.1 region 0,0,40,83,83,40
> volume #1.1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 15.18 tiltedSlabSpacing 0.2 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.1 tiltedSlabAxis -0.1415,0.9898,0.018 tiltedSlabOffset 14.16
> volume #1.1 tiltedSlabAxis -0.8875,-0.3078,-0.343 tiltedSlabOffset -23.29
> volume #!1.1 region all imageMode "full region"
> volume unzone #!1.1
> mousemode rightMode "crop volume"
> volume #1.1 region 0,0,0,83,83,83
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> volume #!1.1 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1.1 region 0,0,38,83,83,38
> volume #1.1 region 0,0,51,83,83,51
> volume #1.1 region 0,0,0,83,83,83 step 1
> volume #1.1 style surface region 0,0,0,83,83,83 step 1
> volume #!1.1 showOutlineBox false
> volume #!1.1 showOutlineBox true
> volume #!1.1 showOutlineBox false
> volume #!1.1 style image
> volume #!1.1 style surface
> volume #!1.1 style mesh
> volume #!1.1 style image
> volume #!1.1 showOutlineBox true
> volume #!1.1 showOutlineBox false
> volume #!1.1 style surface
> volume show
> volume hide
> volume show
> volume hide
> volume #1.1 change image level 0,0 level 2.57,0.8 level 26.52,1
> volume #1.1 level 0.1488
> ui tool show "Side View"
> save /Users/floriansestak/Desktop/image1.png supersample 3
> ui mousemode right clip
> volume #1.1 style mesh
> volume #1.1 style image maximumIntensityProjection true
> volume #1.1 level 0,0 level 1.23,0.8462 level 26.52,1
> volume #1.1 level 0,0 level 1.23,0.8462 level 26.59,1
> volume #1.1 step 2
> volume #1.1 step 1
> volume #1.1 maximumIntensityProjection false colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #1.1 style surface
> volume #!1.1 showOutlineBox false
> volume #!1.1 showOutlineBox true
> volume #!1.1 step 2
> volume #!1.1 step 1
> volume #1.1 region 0,0,0,83,48,83
> volume #1.1 region 0,0,0,83,39,83
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right rotate
> volume #!1.1 showOutlineBox false
> volume #!1.1 showOutlineBox true
> volume #!1.1 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1.1 region 0,0,33,83,39,33
> volume #1.1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 15.18 tiltedSlabSpacing 0.2 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #1.1 tiltedSlabAxis 0.04663,-0.3626,0.9308 tiltedSlabOffset 9.403
> volume #!1.1 region all imageMode "full region"
> volume unzone #!1.1
> mousemode rightMode "crop volume"
> volume #1.1 region 0,0,0,83,83,83
> volume #1.1 style surface
> volume #1.1 region 0,0,0,83,42,83
> color gradient #1.1.1 map #1.1
Map values for surface "surface": minimum 0.6059, mean 2.869, maximum 60.35
> volume #1.1 region 0,0,0,83,37,83
> color gradient #1.1.1 map #1.1
Map values for surface "surface": minimum 0.6059, mean 3.303, maximum 59.29
> color gradient #1 map #1.1
Map values for surface "surface": minimum 0.6059, mean 3.303, maximum 59.29
Map values for surface "surface": minimum 1.731e-06, mean 1.252, maximum 28.58
Map values for surface "surface": minimum 0, mean 2.487, maximum 65.75
Map values for surface "surface": minimum 0, mean 3.985, maximum 86.56
Map values for surface "surface": minimum 0, mean 1.409, maximum 47.81
Map values for surface "surface": minimum 0, mean 2.295, maximum 73.77
Map values for surface "surface": minimum 0, mean 2.053, maximum 64.8
Map values for surface "surface": minimum 0, mean 3.591, maximum 87.56
Map values for surface "surface": minimum 0, mean 2.972, maximum 59.29
Map values for surface "surface": minimum 0, mean 2.602, maximum 73.42
Map values for surface "surface": minimum 0, mean 3.888, maximum 87.18
Map values for surface "surface": minimum 0, mean 3.503, maximum 88.2
Map values for surface "surface": minimum 0, mean 3.619, maximum 88.6
Map values for surface "surface": minimum 0, mean 4.234, maximum 66.5
Map values for surface "surface": minimum 0, mean 3.116, maximum 78.98
Map values for surface "surface": minimum 0, mean 3.648, maximum 88.24
Map values for surface "surface": minimum 0, mean 2.307, maximum 79.81
Map values for surface "surface": minimum 0, mean 3.113, maximum 70.6
Map values for surface "surface": minimum 0, mean 3.26, maximum 86.66
Map values for surface "surface": minimum 0, mean 3.386, maximum 83.56
Map values for surface "surface": minimum 0, mean 3.471, maximum 78.2
Map values for surface "surface": minimum 0, mean 2.607, maximum 60.08
Map values for surface "surface": minimum 0, mean 3.68, maximum 66.05
Map values for surface "surface": minimum 0, mean 2.774, maximum 66.46
Map values for surface "surface": minimum 0, mean 3.754, maximum 88.78
Map values for surface "surface": minimum 0, mean 3.978, maximum 65.87
Map values for surface "surface": minimum 0, mean 4.034, maximum 67.17
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Map values for surface "surface": minimum 0, mean 2.223, maximum 88.15
Map values for surface "surface": minimum 0, mean 2.117, maximum 88.06
Map values for surface "surface": minimum 0, mean 1.845, maximum 75.65
Map values for surface "surface": minimum 0, mean 1.889, maximum 80.81
Map values for surface "surface": minimum 0, mean 1.695, maximum 73.55
Map values for surface "surface": minimum 0, mean 1.353, maximum 64.08
Map values for surface "surface": minimum 0, mean 1.808, maximum 73.76
Map values for surface "surface": minimum 0, mean 1.804, maximum 67.89
Map values for surface "surface": minimum 0, mean 1.372, maximum 65.19
Map values for surface "surface": minimum 0, mean 1.823, maximum 63.34
Map values for surface "surface": minimum 0, mean 1.766, maximum 90.03
Map values for surface "surface": minimum 0, mean 2.226, maximum 87.56
Map values for surface "surface": minimum 0, mean 1.708, maximum 70.71
Map values for surface "surface": minimum 0, mean 1.974, maximum 80.33
Map values for surface "surface": minimum 0, mean 2.078, maximum 84.18
Map values for surface "surface": minimum 0, mean 1.589, maximum 75.33
Map values for surface "surface": minimum 0, mean 2.066, maximum 79.84
Map values for surface "surface": minimum 0, mean 2.216, maximum 86.9
Map values for surface "surface": minimum 0, mean 1.619, maximum 74.62
Map values for surface "surface": minimum 0, mean 1.61, maximum 75.22
Map values for surface "surface": minimum 0, mean 2.25, maximum 83.29
Map values for surface "surface": minimum 0, mean 2.11, maximum 77.94
Map values for surface "surface": minimum 0, mean 1.94, maximum 86.39
Map values for surface "surface": minimum 0, mean 1.998, maximum 87.72
Map values for surface "surface": minimum 0, mean 1.968, maximum 87.77
Map values for surface "surface": minimum 0, mean 1.691, maximum 86.77
Map values for surface "surface": minimum 0, mean 2.134, maximum 86.55
Map values for surface "surface": minimum 0, mean 1.753, maximum 71.5
Map values for surface "surface": minimum 0, mean 1.778, maximum 86.54
Map values for surface "surface": minimum 0, mean 2.123, maximum 84.62
Map values for surface "surface": minimum 0, mean 2.277, maximum 87.24
Map values for surface "surface": minimum 0, mean 1.688, maximum 82.23
Map values for surface "surface": minimum 0, mean 1.482, maximum 73.89
Map values for surface "surface": minimum 0, mean 1.926, maximum 91.6
Map values for surface "surface": minimum 0, mean 1.265, maximum 86.18
Map values for surface "surface": minimum 0, mean 1.573, maximum 83.96
Map values for surface "surface": minimum 0, mean 1.521, maximum 86.85
Map values for surface "surface": minimum 0, mean 1.712, maximum 81.98
Map values for surface "surface": minimum 0, mean 1.428, maximum 86.41
Map values for surface "surface": minimum 0, mean 2.339, maximum 88.88
Map values for surface "surface": minimum 0, mean 0.8796, maximum 70.83
Map values for surface "surface": minimum 0, mean 0.9247, maximum 70.38
Map values for surface "surface": minimum 0, mean 1.572, maximum 67.14
Map values for surface "surface": minimum 0, mean 1.166, maximum 63.74
Map values for surface "surface": minimum 0, mean 1.566, maximum 66.93
Map values for surface "surface": minimum 0, mean 1.557, maximum 66.22
Map values for surface "surface": minimum 0, mean 2.313, maximum 84.1
Map values for surface "surface": minimum 0, mean 2.061, maximum 82.07
Map values for surface "surface": minimum 0, mean 1.584, maximum 73.24
Map values for surface "surface": minimum 0, mean 1.969, maximum 92.44
Map values for surface "surface": minimum 0, mean 1.21, maximum 71.08
Map values for surface "surface": minimum 0, mean 1.257, maximum 81.88
Map values for surface "surface": minimum 0, mean 1.2, maximum 75.36
Map values for surface "surface": minimum 0, mean 1.208, maximum 69.62
Map values for surface "surface": minimum 0, mean 1.346, maximum 77.72
Map values for surface "surface": minimum 0, mean 1.3, maximum 62.78
Map values for surface "surface": minimum 0, mean 1.467, maximum 67.73
Map values for surface "surface": minimum 0, mean 1.456, maximum 81.18
Map values for surface "surface": minimum 0, mean 1.98, maximum 84.67
Map values for surface "surface": minimum 0, mean 1.416, maximum 64.25
Map values for surface "surface": minimum 0, mean 2.03, maximum 86.71
Map values for surface "surface": minimum 0, mean 1.868, maximum 86.8
Map values for surface "surface": minimum 0, mean 1.973, maximum 87.03
Map values for surface "surface": minimum 0, mean 1.793, maximum 89.43
Map values for surface "surface": minimum 0, mean 1.818, maximum 84.49
Map values for surface "surface": minimum 0, mean 1.905, maximum 83.06
Map values for surface "surface": minimum 0, mean 1.701, maximum 83.08
Map values for surface "surface": minimum 0, mean 1.796, maximum 83.99
Map values for surface "surface": minimum 0, mean 1.681, maximum 62.49
Map values for surface "surface": minimum 0, mean 1.694, maximum 65.54
Map values for surface "surface": minimum 0, mean 2.012, maximum 75.97
Map values for surface "surface": minimum 0, mean 2.177, maximum 85.52
Map values for surface "surface": minimum 0, mean 2.343, maximum 86.77
Map values for surface "surface": minimum 0, mean 2.085, maximum 87.79
Map values for surface "surface": minimum 0, mean 1.867, maximum 84.64
Map values for surface "surface": minimum 0, mean 1.819, maximum 78.37
Map values for surface "surface": minimum 0, mean 1.988, maximum 86.81
Map values for surface "surface": minimum 0, mean 2.279, maximum 89.52
Map values for surface "surface": minimum 0, mean 2.174, maximum 90.38
Map values for surface "surface": minimum 0, mean 2.001, maximum 86
Map values for surface "surface": minimum 0, mean 1.778, maximum 64.93
Map values for surface "surface": minimum 0, mean 1.404, maximum 62.07
Map values for surface "surface": minimum 0, mean 1.779, maximum 85.27
Map values for surface "surface": minimum 0, mean 1.295, maximum 90.58
Map values for surface "surface": minimum 0, mean 1.826, maximum 79.87
Map values for surface "surface": minimum 0, mean 1.65, maximum 84.9
Map values for surface "surface": minimum 0, mean 1.562, maximum 87.94
Map values for surface "surface": minimum 0, mean 1.399, maximum 67.12
Map values for surface "surface": minimum 0, mean 1.66, maximum 78.69
Map values for surface "surface": minimum 0, mean 1.363, maximum 63.3
Map values for surface "surface": minimum 0, mean 1.677, maximum 90.76
Map values for surface "surface": minimum 0, mean 1.998, maximum 79.6
Map values for surface "surface": minimum 0, mean 1.165, maximum 65.58
Map values for surface "surface": minimum 0, mean 2.05, maximum 75.74
Map values for surface "surface": minimum 0, mean 1.646, maximum 73.81
Map values for surface "surface": minimum 0, mean 2.619, maximum 88.84
Map values for surface "surface": minimum 0, mean 2.186, maximum 79.73
Map values for surface "surface": minimum 0, mean 1.989, maximum 75.43
Map values for surface "surface": minimum 0, mean 2.25, maximum 87.6
Map values for surface "surface": minimum 0, mean 1.923, maximum 88.66
Map values for surface "surface": minimum 0, mean 1.721, maximum 83.59
Map values for surface "surface": minimum 0, mean 1.719, maximum 84.3
Map values for surface "surface": minimum 0, mean 2.521, maximum 79.69
Map values for surface "surface": minimum 0, mean 2.248, maximum 87.21
Map values for surface "surface": minimum 0, mean 1.858, maximum 80.88
Map values for surface "surface": minimum 0, mean 1.708, maximum 67.1
Map values for surface "surface": minimum 0, mean 2.154, maximum 75.69
Map values for surface "surface": minimum 0, mean 2.296, maximum 91.16
Map values for surface "surface": minimum 0, mean 1.539, maximum 61.85
Map values for surface "surface": minimum 0, mean 1.843, maximum 65.83
Map values for surface "surface": minimum 0, mean 1.933, maximum 83.86
Map values for surface "surface": minimum 0, mean 2.199, maximum 89.39
Map values for surface "surface": minimum 0, mean 1.631, maximum 79.14
Map values for surface "surface": minimum 0, mean 2.313, maximum 82.35
Map values for surface "surface": minimum 0, mean 1.729, maximum 76.37
Map values for surface "surface": minimum 0, mean 1.272, maximum 83.06
Map values for surface "surface": minimum 0, mean 2.009, maximum 86.8
Map values for surface "surface": minimum 0, mean 1.97, maximum 83.55
Map values for surface "surface": minimum 0, mean 1.74, maximum 86.5
Map values for surface "surface": minimum 0, mean 2.341, maximum 83
Map values for surface "surface": minimum 0, mean 2.069, maximum 73.87
Map values for surface "surface": minimum 0, mean 2.566, maximum 84.86
Map values for surface "surface": minimum 0, mean 2.615, maximum 85.79
Map values for surface "surface": minimum 0, mean 1.752, maximum 62.76
Map values for surface "surface": minimum 0, mean 2.355, maximum 82.92
Map values for surface "surface": minimum 0, mean 2.335, maximum 88.19
Map values for surface "surface": minimum 0, mean 2.068, maximum 80.97
Map values for surface "surface": minimum 0, mean 2.111, maximum 66.64
Map values for surface "surface": minimum 0, mean 1.829, maximum 79.32
Map values for surface "surface": minimum 0, mean 2.226, maximum 86.93
Map values for surface "surface": minimum 0, mean 1.941, maximum 64.59
Map values for surface "surface": minimum 0, mean 2.147, maximum 62.35
Map values for surface "surface": minimum 0, mean 2.165, maximum 73.87
Map values for surface "surface": minimum 0, mean 2.904, maximum 86.42
Map values for surface "surface": minimum 0, mean 2.724, maximum 87.02
Map values for surface "surface": minimum 0, mean 2.086, maximum 84.76
Map values for surface "surface": minimum 0, mean 1.823, maximum 75.41
Map values for surface "surface": minimum 0, mean 2.265, maximum 85.82
Map values for surface "surface": minimum 0, mean 2.119, maximum 68.12
Map values for surface "surface": minimum 0, mean 2.174, maximum 84.34
Map values for surface "surface": minimum 0, mean 2.52, maximum 86.95
Map values for surface "surface": minimum 0, mean 1.997, maximum 83.73
Map values for surface "surface": minimum 0, mean 2.169, maximum 82.53
Map values for surface "surface": minimum 0, mean 2.301, maximum 85.74
Map values for surface "surface": minimum 0, mean 1.792, maximum 73.75
Map values for surface "surface": minimum 0, mean 2.188, maximum 87.89
Map values for surface "surface": minimum 0, mean 1.858, maximum 76.59
Map values for surface "surface": minimum 0, mean 1.635, maximum 76.3
Map values for surface "surface": minimum 0, mean 1.883, maximum 91.12
Map values for surface "surface": minimum 0, mean 1.854, maximum 72.21
Map values for surface "surface": minimum 0, mean 1.577, maximum 73.55
Map values for surface "surface": minimum 0, mean 1.83, maximum 74.45
Map values for surface "surface": minimum 0, mean 2.072, maximum 81.54
Map values for surface "surface": minimum 0, mean 2.224, maximum 75.32
Map values for surface "surface": minimum 0, mean 2.084, maximum 74.09
Map values for surface "surface": minimum 0, mean 2.084, maximum 77.22
Map values for surface "surface": minimum 0, mean 1.941, maximum 71.97
Map values for surface "surface": minimum 0, mean 1.837, maximum 74.36
Map values for surface "surface": minimum 0, mean 2.016, maximum 73.86
Map values for surface "surface": minimum 0, mean 2.429, maximum 87.14
Map values for surface "surface": minimum 0, mean 1.844, maximum 81.92
Map values for surface "surface": minimum 0, mean 2.147, maximum 79.13
Map values for surface "surface": minimum 0, mean 2.079, maximum 75.82
Map values for surface "surface": minimum 0, mean 2.482, maximum 88.35
Map values for surface "surface": minimum 0, mean 2.116, maximum 75.94
Map values for surface "surface": minimum 0, mean 2.295, maximum 73.09
Map values for surface "surface": minimum 0, mean 1.973, maximum 73.78
Map values for surface "surface": minimum 0, mean 2.038, maximum 77.12
Map values for surface "surface": minimum 0, mean 2.376, maximum 76.09
Map values for surface "surface": minimum 0, mean 2.249, maximum 77.97
Map values for surface "surface": minimum 0, mean 2.25, maximum 73.19
Map values for surface "surface": minimum 0, mean 2.54, maximum 84.74
Map values for surface "surface": minimum 0, mean 2.104, maximum 70.57
Map values for surface "surface": minimum 0, mean 2.356, maximum 83.37
Map values for surface "surface": minimum 0, mean 1.939, maximum 74.35
Map values for surface "surface": minimum 0, mean 1.966, maximum 79.32
Map values for surface "surface": minimum 0, mean 1.982, maximum 78.29
Map values for surface "surface": minimum 0, mean 2.035, maximum 74.52
Map values for surface "surface": minimum 0, mean 1.754, maximum 75.59
Map values for surface "surface": minimum 0, mean 2.689, maximum 83.91
Map values for surface "surface": minimum 0, mean 1.941, maximum 73.5
Map values for surface "surface": minimum 0, mean 2.12, maximum 78.84
Map values for surface "surface": minimum 0, mean 1.792, maximum 76.4
Map values for surface "surface": minimum 0, mean 1.458, maximum 80.95
Map values for surface "surface": minimum 0, mean 2.18, maximum 84.3
Map values for surface "surface": minimum 0, mean 1.994, maximum 76.52
Map values for surface "surface": minimum 0, mean 2.016, maximum 76.29
Map values for surface "surface": minimum 0, mean 2.232, maximum 85.6
Map values for surface "surface": minimum 0, mean 2.224, maximum 85.02
Map values for surface "surface": minimum 0, mean 2.414, maximum 84.01
Map values for surface "surface": minimum 0, mean 2.132, maximum 73.62
Map values for surface "surface": minimum 0, mean 2.185, maximum 74.41
Map values for surface "surface": minimum 0, mean 2.007, maximum 75.22
Map values for surface "surface": minimum 0, mean 2.033, maximum 77.41
Map values for surface "surface": minimum 0, mean 2.155, maximum 78.91
Map values for surface "surface": minimum 0, mean 1.665, maximum 74.85
Map values for surface "surface": minimum 0, mean 2.25, maximum 87.97
Map values for surface "surface": minimum 0, mean 1.652, maximum 62.39
Map values for surface "surface": minimum 0, mean 2.199, maximum 88.78
Map values for surface "surface": minimum 0, mean 1.506, maximum 67.22
Map values for surface "surface": minimum 0, mean 1.862, maximum 62.75
Map values for surface "surface": minimum 0, mean 2.019, maximum 68.87
Map values for surface "surface": minimum 0, mean 1.854, maximum 86.09
Map values for surface "surface": minimum 0, mean 1.407, maximum 62.39
> volume #1.361 region 0,0,0,83,24,83
> volume #1.1 region 0,0,0,83,50,83
> color gradient #1
volume gradient command must specify "map" option
> color gradient #1 map
Missing "map" keyword's argument
Must specify one map, got 1000
> color gradient #1 map #1.1 offset 60,100,10
Map values for surface "surface": minimum 0, mean 0, maximum 0
> volume #1.814 region 0,0,0,83,53,83
> volume #1.814 region 0,0,0,83,39,83
> color gradient #1 map #1.1 offset 0,10,15,20,25,30,35
Invalid "offset" argument: Expected a number or 3-tuple of numbers
> color gradient #1 map #1.1 offset 0,15,30
Map values for surface "surface": minimum 0.4865, mean 3.286, maximum 85.48
Map values for surface "surface": minimum 1.731e-06, mean 1.252, maximum 28.58
Map values for surface "surface": minimum 0, mean 2.487, maximum 65.75
Map values for surface "surface": minimum 0, mean 3.985, maximum 86.56
Map values for surface "surface": minimum 0, mean 2.584, maximum 67.36
Map values for surface "surface": minimum 0, mean 2.295, maximum 73.77
Map values for surface "surface": minimum 0, mean 2.053, maximum 64.8
Map values for surface "surface": minimum 0, mean 3.591, maximum 87.56
Map values for surface "surface": minimum 0, mean 2.972, maximum 59.29
Map values for surface "surface": minimum 0, mean 2.602, maximum 73.42
Map values for surface "surface": minimum 0, mean 3.888, maximum 87.18
Map values for surface "surface": minimum 0, mean 3.503, maximum 88.2
Map values for surface "surface": minimum 0, mean 3.619, maximum 88.6
Map values for surface "surface": minimum 0, mean 4.662, maximum 85.48
Map values for surface "surface": minimum 0, mean 3.116, maximum 78.98
Map values for surface "surface": minimum 0, mean 3.648, maximum 88.24
Map values for surface "surface": minimum 0, mean 2.307, maximum 79.81
Map values for surface "surface": minimum 0, mean 3.113, maximum 70.6
Map values for surface "surface": minimum 0, mean 3.26, maximum 86.66
Map values for surface "surface": minimum 0, mean 3.386, maximum 83.56
Map values for surface "surface": minimum 0, mean 3.471, maximum 78.2
Map values for surface "surface": minimum 0, mean 2.607, maximum 60.08
Map values for surface "surface": minimum 0, mean 3.68, maximum 66.05
Map values for surface "surface": minimum 0, mean 2.774, maximum 66.46
Map values for surface "surface": minimum 0, mean 3.754, maximum 88.78
Map values for surface "surface": minimum 0, mean 5.458, maximum 85.48
Map values for surface "surface": minimum 0, mean 4.034, maximum 67.17
Map values for surface "surface": minimum 0, mean 3.717, maximum 91.02
Map values for surface "surface": minimum 0, mean 3.515, maximum 73.49
Map values for surface "surface": minimum 0, mean 3.339, maximum 80.15
Map values for surface "surface": minimum 0, mean 2.363, maximum 62.37
Map values for surface "surface": minimum 0, mean 4.086, maximum 78.83
Map values for surface "surface": minimum 0, mean 3.254, maximum 87.38
Map values for surface "surface": minimum 0, mean 2.507, maximum 75.82
Map values for surface "surface": minimum 0, mean 3.652, maximum 76.42
Map values for surface "surface": minimum 0, mean 3.078, maximum 83.54
Map values for surface "surface": minimum 0, mean 2.688, maximum 82.93
Map values for surface "surface": minimum 0, mean 2.666, maximum 80.74
Map values for surface "surface": minimum 0, mean 4.311, maximum 60.28
Map values for surface "surface": minimum 0, mean 3.531, maximum 89.23
Map values for surface "surface": minimum 0, mean 3.216, maximum 88.32
Map values for surface "surface": minimum 0, mean 3.492, maximum 88.34
Map values for surface "surface": minimum 0, mean 4.103, maximum 67.76
Map values for surface "surface": minimum 0, mean 3.447, maximum 86.8
Map values for surface "surface": minimum 0, mean 2.955, maximum 69.92
Map values for surface "surface": minimum 0, mean 3.242, maximum 83.18
Map values for surface "surface": minimum 0, mean 3.118, maximum 78.22
Map values for surface "surface": minimum 0, mean 6.224, maximum 88.15
Map values for surface "surface": minimum 0, mean 3.098, maximum 85.96
Map values for surface "surface": minimum 0, mean 2.542, maximum 66.87
Map values for surface "surface": minimum 0, mean 2.099, maximum 59.5
Map values for surface "surface": minimum 6.637e-07, mean 6.086, maximum 86.28
Map values for surface "surface": minimum 0, mean 3.987, maximum 89.8
Map values for surface "surface": minimum 0, mean 3.789, maximum 81.57
Map values for surface "surface": minimum 0, mean 3.356, maximum 81.94
Map values for surface "surface": minimum 0, mean 4.913, maximum 85.48
Map values for surface "surface": minimum 0, mean 3.131, maximum 87.63
Map values for surface "surface": minimum 0, mean 3.367, maximum 88.76
Map values for surface "surface": minimum 0, mean 2.464, maximum 65.02
Map values for surface "surface": minimum 0, mean 7.218, maximum 85
Map values for surface "surface": minimum 0, mean 3.298, maximum 86.78
Map values for surface "surface": minimum 0, mean 2.972, maximum 76.81
Map values for surface "surface": minimum 0, mean 3.61, maximum 85.04
Map values for surface "surface": minimum 0, mean 5.142, maximum 88.45
Map values for surface "surface": minimum 0, mean 3.26, maximum 89.67
Map values for surface "surface": minimum 0, mean 3.544, maximum 76.58
Map values for surface "surface": minimum 0, mean 3.131, maximum 79.09
Map values for surface "surface": minimum 0, mean 3.636, maximum 84.36
Map values for surface "surface": minimum 0, mean 4.954, maximum 85.48
Map values for surface "surface": minimum 0, mean 3.419, maximum 87.84
Map values for surface "surface": minimum 0, mean 3.412, maximum 86.13
Map values for surface "surface": minimum 0, mean 3.589, maximum 72.85
Map values for surface "surface": minimum 0, mean 5.011, maximum 84.54
Map values for surface "surface": minimum 0, mean 3.522, maximum 90
Map values for surface "surface": minimum 0, mean 3.033, maximum 81.99
Map values for surface "surface": minimum 0, mean 3.203, maximum 88.94
Map values for surface "surface": minimum 0, mean 4.779, maximum 88.99
Map values for surface "surface": minimum 0, mean 3.24, maximum 87.3
Map values for surface "surface": minimum 0, mean 3.18, maximum 88.17
Map values for surface "surface": minimum 0, mean 3.076, maximum 88.69
Map values for surface "surface": minimum 0, mean 6.482, maximum 66.86
Map values for surface "surface": minimum 0, mean 3.228, maximum 87.47
Map values for surface "surface": minimum 0, mean 3.281, maximum 89.87
Map values for surface "surface": minimum 0, mean 3.385, maximum 86.11
Map values for surface "surface": minimum 0, mean 3.307, maximum 89.78
Map values for surface "surface": minimum 7.438e-07, mean 7.113, maximum 87.47
Map values for surface "surface": minimum 0, mean 2.908, maximum 91.85
Map values for surface "surface": minimum 0, mean 3.317, maximum 80.2
Map values for surface "surface": minimum 0, mean 3.476, maximum 76.39
Map values for surface "surface": minimum 0, mean 5.549, maximum 85.03
Map values for surface "surface": minimum 0, mean 3.53, maximum 82.19
Map values for surface "surface": minimum 0, mean 3.236, maximum 65.86
Map values for surface "surface": minimum 0, mean 3.119, maximum 84.73
Map values for surface "surface": minimum 0, mean 5.523, maximum 87.36
Map values for surface "surface": minimum 0, mean 3.236, maximum 85.33
Map values for surface "surface": minimum 0, mean 3.649, maximum 82.51
Map values for surface "surface": minimum 0, mean 2.816, maximum 73.76
Map values for surface "surface": minimum 0, mean 5.169, maximum 84.5
Map values for surface "surface": minimum 0, mean 3.402, maximum 90.77
Map values for surface "surface": minimum 0, mean 3.098, maximum 75.11
Map values for surface "surface": minimum 0, mean 2.287, maximum 67.16
Map values for surface "surface": minimum 0, mean 3.441, maximum 86.12
Map values for surface "surface": minimum 0, mean 4.171, maximum 68.18
Map values for surface "surface": minimum 0, mean 3.502, maximum 77.45
Map values for surface "surface": minimum 0, mean 3.635, maximum 86.32
Map values for surface "surface": minimum 0, mean 3.666, maximum 89.32
Map values for surface "surface": minimum 0, mean 3.216, maximum 73.5
Map values for surface "surface": minimum 0, mean 3.122, maximum 91.77
Map values for surface "surface": minimum 0, mean 3.791, maximum 84.75
Map values for surface "surface": minimum 0, mean 3.755, maximum 90.8
Map values for surface "surface": minimum 0, mean 4.318, maximum 66.99
Map values for surface "surface": minimum 0, mean 3.142, maximum 86.48
Map values for surface "surface": minimum 0, mean 2.882, maximum 82.76
Map values for surface "surface": minimum 0, mean 2.461, maximum 73.12
Map values for surface "surface": minimum 0, mean 2.357, maximum 73.76
Map values for surface "surface": minimum 0, mean 2.142, maximum 84.2
Map values for surface "surface": minimum 0, mean 2.081, maximum 84.33
Map values for surface "surface": minimum 0, mean 2.149, maximum 85.56
Map values for surface "surface": minimum 0, mean 2.197, maximum 77.6
Map values for surface "surface": minimum 0, mean 0.9643, maximum 44.95
Map values for surface "surface": minimum 0, mean 3.071, maximum 79
Map values for surface "surface": minimum 0, mean 2.849, maximum 87.87
Map values for surface "surface": minimum 0, mean 2.596, maximum 82.25
Map values for surface "surface": minimum 0, mean 2.545, maximum 72.49
Map values for surface "surface": minimum 0, mean 2.539, maximum 80.43
Map values for surface "surface": minimum 0, mean 3.618, maximum 90.06
Map values for surface "surface": minimum 0, mean 2.888, maximum 79.75
Map values for surface "surface": minimum 0, mean 3.478, maximum 85.48
Map values for surface "surface": minimum 0, mean 2.122, maximum 84.88
Map values for surface "surface": minimum 0, mean 3.32, maximum 87.74
Map values for surface "surface": minimum 0, mean 3.071, maximum 84.34
Map values for surface "surface": minimum 0, mean 3.134, maximum 83.99
Map values for surface "surface": minimum 0, mean 2.186, maximum 83.31
Map values for surface "surface": minimum 0, mean 2.647, maximum 90.06
Map values for surface "surface": minimum 0, mean 2.32, maximum 72.99
Map values for surface "surface": minimum 0, mean 2.924, maximum 73.31
Map values for surface "surface": minimum 0, mean 2.612, maximum 80.65
Map values for surface "surface": minimum 0, mean 2.173, maximum 76.41
Map values for surface "surface": minimum 0, mean 2.151, maximum 79.17
Map values for surface "surface": minimum 0, mean 2.755, maximum 87.49
Map values for surface "surface": minimum 0, mean 6.229, maximum 67.12
Map values for surface "surface": minimum 0, mean 3.692, maximum 87.15
Map values for surface "surface": minimum 0, mean 2.59, maximum 73.06
Map values for surface "surface": minimum 0, mean 2.739, maximum 82.02
Map values for surface "surface": minimum 0, mean 2.414, maximum 75.5
Map values for surface "surface": minimum 0, mean 2.428, maximum 84.27
Map values for surface "surface": minimum 0, mean 2.8, maximum 73.28
Map values for surface "surface": minimum 0, mean 3.003, maximum 80.06
Map values for surface "surface": minimum 0, mean 2.699, maximum 71.19
Map values for surface "surface": minimum 0, mean 3.154, maximum 88.16
Map values for surface "surface": minimum 0, mean 2.769, maximum 92.35
Map values for surface "surface": minimum 0, mean 2.638, maximum 77.3
Map values for surface "surface": minimum 0, mean 2.855, maximum 75.11
Map values for surface "surface": minimum 0, mean 2.202, maximum 65.55
Map values for surface "surface": minimum 0, mean 1.587, maximum 63.8
Map values for surface "surface": minimum 0, mean 1.877, maximum 77.78
Map values for surface "surface": minimum 0, mean 1.496, maximum 67.1
Map values for surface "surface": minimum 0, mean 0.6366, maximum 31.32
Map values for surface "surface": minimum 0, mean 1.31, maximum 65.82
Map values for surface "surface": minimum 0, mean 1.585, maximum 77.45
Map values for surface "surface": minimum 0, mean 2.006, maximum 72.39
Map values for surface "surface": minimum 0, mean 1.643, maximum 64.53
Map values for surface "surface": minimum 0, mean 1.266, maximum 78.62
Map values for surface "surface": minimum 0, mean 1.261, maximum 65.14
Map values for surface "surface": minimum 0, mean 1.665, maximum 72.22
Map values for surface "surface": minimum 0, mean 0.7363, maximum 29.85
Map values for surface "surface": minimum 0, mean 1.982, maximum 79.47
Map values for surface "surface": minimum 0, mean 1.584, maximum 77.76
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Map values for surface "surface": minimum 0, mean 0.5216, maximum 31.93
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> volume #1.814 region 0,0,0,83,31,83
> volume #1.814 region 0,0,0,83,46,83
> volume #1.814 region 0,0,0,83,83,83
> volume #1.814 region 39,0,0,83,83,83
> color gradient #1 map #1.1 offset 0,10,30
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Map values for surface "surface": minimum 0, mean 0.3218, maximum 12.22
Map values for surface "surface": minimum 0, mean 0.3362, maximum 12.4
Map values for surface "surface": minimum 0, mean 0.3014, maximum 12.54
Map values for surface "surface": minimum 0, mean 0.2722, maximum 12.09
Map values for surface "surface": minimum 0, mean 0.2668, maximum 11.2
Map values for surface "surface": minimum 0, mean 0.2908, maximum 12.4
Map values for surface "surface": minimum 0, mean 0.3299, maximum 12.79
Map values for surface "surface": minimum 0, mean 0.3124, maximum 12.91
Map values for surface "surface": minimum 0, mean 0.2945, maximum 12.29
Map values for surface "surface": minimum 0, mean 0.2575, maximum 9.275
Map values for surface "surface": minimum 0, mean 0.2019, maximum 8.868
Map values for surface "surface": minimum 0, mean 0.263, maximum 12.18
Map values for surface "surface": minimum 0, mean 0.1866, maximum 12.94
Map values for surface "surface": minimum 0, mean 0.2643, maximum 11.41
Map values for surface "surface": minimum 0, mean 0.24, maximum 12.13
Map values for surface "surface": minimum 0, mean 0.2282, maximum 12.56
Map values for surface "surface": minimum 0, mean 0.2041, maximum 9.589
Map values for surface "surface": minimum 0, mean 0.2412, maximum 11.24
Map values for surface "surface": minimum 0, mean 0.2007, maximum 9.043
Map values for surface "surface": minimum 0, mean 0.2461, maximum 12.97
Map values for surface "surface": minimum 0, mean 0.291, maximum 11.56
Map values for surface "surface": minimum 0, mean 0.1692, maximum 9.369
Map values for surface "surface": minimum 0, mean 0.3023, maximum 10.82
Map values for surface "surface": minimum 0, mean 0.241, maximum 10.56
Map values for surface "surface": minimum 0, mean 0.3805, maximum 12.69
Map values for surface "surface": minimum 0, mean 0.3195, maximum 11.39
Map values for surface "surface": minimum 0, mean 0.2871, maximum 10.78
Map values for surface "surface": minimum 0, mean 0.3257, maximum 12.51
Map values for surface "surface": minimum 0, mean 0.2777, maximum 12.67
Map values for surface "surface": minimum 0, mean 0.2507, maximum 11.94
Map values for surface "surface": minimum 0, mean 0.247, maximum 12.04
Map values for surface "surface": minimum 0, mean 0.3623, maximum 11.38
Map values for surface "surface": minimum 0, mean 0.3282, maximum 12.46
Map values for surface "surface": minimum 0, mean 0.2721, maximum 11.55
Map values for surface "surface": minimum 0, mean 0.2467, maximum 9.586
Map values for surface "surface": minimum 0, mean 0.3127, maximum 10.81
Map values for surface "surface": minimum 0, mean 0.3373, maximum 13.02
Map values for surface "surface": minimum 0, mean 0.2226, maximum 8.836
Map values for surface "surface": minimum 0, mean 0.2678, maximum 9.404
Map values for surface "surface": minimum 0, mean 0.2791, maximum 11.98
Map values for surface "surface": minimum 0, mean 0.3183, maximum 12.77
Map values for surface "surface": minimum 0, mean 0.2384, maximum 11.31
Map values for surface "surface": minimum 0, mean 0.3398, maximum 11.76
Map values for surface "surface": minimum 0, mean 0.2487, maximum 10.91
Map values for surface "surface": minimum 0, mean 0.1854, maximum 11.87
Map values for surface "surface": minimum 0, mean 0.2938, maximum 12.4
Map values for surface "surface": minimum 0, mean 0.2839, maximum 11.94
Map values for surface "surface": minimum 0, mean 0.2515, maximum 12.36
Map values for surface "surface": minimum 0, mean 0.3427, maximum 11.86
Map values for surface "surface": minimum 0, mean 0.2986, maximum 10.55
Map values for surface "surface": minimum 0, mean 0.3723, maximum 12.12
Map values for surface "surface": minimum 0, mean 0.38, maximum 12.26
Map values for surface "surface": minimum 0, mean 0.2581, maximum 8.966
Map values for surface "surface": minimum 0, mean 0.3416, maximum 11.85
Map values for surface "surface": minimum 0, mean 0.339, maximum 12.6
Map values for surface "surface": minimum 0, mean 0.2986, maximum 11.57
Map values for surface "surface": minimum 0, mean 0.3055, maximum 9.52
Map values for surface "surface": minimum 0, mean 0.2675, maximum 11.33
Map values for surface "surface": minimum 0, mean 0.3205, maximum 12.42
Map values for surface "surface": minimum 0, mean 0.2847, maximum 9.227
Map values for surface "surface": minimum 0, mean 0.3156, maximum 11.28
Map values for surface "surface": minimum 0, mean 0.3125, maximum 10.55
Map values for surface "surface": minimum 0, mean 0.4217, maximum 12.35
Map values for surface "surface": minimum 0, mean 0.3974, maximum 12.43
Map values for surface "surface": minimum 0, mean 0.3016, maximum 12.11
Map values for surface "surface": minimum 0, mean 0.2662, maximum 10.77
Map values for surface "surface": minimum 0, mean 0.3273, maximum 12.26
Map values for surface "surface": minimum 0, mean 0.3073, maximum 9.746
Map values for surface "surface": minimum 0, mean 0.3138, maximum 12.05
Map values for surface "surface": minimum 0, mean 0.3664, maximum 12.42
Map values for surface "surface": minimum 0, mean 0.2935, maximum 11.96
Map values for surface "surface": minimum 0, mean 0.3159, maximum 11.79
Map values for surface "surface": minimum 0, mean 0.3377, maximum 12.25
Map values for surface "surface": minimum 0, mean 0.2622, maximum 10.54
Map values for surface "surface": minimum 0, mean 0.3206, maximum 12.56
Map values for surface "surface": minimum 0, mean 0.2681, maximum 10.94
Map values for surface "surface": minimum 0, mean 0.2396, maximum 10.9
Map values for surface "surface": minimum 0, mean 0.2718, maximum 13.02
Map values for surface "surface": minimum 0, mean 0.2676, maximum 10.32
Map values for surface "surface": minimum 0, mean 0.2277, maximum 10.51
Map values for surface "surface": minimum 0, mean 0.2658, maximum 10.64
Map values for surface "surface": minimum 0, mean 0.2983, maximum 11.65
Map values for surface "surface": minimum 0, mean 0.3197, maximum 10.76
Map values for surface "surface": minimum 0, mean 0.3021, maximum 10.58
Map values for surface "surface": minimum 0, mean 0.3014, maximum 11.03
Map values for surface "surface": minimum 0, mean 0.2844, maximum 10.28
Map values for surface "surface": minimum 0, mean 0.2662, maximum 10.62
Map values for surface "surface": minimum 0, mean 0.2932, maximum 10.55
Map values for surface "surface": minimum 0, mean 0.35, maximum 12.45
Map values for surface "surface": minimum 0, mean 0.2699, maximum 11.7
Map values for surface "surface": minimum 0, mean 0.3106, maximum 11.3
Map values for surface "surface": minimum 0, mean 0.302, maximum 10.83
Map values for surface "surface": minimum 0, mean 0.3608, maximum 12.62
Map values for surface "surface": minimum 0, mean 0.3054, maximum 10.85
Map values for surface "surface": minimum 0, mean 0.3352, maximum 10.44
Map values for surface "surface": minimum 0, mean 0.2837, maximum 10.54
Map values for surface "surface": minimum 0, mean 0.296, maximum 11.02
Map values for surface "surface": minimum 0, mean 0.3502, maximum 10.87
Map values for surface "surface": minimum 0, mean 0.3305, maximum 11.14
Map values for surface "surface": minimum 0, mean 0.3328, maximum 10.46
Map values for surface "surface": minimum 0, mean 0.3739, maximum 12.11
Map values for surface "surface": minimum 0, mean 0.304, maximum 10.08
Map values for surface "surface": minimum 0, mean 0.3387, maximum 11.91
Map values for surface "surface": minimum 0, mean 0.2831, maximum 10.62
Map values for surface "surface": minimum 0, mean 0.2858, maximum 11.33
Map values for surface "surface": minimum 0, mean 0.2869, maximum 11.18
Map values for surface "surface": minimum 0, mean 0.3001, maximum 10.65
Map values for surface "surface": minimum 0, mean 0.2534, maximum 10.8
Map values for surface "surface": minimum 0, mean 0.3906, maximum 11.99
Map values for surface "surface": minimum 0, mean 0.2925, maximum 10.5
Map values for surface "surface": minimum 0, mean 0.3057, maximum 11.26
Map values for surface "surface": minimum 0, mean 0.2582, maximum 10.91
Map values for surface "surface": minimum 0, mean 0.2097, maximum 11.56
Map values for surface "surface": minimum 0, mean 0.3136, maximum 12.04
Map values for surface "surface": minimum 0, mean 0.2886, maximum 10.93
Map values for surface "surface": minimum 0, mean 0.2918, maximum 10.9
Map values for surface "surface": minimum 0, mean 0.3239, maximum 12.23
Map values for surface "surface": minimum 0, mean 0.3193, maximum 12.15
Map values for surface "surface": minimum 0, mean 0.3495, maximum 12
Map values for surface "surface": minimum 0, mean 0.3097, maximum 10.52
Map values for surface "surface": minimum 0, mean 0.3187, maximum 10.63
Map values for surface "surface": minimum 0, mean 0.2905, maximum 10.75
Map values for surface "surface": minimum 0, mean 0.2946, maximum 11.06
Map values for surface "surface": minimum 0, mean 0.3096, maximum 11.27
Map values for surface "surface": minimum 0, mean 0.2395, maximum 10.69
Map values for surface "surface": minimum 0, mean 0.3273, maximum 12.57
Map values for surface "surface": minimum 0, mean 0.238, maximum 8.913
Map values for surface "surface": minimum 0, mean 0.3169, maximum 12.68
Map values for surface "surface": minimum 0, mean 0.2196, maximum 9.602
Map values for surface "surface": minimum 0, mean 0.2703, maximum 8.964
Map values for surface "surface": minimum 0, mean 0.292, maximum 9.839
Map values for surface "surface": minimum 0, mean 0.2728, maximum 12.3
Map values for surface "surface": minimum 0, mean 0.205, maximum 8.912
> volume #1.814 region 51,0,0,83,83,83
> volume #1.1 region 32,0,0,83,83,83
> color gradient #1 offset 0,30,5 palette paegreen
volume gradient command must specify "map" option
> volume #1 colormapSize viridis
Invalid "colormapSize" argument: Expected an integer
> volume #1 colormapSize 1
> volume #1.1 region 26,0,0,83,83,83
> volume #1.1 region 43,0,0,83,83,83
> volume #1 colormapSize viridis
Invalid "colormapSize" argument: Expected an integer
> volume #1 color 0,0.5,1 palette red:white:blue
Expected a keyword
> volume #1 color maroon
> volume #1.1 region 13,0,0,83,83,83
> volume #1 colormapSize palette red:white:blue range 0,1
Invalid "colormapSize" argument: Expected an integer
> volume #1 color palette red:white:blue range 0,1
Invalid "color" argument: Invalid color name or specifier
> volume #1 color palette maroon red:white:blue range 0,1
Invalid "color" argument: Invalid color name or specifier
> volume #1 color maroon red:white:blue range 0,1
Expected a keyword
> volume #1 color maroon range 0,1
Expected a keyword
> volume #1.1 region 43,0,0,83,83,83
> volume #1 style mesh level 0.8 color red level 1.2 color 0,50,80
> volume #1.1 region 27,0,0,83,83,83
> volume #1.1 level 0.8 level 4.474
> volume #1.1 level 0.2232 level 4.474
> volume #1.1 level 0.2232 level 0.9768
> volume #1.1 style mesh
> volume #1.1 level 0.2232 level 4.846
> volume #1.1 level 0.1488 level 4.846
> volume #1 level 10,0 level 100,1 level 400,1 color hot pink style image
> volume #1.1 region 0,0,0,83,83,83
> volume #1.1 style surface
> volume #1.1 region 48,0,0,83,83,83
> volume #1 level 10,0 level 100,1 level 400,1 color hot pink style image
> volume #1.1 level 0.258,0.1538 level 100,1 level 400,1
> volume #1.1 level 0.258,0.1538 level 100,1 level 23.29,0.1692
> volume #1.1 region 0,0,0,83,83,83
> close
> open /Users/floriansestak/Code/chimerax_scripts/volumes/*.mrc format mrc
> vseries true
Opened map series volume_001.mrc as #1, 1000 images, grid size 84,84,84, pixel
0.2, shown at level 0.0145, step 1, values float32
> volume #1.001-1.100 style mesh level 0.8 color red level 1.2 color 0,50,80
No volumes specified
> volume #1.1-1.100 style mesh level 0.8 color red level 1.2 color 0,50,80
No volumes specified
> volume #1.1-1.20 style mesh level 0.8 color red level 1.2 color 0,50,80
No volumes specified
> ui mousemode right windowing
> ui mousemode right "tape measure"
> marker segment #2 position 13.8,16.29,15.99 toPosition 13.92,13.61,15.32
> color yellow radius 0.05 label 2.759 labelHeight 0.2759 labelColor yellow
> ui mousemode right "rotate slab"
> volume #1.1 tiltedSlabAxis -0.5213,-0.0171,0.8532 tiltedSlabOffset 2.188
> volume #1.1 tiltedSlabAxis 0.1979,0.02421,-0.9799 tiltedSlabOffset -11.89
> volume #1.1 tiltedSlabAxis 0.3298,-0.9435,0.03273 tiltedSlabOffset -13.15
> volume #!1.1 showOutlineBox false
> ui mousemode right "move planes"
> volume #1.1 region 0,0,0,83,83,83
> ui mousemode right "tape measure"
> close #2
> volume defaultvalues initialColors salmon,lime,#ff805c saveSettings true
Saved volume settings
> marker segment #2 position 14.66,17.2,16.32 toPosition 14.54,14.65,12.29
> color yellow radius 0.05 label 4.764 labelHeight 0.4764 labelColor yellow
> close #2
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202406042103 (2024-06-04)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,7
Model Number: MRW23D/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 7 days, 10 hours, 40 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
HP E24i G4:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E24i G4:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202406042103
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.4
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.46
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.12.1
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
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