![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17474 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-14.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000002067acc00 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 62)
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{
"uptime" : 20000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,7",
"coalitionID" : 739,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2025-04-23 23:15:56.6980 -0500",
"codeSigningMonitor" : 1,
"incident" : "07A4A8C8-E380-48FA-AC4E-D3E350D31C92",
"pid" : 3695,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-23 18:56:34.6218 -0500",
"procStartAbsTime" : 160812905774,
"procExitAbsTime" : 500545871031,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"4FE1FF3F-D256-597B-8D28-2D9970CD1179","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7CBB956D-EE73-7D9F-180F-A2ECC121435D",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 24,
"sleepWakeUUID" : "C03A97A2-FCE9-478A-8833-6D8D138DD593",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4330258408\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1021a8000-1021ac000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":3695},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4330258408\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1021a8000-1021ac000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/lianqi/Files/Postdoc/VEGF/Figures/b1.cxs format session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.00311, step 2, values float32
opened ChimeraX session
> show #!1 models
> volume step 1
> surface dust #1 size 10.8
> color zone #1 near #3 distance 6.48
> volume style surface
> volume hide
> volume show
> transparency 50
> volume style surface
> volume show
> volume style surface
> transparency 0
> volume style mesh
> volume style surface
> color zone #1 near #3 distance 6.48
> volume #1 color silver
> volume #1 color #ebebeb
> hide surfaces
> show cartoons
> volume hide
> select add #3.3
2290 atoms, 146 residues, 1 model selected
> color #3.3 #0096ffff
> ui tool show "Color Actions"
> color (#!3 & sel) #0096ffff
> color (#!3 & sel) #76d6ffff
> select add #3.4
4580 atoms, 292 residues, 2 models selected
> select subtract #3.3
2290 atoms, 146 residues, 3 models selected
> select add #3.5
11692 atoms, 750 residues, 2 models selected
> select subtract #3.4
9402 atoms, 604 residues, 3 models selected
> select add #3.6
18804 atoms, 1208 residues, 2 models selected
> select subtract #3.5
9402 atoms, 604 residues, 3 models selected
> select add #3.5
18804 atoms, 1208 residues, 2 models selected
> select subtract #3.6
9402 atoms, 604 residues, 3 models selected
> color #3.5 #ff2f92ff
> color #3.5 #ff8ad8ff
> select subtract #3.5
1 model selected
> select add #3.5
9402 atoms, 604 residues, 1 model selected
> select add #3.6
18804 atoms, 1208 residues, 2 models selected
> select subtract #3.6
9402 atoms, 604 residues, 3 models selected
> select subtract #3.5
1 model selected
> select add #3.7
8330 atoms, 537 residues, 1 model selected
> color #3.7 #73fcd6ff
> color #3.7 #00f900ff
> color #3.7 #73fa79ff
> hide #3.7 models
> show #3.7 models
> ui tool show "Color Actions"
> color (#!3 & sel) #00f900ff
> color (#!3 & sel) #73fa79ff
> color (#!3 & sel) #00f900ff
> color (#!3 & sel) #73fa79ff
> select subtract #3.7
1 model selected
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #009193ff
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #008f00ff
> color (#!3 & sel) #009051ff
> select subtract #3.8
1 model selected
> select add #3.3
2290 atoms, 146 residues, 1 model selected
> select subtract #3.3
1 model selected
> select add #3.4
2290 atoms, 146 residues, 1 model selected
> select subtract #3.4
1 model selected
> show surfaces
> hide surfaces
> turn y 90
> show surfaces
> color #3.5 #ff2f92ff
> color #3.5 #ff8ad8ff
> color #3.5 #ff85ffff
> color #3.5 #ff40ffff
> color #3.5 #941751ff
> color #3.5 #ff2600ff
> color #3.5 #ff7e79ff
> color #3.6 #ff40ffff
> color #3.6 #ff85ffff
> color #3.6 #9437ffff
> color #3.6 #ff85ffff
> color #3.6 #ff7e79ff
> color #3.6 #ffd479ff
> color #3.6 #ff2600ff
> color #3.6 #941100ff
> color #3.6 #945200ff
> color #3.6 #ff9300ff
> color #3.6 #ff2f92ff
> color #3.6 #ff8ad8ff
> color #3.5 #ff85ffff
> color #3.5 #9437ffff
> color #3.5 #ff40ffff
> color #3.5 #d783ffff
> color #3.5 #ff40ffff
> turn y 90
> color #3.5 #ff7e79ff
> color #3.5 #ff2600ff
> color #3.5 #ff9300ff
> color #3.5 #ff7e79ff
> color #3.5 #d783ffff
> color #3.5 #ff85ffff
> color #3.5 #ff8ad8ff
> color #3.5 #ff85ffff
> color #3.5 #ff40ffff
> color #3.5 #ff2f92ff
> color #3.5 #9437ffff
> color #3.5 #941751ff
> color #3.5 #942193ff
> color #3.5 #531b93ff
> color #3.5 #ff9300ff
> color #3.5 #945200ff
> color #3.5 #ff2600ff
> color #3.5 #ff7e79ff
> color #3.5 #ff85ffff
> color #3.5 #ff9300ff
> color #3.5 #ff7e79ff
> color #3.5 #ff2600ff
> color #3.5 #941100ff
> color #3.5 #ff2600ff
> color #3.5 #ff7e79ff
Unsupported scale factor (0.000000) detected on Display1
> open "/Users/lianqi/Files/Postdoc/VEGF/model colored.cxs"
opened ChimeraX session
> open /Users/lianqi/Files/Postdoc/VEGF/Figures/b1.cxs format session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.00311, step 2, values float32
opened ChimeraX session
> hide surfaces
> show cartoons
> select add #3.3
2290 atoms, 146 residues, 1 model selected
> select add #3.2
2290 atoms, 12 pseudobonds, 146 residues, 3 models selected
> select subtract #3.3
11 pseudobonds, 2 models selected
> select add #3.3
2290 atoms, 11 pseudobonds, 146 residues, 2 models selected
> select add #3.2
2290 atoms, 12 pseudobonds, 146 residues, 3 models selected
> select subtract #3.2
2290 atoms, 146 residues, 2 models selected
> select add #3.4
4580 atoms, 292 residues, 2 models selected
> select subtract #3.3
2290 atoms, 146 residues, 3 models selected
> select add #3.5
11692 atoms, 750 residues, 2 models selected
> select subtract #3.4
9402 atoms, 604 residues, 3 models selected
> cartoon style (#!3 & sel) xsection oval modeHelix default
> hide #!3 models
> show #!3 models
> select add #3
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 4 models selected
> select subtract #3
6 models selected
> hide #!3 models
> show #!3 models
> hide #3.1 models
> hide #!3 models
> show #!3 models
> show #3.1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 3 models selected
> select subtract #3
6 models selected
> hide #!3 models
> hide #3.1 models
> show #3.1 models
> hide #3.8 models
> hide #3.7 models
> show #3.7 models
> hide #3.7 models
> hide #3.6 models
> hide #3.5 models
> hide #3.4 models
> hide #3.3 models
> hide #3.2 models
> show #3.2 models
> hide #3.1 models
> hide #!3 models
> show #3.1 models
> hide #3.2 models
> show #3.2 models
> hide #3.1 models
> show #3.1 models
> hide #3.2 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> select add #3.3
2290 atoms, 146 residues, 1 model selected
> show #3.3 models
> hide #3.3 models
> show sel cartoons
> ui tool show "Color Actions"
> color (#!3 & sel) #76d6ffff
> select add #3.4
4580 atoms, 292 residues, 2 models selected
> select subtract #3.3
2290 atoms, 146 residues, 3 models selected
> ui tool show "Color Actions"
> color (#!3 & sel) #76d6ffff
> color (#!3 & sel) #0096ffff
> select add #3.5
11692 atoms, 750 residues, 2 models selected
> select subtract #3.4
9402 atoms, 604 residues, 3 models selected
> color (#!3 & sel) #ff8ad8ff
> color (#!3 & sel) #ff557fff
> select add #3.6
18804 atoms, 1208 residues, 2 models selected
> select subtract #3.5
9402 atoms, 604 residues, 3 models selected
> color (#!3 & sel) #ffaaffff
> select add #3.7
17732 atoms, 1141 residues, 2 models selected
> select subtract #3.6
8330 atoms, 537 residues, 3 models selected
> color (#!3 & sel) #76d6ffff
> color (#!3 & sel) #73fa79ff
> select add #3.8
16660 atoms, 1074 residues, 2 models selected
> select subtract #3.7
8330 atoms, 537 residues, 3 models selected
> color (#!3 & sel) #009051ff
> select subtract #3.8
1 model selected
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> ui tool show "Side View"
> turn y 90
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> show #!1 models
> transparency #1.1 50
> volume step 1
> surface dust #1 size 10.8
> volume style surface
> volume hide
> volume show
> volume #1 level 0.003198
> color zone #1 near #3 distance 6.48
> volume #1 level 0.003554
> hide #!3 models
> turn y 90
> volume style surface
> show #3.2 models
> hide #3.2 models
> select ::name="CA"::name="NAG"
88 atoms, 84 bonds, 10 residues, 1 model selected
> color sel white
> volume #1 color #ebebeb
> transparency #1.1 50
> volume style surface
> volume #1 color #d6d6d6
> volume #1 color darkgrey
> volume #1 color silver
> volume #1 color #d6d6d6
> transparency #1.1 50
> volume #1 color silver
> transparency #1.1 50
> volume #1 color #ebebeb
> color zone #1 near sel & #3 distance 6.48
> hide #!3 models
> show #!3 models
> color zone #1 near sel & #3 distance 6.48
> hide #!1 models
> show #!1 models
> volume style surface
> volume style mesh
> volume style image
> volume style surface
> volume hide
> volume show
> color zone #1 near sel & #3 distance 6.48
> select ::name="NAG"
84 atoms, 84 bonds, 6 residues, 1 model selected
> show sel atoms
> hide #!1 models
> color sel gray
> select ::name="NAG"
84 atoms, 84 bonds, 6 residues, 1 model selected
> select ::name="CA"
4 atoms, 4 residues, 1 model selected
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> color (#!3 & sel) dark gray
> show #!1 models
> color zone #1 near sel & #3 distance 6.48
> hide #!3 models
> show #!3 models
> show #3.1 models
> hide #!3 models
> show #!3 models
> show #3.8 models
> show #3.7 models
> show #3.6 models
> show #3.5 models
> show #3.4 models
> show #3.3 models
> show #3.2 models
> select subtract #3.10
2 atoms, 2 residues, 3 models selected
> select subtract #3.9
1 model selected
> select add #1
3 models selected
> color zone #1 near #3 distance 6.48
> select add #1
3 models selected
> select add #1
3 models selected
> ui mousemode right select
> select clear
> hide #!3 models
> volume #1 change image level -0.0006805,0 level 0.003109,0.8 level 0.03586,1
> volume #1 level 0.003732
> volume #1 level 0.003643
> volume #1 level 0.003732
> volume #1 level 0.003376
> volume #1 level 0.003198
> color zone #1 near #3 distance 7
> color zone #1 near #3 distance 8
> color zone #1 near #3 distance 10
> color zone #1 near #3 distance 11
> volume #1 level 0.003554
> volume #1 level 0.0036
> volume #1 level 0.00355
> show #!3 models
> hide #!3 models
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting soft
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> turn y 45
> turn y 30
> turn y 90
> turn y 30
> save "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure 1/a1.cxs"
> turn y 90
> save "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure 1/a2.cxs"
> open /Users/lianqi/Files/Postdoc/VEGF/Figures/b1.cxs format session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.00311, step 2, values float32
opened ChimeraX session
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure 1/a1.cxs" format
> session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.00355, step 1, values float32
opened ChimeraX session
> save /Users/lianqi/Desktop/image1.png supersample 3
> turn y 90
> save /Users/lianqi/Desktop/image2.png supersample 3
> show #!3 models
> hide #!1 models
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure 1/a1.cxs" format
> session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.00355, step 1, values float32
opened ChimeraX session
> show #!3 models
> hide #!1 models
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> save /Users/lianqi/Desktop/image3.png supersample 3
> turn y 90
> save /Users/lianqi/Desktop/image4.png supersample 3
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> turn y 90
> select add #3
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 3 models selected
> select clear
> select /F:54
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select /F:26
22 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select /F:26
22 atoms, 21 bonds, 1 residue, 1 model selected
> select add /F:265
41 atoms, 39 bonds, 2 residues, 2 models selected
> select add /F:266
58 atoms, 55 bonds, 3 residues, 2 models selected
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 238 of 296 triangles, 42 atoms, 575 residues, 2 pseudobonds, 42 bonds
> select clear
> select /F:266
17 atoms, 16 bonds, 1 residue, 1 model selected
> select clear
> select add #3
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 3 models selected
> color (#!3 & sel) gray
> color (#!3 & sel) light gray
> select clear
> select add #3
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 3 models selected
> color (#!3 & sel) gray
> select clear
> select /F:26-266
3710 atoms, 3775 bonds, 241 residues, 1 model selected
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #009193ff
> color (#!3 & sel) #00fa92ff
> color (#!3 & sel) #008f00ff
> color (#!3 & sel) #009051ff
> select /C:330-420
1396 atoms, 1411 bonds, 91 residues, 1 model selected
> color (#!3 & sel) #ff85ffff
> color (#!3 & sel) #ff557fff
> show #!1 models
> hide #!1 models
> show #!1 models
> color zone #1 near sel & #3 distance 6.48
> select add #3.8
9726 atoms, 1411 bonds, 628 residues, 2 models selected
> color zone #1 near sel & #3 distance 6.48
> select add #1
9726 atoms, 1411 bonds, 628 residues, 6 models selected
> select add #3
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 8 models selected
> color zone #1 near sel & #3 distance 6.48
> select clear
> transparency 50
> view
> view orient
> turn z 90
> turn x 90
> view
> hide #!3 models
> transparency #1.1 0
> color #3 #ebebebff
> select add #1
3 models selected
> select add #3
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 6 models selected
> show #!3 models
> hide #!3 models
> show #!3 models
> color zone #1 near sel & #3 distance 6.48
> transparency sel 50
> select clear
> volume #1 color #d6d6d6
> volume #1 color #ebebeb
> volume #1 color darkgrey
> volume #1 color silver
> volume #1 color #ebebeb
> volume #1 color #d6d6d6
> transparency 0
> lighting soft
> lighting flat
> lighting soft
> volume #1 color white
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> view
> transparency 50
> volume style surface
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> volume #1 color #ebebeb
> volume #1 color #d6d6d6
> transparency 0
> transparency 50
> volume style surface
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> view orient
> turn x 90
> view
> select /F:26-266
3710 atoms, 3775 bonds, 241 residues, 1 model selected
> color (#!3 & sel) #d6d6d6ff
> color (#!3 & sel) #009051ff
> select /C330-420
Nothing selected
> color #3#1.1#!1 #ff557fff
> undo
> select /C330-420
Nothing selected
> select /C:330-420
1396 atoms, 1411 bonds, 91 residues, 1 model selected
> select clear
> select /C:330-420
1396 atoms, 1411 bonds, 91 residues, 1 model selected
> color (#!3 & sel) #ffaaffff
> color (#!3 & sel) #ff557fff
> select clear
> volume #1 level 0.003461
> volume #1 level 0.00355
> hide #!3 models
> select /C:330-420
1396 atoms, 1411 bonds, 91 residues, 1 model selected
> show #!3 models
> hide #3.1 models
> show #3.1 models
> hide #3.4 models
> hide #3.2 models
> hide #3.3 models
> hide #3.1 models
> hide #3.6 models
> hide #3.7 models
> hide #3.8 models
> hide #3.9 models
> hide #3.10 models
> select add #3
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 4 models selected
> select subtract #3
8 models selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #3.5 models
> show #3.5 models
> hide #3.5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select /A
2290 atoms, 2319 bonds, 1 pseudobond, 146 residues, 2 models selected
> hide sel cartoons
> select /B
2290 atoms, 2319 bonds, 1 pseudobond, 146 residues, 2 models selected
> hide sel cartoons
> select subtract #3.4
1 model selected
> select add #3.4
2290 atoms, 146 residues, 1 model selected
> select subtract #3.4
1 model selected
> show #3.4 models
> hide #3.4 models
> select add #3.4
2290 atoms, 146 residues, 1 model selected
> select subtract #3.4
1 model selected
> select add #3.5
9402 atoms, 604 residues, 1 model selected
> hide sel cartoons
> select add #3.6
18804 atoms, 1208 residues, 2 models selected
> select add #3.7
27134 atoms, 1745 residues, 3 models selected
> select add #3.8
35464 atoms, 2282 residues, 4 models selected
> select add #3.9
35466 atoms, 2284 residues, 5 models selected
> select add #3.10
35468 atoms, 2286 residues, 6 models selected
> hide sel cartoons
> select subtract #3.5
26066 atoms, 1682 residues, 7 models selected
> select subtract #3.6
16664 atoms, 1078 residues, 6 models selected
> select subtract #3.7
8334 atoms, 541 residues, 5 models selected
> select subtract #3.8
4 atoms, 4 residues, 4 models selected
> select subtract #3.9
2 atoms, 2 residues, 3 models selected
> select subtract #3.10
1 model selected
> select add #3.2
12 pseudobonds, 1 model selected
> hide atoms
> select subtract #3.2
Nothing selected
> select add #3.1
26 pseudobonds, 1 model selected
> show atoms
> hide atoms
> show cartoons
> hide cartoons
> select subtract #3.1
Nothing selected
> select /C:330-420
1396 atoms, 1411 bonds, 91 residues, 1 model selected
> show sel cartoons
> select /F:26-266
3710 atoms, 3775 bonds, 241 residues, 1 model selected
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> select clear
> hide #!3 models
> show #!3 models
> show #3.1 models
> hide #3.1 models
> show #3.3 models
> hide #3.3 models
> view orient
> view
> view orient
> turn x 180
> turn z 90
> turn y 90
> turn x 90
> view
> turn y 30
> color zone #1 near #3 distance 6.48
> undo
> turn y 30
> color zone #1 near #3 distance 6.48
> turn y 30
> transparency #1.1#3.8 0
> transparency #1.1#3.8 50
> transparency #1.1#3.8 0
> volume style surface
> transparency #1.1#3.8 50
> transparency #1.1#3.8 0
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> turn y 30
> turn y 10
> save /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/a1.cxs
> select /C:330-420
1396 atoms, 1411 bonds, 91 residues, 1 model selected
> show sel cartoons
> hide #!1 models
> select clear
> undo
> open /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/a1.cxs format session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.00355, step 1, values float32
opened ChimeraX session
> hide #!1 models
Drag select of 332 residues
> volume zone #1 nearAtoms sel range 3
> show #!1 models
> select clear
> volume zone #1 nearAtoms sel range 4
no atoms specified for zone
Drag select of 332 residues, 1 postprocess_b20_3.3A.mrc
> volume zone #1 nearAtoms sel range 4
> volume zone #1 nearAtoms sel range 5
> volume zone #1 nearAtoms sel range 4
> surface dust #1 size 10.8
> volume zone #1 nearAtoms sel range 4
> transparency sel & #1.1#3.8 50
> select clear
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/a2.cxs
> select clear
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
Drag select of 6 residues, 1 postprocess_b20_3.3A.mrc
> select clear
> ui mousemode right translate
> volume #1 level 0.004439
> volume #1 level 0.006396
> volume #1 level 0.007107
> ui mousemode right select
> select #1
3 models selected
> select clear
> view orient
> view
> turn x 90
> select /F:38
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 21 atom styles
> color sel byhetero
> Hide H
Unknown command: Hide H
> Hide atom H
Unknown command: Hide atom H
> ~hbonds
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Alignment identifier is 3/F
> hbonds sel reveal true
2 hydrogen bonds found
> undo
> select /F:137@CD
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /F:137@NH1
1 atom, 1 residue, 1 model selected
> select /F:137@HD3
1 atom, 1 residue, 1 model selected
Drag select of 22 atoms, 20 residues, 1 pseudobonds, 1
postprocess_b20_3.3A.mrc
> select clear
> select /F:137@NH1
1 atom, 1 residue, 1 model selected
> select /F:137@HD3
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /F:137
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
Drag select of 22 atoms, 329 residues, 1 pseudobonds, 1
postprocess_b20_3.3A.mrc
> hide sel atoms
> select clear
> select /F:38
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 21 atom styles
> style sel sphere
Changed 21 atom styles
> style sel stick
Changed 21 atom styles
> style sel ball
Changed 21 atom styles
> style sel stick
Changed 21 atom styles
> select clear
> hide h
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide h atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide atoms H
Expected ',' or a keyword
> hide atoms h
Expected ',' or a keyword
> hide atoms hydrogen
Expected ',' or a keyword
> select #1
3 models selected
> select /F:38
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel & @H
> hide sel atoms
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> color sel byhetero
> hide (#!3 & sel) target a
> show sel atoms
> select clear
> select #1
3 models selected
> select clear
> hide sel & @H
> select clear
> hide H
> select /C:410
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> style sel sphere
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> hide sel cartoons
> show sel cartoons
> select clear
> hide H
> select ::name="CA"
4 atoms, 4 residues, 1 model selected
> style sel sphere
Changed 4 atom styles
> show sel surfaces
> color (#!3 & sel) dark gray
> color (#!3 & sel) cornflower blue
> select clear
> select /H:3@CA
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select /H:2@CA
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 15 atoms, 332 residues, 14 bonds, 1 postprocess_b20_3.3A.mrc
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> select #1
3 models selected
> select clear
> view orient
> view
> turn x 90
> volume #1 level 0.009508
> volume #1 level 0.01013
> ui tool show "Side View"
> view
> turn x 90
> view
> turn x 90
> view
> turn x 90
> view
> turn x 90
> view
> turn x 90
> view orient
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 15 atoms, 332 residues, 14 bonds, 1 postprocess_b20_3.3A.mrc
> hide sel atoms
> select clear
> save /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/b1.cxs
> turn x 90
> turn y 10
> turn y -10
> save /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/b2.cxs
> turn x 90
> turn y 10
Drag select of 87 residues, 1 postprocess_b20_3.3A.mrc
> view sel
> undo
> select clear
> select /C:410
22 atoms, 21 bonds, 1 residue, 1 model selected
> view
> undo
> view
> view orient
> open /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/b2.cxs format session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> turn y 10
> ui tool show "Side View"
> turn y 10
> turn y -5
> turn y 5
> turn y -5
> select /C:410
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide H
> select /C:410@NZ
1 atom, 1 residue, 1 model selected
> show sel | contacts
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel contacts
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> contacts sel restrict otherAtoms distance 4 make true
Invalid "restrict" argument: Expected one of 'any', 'both', or 'cross' or an
atoms specifier
> contacts sel restrict other Atoms distance 4 make true
Invalid "restrict" argument: Expected one of 'any', 'both', or 'cross' or an
atoms specifier
> contacts sel restrict any atoms distance 4 make true
Expected a keyword
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui tool show Contacts
> contacts distanceOnly 4.0 ignoreHiddenModels true
146479 distances
> undo
> close #3.12
> select add #3.11
2 pseudobonds, 1 model selected
> select subtract #3.11
Nothing selected
> hide #3.11 models
> select /C:410@NZ
1 atom, 1 residue, 1 model selected
> hide #!1 models
Drag select of 1 atoms, 88 residues
> select clear
Drag select of 6 atoms, 94 residues, 5 bonds
> select clear
Drag select of 3 atoms, 91 residues, 3 bonds
> color (#!3 & sel) #ffaaffff
> color (#!3 & sel) #ff557fff
> color (#!3 & sel) #ff557ff1
> color (#!3 & sel) #ff557fe4
> color (#!3 & sel) #ff557fdc
> color (#!3 & sel) #ff557fd4
> color (#!3 & sel) #ff557fd0
> color (#!3 & sel) #ff557fcb
> color (#!3 & sel) #ff557fc2
> color (#!3 & sel) #ff557fbf
> color (#!3 & sel) #ff557fb9
> color (#!3 & sel) #ff557fb2
> color (#!3 & sel) #ff557fab
> color (#!3 & sel) #ff557fa3
> color (#!3 & sel) #ff557f9f
> color (#!3 & sel) #ff557f9b
> color (#!3 & sel) #ff557f98
> color (#!3 & sel) #ff557f97
> color (#!3 & sel) #ff557f94
> color (#!3 & sel) #ff557f8e
> color (#!3 & sel) #ff557f8b
> color (#!3 & sel) #ff557f8a
> color (#!3 & sel) #ff557f8e
> color (#!3 & sel) #ff557f94
> color (#!3 & sel) #ff557f95
> color (#!3 & sel) #ff557f9a
> color (#!3 & sel) #ff557f9d
> color (#!3 & sel) #ff557f97
> color (#!3 & sel) #ff557f90
> color (#!3 & sel) #ff557f8d
> color (#!3 & sel) #ff557f89
> color (#!3 & sel) #ff557f87
> color (#!3 & sel) #ff557f86
> color (#!3 & sel) #ff557f84
> color (#!3 & sel) #ff557f83
> color (#!3 & sel) #ff557f81
> color (#!3 & sel) #ff557f80
> select clear
> select /C:410@CD
1 atom, 1 residue, 1 model selected
> select /C:410
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /C:410
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /C:410
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /C:410
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /C:410
22 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!3 & sel) #ff557f80
> color (#!3 & sel) #ff557f81
> color (#!3 & sel) #ff557f88
> color (#!3 & sel) #ff557f97
> color (#!3 & sel) #ff557fa4
> color (#!3 & sel) #ff557fb3
> color (#!3 & sel) #ff557fb8
> color (#!3 & sel) #ff557fc3
> color (#!3 & sel) #ff557fc6
> color (#!3 & sel) #ff557fcc
> color (#!3 & sel) #ff557fd2
> color (#!3 & sel) #ff557fde
> color (#!3 & sel) #ff557fe3
> color (#!3 & sel) #ff557fe8
> color (#!3 & sel) #ff557fed
> color (#!3 & sel) #ff557ff1
> color (#!3 & sel) #ff557ff6
> color (#!3 & sel) #ff557ff9
> color (#!3 & sel) #ff557ffd
> color (#!3 & sel) #ff557fff
> undo
Unknown command: ui undo
> reset
Unknown command: reset
> ui tool show "Side View"
> view sel
> view
> open /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/a2.cxs format session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.00355, step 1, values float32
opened ChimeraX session
> open /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/b2.cxs format session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> turn y 5
> turn y -5
> turn y 30
> turn y -5
> turn y 5
> turn y -5
> save "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2.cxs"
> turn y -5
> turn y 5
> turn y -5
> turn y 5
> save "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1.cxs"
> hide #!1 models
Drag select of 89 residues
> color (#!3 & sel) #ff557fff
> color (#!3 & sel) #ff557ffd
> color (#!3 & sel) #ff557ff0
> color (#!3 & sel) #ff557fe3
> color (#!3 & sel) #ff557fdb
> color (#!3 & sel) #ff557fd4
> color (#!3 & sel) #ff557fce
> color (#!3 & sel) #ff557fc5
> color (#!3 & sel) #ff557fbe
> color (#!3 & sel) #ff557fba
> color (#!3 & sel) #ff557fb9
> color (#!3 & sel) #ff557fb7
> color (#!3 & sel) #ff557fb6
> color (#!3 & sel) #ff557fab
> color (#!3 & sel) #ff557f99
> color (#!3 & sel) #ff557f82
> color (#!3 & sel) #ff557f7c
> color (#!3 & sel) #ff557f74
> color (#!3 & sel) #ff557f6e
> color (#!3 & sel) #ff557f6a
> color (#!3 & sel) #ff557f68
> color (#!3 & sel) #ff557f65
> color (#!3 & sel) #ff557f63
> color (#!3 & sel) #ff557f62
> color (#!3 & sel) #ff557f5f
> color (#!3 & sel) #ff557f5e
> color (#!3 & sel) #ff557f5c
> color (#!3 & sel) #ff557f5b
> color (#!3 & sel) #ff557f59
> color (#!3 & sel) #ff557f58
> color (#!3 & sel) #ff557f56
> color (#!3 & sel) #ff557f55
> color (#!3 & sel) #ff557f54
> color (#!3 & sel) #ff557f52
> color (#!3 & sel) #ff557f51
> color (#!3 & sel) #ff557f50
> color (#!3 & sel) #ff557f4f
> color (#!3 & sel) #ff557f4e
> color (#!3 & sel) #ff557f4c
> color (#!3 & sel) #ff557f4b
> select clear
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 148 of 296 triangles, 116 residues
> select clear
> graphics silhouettes false
> graphics silhouettes true
> select add #3
40132 atoms, 40646 bonds, 40 pseudobonds, 2584 residues, 6 models selected
> select subtract #3
8 models selected
> select /F:53
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /F:53
22 atoms, 21 bonds, 1 residue, 1 model selected
> select subtract #3.8
1 model selected
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> select add #3.9
8332 atoms, 539 residues, 4 models selected
> select subtract #3.9
8330 atoms, 537 residues, 3 models selected
> select subtract #3.8
1 model selected
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> color (#!3 & sel) #ff557f4d
> color (#!3 & sel) #0090514d
> select clear
> show atoms
> style stick
Changed 40132 atom styles
> color byhetero
> select clear
> hide H
> select clear
> ui mousemode right translate
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1.cxs" format
> session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> select add #1
5 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> ui mousemode right select
> select /C:402
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /C:402
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /C:400
16 atoms, 15 bonds, 1 residue, 1 model selected
Drag select of 91 residues
> select clear
Drag select of 89 residues
> select subtract #3.5
1 model selected
> select add #3.5
9402 atoms, 604 residues, 1 model selected
> color (#!3 & sel) #ff557f4d
> select subtract #3.5
1 model selected
> select /F:69
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /F:69
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /F:89
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /F:120
20 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #3.8
1 model selected
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> hide #3.8 models
> color (#!3 & sel) #0090514d
> select clear
> select /F:38 /C:413,334
58 atoms, 58 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 58 atom styles
> hide H
> color sel byhetero
> select clear
> select /F:38@CG
1 atom, 1 residue, 1 model selected
> select clear
> select /F:38@CG
1 atom, 1 residue, 1 model selected
> select clear
> select /F:38
21 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!3 & sel) #0090514d
> color (#!3 & sel) #00905184
> color (#!3 & sel) #009051b7
> color (#!3 & sel) #009051ce
> color (#!3 & sel) #009051e6
> color (#!3 & sel) #009051f3
> color (#!3 & sel) #009051f9
> color (#!3 & sel) #009051ff
> color sel byhetero
> select /C:334,413
37 atoms, 37 bonds, 2 residues, 1 model selected
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #009051f8
> color (#!3 & sel) #009051d2
> color (#!3 & sel) #009051c2
> color (#!3 & sel) #009051c0
> color (#!3 & sel) #009051cd
> color (#!3 & sel) #009051df
> color (#!3 & sel) #009051e8
> color (#!3 & sel) #009051f0
> color (#!3 & sel) #009051f4
> color (#!3 & sel) #009051fd
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #ff557fff
> select clear
> turn y 5
> select /F:38@CZ
1 atom, 1 residue, 1 model selected
> select /C:334@CA
1 atom, 1 residue, 1 model selected
> select /C:413
17 atoms, 17 bonds, 1 residue, 1 model selected
> select add /F:38
38 atoms, 38 bonds, 2 residues, 2 models selected
> select add /C:334
58 atoms, 58 bonds, 3 residues, 3 models selected
> view sel
> view
> turn y -5
> turn y 5
> select /F:144-266
1868 atoms, 1898 bonds, 123 residues, 1 model selected
> hide sel cartoons
> select /G:2@CA
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel surfaces
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 148 of 296 triangles, 24 atoms, 209 residues, 24 bonds
> select clear
> show #!1 models
> transparency #1.1#3.9-10 0
> volume style surface
> select clear
> transparency #1.1#3.9-10 50
> hide #!1 models
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 148 of 296 triangles, 24 atoms, 209 residues, 24 bonds
> volume zone #1 nearAtoms sel range 4
> show #!1 models
> select clear
> transparency #1.1#3.9-10 0
> volume style surface
> transparency #1.1#3.9-10 50
> volume style mesh
> volume style surface
> transparency #1.1#3.9-10 0
> volume style surface
> volume hide
> volume show
> volume style surface
> transparency #1.1#3.9-10 50
> volume style image
> volume style mesh
> volume style surface
> transparency #1.1#3.9-10 0
> transparency #1.1#3.9-10 50
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 148 of 296 triangles, 24 atoms, 209 residues, 24 bonds, 1
postprocess_b20_3.3A.mrc
> hide #!1 models
> show sel cartoons
> show sel atoms
> hide sel atoms
> show sel surfaces
> hide sel surfaces
> show #!1 models
> transparency sel 0
> volume sel style surface
> transparency sel 0
> volume #1 color #d6d6d6
> transparency sel 0
> volume sel style surface
> volume sel style mesh
> volume sel style image
> transparency sel & #3.5,8 0
> transparency sel & #3.5,8 50
> volume sel style surface
> transparency sel 0
> select clear
> transparency #1.1#3.5,8-10 0
> volume style surface
> volume style mesh
> volume style surface
> transparency #1.1#3.5,8-10 50
> transparency #1.1#3.5,8-10 0
> transparency #1.1#3.5,8-10 50
> transparency #1.1#3.5,8-10 0
> transparency #1.1#3.5,8-10 50
> transparency #1.1#3.5,8-10 0
> transparency #1.1#3.5,8-10 50
> transparency #1.1#3.5,8-10 20
> transparency #1.1#3.5,8-10 90
> transparency #1.1#3.5,8-10 0
> transparency #1.1#3.5,8-10 50
> transparency #1 50
> transparency #1 20
> transparency #1 0
> transparency #1 90
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1.cxs" format
> session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> select /F144-266
Nothing selected
> hide cartoons
> undo
> select /F:144-266
1868 atoms, 1898 bonds, 123 residues, 1 model selected
> hide sel cartoons
> select #1
5 models selected
> select clear
> hide #!1 models
> select /G:2@CA
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel surfaces
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 148 of 296 triangles, 208 residues
> select clear
> select /F:68
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /F:90
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /F:89
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /F:68
17 atoms, 16 bonds, 1 residue, 1 model selected
> select subtract #3.8
1 model selected
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> color (#!3 & sel) #d6d6d680
> color (#!3 & sel) #d6d6d68a
> color (#!3 & sel) #d6d6d6a3
> color (#!3 & sel) #d6d6d6c3
> color (#!3 & sel) #d6d6d6e8
> color (#!3 & sel) #d6d6d6fd
> color (#!3 & sel) #d6d6d6ff
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #009051f0
> color (#!3 & sel) #009051db
> color (#!3 & sel) #009051c8
> color (#!3 & sel) #009051bc
> color (#!3 & sel) #009051b1
> color (#!3 & sel) #009051a5
> color (#!3 & sel) #009051a0
> color (#!3 & sel) #0090519f
> color (#!3 & sel) #0090519c
> color (#!3 & sel) #00905194
> color (#!3 & sel) #0090518d
> color (#!3 & sel) #0090518e
> color (#!3 & sel) #0090518f
> color (#!3 & sel) #00905190
> color (#!3 & sel) #00905192
> color (#!3 & sel) #0090519d
> color (#!3 & sel) #009051a9
> color (#!3 & sel) #009051ab
> color (#!3 & sel) #009051b0
> color (#!3 & sel) #009051b8
> color (#!3 & sel) #009051c0
> color (#!3 & sel) #009051c1
> color (#!3 & sel) #009051c0
> color (#!3 & sel) #009051be
> color (#!3 & sel) #009051b8
> color (#!3 & sel) #009051b4
> color (#!3 & sel) #009051b1
> color (#!3 & sel) #009051b0
> color (#!3 & sel) #009051b1
> color (#!3 & sel) #009051b4
> color (#!3 & sel) #009051b3
> select /C:400
16 atoms, 15 bonds, 1 residue, 1 model selected
> select subtract #3.5
1 model selected
> select add #3.5
9402 atoms, 604 residues, 1 model selected
> color (#!3 & sel) #ff557fb3
> undo
> view
> view orient
> view
> view orient
> turn y 90
> turn x 90
> turn z 90
> turn y 90
> turn y 10
> select /C:411
17 atoms, 16 bonds, 1 residue, 1 model selected
> select subtract #3.5
1 model selected
> select add #3.5
9402 atoms, 604 residues, 1 model selected
> select clear
> ui mousemode right zoom
> show #!1 models
> hide #!1 models
> ui mousemode right select
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 148 of 296 triangles, 209 residues
> volume zone #mapID near sel range 4
Missing or invalid "volumes" argument: invalid density maps specifier
> show #!1 models
> volume zone #1 nearAtoms sel range 4
> select clear
> transparency #1.1#3.8-10 0
> transparency #1.1#3.8-10 50
> hide #!1 models
> save "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 2.cxs"
> show #!1 models
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> select add #3.9
8332 atoms, 539 residues, 2 models selected
> select subtract #3.8
2 atoms, 2 residues, 3 models selected
> select add #3.10
4 atoms, 4 residues, 2 models selected
> select subtract #3.9
2 atoms, 2 residues, 3 models selected
> select add #3.9
4 atoms, 4 residues, 2 models selected
> select subtract #3.10
2 atoms, 2 residues, 3 models selected
> select add #3.8
8332 atoms, 539 residues, 2 models selected
> select subtract #3.9
8330 atoms, 537 residues, 3 models selected
> select subtract #3.8
1 model selected
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> select add #3.5
17732 atoms, 1141 residues, 2 models selected
> show #3.5 models
> hide #3.5 models
> hide #3.8 models
> select subtract #3.5
8330 atoms, 537 residues, 3 models selected
> select subtract #3.8
1 model selected
> show #3.8 models
> hide #3.8 models
> color #3.8 #009051b1
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #3.8 models
> show #3.5 models
> hide #3.5 models
> show #3.4 models
> select add #3.4
2290 atoms, 146 residues, 1 model selected
> select subtract #3.4
1 model selected
> hide #3.4 models
> select add #3.5
9402 atoms, 604 residues, 1 model selected
> show #3.5 models
> select add #3.8
17732 atoms, 1141 residues, 2 models selected
> show #!1 models
> hide #!1 models
> show #3.7 models
> hide #3.7 models
> show #3.7 models
> show #3.6 models
> hide #3.7 models
> hide #3.6 models
> hide #3.8 models
> show #3.8 models
> show sel cartoons
> hide sel cartoons
> hide #3.8 models
> hide #3.5 models
> show #3.5 models
> show #3.8 models
> hide #3.8 models
> hide #3.5 models
> select subtract #3.5
8330 atoms, 537 residues, 3 models selected
> select add #3.5
17732 atoms, 1141 residues, 2 models selected
> select subtract #3.8
9402 atoms, 604 residues, 3 models selected
> select subtract #3.5
1 model selected
> hide #3.11 models
> show #3.11 models
> close #3.11
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 2.cxs" format
> session
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> hide #3.8 models
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> select add #3.4
10620 atoms, 683 residues, 2 models selected
> select subtract #3.4
8330 atoms, 537 residues, 3 models selected
> select add #3.5
17732 atoms, 1141 residues, 2 models selected
> show #!1 models
> hide #!1 models
> raise #3
Unknown command: raise #3
> raise #3.8
Unknown command: raise #3.8
> raise #3
Unknown command: raise #3
> select clear
> modeldisplay #3 front
Unknown command: modeldisplay #3 front
> clip auto
Expected a keyword
> clip off
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 color #d6d6d680
> volume #1 color #d6d6d6
> volume #1 color #d6d6d680
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> color (#!3 & sel) #d6d6d680
> color (#!3 & sel) #d6d6d68c
> color (#!3 & sel) #d6d6d69e
> color (#!3 & sel) #d6d6d6aa
> color (#!3 & sel) #d6d6d6b8
> color (#!3 & sel) #d6d6d6c3
> color (#!3 & sel) #d6d6d6cf
> color (#!3 & sel) #d6d6d6d3
> color (#!3 & sel) #d6d6d6d5
> color (#!3 & sel) #d6d6d6d8
> color (#!3 & sel) #d6d6d6dd
> color (#!3 & sel) #d6d6d6e0
> color (#!3 & sel) #d6d6d6e3
> color (#!3 & sel) #d6d6d6e6
> color (#!3 & sel) #d6d6d6e7
> color (#!3 & sel) #d6d6d6e8
> color (#!3 & sel) #009051e8
> color (#!3 & sel) #009051f3
> color (#!3 & sel) #009051f8
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #009051f5
> color (#!3 & sel) #009051f1
> color (#!3 & sel) #009051f0
> color (#!3 & sel) #009051ea
> color (#!3 & sel) #009051eb
> color (#!3 & sel) #009051ec
> color (#!3 & sel) #009051ee
> color (#!3 & sel) #009051f0
> color (#!3 & sel) #009051f5
> color (#!3 & sel) #009051f6
> color (#!3 & sel) #009051f8
> color (#!3 & sel) #009051fb
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #009051f6
> color (#!3 & sel) #009051f5
> color (#!3 & sel) #009051f6
> color (#!3 & sel) #009051f9
> color (#!3 & sel) #009051fb
> color (#!3 & sel) #009051fd
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #009051f5
> color (#!3 & sel) #009051ed
> color (#!3 & sel) #009051ec
> color (#!3 & sel) #009051e7
> color (#!3 & sel) #009051e4
> color (#!3 & sel) #009051e0
> color (#!3 & sel) #009051e7
> color (#!3 & sel) #009051fd
> color (#!3 & sel) #009051ff
> show #3.8 models
> hide #3.8 models
> color #3.8 #ebebebff
> color #3.8 white
> color #3.8 #ebebebff
> color #3.8 #ebebeb00
> select subtract #3.8
1 model selected
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> select subtract #3.8
1 model selected
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> select clear
> hide #!1 models
> select add #3.4
2290 atoms, 146 residues, 1 model selected
> select subtract #3.4
1 model selected
> select add #3.5
9402 atoms, 604 residues, 1 model selected
> select subtract #3.5
1 model selected
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> select subtract #3.8
1 model selected
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> color (#!3 & sel) #ebebeb00
> color (#!3 & sel) #00905100
> color (#!3 & sel) #00905107
> color (#!3 & sel) #00905116
> color (#!3 & sel) #00905125
> color (#!3 & sel) #00905138
> color (#!3 & sel) #00905148
> color (#!3 & sel) #0090514e
> color (#!3 & sel) #00905151
> color (#!3 & sel) #0090515b
> color (#!3 & sel) #00905167
> color (#!3 & sel) #0090516a
> color (#!3 & sel) #0090516c
> color (#!3 & sel) #0090516e
> color (#!3 & sel) #00905171
> color (#!3 & sel) #00905177
> color (#!3 & sel) #0090517b
> color (#!3 & sel) #00905180
> color (#!3 & sel) #00905189
> color (#!3 & sel) #0090518d
> color (#!3 & sel) #0090518e
> color (#!3 & sel) #00905191
> color (#!3 & sel) #00905194
> color (#!3 & sel) #0090519a
> color (#!3 & sel) #009051a0
> color (#!3 & sel) #009051a6
> color (#!3 & sel) #009051b3
> color (#!3 & sel) #009051b7
> color (#!3 & sel) #009051b8
> color (#!3 & sel) #009051b9
> color (#!3 & sel) #009051bb
> color (#!3 & sel) #009051be
> color (#!3 & sel) #009051c0
> color (#!3 & sel) #009051c2
> color (#!3 & sel) #009051c3
> color (#!3 & sel) #009051c4
> show #!1 models
> color (#!3 & sel) #009051c4
> color (#!3 & sel) #009051c7
> color (#!3 & sel) #009051cf
> color (#!3 & sel) #009051d6
> color (#!3 & sel) #009051dd
> color (#!3 & sel) #009051e2
> color (#!3 & sel) #009051e6
> color (#!3 & sel) #009051e9
> color (#!3 & sel) #009051eb
> color (#!3 & sel) #009051ed
> color (#!3 & sel) #009051f0
> color (#!3 & sel) #009051f3
> color (#!3 & sel) #009051f4
> color (#!3 & sel) #009051f5
> color (#!3 & sel) #009051f7
> color (#!3 & sel) #009051f9
> color (#!3 & sel) #009051fb
> color (#!3 & sel) #009051fd
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #009051fc
> color (#!3 & sel) #009051f8
> color (#!3 & sel) #009051f4
> color (#!3 & sel) #009051f0
> color (#!3 & sel) #009051ed
> color (#!3 & sel) #009051eb
> color (#!3 & sel) #009051ee
> color (#!3 & sel) #009051f9
> color (#!3 & sel) #009051fc
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #009051f7
> color (#!3 & sel) #009051ee
> color (#!3 & sel) #009051e8
> color (#!3 & sel) #009051e4
> color (#!3 & sel) #009051ea
> color (#!3 & sel) #009051fd
> color (#!3 & sel) #009051ff
> color #3.8 #ebebebff
> color #3.8 #ebebeb80
> select clear
> hide #!1 models
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 148 of 296 triangles, 120 residues
> select clear
> select /F:26-143
1842 atoms, 1876 bonds, 1 pseudobond, 118 residues, 2 models selected
> color (#!3 & sel) #ebebeb80
> color (#!3 & sel) #00905180
> color (#!3 & sel) #00905181
> color (#!3 & sel) #00905186
> color (#!3 & sel) #0090518b
> color (#!3 & sel) #00905193
> color (#!3 & sel) #00905198
> color (#!3 & sel) #0090519b
> color (#!3 & sel) #0090519d
> color (#!3 & sel) #0090519f
> color (#!3 & sel) #009051a1
> color (#!3 & sel) #009051a3
> color (#!3 & sel) #009051a4
> color (#!3 & sel) #009051a5
> color (#!3 & sel) #009051a6
> color (#!3 & sel) #009051a7
> color (#!3 & sel) #009051aa
> color (#!3 & sel) #009051ae
> color (#!3 & sel) #009051af
> color (#!3 & sel) #009051b1
> color (#!3 & sel) #009051b2
> show #!1 models
> color (#!3 & sel) #009051b2
> color (#!3 & sel) #009051b5
> color (#!3 & sel) #009051b8
> color (#!3 & sel) #009051bc
> color (#!3 & sel) #009051bd
> color (#!3 & sel) #009051c1
> color (#!3 & sel) #009051c4
> color (#!3 & sel) #009051c6
> color (#!3 & sel) #009051cb
> color (#!3 & sel) #009051ce
> color (#!3 & sel) #009051d0
> color (#!3 & sel) #009051d3
> color (#!3 & sel) #009051d4
> color (#!3 & sel) #009051d7
> color (#!3 & sel) #009051d9
> color (#!3 & sel) #009051da
> color (#!3 & sel) #009051db
> color (#!3 & sel) #009051dc
> color (#!3 & sel) #009051de
> color (#!3 & sel) #009051e1
> color (#!3 & sel) #009051e2
> color (#!3 & sel) #009051e3
> color (#!3 & sel) #009051e4
> color (#!3 & sel) #009051e5
> color (#!3 & sel) #009051e7
> color (#!3 & sel) #009051e8
> color (#!3 & sel) #009051e9
> color (#!3 & sel) #009051eb
> color (#!3 & sel) #009051ec
> color (#!3 & sel) #009051ee
> color (#!3 & sel) #009051f0
> color (#!3 & sel) #009051f2
> color (#!3 & sel) #009051f4
> color (#!3 & sel) #009051f5
> color (#!3 & sel) #009051f6
> color (#!3 & sel) #009051f9
> color (#!3 & sel) #009051fe
> color (#!3 & sel) #009051ff
> volume #1 color #d6d6d64c
> select clear
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> color (#!3 & sel) #d6d6d64d
> color (#!3 & sel) #0090514d
> color (#!3 & sel) #0090515d
> color (#!3 & sel) #00905189
> color (#!3 & sel) #009051a6
> color (#!3 & sel) #009051cf
> color (#!3 & sel) #009051e2
> color (#!3 & sel) #009051ed
> color (#!3 & sel) #009051fe
> color (#!3 & sel) #009051ff
> color (#!3 & sel) #008f00ff
> color (#!3 & sel) #00fa92ff
> color (#!3 & sel) #73fcd6ff
> color (#!3 & sel) #73fa79ff
> select subtract #3.8
1 model selected
> select add #3.5
9402 atoms, 604 residues, 1 model selected
> color (#!3 & sel) #73fa79ff
> color (#!3 & sel) #ffaaffff
> select clear
> save "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 3.cxs"
> select /F:38
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> color (#!3 & sel) #009051ff
> ui mousemode right zoom
> select /C:413,334
37 atoms, 37 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 37 atom styles
> color sel byhetero
> color (#!3 & sel) #ff557fff
> hide H
> select /F:38
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> style sel ball
Changed 21 atom styles
> style sel sphere
Changed 21 atom styles
> style sel stick
Changed 21 atom styles
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide H
> color sel byhetero
> ui mousemode right select
> ui mousemode right zoom
> ui mousemode right select
> select clear
> ui mousemode right zoom
> ui mousemode right select
> color byhetero
> select #1
3 models selected
> select clear
> select #1
3 models selected
> select clear
> ui mousemode right zoom
> save "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 4.cxs"
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2.cxs"
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> hide #3.8 models
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> select /F:26-143
1842 atoms, 1876 bonds, 1 pseudobond, 118 residues, 2 models selected
> hide sel cartoons
> hide #!1 models
> ui mousemode right select
> select /G:3@CA
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel surfaces
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 148 of 296 triangles, 214 residues
> view sel
> view
> view orient
> turn x 90
> select clear
> turn y 90
> turn z 90
> turn x 90
> turn y 10
> turn y -5
> select add #3.3
2290 atoms, 146 residues, 1 model selected
> select subtract #3.3
1 model selected
> select add #3.4
2290 atoms, 146 residues, 1 model selected
> select subtract #3.4
1 model selected
> select add #3.4
2290 atoms, 146 residues, 1 model selected
> select subtract #3.4
1 model selected
> select add #3.5
9402 atoms, 604 residues, 1 model selected
> color (#!3 & sel) #ffaaffff
> select subtract #3.5
1 model selected
> select add #3.5
9402 atoms, 604 residues, 1 model selected
> color (#!3 & sel) #ffaaff
> select clear
> select add #3.8
8330 atoms, 537 residues, 1 model selected
> color (#!3 & sel) #73fa79ff
> select clear
Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES
surface, 148 of 296 triangles, 214 residues
> volume zone #1 nearAtoms sel range 4
> show #!1 models
> select clear
> turn y 5
> turn y -5
> select /C:410
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!3 & sel) #ff557fff
> select /F:250,209,195
39 atoms, 36 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 39 atom styles
> color sel byhetero
> ui tool show "Color Actions"
> color (#!3 & sel) #009051ff
> hide H
> select clear
> color byhetero
> close #3.11
> select add #3.10
2 atoms, 2 residues, 1 model selected
> select subtract #3.10
1 model selected
> select add #3.9
2 atoms, 2 residues, 1 model selected
> color #3.9 #0096ffff
> select clear
> save "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2 1.cxs"
> turn x 5
> turn x -5
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2 1.cxs"
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> select clear
> ui mousemode right zoom
> hide #!1 models
> ui mousemode right select
> select /F:208
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 21 atom styles
> hide sel atoms
> select clear
> show #!1 models
> select clear
> ui mousemode right zoom
> select clear
> save "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2 2.cxs"
> save /Users/lianqi/Desktop/image5.png supersample 3
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2 1.cxs"
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> save /Users/lianqi/Desktop/image6.png supersample 3
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 4.cxs"
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> save /Users/lianqi/Desktop/image7.png supersample 3
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 3.cxs"
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> save /Users/lianqi/Desktop/image8.png supersample 3
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 2.cxs"
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.0101, step 1, values float32
opened ChimeraX session
> open "/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure 1/a1.cxs"
Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08,
shown at level 0.00355, step 1, values float32
opened ChimeraX session
> open "/Users/lianqi/Files/Postdoc/VEGF/EM
> Data/Cis/relion_locres_filtered_job187.mrc"
> "/Users/lianqi/Files/Postdoc/VEGF/EM
> Data/Cis/tetramer_cis_13-coot-47_isolde_real_space_refined_057.pdb"
Opened relion_locres_filtered_job187.mrc as #2, grid size 400,400,400, pixel
0.936, shown at level 0.0027, step 2, values float32
Chain information for
tetramer_cis_13-coot-47_isolde_real_space_refined_057.pdb #4
---
Chain | Description
A B G H | No description available
C I | No description available
D J | No description available
E K | No description available
F L | No description available
> select add #1
3 models selected
> select add #2
5 models selected
> select subtract #2
3 models selected
> select add #3
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 6 models selected
> select subtract #3
11 models selected
> select add #3
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 6 models selected
> select subtract #1
40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 11 models selected
> show #!3 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,7
Model Number: MRW13LL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 3 days, 1 hour, 37 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL E2218HN:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 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 , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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