![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15745 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| 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-13.6.7-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 110000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 14554,
"osVersion" : {
"train" : "macOS 13.6.7",
"build" : "22G720",
"releaseType" : "User"
},
"captureTime" : "2024-08-07 21:58:56.7244 -0700",
"incident" : "FD2DB828-5415-43A8-860B-61AE22F0E765",
"pid" : 11636,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-05 12:49:49.8355 -0700",
"procStartAbsTime" : 702652693754,
"procExitAbsTime" : 2755222625348,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5EAECDE7-CBF1-5097-855E-E117783BF094","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C819F76F-3813-8349-EFEF-695E46CF7FE0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 28502,
"sleepWakeUUID" : "B124A416-9AA5-494E-BF2E-2E976202EBAE",
"sip" : "enabled",
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"name" : "_version.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6340427776,
"size" : 212992,
"uuid" : "9ff84874-4ecd-3fed-ba32-23b23bfaaecc",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6360694784,
"size" : 131072,
"uuid" : "272f9886-859c-3c84-8ea4-2bde196ca08b",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6172770304,
"size" : 131072,
"uuid" : "99497e49-7155-3c86-b62e-dd8a79f1be5d",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6597279744,
"size" : 737280,
"uuid" : "85293474-c54e-32bd-967c-f9f9839646ae",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6149144576,
"size" : 49152,
"uuid" : "0e674aef-d74d-34e9-a46b-63ce1a6729b4",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6146179072,
"size" : 49152,
"uuid" : "c84a9a90-56dd-385a-aad3-a15d44bc216b",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
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"arch" : "x86_64",
"base" : 6146383872,
"size" : 524288,
"uuid" : "58e1300b-c472-3863-8fc4-4eb27185cbbf",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 6252494848,
"size" : 442368,
"uuid" : "9141612b-bf67-390f-8b66-18a585729cab",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
},
{
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"base" : 5949980672,
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"uuid" : "6d0a4aa1-f80b-3e16-baed-3f694111a75d",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 6440796160,
"size" : 4210688,
"uuid" : "08a0cdf4-85d3-328a-98ac-8a7ec48356eb",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
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"base" : 5944410112,
"size" : 147456,
"uuid" : "a66bb1e2-ecf4-3220-9c8e-a465d9305940",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5937741824,
"size" : 16384,
"uuid" : "67c108ea-3b9a-3731-a794-8ca4049035a3",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-311-darwin.so",
"name" : "_sw.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 5938085888,
"size" : 16384,
"uuid" : "0cf88116-cc85-32ed-b523-593e852fc25f",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/libalign_algs.dylib",
"name" : "libalign_algs.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5922832384,
"size" : 16384,
"uuid" : "ce412e76-387f-357d-b7be-b4654bc453d4",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/dssp\/_dssp.cpython-311-darwin.so",
"name" : "_dssp.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6032228352,
"size" : 32768,
"uuid" : "ad017f10-16c5-3c7b-8ee2-47e1604a376a",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-311-darwin.so",
"name" : "_nw.cpython-311-darwin.so"
},
{
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"base" : 5934387200,
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"uuid" : "e85fa1ce-f4e4-3454-9368-bd7d363c7e9e",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/iconengines\/libqsvgicon.dylib",
"name" : "libqsvgicon.dylib"
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"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/morph\/_morph.cpython-311-darwin.so",
"name" : "_morph.cpython-311-darwin.so"
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"size" : 16814080,
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"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.77.138"
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"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> alias nice cartoon suppressBackboneDisplay false; cartoon style width 1;
> size stickRadius 0.12
> lighting soft
> nice
Changed 0 bond radii
> alias voltr5 vol transparency 0.5
> alias voltroff vol transparency 0
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> alias cartoonDefaults cartoon style protein modeh default
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2922_005_volume_mask_refine.mrc"
Opened cryosparc_P120_J2922_005_volume_mask_refine.mrc as #1, grid size
200,200,200, pixel 1.04, shown at level 1, step 1, values float32
> volume #1 level 0.9731
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2922_005_volume_map_sharp.mrc"
Opened cryosparc_P120_J2922_005_volume_map_sharp.mrc as #2, grid size
200,200,200, pixel 1.04, shown at level 0.0781, step 1, values float32
> volume #1 level 0.1454
> volume #1 level 1
> ui tool show "Side View"
> volume #1 level 1
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J3552_map_locres.mrc"
Opened cryosparc_P120_J3552_map_locres.mrc as #3, grid size 200,200,200, pixel
1.04, shown at level 5.73, step 1, values float32
> volume #3 level 2.802
> volume #2 level 0.1843
> color sample #2 map #3 range 2.7,4.5 palette rainbow
Map values for surface "surface": minimum 2.75, mean 2.955, maximum 4.662
> volume #2 level 0.231
> volume #2 level 0.07172
> volume #2 level 0.1703
> volume #2 level 0.14
> volume #2 level 0.17
> view locres_side
Expected an objects specifier or a view name or a keyword
> view orient
> turn x -90
> ui tool show "Color Key"
> ui mousemode right "color key"
> key blue-white-red :min : :max white:
> key blue:min white: red:max white: white:
> key blue:2 white: red:max white: white:
> key blue:2. white: red:max white: white:
> key blue:2.7 white: red:max white: white:
> key blue:2.7 white: red: white: white:
> key blue:2.7 white:3 red: white: white:
> key blue:2.7 white:3. red: white: white:
> key blue:2.7 white:3.1 red: white: white:
> key blue:2.7 white:3.1 red:3 white: white:
> key blue:2.7 white:3.1 red:3. white: white:
> key blue:2.7 white:3.1 red:3.5 white: white:
> key blue:2.7 white:3.1 red:3.5 white:3 white:
> key blue:2.7 white:3.1 red:3.5 white:3. white:
> key blue:2.7 white:3.1 red:3.5 white:3.9 white:
> key blue:2.7 white:3.1 red:3.5 white:3.9 white:4
> key blue:2.7 white:3.1 red:3.5 white:3.9 white:4.
> key blue:2.7 white:3.1 red:3.5 white:3.9 white:4.3
> key rainbow :2.7 :3.1 :3.5 :3.9 :4.3
> color sample #2 map #3 range 2.7,4.3 palette rainbow
Map values for surface "surface": minimum 2.75, mean 2.971, maximum 4.766
> key fontSize 40
> hide #!2 models
> key pos 0.0575451,0.553904 size 0.911327,0.0955666
> key pos 0.0523717,0.482386
> pwd
Current working directory is: /Users/bburendei/Desktop
> cd "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing"
Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing
> save J2922_locresJ3552_colorkey.png supersample 3 transparentBackground true
> hide #4 models
> show #!2 models
> save J2922_locresJ3552_otherSide.png supersample 3 transparentBackground
> true
> turn y 90
> save J2922_locresJ3552_side.png supersample 3 transparentBackground true
> view initial
> color #2 #B2B2B2
> lighting soft
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> camera ortho
> color sample #2 map #3 range 2.7,4.3 palette rainbow
Map values for surface "surface": minimum 2.75, mean 2.971, maximum 4.766
> save J2922_locresJ3552_side.png supersample 3 transparentBackground true
> turn y -90
> save J2922_locresJ3552_otherSide.png supersample 3 transparentBackground
> true
> turn y -90
> surface dust #2
> color #2 #B2B2B2
> save J2922_NC36_final_side.png supersample 3 transparentBackground true
> color sample #2 map #3 range 2.7,4.3 palette rainbow
Map values for surface "surface": minimum 2.75, mean 2.971, maximum 4.766
> save J2922_locresJ3552_side.png supersample 3 transparentBackground true
> turn y -90
> save J2922_locresJ3552_otherSide.png supersample 3 transparentBackground
> true
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2704_class_04_00162_volume.mrc"
Opened cryosparc_P120_J2704_class_04_00162_volume.mrc as #5, grid size
100,100,100, pixel 2.09, shown at level 0.139, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2704_class_03_00162_volume.mrc"
Opened cryosparc_P120_J2704_class_03_00162_volume.mrc as #6, grid size
100,100,100, pixel 2.09, shown at level 0.151, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2704_class_02_00162_volume.mrc"
Opened cryosparc_P120_J2704_class_02_00162_volume.mrc as #7, grid size
100,100,100, pixel 2.09, shown at level 0.126, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2704_class_01_00162_volume.mrc"
Opened cryosparc_P120_J2704_class_01_00162_volume.mrc as #8, grid size
100,100,100, pixel 2.09, shown at level 0.15, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2704_class_00_00162_volume.mrc"
Opened cryosparc_P120_J2704_class_00_00162_volume.mrc as #9, grid size
100,100,100, pixel 2.09, shown at level 0.123, step 1, values float32
> hide #!2 models
> tile
5 models tiled
> color #B2B2B2
> lighting soft
> volume #5 level 0.2126
> volume #6 level 0.2515
> volume #7 level 0.2288
> volume #8 level 0.2354
> volume #9 level 0.2117
> volume #5-9 level 0.15
> volume #5-9 level 0.2
> volume #5-9 level 0.18
> volume #5-9 level 0.19
> volume #5-9 level 0.2
> save J2704_hetero_coll3.png supersample 3 transparentBackground true
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2723_class_04_00122_volume.mrc"
Opened cryosparc_P120_J2723_class_04_00122_volume.mrc as #10, grid size
100,100,100, pixel 2.09, shown at level 0.15, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2723_class_03_00122_volume.mrc"
Opened cryosparc_P120_J2723_class_03_00122_volume.mrc as #11, grid size
100,100,100, pixel 2.09, shown at level 0.156, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2723_class_02_00122_volume.mrc"
Opened cryosparc_P120_J2723_class_02_00122_volume.mrc as #12, grid size
100,100,100, pixel 2.09, shown at level 0.156, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2723_class_01_00122_volume.mrc"
Opened cryosparc_P120_J2723_class_01_00122_volume.mrc as #13, grid size
100,100,100, pixel 2.09, shown at level 0.159, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2723_class_00_00122_volume.mrc"
Opened cryosparc_P120_J2723_class_00_00122_volume.mrc as #14, grid size
100,100,100, pixel 2.09, shown at level 0.159, step 1, values float32
> tile off
> view initial
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> tile
5 models tiled
> lighting soft
> color #B2B2B2
> volume #14 level 0.2039
> volume #13 level 0.2518
> volume #12 level 0.2601
> volume #11 level 0.2174
> volume #10 level 0.2153
> volume #11 level 0.2349
> key pos 0.475164,0.446975 size 0.00838926,0.000748005
> save J2723_hetero_coll3.png supersample 3 transparentBackground true
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2725_002_volume_map_sharp.mrc"
Opened cryosparc_P120_J2725_002_volume_map_sharp.mrc as #15, grid size
100,100,100, pixel 2.09, shown at level 3.77, step 1, values float32
> tile off
> view initial
> view orient
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> volume #15 level 6.365
> view orient
> turn y -90
> turn x -90
> turn y -90
> volume #15 level 7.107
> volume #15 level 6.489
> color #b2b2b2
> color #B2B2B2
> save J2725_NUref_coll3.png supersample 3 transparentBackground true
> hide #!15 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2527_class_02_00182_volume.mrc"
Opened cryosparc_P120_J2527_class_02_00182_volume.mrc as #16, grid size
128,128,128, pixel 1.63, shown at level 0.103, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2527_class_04_00182_volume.mrc"
Opened cryosparc_P120_J2527_class_04_00182_volume.mrc as #17, grid size
128,128,128, pixel 1.63, shown at level 0.0987, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2527_class_03_00182_volume.mrc"
Opened cryosparc_P120_J2527_class_03_00182_volume.mrc as #18, grid size
128,128,128, pixel 1.63, shown at level 0.0985, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2527_class_01_00182_volume.mrc"
Opened cryosparc_P120_J2527_class_01_00182_volume.mrc as #19, grid size
128,128,128, pixel 1.63, shown at level 0.0976, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2527_class_00_00182_volume.mrc"
Opened cryosparc_P120_J2527_class_00_00182_volume.mrc as #20, grid size
128,128,128, pixel 1.63, shown at level 0.117, step 1, values float32
> view initial
> tile
5 models tiled
> lighting soft
> color #B2B2B2
> volume #20 level 0.1445
> volume #19 level 0.1343
> volume #18 level 0.1302
> volume #17 level 0.128
> volume #16 level 0.1298
> save J2527_hetero_coll2.png supersample 3 transparentBackground true
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2537_class_04_00142_volume.mrc"
Opened cryosparc_P120_J2537_class_04_00142_volume.mrc as #21, grid size
128,128,128, pixel 1.63, shown at level 0.112, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2537_class_03_00142_volume.mrc"
Opened cryosparc_P120_J2537_class_03_00142_volume.mrc as #22, grid size
128,128,128, pixel 1.63, shown at level 0.114, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2537_class_02_00142_volume.mrc"
Opened cryosparc_P120_J2537_class_02_00142_volume.mrc as #23, grid size
128,128,128, pixel 1.63, shown at level 0.116, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2537_class_01_00142_volume.mrc"
Opened cryosparc_P120_J2537_class_01_00142_volume.mrc as #24, grid size
128,128,128, pixel 1.63, shown at level 0.112, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2537_class_00_00142_volume.mrc"
Opened cryosparc_P120_J2537_class_00_00142_volume.mrc as #25, grid size
128,128,128, pixel 1.63, shown at level 0.116, step 1, values float32
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> show #!21 models
> view initial
> select ~sel & ##selected
Nothing selected
> tile off
> tile
5 models tiled
> lighting soft
> volume #25 level 0.1585
> volume #24 level 0.1873
> volume #23 level 0.1609
> volume #22 level 0.1615
> volume #21 level 0.149
> save J2537_hetero_coll2.png supersample 3 transparentBackground true
> color #B2B2B2
> save J2537_hetero_coll2.png supersample 3 transparentBackground true
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/csparc_otop/20230125_bburendei_zfO1_WT_ND_5mgml_NC36_1mM_grid6_collection/cryosparc_P120_J2540_006_volume_map_sharp.mrc"
Opened cryosparc_P120_J2540_006_volume_map_sharp.mrc as #26, grid size
200,200,200, pixel 1.04, shown at level 0.0843, step 1, values float32
> view initial
> tile off
> hide #!21 models
> hide #!22 models
> hide #!23 models
> hide #!24 models
> hide #!25 models
> select down
Nothing selected
> save J2537_hetero_coll2.png supersample 3 transparentBackground true
> select down
Nothing selected
> color #B2B2B2
> volume #26 level 0.162
> save J2540_NUref_coll2.png supersample 3 transparentBackground true
> hide #!26 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2484_class_04_00202_volume.mrc"
Opened cryosparc_P120_J2484_class_04_00202_volume.mrc as #27, grid size
128,128,128, pixel 1.63, shown at level 0.103, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2484_class_03_00202_volume.mrc"
Opened cryosparc_P120_J2484_class_03_00202_volume.mrc as #28, grid size
128,128,128, pixel 1.63, shown at level 0.104, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2484_class_02_00202_volume.mrc"
Opened cryosparc_P120_J2484_class_02_00202_volume.mrc as #29, grid size
128,128,128, pixel 1.63, shown at level 0.0963, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2484_class_01_00202_volume.mrc"
Opened cryosparc_P120_J2484_class_01_00202_volume.mrc as #30, grid size
128,128,128, pixel 1.63, shown at level 0.0965, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2484_class_00_00202_volume.mrc"
Opened cryosparc_P120_J2484_class_00_00202_volume.mrc as #31, grid size
128,128,128, pixel 1.63, shown at level 0.0877, step 1, values float32
> view initial
> tile
5 models tiled
> lighting soft
> color #B2B2B2
> volume #31 level 0.1001
> volume #30 level 0.1265
> volume #29 level 0.1236
> volume #28 level 0.1249
> volume #27 level 0.1298
> volume #26 level 0.166
> volume #27 level 0.1338
> volume #28 level 0.1349
> volume #29 level 0.1353
> save J2484_hetero_coll1.png supersample 3 transparentBackground true
> hide #!27 models
> hide #!28 models
> hide #!29 models
> hide #!30 models
> hide #!31 models
> tile off
No models found for tiling.
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2506_class_04_00122_volume.mrc"
Opened cryosparc_P120_J2506_class_04_00122_volume.mrc as #32, grid size
128,128,128, pixel 1.63, shown at level 0.101, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2506_class_03_00122_volume.mrc"
Opened cryosparc_P120_J2506_class_03_00122_volume.mrc as #33, grid size
128,128,128, pixel 1.63, shown at level 0.101, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2506_class_02_00122_volume.mrc"
Opened cryosparc_P120_J2506_class_02_00122_volume.mrc as #34, grid size
128,128,128, pixel 1.63, shown at level 0.102, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2506_class_01_00122_volume.mrc"
Opened cryosparc_P120_J2506_class_01_00122_volume.mrc as #35, grid size
128,128,128, pixel 1.63, shown at level 0.102, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2506_class_00_00122_volume.mrc"
Opened cryosparc_P120_J2506_class_00_00122_volume.mrc as #36, grid size
128,128,128, pixel 1.63, shown at level 0.11, step 1, values float32
> tile off
> tile
5 models tiled
> volume #36 level 0.1621
> tile
5 models tiled
> tile spacingFactor 1
5 models tiled
> tile spacingFactor 1.1
5 models tiled
> volume #35 level 0.1622
> volume #34 level 0.1792
> volume #33 level 0.1406
> volume #32 level 0.1384
> color #B2B2B2
> lighting soft
> tile spacingFactor 1
5 models tiled
> tile spacingFactor 1.1
5 models tiled
> lighting soft
> save J2506_hetero_coll1.png supersample 3 transparentBackground true
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2530_005_volume_map_sharp.mrc"
Opened cryosparc_P120_J2530_005_volume_map_sharp.mrc as #37, grid size
200,200,200, pixel 1.04, shown at level 0.0821, step 1, values float32
> tile off
> view initial
> hide #!32 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> hide #!36 models
> volume #37 level 0.1758
> color #B2B2B2
> lighting soft
> save J2530_NUref_coll1.png supersample 3 transparentBackground true
> hide #!37 models
> show #!27 models
> show #!28 models
> show #!29 models
> show #!30 models
> show #!31 models
> tile
5 models tiled
> lighting soft
> hide #!28 models
> show #!28 models
> hide #!29 models
> hide #!31 models
> hide #!27 models
> hide #!28 models
> hide #!30 models
> show #!16 models
> show #!17 models
> show #!18 models
> show #!19 models
> show #!20 models
> tile
5 models tiled
> lighting soft
> hide #!16 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> hide #!20 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> tile
5 models tiled
> lighting soft
> hide #!5 models
> hide #!9 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2756_004_volume_map_sharp.mrc"
Opened cryosparc_P120_J2756_004_volume_map_sharp.mrc as #38, grid size
200,200,200, pixel 1.04, shown at level 0.0777, step 1, values float32
> tile off
> hide #!8 models
> hide #!7 models
> hide #!6 models
> volume #38 level 0.156
> view orient
> turn x -90
> turn y 90
> color #b2b2b2
> save J2756_NUref_merged.png supersample 3 transparentBackground true
> hide #!38 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2809_class_02_final_volume.mrc"
Opened cryosparc_P120_J2809_class_02_final_volume.mrc as #39, grid size
200,200,200, pixel 1.04, shown at level 0.029, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2809_class_01_final_volume.mrc"
Opened cryosparc_P120_J2809_class_01_final_volume.mrc as #40, grid size
200,200,200, pixel 1.04, shown at level 0.0522, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2809_class_00_final_volume.mrc"
Opened cryosparc_P120_J2809_class_00_final_volume.mrc as #41, grid size
200,200,200, pixel 1.04, shown at level 0.0322, step 1, values float32
> view
> view initial
> tile
3 models tiled
> lighting soft
> key pos 0.939082,0.123641 size 0.0096127,0.0246367
> tile columns 3
3 models tiled
> volume #40 level 0.1011
> tile columns 3 spacingFactor 1
3 models tiled
> volume #41 level 0.04092
> volume #39 level 0.03316
> lighting soft
> volume #40 level 0.1175
> color #b2b2b2
> tile columns 3 spacingFactor 0.9
3 models tiled
> lighting soft
> tile columns 3 spacingFactor 1
3 models tiled
> lighting soft
> save J2809_abInit_merged.png supersample 3 transparentBackground true
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2758_class_02_final_volume.mrc"
Opened cryosparc_P120_J2758_class_02_final_volume.mrc as #42, grid size
200,200,200, pixel 1.04, shown at level 0.0319, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2758_class_01_final_volume.mrc"
Opened cryosparc_P120_J2758_class_01_final_volume.mrc as #43, grid size
200,200,200, pixel 1.04, shown at level 0.0299, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2758_class_00_final_volume.mrc"
Opened cryosparc_P120_J2758_class_00_final_volume.mrc as #44, grid size
200,200,200, pixel 1.04, shown at level 0.0439, step 1, values float32
> hide #!39 models
> hide #!40 models
> hide #!41 models
> tile columns 3 spacingFactor 1
3 models tiled
> tile columns 3
3 models tiled
> color #b2b2b2
> volume #43 level 0.06142
> volume #44 level 0.05758
> volume #42 level 0.04794
> lighting soft
> volume #43 level 0.06482
> volume #42 level 0.0565
> volume #44 level 0.06123
> volume #43 level 0.06738
> volume #42 level 0.05436
> save J2758_abInit_merged.png supersample 3 transparentBackground true
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2759_class_02_01600_volume.mrc"
Opened cryosparc_P120_J2759_class_02_01600_volume.mrc as #45, grid size
128,128,128, pixel 1.63, shown at level 0.0632, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2759_class_01_01600_volume.mrc"
Opened cryosparc_P120_J2759_class_01_01600_volume.mrc as #46, grid size
128,128,128, pixel 1.63, shown at level 0.0884, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2759_class_00_01600_volume.mrc"
Opened cryosparc_P120_J2759_class_00_01600_volume.mrc as #47, grid size
128,128,128, pixel 1.63, shown at level 0.0662, step 1, values float32
> hide #!42 models
> hide #!43 models
> hide #!44 models
> tile off
> view initial
> tile columns 3
3 models tiled
> lighting soft
> color #b2b2b2
> volume #46 level 0.1341
> volume #47 level 0.1393
> volume #45 level 0.1553
> volume #45 level 0.1653
> volume #47 level 0.1451
> volume #46 level 0.1382
> save J2759_abInit_merged.png supersample 3 transparentBackground true
> view initial
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2812_class_01_final_volume.mrc"
Opened cryosparc_P120_J2812_class_01_final_volume.mrc as #48, grid size
200,200,200, pixel 1.04, shown at level 0.049, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2812_class_00_final_volume.mrc"
Opened cryosparc_P120_J2812_class_00_final_volume.mrc as #49, grid size
200,200,200, pixel 1.04, shown at level 0.0516, step 1, values float32
> view
> tile
2 models tiled
> volume #48 level 0.1112
> volume #49 level 0.1113
> lighting soft
> volume #49 level 0.09486
> volume #48 level 0.1286
> volume #49 level 0.1113
> color #b2b2b2
> save J2812_abInit_merged_k2.png supersample 3 transparentBackground true
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2813_class_01_final_volume.mrc"
Opened cryosparc_P120_J2813_class_01_final_volume.mrc as #50, grid size
200,200,200, pixel 1.04, shown at level 0.0509, step 1, values float32
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2813_class_00_final_volume.mrc"
Opened cryosparc_P120_J2813_class_00_final_volume.mrc as #51, grid size
200,200,200, pixel 1.04, shown at level 0.0423, step 1, values float32
> hide #!48 models
> hide #!49 models
> view initial
> tile
2 models tiled
> volume #50 level 0.09709
> lighting soft
> volume #51 level 0.08004
> volume #50 level 0.1086
> color #b2b2b2
> save J2813_abInit_merged_k2.png supersample 3 transparentBackground true
> save "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/240805_NC36_processing.cxs"
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/240801_C11_processing.cxs"
> format session
> ui mousemode right translate
Opened cryosparc_P120_cryosparc_P120_J2126_class_05_00202_volume.mrc as #1,
grid size 256,256,256, pixel 1.15, shown at level 0.0983, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2126_class_04_00202_volume.mrc as #2,
grid size 256,256,256, pixel 1.15, shown at level 0.103, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2126_class_03_00202_volume.mrc as #3,
grid size 256,256,256, pixel 1.15, shown at level 0.104, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2126_class_02_00202_volume.mrc as #4,
grid size 256,256,256, pixel 1.15, shown at level 0.128, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2126_class_01_00202_volume.mrc as #5,
grid size 256,256,256, pixel 1.15, shown at level 0.149, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2126_class_00_00202_volume.mrc as #6,
grid size 256,256,256, pixel 1.15, shown at level 0.109, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2136_class_02_final_volume.mrc as #13,
grid size 256,256,256, pixel 1.15, shown at level 0.202, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2136_class_01_final_volume.mrc as #14,
grid size 256,256,256, pixel 1.15, shown at level 0.212, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2136_class_00_final_volume.mrc as #15,
grid size 256,256,256, pixel 1.15, shown at level 0.219, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2132_class_00_00162_volume.mrc as #7,
grid size 256,256,256, pixel 1.15, shown at level 0.162, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2132_class_05_00162_volume.mrc as #12,
grid size 256,256,256, pixel 1.15, shown at level 0.133, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2132_class_04_00162_volume.mrc as #8,
grid size 256,256,256, pixel 1.15, shown at level 0.128, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2132_class_03_00162_volume.mrc as #9,
grid size 256,256,256, pixel 1.15, shown at level 0.124, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2132_class_02_00162_volume.mrc as #10,
grid size 256,256,256, pixel 1.15, shown at level 0.114, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2132_class_01_00162_volume.mrc as #11,
grid size 256,256,256, pixel 1.15, shown at level 0.0912, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2140_006_volume_map_sharp.mrc as #16,
grid size 256,256,256, pixel 1.15, shown at level 0.279, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2142_010_volume_map_sharp.mrc as #17,
grid size 256,256,256, pixel 1.15, shown at level 0.397, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2146_006_volume_map_sharp.mrc as #18,
grid size 256,256,256, pixel 1.15, shown at level 0.399, step 1, values
float32
Opened cryosparc_P120_cryosparc_P120_J2188_cluster_000.mrc as #19, grid size
256,256,256, pixel 1.15, shown at level 0.0801, step 1, values float32
Opened cryosparc_P120_J2188_cluster_001.mrc as #20, grid size 256,256,256,
pixel 1.15, shown at level 0.108, step 1, values float32
Opened cryosparc_P120_J2188_cluster_002.mrc as #21, grid size 256,256,256,
pixel 1.15, shown at level 0.101, step 1, values float32
Opened cryosparc_P120_J2188_cluster_003.mrc as #22, grid size 256,256,256,
pixel 1.15, shown at level 0.0954, step 1, values float32
Opened cryosparc_P120_J2188_cluster_004.mrc as #23, grid size 256,256,256,
pixel 1.15, shown at level 0.0801, step 1, values float32
Opened cryosparc_P120_J2235_map_locres.mrc as #24, grid size 256,256,256,
pixel 1.15, shown at level 2.98, step 1, values float32
Opened cryosparc_P120_J2190_007_volume_map_sharp.mrc as #25, grid size
256,256,256, pixel 1.15, shown at level 0.35, step 1, values float32
Opened cryosparc_P120_cryosparc_P120_J2157_007_volume_map.mrc as #27, grid
size 256,256,256, pixel 1.15, shown at level 0.248, step 1, values float32
Opened cryosparc_P120_J2157_007_volume_map_sharp.mrc as #28, grid size
256,256,256, pixel 1.15, shown at level 0.281, step 1, values float32
opened ChimeraX session
> hide #!30 models
> show #!29 models
> hide #!29 models
> show #!28 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> show #!2 models
> show #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> tile
6 models tiled
> tile columns 6
6 models tiled
> hide #!6 models
> hide #!3 models
> hide #!2 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> hide #!5 models
> hide #!1 models
> show #!20 models
> show #!22 models
> show #!19 models
> show #!21 models
> show #!23 models
> tile columns 5
5 models tiled
> voltroff
> lighting soft
> hide #!20 models
> hide #!22 models
> show #!22 models
> show #!20 models
> hide #!20 models
> hide #!22 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/240805_NC36_processing.cxs"
> format session
Opened cryosparc_P120_J2922_005_volume_mask_refine.mrc as #1, grid size
200,200,200, pixel 1.04, shown at level 1, step 1, values float32
Opened cryosparc_P120_J2922_005_volume_map_sharp.mrc as #2, grid size
200,200,200, pixel 1.04, shown at level 0.17, step 1, values float32
Opened cryosparc_P120_J3552_map_locres.mrc as #3, grid size 200,200,200, pixel
1.04, shown at level 2.8, step 1, values float32
Opened cryosparc_P120_J2704_class_04_00162_volume.mrc as #5, grid size
100,100,100, pixel 2.09, shown at level 0.2, step 1, values float32
Opened cryosparc_P120_J2704_class_03_00162_volume.mrc as #6, grid size
100,100,100, pixel 2.09, shown at level 0.2, step 1, values float32
Opened cryosparc_P120_J2704_class_02_00162_volume.mrc as #7, grid size
100,100,100, pixel 2.09, shown at level 0.2, step 1, values float32
Opened cryosparc_P120_J2704_class_01_00162_volume.mrc as #8, grid size
100,100,100, pixel 2.09, shown at level 0.2, step 1, values float32
Opened cryosparc_P120_J2704_class_00_00162_volume.mrc as #9, grid size
100,100,100, pixel 2.09, shown at level 0.2, step 1, values float32
Opened cryosparc_P120_J2723_class_04_00122_volume.mrc as #10, grid size
100,100,100, pixel 2.09, shown at level 0.215, step 1, values float32
Opened cryosparc_P120_J2723_class_03_00122_volume.mrc as #11, grid size
100,100,100, pixel 2.09, shown at level 0.235, step 1, values float32
Opened cryosparc_P120_J2723_class_02_00122_volume.mrc as #12, grid size
100,100,100, pixel 2.09, shown at level 0.26, step 1, values float32
Opened cryosparc_P120_J2723_class_01_00122_volume.mrc as #13, grid size
100,100,100, pixel 2.09, shown at level 0.252, step 1, values float32
Opened cryosparc_P120_J2723_class_00_00122_volume.mrc as #14, grid size
100,100,100, pixel 2.09, shown at level 0.204, step 1, values float32
Opened cryosparc_P120_J2725_002_volume_map_sharp.mrc as #15, grid size
100,100,100, pixel 2.09, shown at level 6.49, step 1, values float32
Opened cryosparc_P120_J2527_class_02_00182_volume.mrc as #16, grid size
128,128,128, pixel 1.63, shown at level 0.13, step 1, values float32
Opened cryosparc_P120_J2527_class_04_00182_volume.mrc as #17, grid size
128,128,128, pixel 1.63, shown at level 0.128, step 1, values float32
Opened cryosparc_P120_J2527_class_03_00182_volume.mrc as #18, grid size
128,128,128, pixel 1.63, shown at level 0.13, step 1, values float32
Opened cryosparc_P120_J2527_class_01_00182_volume.mrc as #19, grid size
128,128,128, pixel 1.63, shown at level 0.134, step 1, values float32
Opened cryosparc_P120_J2527_class_00_00182_volume.mrc as #20, grid size
128,128,128, pixel 1.63, shown at level 0.144, step 1, values float32
Opened cryosparc_P120_J2537_class_04_00142_volume.mrc as #21, grid size
128,128,128, pixel 1.63, shown at level 0.149, step 1, values float32
Opened cryosparc_P120_J2537_class_03_00142_volume.mrc as #22, grid size
128,128,128, pixel 1.63, shown at level 0.162, step 1, values float32
Opened cryosparc_P120_J2537_class_02_00142_volume.mrc as #23, grid size
128,128,128, pixel 1.63, shown at level 0.161, step 1, values float32
Opened cryosparc_P120_J2537_class_01_00142_volume.mrc as #24, grid size
128,128,128, pixel 1.63, shown at level 0.187, step 1, values float32
Opened cryosparc_P120_J2537_class_00_00142_volume.mrc as #25, grid size
128,128,128, pixel 1.63, shown at level 0.159, step 1, values float32
Opened cryosparc_P120_J2540_006_volume_map_sharp.mrc as #26, grid size
200,200,200, pixel 1.04, shown at level 0.166, step 1, values float32
Opened cryosparc_P120_J2484_class_04_00202_volume.mrc as #27, grid size
128,128,128, pixel 1.63, shown at level 0.134, step 1, values float32
Opened cryosparc_P120_J2484_class_03_00202_volume.mrc as #28, grid size
128,128,128, pixel 1.63, shown at level 0.135, step 1, values float32
Opened cryosparc_P120_J2484_class_02_00202_volume.mrc as #29, grid size
128,128,128, pixel 1.63, shown at level 0.135, step 1, values float32
Opened cryosparc_P120_J2484_class_01_00202_volume.mrc as #30, grid size
128,128,128, pixel 1.63, shown at level 0.127, step 1, values float32
Opened cryosparc_P120_J2484_class_00_00202_volume.mrc as #31, grid size
128,128,128, pixel 1.63, shown at level 0.1, step 1, values float32
Opened cryosparc_P120_J2506_class_04_00122_volume.mrc as #32, grid size
128,128,128, pixel 1.63, shown at level 0.138, step 1, values float32
Opened cryosparc_P120_J2506_class_03_00122_volume.mrc as #33, grid size
128,128,128, pixel 1.63, shown at level 0.141, step 1, values float32
Opened cryosparc_P120_J2506_class_02_00122_volume.mrc as #34, grid size
128,128,128, pixel 1.63, shown at level 0.179, step 1, values float32
Opened cryosparc_P120_J2506_class_01_00122_volume.mrc as #35, grid size
128,128,128, pixel 1.63, shown at level 0.162, step 1, values float32
Opened cryosparc_P120_J2506_class_00_00122_volume.mrc as #36, grid size
128,128,128, pixel 1.63, shown at level 0.162, step 1, values float32
Opened cryosparc_P120_J2530_005_volume_map_sharp.mrc as #37, grid size
200,200,200, pixel 1.04, shown at level 0.176, step 1, values float32
Opened cryosparc_P120_J2756_004_volume_map_sharp.mrc as #38, grid size
200,200,200, pixel 1.04, shown at level 0.156, step 1, values float32
Opened cryosparc_P120_J2809_class_02_final_volume.mrc as #39, grid size
200,200,200, pixel 1.04, shown at level 0.0332, step 1, values float32
Opened cryosparc_P120_J2809_class_01_final_volume.mrc as #40, grid size
200,200,200, pixel 1.04, shown at level 0.117, step 1, values float32
Opened cryosparc_P120_J2809_class_00_final_volume.mrc as #41, grid size
200,200,200, pixel 1.04, shown at level 0.0409, step 1, values float32
Opened cryosparc_P120_J2758_class_02_final_volume.mrc as #42, grid size
200,200,200, pixel 1.04, shown at level 0.0544, step 1, values float32
Opened cryosparc_P120_J2758_class_01_final_volume.mrc as #43, grid size
200,200,200, pixel 1.04, shown at level 0.0674, step 1, values float32
Opened cryosparc_P120_J2758_class_00_final_volume.mrc as #44, grid size
200,200,200, pixel 1.04, shown at level 0.0612, step 1, values float32
Opened cryosparc_P120_J2759_class_02_01600_volume.mrc as #45, grid size
128,128,128, pixel 1.63, shown at level 0.165, step 1, values float32
Opened cryosparc_P120_J2759_class_01_01600_volume.mrc as #46, grid size
128,128,128, pixel 1.63, shown at level 0.138, step 1, values float32
Opened cryosparc_P120_J2759_class_00_01600_volume.mrc as #47, grid size
128,128,128, pixel 1.63, shown at level 0.145, step 1, values float32
Opened cryosparc_P120_J2812_class_01_final_volume.mrc as #48, grid size
200,200,200, pixel 1.04, shown at level 0.129, step 1, values float32
Opened cryosparc_P120_J2812_class_00_final_volume.mrc as #49, grid size
200,200,200, pixel 1.04, shown at level 0.111, step 1, values float32
Opened cryosparc_P120_J2813_class_01_final_volume.mrc as #50, grid size
200,200,200, pixel 1.04, shown at level 0.109, step 1, values float32
Opened cryosparc_P120_J2813_class_00_final_volume.mrc as #51, grid size
200,200,200, pixel 1.04, shown at level 0.08, step 1, values float32
opened ChimeraX session
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/nc36_processing_csparc_files/cryosparc_P120_J2811_005_volume_map_sharp.mrc"
Opened cryosparc_P120_J2811_005_volume_map_sharp.mrc as #52, grid size
200,200,200, pixel 1.04, shown at level 0.0736, step 1, values float32
> hide #!50 models
> hide #!51 models
> tile off
> view
> view initial
> volume #52 level 0.1573
> volume #52 level 0.1693
> view orient
> turn x -90
> turn y 90
> save J2811_NUref_merged.png supersample 3 transparentBackground true
> show #4 models
> hide #!52 models
> ui tool show "Color Key"
> ui mousemode right "color key"
> key pos 0.504457,0.0682585 size 0.0474474,0.830529
> save J2922_locresJ3552_colorkey.png supersample 3 transparentBackground true
> save "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing/240805_NC36_processing_v2.cxs"
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/240709_zfO1_final_structures_maps_comparison_12.cxs"
> ui mousemode right translate
Opened emd_9360.map as #1, grid size 200,200,200, pixel 1.03, shown at level
3.67, step 1, values float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc as #3,
grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values float32
Opened
zfO1_C11_1mM_final_cryosparc_P120_cryosparc_P120_J2190_007_volume_map.mrc as
#4, grid size 256,256,256, pixel 1.15, shown at level 0.176, step 1, values
float32
Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map.mrc as #7, grid
size 200,200,200, pixel 1.07, shown at level 0.34, step 1, values float32
Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map_sharp.mrc as #8,
grid size 200,200,200, pixel 1.07, shown at level 0.272, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map.mrc as #11,
grid size 200,200,200, pixel 1.07, shown at level 0.242, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc as
#12, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map.mrc as #15,
grid size 200,200,200, pixel 1.04, shown at level 0.0979, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc as
#16, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 0 as
#25.1, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 1 as
#25.2, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 2 as
#25.3, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 3 as
#25.4, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 4 as
#25.5, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 5 as
#25.6, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened emd_9360.map 0 as #24.1, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 1 as #24.2, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 2 as #24.3, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 3 as #24.4, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 4 as #24.5, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 0 as
#31.1, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 1 as
#31.2, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 2 as
#31.3, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 3 as
#31.4, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 4 as
#31.5, grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 5 as
#31.6, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 0 as
#30.1, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 1 as
#30.2, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 2 as
#30.3, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 3 as
#30.4, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 4 as
#30.5, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 5 as
#30.6, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
opened ChimeraX session
> view
> hide #!17 models
> hide #!5 models
> hide #!2 models
> show #!2 models
> show #!9 models
> hide #!9 models
> show #!13 models
> hide #!2 models
> select add #13
6846 atoms, 7036 bonds, 18 pseudobonds, 800 residues, 3 models selected
> show #14 surfaces
> show #!14 models
> select subtract #13
Nothing selected
> hide #!13 models
> hide #!14 models
> show #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> surface #14 transparency 0
> hide #14/B target s
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
37 atoms, 38 bonds, 1 residue, 1 model selected
> show sphere sel
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel sphere
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> atom sel style phere
Unknown command: atom sel style phere
> atom sel style sphere
Unknown command: atom sel style sphere
> style sel sphere
Changed 37 atom styles
> select clear
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #2/A surfaces
> show #!2 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!2 models
> style #13:NC2 stick
Changed 296 atom styles
> select clear
> hide HC
> view list
Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, outer_site_45, side_view,
side_view_NdomAligned, side_view_models, top_view
> view F570outer_resi_comp
> view F570outer
> view F570outer_site_modelComp2
> camera mono
> show #!2 models
> hide #!13 models
> hide #2 surfaces
> show #!13 models
> hide #!2 models
> show #!2 models
> hide #!13 models
> show #!13 models
> hide #!2 models
> show #!23 models
> ui tool show Distances
> select #13/A:267@OE2
1 atom, 1 residue, 1 model selected
> select add #13/A:609@O14
2 atoms, 2 residues, 1 model selected
> distance #13/A:267@OE2 #13/A:609@O14
Distance already exists; modify distance properties with 'distance style'
> show #23.1 models
> hide #23.1 models
> show #23.1 models
> show #23 target p
> show #!12 models
> hide #!12 models
> lighting simple
> lighting soft
> hide #13/A:111-140 target c
> show #13/A:111-140 target c
> transparency #13/A:111-140 0.9 target c
> transparency #13/A:111-140 90 target c
> hide #23.1 models
> show #!2 models
> hide #!13 models
> select add #13
6846 atoms, 7036 bonds, 18 pseudobonds, 800 residues, 3 models selected
> select subtract #13
Nothing selected
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!2 models
> hide #13/A:111-140 target c
> hide #13/A:111-140:C,CA,N,O
> show #13/A:111-140:C,CA,N,O
> hide #!13 cartoons
> show #!13 cartoons
> show #13/A:111-140@C,CA,N,O
> hide #13/A:111-140@C,CA,N,O
> hide #13/A:111-140 target c
> show #13/A:111-140 target c
> show #13/A:111-140@C,CA,N,O
> hide #13:CLR,CHS
> select clear
> view name outer_site_NC2_flat_view
> lighting soft
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting soft
> lighting simple
> lighting soft
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select ~sel & ##selected
Nothing selected
> view outer_site_NC2_flat_view
> show #23.1 models
> hide #23.1 models
> show #23.1 models
> hide #23.1 models
> pwd
Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig_S3_C11_NC36_cryoEM_processing
> cd "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM"
Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM
> save outer_site_NC2_flatView_2HBs.png supersample 3 transparentBackground
> true
> turn y 180
> transparency #13 0 target c
> save outer_site_NC2_flatView_2HBs_fromCdom.png supersample 3
> transparentBackground true
> cd images
Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/images
> view list
Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, outer_site_45, outer_site_NC2_flat_view,
side_view, side_view_NdomAligned, side_view_models, top_view
> view outer_site_NC2_flat_view
> view F570central_densityComp
> view F570central_resi_comp
> view F570central_modelComp2
> hide #13:Y01
> hide #!23 models
> show #!23 models
> show #!2 models
> view F570central_modelComp
> view F570central_densityComp
> view F570central_resi_comp
> view F570central_modelComp2
> hide #!2 models
> hide #!23 models
> show #!23 models
> select #13/A:607@H181
1 atom, 1 residue, 1 model selected
> select #13/A:384@OE1
1 atom, 1 residue, 1 model selected
> select add #13/A:607@H181
2 atoms, 2 residues, 1 model selected
> distance #13/A:384@OE1 #13/A:607@H181
Distance between zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/A
GLU 384 OE1 and NC2 607 H181: 2.037Å
> show #23.1 models
> hide #23.1 models
> show #23.1 models
> show #!12 models
> hide #!12 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!13 models
> show #!13 models
> style sel sphere
Changed 2 atom styles
> style sel sphere
Changed 2 atom styles
> style sel stick
Changed 2 atom styles
> select clear
> select add #13
6846 atoms, 7036 bonds, 19 pseudobonds, 800 residues, 3 models selected
> style sel sphere
Changed 6846 atom styles
> style sel stick
Changed 6846 atom styles
> style sel ball
Changed 6846 atom styles
> style sel stick
Changed 6846 atom styles
> style sel sphere
Changed 6846 atom styles
> lighting simple
> style sel stick
Changed 6846 atom styles
> lighting soft
> select clear
> select #13/A:278@CB
1 atom, 1 residue, 1 model selected
> select add #13/A:381@CG
2 atoms, 2 residues, 1 model selected
> distance #13/A:278@CB #13/A:381@CG
Distance between zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/A
VAL 278 CB and LEU 381 CG: 5.537Å
> select add #13/A:275@CE
3 atoms, 3 residues, 1 model selected
> select clear
> select #13/A:275@CE
1 atom, 1 residue, 1 model selected
> select add #13/A:385@CG
2 atoms, 2 residues, 1 model selected
> select subtract #13/A:385@CG
1 atom, 1 residue, 1 model selected
> select add #13/A:385@CG
2 atoms, 2 residues, 1 model selected
> select clear
> select add #13/A:385@CG
1 atom, 1 residue, 1 model selected
> select add #13/A:275@CE
2 atoms, 2 residues, 1 model selected
> distance #13/A:385@CG #13/A:275@CE
Distance between zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/A
LEU 385 CG and MET 275 CE: 4.390Å
> show HC
> hide HC
> select clear
> select #13/A:281@NZ
1 atom, 1 residue, 1 model selected
> select add #13/A:607@O14
2 atoms, 2 residues, 1 model selected
> distance #13/A:281@NZ #13/A:607@O14
Distance between zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/A
LYS 281 NZ and NC2 607 O14: 4.723Å
> select clear
> select #13/A:281@NZ
1 atom, 1 residue, 1 model selected
> ui tool show "Add Hydrogens"
> select clear
> hide #!23 models
> show #!23 models
> ui tool show Distances
> ~distance #13/A:385@CG #13/A:275@CE
> ~distance #13/A:278@CB #13/A:381@CG
> select #13/A:281@NZ
1 atom, 1 residue, 1 model selected
> select clear
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> ~distance #13/A:281@NZ #13/A:607@O14
> view name central_site_flatView
> save central_site_NC2_flatView_HB.png supersample 3 transparentBackground
> true
> view central_site_flatView
> view name central_site_flatView
> save central_site_NC2_flatView_HB.png supersample 3 transparentBackground
> true
> ui mousemode right "tape measure"
> marker segment #29 position 109.7,99.11,95.93 toPosition 107.4,96.8,92.97
> color yellow radius 0.2666 label 4.38 labelHeight 0.5331 labelColor yellow
> marker segment #29 position 109.4,91.97,100.8 toPosition 107.7,96.78,92.57
> color yellow radius 0.261 label 9.721 labelHeight 0.9721 labelColor yellow
> hide #!29 models
> show #!28 models
> hide #!28 models
> show #!29 models
> close #29
> marker segment #29 position 109.9,99.24,95.9 toPosition 107.7,96.7,92.66
> color yellow radius 0.2666 label 4.646 labelHeight 0.5331 labelColor yellow
> hide #!29 models
> ui mousemode right translate
> select add #13/A:277@CE2
1 atom, 1 residue, 1 model selected
> select add #13/A:277@CG
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #13/A:277@CE1
3 atoms, 2 bonds, 1 residue, 1 model selected
> select add #13/A:277@CZ
4 atoms, 2 bonds, 1 residue, 1 model selected
> select clear
> select add #13/A:277@CD2
1 atom, 1 residue, 1 model selected
> select add #13/A:277@CE2
2 atoms, 1 residue, 1 model selected
> select add #13/A:277@CG
3 atoms, 1 residue, 1 model selected
> select add #13/A:277@CD1
4 atoms, 1 residue, 1 model selected
> select add #13/A:277@CE1
5 atoms, 1 residue, 1 model selected
> select add #13/A:277@CZ
6 atoms, 1 residue, 1 model selected
> define centroid sel name F277_centroid
Centroid 'F277_centroid' placed at [111.43766658 100.26916631 96.34250005]
> define centroid sel name F277_centroid radius 0.2
Centroid 'F277_centroid' placed at [111.43766658 100.26916631 96.34250005]
> select clear
> view list
Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, central_site_flatView, outer_site_45,
outer_site_NC2_flat_view, side_view, side_view_NdomAligned, side_view_models,
top_view
> view central_site_flatView
> select #!13/A:607@C10
1 atom, 1 residue, 1 model selected
> select add #13.3
2 atoms, 2 residues, 2 models selected
> distance #!13/A:607@C10 #13.3
Distance between zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb
#!13/A NC2 607 C10 and F277_centroid #13.3: 4.501Å
> ~select #13.3
1 atom, 1 residue, 1 model selected
> select #13.3
1 atom, 1 residue, 1 model selected
> ~select #13.3
Nothing selected
> transparency sel 100
> transparency sel 100 target a
> select #13.3
1 atom, 1 residue, 1 model selected
> hide #13.3 models
> show #13.3 models
> transparency #13.3 1
> color #13.3 #aa5ee8e1
> color #13.3 #aa5ee800
> select clear
> save central_site_NC2_flatView_HB.png supersample 3 transparentBackground
> true
> view central_site_flatView
> hide #13.3 models
> show #13.3 models
> close #13.2
> select #13.3
1 atom, 1 residue, 1 model selected
> ~select #13.3
Nothing selected
> ui tool show Distances
> select #13.3
1 atom, 1 residue, 1 model selected
> ~select #13.3
Nothing selected
> view central_site_flatView
> hide #23.1 models
> save central_site_NC2_flatView_HB.png supersample 3 transparentBackground
> true
> distance save "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/distances.txt"
> save central_site_NC2_flatView_HB.png supersample 3 transparentBackground
> trueview
Invalid "transparentBackground" argument: Expected true or false (or 1 or 0)
> view
> hide #13.3 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!14 models
> save "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/240807_zfO1_final_structures_maps_comparison_13.cxs"
> hide #!14 models
> show #!13 models
> hide #13.1 models
> hide atoms
> cartoon style width 2
> hide /B target c
> show #!2 models
> view orient
> view list
Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, central_site_flatView, outer_site_45,
outer_site_NC2_flat_view, side_view, side_view_NdomAligned, side_view_models,
top_view
> view side_view
> view side_view_NdomAligned
> view side_view_models
> view side_view_NdomAligned
> view side_view_models
> view side_view_NdomAligned
> view side_view_models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> show #!5 models
> hide #!5 models
> show #!5 models
> mmaker #5,13,17 to #2
No matrix compatible with both reference structure and all match structures
> hide #!23 models
> mmaker #5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 1579.5
RMSD between 329 pruned atom pairs is 0.742 angstroms; (across all 354 pairs:
1.052)
> mmaker #13 to #2
No matrix compatible with both reference structure and all match structures
> close #13.3
> mmaker #13 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)
> mmaker #5,13,17 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 1579.5
RMSD between 329 pruned atom pairs is 0.742 angstroms; (across all 354 pairs:
1.052)
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC36_1mM_final_240319_zfO1_NC36_bestModel_NC36_6copies.pdb, chain A
(#17), sequence alignment score = 1670.9
RMSD between 358 pruned atom pairs is 0.679 angstroms; (across all 367 pairs:
1.167)
> view side_view_models
> pwd
Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/images
> save all_models_alTo6nf4_Cdom_slanted_side_view.png supersample 3
> transparentBackground true
> save all_models_alTo6nf4_Ndom_slanted_side_view.png supersample 3
> transparentBackground true
> mmaker #13:1-300 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)
> mmaker #5,13,17:1-300 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 810.1
RMSD between 163 pruned atom pairs is 0.668 angstroms; (across all 172 pairs:
0.956)
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC36_1mM_final_240319_zfO1_NC36_bestModel_NC36_6copies.pdb, chain A
(#17), sequence alignment score = 773.2
RMSD between 164 pruned atom pairs is 0.611 angstroms; (across all 167 pairs:
1.283)
> mmaker #5,13,17/A:1-300 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 810.1
RMSD between 163 pruned atom pairs is 0.668 angstroms; (across all 172 pairs:
0.956)
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC36_1mM_final_240319_zfO1_NC36_bestModel_NC36_6copies.pdb, chain A
(#17), sequence alignment score = 773.2
RMSD between 164 pruned atom pairs is 0.611 angstroms; (across all 167 pairs:
1.283)
> mmaker #5:1-300 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 810.1
RMSD between 163 pruned atom pairs is 0.668 angstroms; (across all 172 pairs:
0.956)
> mmaker #5/A:1-300 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 810.1
RMSD between 163 pruned atom pairs is 0.668 angstroms; (across all 172 pairs:
0.956)
> hide #2,5,13,17:300-586
> hide #2,5,13,17:300-586 target c
> hide #!5 models
> hide #!17 models
> select #13/A:1-300
1508 atoms, 1548 bonds, 4 pseudobonds, 185 residues, 2 models selected
> select #2/A:1-300
1647 atoms, 1692 bonds, 2 pseudobonds, 203 residues, 2 models selected
> show #2,5,13,17:300-586 target c
> hide #2,5,13,17:1-300 target c
> hide /B target c
> mmaker #5,13,17/A:300-599 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_C11_1mM_final_bestModel1_w4copiesOfC11.pdb, chain A (#5), sequence
alignment score = 803.4
RMSD between 174 pruned atom pairs is 0.646 angstroms; (across all 182 pairs:
0.853)
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 974.9
RMSD between 195 pruned atom pairs is 0.511 angstroms; (across all 206 pairs:
1.101)
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC36_1mM_final_240319_zfO1_NC36_bestModel_NC36_6copies.pdb, chain A
(#17), sequence alignment score = 921.7
RMSD between 197 pruned atom pairs is 0.599 angstroms; (across all 200 pairs:
0.908)
> rmsd
Missing or invalid "atoms" argument: empty atom specifier
> show #!17 models
> hide #!13 models
> show #!13 models
> hide #!17 models
> show #2,5,13,17/A target c
> select clear
> show #!17 models
> hide #!13 models
> hide #!17 models
> show #!13 models
> transparency #2 0 target c
> mmaker #13 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)
> mmaker #13/A:1-300 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)
> rmsd #13 #2
Missing required "to" argument
> rmsd #13 to #2
Number of atoms from first atom spec (6846) differs from number in second
(6960)
> rmsd #13@CA to #2@CA
Number of atoms from first atom spec (782) differs from number in second (842)
> rmsd #13/A@CA to #2@CA
Number of atoms from first atom spec (391) differs from number in second (842)
> rmsd #13/A@CA to #2/A@CA
Number of atoms from first atom spec (391) differs from number in second (421)
> select #2/A:300-599
1700 atoms, 1739 bonds, 1 pseudobond, 218 residues, 2 models selected
value: None default: None
> define axis sel name axis
Axis '6nf4.cif #2/axis' centered at [120.65083896 118.77276092 100.9266898 ]
with direction [ 0.00180921 -0.03751698 0.99929435], radius 10.7681, and
length 60.0678
> select #13/A:300-599
1613 atoms, 1649 bonds, 3 pseudobonds, 206 residues, 2 models selected
value: None default: None
> define axis sel name axis_NC2
Axis 'zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/axis_NC2'
centered at [121.3391677 118.7759146 101.6475822] with direction [-0.13294866
-0.06416798 0.98904354], radius 10.2564, and length 56.0317
value: None default: None
> define axis sel name axis_apo radius 1
Axis 'zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/axis_apo'
centered at [121.3391677 118.7759146 101.6475822] with direction [-0.13294866
-0.06416798 0.98904354], radius 1, and length 56.0317
> close #13.3
> close #2.3
> close #13.2
> select #2/A:300-599
1700 atoms, 1739 bonds, 1 pseudobond, 218 residues, 2 models selected
value: None default: None
> define axis sel name axis_apo radius 0.1
Axis '6nf4.cif #2/axis_apo' centered at [120.65083896 118.77276092 100.9266898
] with direction [ 0.00180921 -0.03751698 0.99929435], radius 0.1, and length
60.0678
> select #13/A:300-599
1613 atoms, 1649 bonds, 3 pseudobonds, 206 residues, 2 models selected
value: None default: None
> define axis sel name axis_C2.2 radius 0.1
Axis 'zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/axis_C2.2'
centered at [121.3391677 118.7759146 101.6475822] with direction [-0.13294866
-0.06416798 0.98904354], radius 0.1, and length 56.0317
> select clear
> select #13.2
1 model selected
> select add #2.3
2 models selected
Either three or four atoms must be selected!
> select clear
> select add #13.2
1 model selected
> select add #2.3
2 models selected
> select clear
> color #2.3 #bffdb78a
> color #2.3 #bffdb7bc
> color #2.3 #bffdb7
> color #2.3 #bffdb7bd
> color #2.3 #bffdb7c9
> color #2.3 #bffdb7d4
> color #2.3 #bffdb7
> color #2.3 #bffdb703
> color #2.3 #bffdb7
> transparency #2.3 0
> select clear
> view side_view_models
> select #2/A:1-300
1647 atoms, 1692 bonds, 2 pseudobonds, 203 residues, 2 models selected
value: None default: None
> define axis sel name axis_N_apo radius 0.1
Axis '6nf4.cif #2/axis_N_apo' centered at [118.54776471 90.8364824
103.97076155] with direction [0.27118103 0.20100905 0.94130559], radius 0.1,
and length 61.1241
> select #13/A:1-300
1508 atoms, 1548 bonds, 4 pseudobonds, 185 residues, 2 models selected
value: None default: None
> define axis sel name axis_N_C2.2 radius 0.1
Axis 'zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb #13/axis_N_C2.2'
centered at [116.76259877 90.30409579 101.24155364] with direction [0.35270227
0.21681833 0.9102697 ], radius 0.1, and length 56.3703
> select clear
> mmaker #13 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)
> mmaker #13/A:1-300 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)
> mmaker #13 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)
> mmaker #13/A:1-300 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)
> mmaker #13/A:300-599 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 974.9
RMSD between 195 pruned atom pairs is 0.511 angstroms; (across all 206 pairs:
1.101)
> mmaker #13/A:1-300 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)
> camera ortho
> select #2.3
1 model selected
> select clear
> ui mousemode right "mark point"
> marker #28 position 122.4,112.2,132.2 color yellow radius 1
> marker #28 position 110.8,133.1,118.3 color yellow radius 1
> select #2.3
1 model selected
> select #13.2
1 model selected
> select #2.3
1 model selected
> select #13.2
1 model selected
> select #2.3
1 model selected
> marker #28 position 136.5,129.1,114.2 color yellow radius 1
> ui mousemode right translate
> select #2.3
1 model selected
> select #13.2
1 model selected
> select #2.3
1 model selected
> select #2.4
1 model selected
> select #2.3
1 model selected
> ~select #2.3
Nothing selected
> select #13.2
1 model selected
> select add #2.3
2 models selected
Either three or four atoms must be selected!
Exactly two atoms must be selected!
> select #2.4
1 model selected
> select #2.3
1 model selected
> select add #13.2
2 models selected
No atoms selected
> ~select #13.2
1 model selected
> ~select #2.3
Nothing selected
> morph #13,2 frames 60 wrap true
Computed 121 frame morph #32
> coordset #32 1,121
> morph #2,13 frames 60
Computed 61 frame morph #33
> coordset #33 1,61
> hide #!32 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #13:NC2
> hide /B
> mmaker #13 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)
> morph #2,13 frames 60
Computed 61 frame morph #34
> coordset #34 1,61
> hide #!33 models
> show #!13 models
> mmaker #13/A:300-586 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 974.9
RMSD between 195 pruned atom pairs is 0.511 angstroms; (across all 206 pairs:
1.101)
> morph #2,13 frames 60
Computed 61 frame morph #35
> coordset #35 1,61
> show #!33 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> show #!35 models
> show #!34 models
> hide #!35 models
> hide #!34 models
> show #!13 models
> show #!2 models
> mmaker #13 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)
> hide #!13 models
> show #!34 models
> show #!13 models
> hide #!2 models
> hide #!13 models
> show #!13 models
> show #13 atoms
> hide /B
> show #!2 models
> show #2/A atoms
> transparency #2 0
> transparency #2 0 target ca
> select clear
> hide #!2 models
> show #34/A atoms
> hide atoms
> hide #!34 models
> hide #13.2 models
> show #13.2 models
> hide #13.2 models
> show #!2 models
> hide #2.3 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> transparency #2 50 target c
> transparency #2 90 target c
> transparency #2 70 target c
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!34 models
> show #34/A atoms
> hide #!13 models
> hide #!34 models
> show #!13 models
> view orient
> turn z 90
> turn x 180
> turn z 180
> ui tool show "Side View"
> camera mono
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting simple
> lighting soft
> transparency #2 00 target c
> transparency #2 80 target c
> transparency #2 90 target c
> save apo_vs_NC2_bottom_view.png supersample 3 transparentBackground true
> mmaker #13/A:1-300 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 833.6
RMSD between 165 pruned atom pairs is 0.622 angstroms; (across all 183 pairs:
2.417)
> show #13/A:NC2
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> hide HC
> style #13/A:NC2 sphere
Changed 148 atom styles
> hide #13:608
> camera ortho
> mmaker #13 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6nf4.cif, chain A (#2) with
zfO1_NC2_10mM_final_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#13),
sequence alignment score = 1783.5
RMSD between 351 pruned atom pairs is 0.732 angstroms; (across all 389 pairs:
1.990)
> view name bottom_view
> save apo_vs_NC2_bottom_view.png supersample 3 transparentBackground true
> hide #13:610
> view side_view
> view bottom_view
> transparency #2 0 target c
> save apo_vs_NC2_bottom_view.png supersample 3 transparentBackground true
> view side_view
> camera mono
> camera ortho
> view bottom_view
> view side_view
> view bottom_view
> view side_view
> save apo_vs_NC2_models_side_view.png supersample 3 transparentBackground
> true
> view bottom_view
> turn x 180
> lighting soft
> lighting simple
> lighting soft
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> hide #23.1 models
> show #23.1 models
> hide #23.1 models
> view bottom_view
> turn x 180
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!34 models
> hide #!2 models
> save "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/240807_zfO1_final_structures_maps_comparison_14.cxs"
> hide #!34 models
> show #!2 models
> save apo_vs_NC2_models_top_view.png supersample 3 transparentBackground true
> camera orho
Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword
> camera ortho
> clip off
> show #!34 models
> hide #!2 models
> hide #!13 models
> show #!13 models
> hide #!34 models
> view list
Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, bottom_view, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, central_site_flatView, outer_site_45,
outer_site_NC2_flat_view, side_view, side_view_NdomAligned, side_view_models,
top_view
> view C_dom_pocket_mirror2docked
> show #13/A atoms
> style #13:NC2 stick
Changed 296 atom styles
> hide HC
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> alias nice cartoon suppressBackboneDisplay false; cartoon style width 1;
> size stickRadius 0.12
> lighting soft
> nice
Changed 0 bond radii
> alias voltr5 vol transparency 0.5
> alias voltroff vol transparency 0
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> alias cartoonDefaults cartoon style protein modeh default
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
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: Mac
Model Identifier: Mac14,2
Model Number: Z15S000D5LL/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.6.7 (22G720)
Kernel Version: Darwin 22.6.0
Time since boot: 6 days, 4 hours, 19 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL P2721Q:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
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: 1.6.4
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: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
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-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: 1.8
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-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: 1.5.17
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: 1.13.5
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
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: 3.0.47
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: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
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
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Probable Mac Qt 6.6 bug. Crash in _NSViewHierarchyDidChangeBackingProperties.