![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16509 closed defect (duplicate)
Crash moving window between screens
| 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-13.1-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 0x00000001e11dba80 (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.surface._surface, chimerax.pdb_lib._load_libs, 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.dssp._dssp (total: 61)
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"procLaunch" : "2024-12-20 09:21:56.9815 -0700",
"procStartAbsTime" : 23908344612660,
"procExitAbsTime" : 23992057798293,
"procName" : "ChimeraX",
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"crashReporterKey" : "C42CA24A-F4BA-B841-EB38-BF08346FFDF1",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
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"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=6.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2944K 8 \nCG image 880K 45 \nColorSync 576K 29 \nCoreAnimation 2096K 108 \nCoreGraphics 96K 6 \nCoreServices 624K 2 \nCoreUI image data 496K 8 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 5.4G 480 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 176.0M 3 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 640K 40 \nStack 193.9M 41 \nStack Guard 56.0M 1 \nVM_ALLOCATE 301.6M 249 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__AUTH 2014K 390 \n__AUTH_CONST 25.4M 624 \n__CTF 756 1 \n__DATA 20.9M 778 \n__DATA_CONST 39.4M 783 \n__DATA_DIRTY 2050K 248 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 797.2M 158 \n__OBJC_CONST 4997K 358 \n__OBJC_RO 65.4M 1 \n__OBJC_RW 1986K 1 \n__TEXT 862.7M 804 \ndyld private memory 304K 3 \nmapped file 549.6M 76 \nshared memory 3280K 33 \n=========== ======= ======= \nTOTAL 8.6G 5308 \nTOTAL, minus reserved VM space 8.2G 5308 \n",
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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/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix_crosslinkResidues.cxs" format
> session
No such file/path: /Users/colinmuir/Desktop/MCU Paper
Figures/DomainSwapFigure/Y289S_lateralhelix_crosslinkResidues.cxs
> open "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix.cxs" format session
No such file/path: /Users/colinmuir/Desktop/MCU Paper
Figures/DomainSwapFigure/Y289S_lateralhelix.cxs
> open "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure2/Y289S_lateralhelix_crosslinkResidues.cxs"
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #1.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0453, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #1.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #1.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 3 as #1.4, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 4 as #1.5, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc as #2, grid size 320,320,320, pixel
0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 0 as #8.1, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 1 as #8.2, grid size 320,320,320,
pixel 0.86, shown at level 0.009, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 2 as #8.3, grid size 320,320,320,
pixel 0.86, shown at level 0.01, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 3 as #8.4, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 4 as #8.5, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
opened ChimeraX session
> open "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure2/Y289S_lateralhelix_crosslinkResidues.cxs"
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #1.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0453, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #1.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #1.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 3 as #1.4, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 4 as #1.5, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc as #2, grid size 320,320,320, pixel
0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 0 as #8.1, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 1 as #8.2, grid size 320,320,320,
pixel 0.86, shown at level 0.009, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 2 as #8.3, grid size 320,320,320,
pixel 0.86, shown at level 0.01, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 3 as #8.4, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 4 as #8.5, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
opened ChimeraX session
> open "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure2/Y289S_lateralhelix_crosslinkResidues.cxs"
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #1.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0453, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #1.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #1.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 3 as #1.4, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 4 as #1.5, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc as #2, grid size 320,320,320, pixel
0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 0 as #8.1, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 1 as #8.2, grid size 320,320,320,
pixel 0.86, shown at level 0.009, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 2 as #8.3, grid size 320,320,320,
pixel 0.86, shown at level 0.01, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 3 as #8.4, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 4 as #8.5, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
opened ChimeraX session
> ui tool show "Side View"
> open
> /Users/colinmuir/Documents/phenix/CM25/RealSpaceRefine_15/CM25_deepEMhancerJ463docked_real_space_refined_015_coot3-2.pdb
Chain information for
CM25_deepEMhancerJ463docked_real_space_refined_015_coot3-2.pdb #9
---
Chain | Description
A B D | No description available
C | No description available
> hide #6 models
> dssp
Computing secondary structure
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.02899
> volume #2 level 0.01187
> hide #!2 models
> select #9/A:316
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
208 atoms, 209 bonds, 25 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> select clear
> select #9/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
80 atoms, 80 bonds, 10 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> select down
80 atoms, 80 bonds, 10 residues, 1 model selected
> select add #9/A:297
90 atoms, 90 bonds, 11 residues, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 1 model selected
> select add #9/A:293
120 atoms, 122 bonds, 14 residues, 1 model selected
> select add #9/A:287
125 atoms, 126 bonds, 15 residues, 1 model selected
> select add #9/A:285
132 atoms, 133 bonds, 16 residues, 1 model selected
> select up
260 atoms, 266 bonds, 30 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #9/D:306
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #9/D:299
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #9/D:295
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #9/D:291
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add #9/D:285
39 atoms, 36 bonds, 5 residues, 1 model selected
> select up
244 atoms, 249 bonds, 28 residues, 1 model selected
> select add #9/D:293
252 atoms, 256 bonds, 29 residues, 1 model selected
> undo
> close #9
> open
> /Users/colinmuir/Documents/phenix/CM25/RealSpaceRefine_15/CM25_deepEMhancerJ463docked_real_space_refined_015_coot3-2.pdb
Chain information for
CM25_deepEMhancerJ463docked_real_space_refined_015_coot3-2.pdb #9
---
Chain | Description
A B D | No description available
C | No description available
> dssp
Computing secondary structure
> open
> /Users/colinmuir/Documents/phenix/CM25/RealSpaceRefine_15/CM25_deepEMhancerJ463docked_real_space_refined_015_coot4.pdb
Chain information for
CM25_deepEMhancerJ463docked_real_space_refined_015_coot4.pdb #10
---
Chain | Description
A B D | No description available
C | No description available
> close #9
> dssp
Computing secondary structure
> select #10/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> transparency #2.1 50
> hide #!2 models
> show #!8 models
> show #!8.5 models
> hide #!8.5 models
> show #!8.4 models
> hide #!8.4 models
> show #!8.3 models
> show #!8.2 models
> transparency #8.2.1#8.3.1 50
> hide #!8.3 models
> hide #!8.2 models
> select up
38 atoms, 38 bonds, 4 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cyan
> show #!8.3 models
> show #!8.2 models
> color sel medium blue
> select clear
> select #8.3
4 models selected
> hide #!8.3 models
> hide #!8.2 models
> select #10/B:288
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
122 atoms, 125 bonds, 14 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel deep sky blue
> select clear
> select #10/C:301
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!8.5 models
> hide #!8.5 models
> show #!8.4 models
> hide #!8.4 models
> select up
143 atoms, 146 bonds, 16 residues, 1 model selected
> select up
1422 atoms, 1451 bonds, 171 residues, 1 model selected
> color sel dark blue
> select clear
> select add #10/D:228
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
88 atoms, 89 bonds, 11 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel dodger blue
> select clear
> show #!8.3 models
> show #!8.2 models
> color #8.3 #76d6ffff models
> transparency #8.2.1#8.3.1 0
> transparency #8.2.1#8.3.1 50
> ui tool show "Side View"
> select #8.3
4 models selected
> hide #!8.3 models
> hide #!8.2 models
> select add #10/B:274
12 atoms, 12 bonds, 1 residue, 3 models selected
> select up
171 atoms, 177 bonds, 21 residues, 3 models selected
> select up
1411 atoms, 1440 bonds, 170 residues, 3 models selected
> show sel atoms
> color sel byhetero
> select clear
> select #10/A:308
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
38 atoms, 38 bonds, 4 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #10/B:209
7 atoms, 7 bonds, 1 residue, 1 model selected
> setattr /B:187-249 res ss_type 1
Assigning ss_type attribute to 189 items
> setattr /B:187-249 res ss_id 200
Assigning ss_id attribute to 189 items
> setattr /B:187-250 res ss_id 200
Assigning ss_id attribute to 192 items
> select #10/A:299
4 atoms, 3 bonds, 1 residue, 1 model selected
> setattr /A:187-250 res ss_id 201
Assigning ss_id attribute to 192 items
> setattr /A:187-250 res ss_type 1
Assigning ss_type attribute to 192 items
> setattr /A:287-299 res ss_type 1
Assigning ss_type attribute to 39 items
> setattr /A:287-299 res ss_id 202
Assigning ss_id attribute to 39 items
> show #!8.3 models
> select clear
> select #10/A:208
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
533 atoms, 542 bonds, 64 residues, 1 model selected
> style sel stick
Changed 533 atom styles
> show sel atoms
> color sel byhetero
> show #!8.2 models
> color #8.2 #0433ffff models
> transparency #8.2.1#8.3.1 0
> transparency #8.2.1#8.3.1 50
> select clear
> hide #10 atoms
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure2/Y289S_showDomainSwapDensity.cxs"
> color #8.2 #0096ffff models
> transparency #8.2.1#8.3.1 0
> transparency #8.2.1#8.3.1 50
> color #8.2 #0433ffff models
> transparency #8.2.1#8.3.1 0
> transparency #8.2.1#8.3.1 50
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure2/Y289S_showDomainSwapDensity.png" width 1500 height
> 1083 supersample 3 transparentBackground true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure2/Y289S_showDomainSwapDensity.cxs"
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #1.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0453, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #1.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #1.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 3 as #1.4, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 4 as #1.5, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc as #2, grid size 320,320,320, pixel
0.86, shown at level 0.0119, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 0 as #8.1, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 1 as #8.2, grid size 320,320,320,
pixel 0.86, shown at level 0.009, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 2 as #8.3, grid size 320,320,320,
pixel 0.86, shown at level 0.01, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 3 as #8.4, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 4 as #8.5, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Log from Fri Dec 20 10:08:48 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure2/Y289S_lateralhelix_crosslinkResidues.cxs"
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #1.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0453, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #1.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #1.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 3 as #1.4, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 4 as #1.5, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc as #2, grid size 320,320,320, pixel
0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 0 as #8.1, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 1 as #8.2, grid size 320,320,320,
pixel 0.86, shown at level 0.009, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 2 as #8.3, grid size 320,320,320,
pixel 0.86, shown at level 0.01, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 3 as #8.4, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 4 as #8.5, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Log from Thu Dec 19 15:55:09 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix.cxs"
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #1.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0453, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #1.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #1.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 3 as #1.4, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 4 as #1.5, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc as #2, grid size 320,320,320, pixel
0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 0 as #8.1, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 1 as #8.2, grid size 320,320,320,
pixel 0.86, shown at level 0.009, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 2 as #8.3, grid size 320,320,320,
pixel 0.86, shown at level 0.01, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 3 as #8.4, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 4 as #8.5, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Log from Thu Dec 19 14:59:01 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/colinmuir/Desktop/MCU Paper Figures/289S_cylinder_model.cxs"
> format session
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #1.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0453, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #1.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #1.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 3 as #1.4, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 4 as #1.5, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc as #2, grid size 320,320,320, pixel
0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 0 as #8.1, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 1 as #8.2, grid size 320,320,320,
pixel 0.86, shown at level 0.009, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 2 as #8.3, grid size 320,320,320,
pixel 0.86, shown at level 0.01, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 3 as #8.4, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 4 as #8.5, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Log from Mon Dec 16 14:31:03 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_deepEMhancer_blue_v2.cxs"
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #1.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0453, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #1.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #1.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 3 as #1.4, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 4 as #1.5, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc as #2, grid size 320,320,320, pixel
0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 0 as #8.1, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 1 as #8.2, grid size 320,320,320,
pixel 0.86, shown at level 0.009, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 2 as #8.3, grid size 320,320,320,
pixel 0.86, shown at level 0.01, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 3 as #8.4, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 4 as #8.5, grid size 320,320,320,
pixel 0.86, shown at level 0.036, step 1, values float32
Log from Mon Dec 16 12:03:21 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/colinmuir/Desktop/MCU Paper Figures/MCU Y289S alone.cxs"
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #1.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0453, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #1.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #1.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 3 as #1.4, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 4 as #1.5, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Log from Sat Nov 9 12:42:50 2024UCSF ChimeraX version: 1.6rc202305021906
(2023-05-02)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/colinmuir/Desktop/MCU alone
> map/Figures/MCU_alone_DimerDimerColor.cxs" format session
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Log from Fri Sep 6 18:02:51 2024UCSF ChimeraX version: 1.6rc202305021906
(2023-05-02)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/colinmuir/Downloads/cryosparc_P36_J252_009_volume_map_sharp.mrc
Opened cryosparc_P36_J252_009_volume_map_sharp.mrc as #1, grid size
360,360,360, pixel 0.86, shown at level 0.0362, step 2, values float32
> volume #1 step 1
> volume #1 level 0.1778
> volume #1 level 0.1185
> volume #1 level 0.1916
> volume #1 level 0.1047
> volume #1 level 0.06819
> volume #1 level 0.2098
> open /Users/colinmuir/Downloads/cryosparc_P36_J252_009_volume_map.mrc
Opened cryosparc_P36_J252_009_volume_map.mrc as #2, grid size 360,360,360,
pixel 0.86, shown at level 0.0358, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1073
> volume #2 level 0.07868
> volume #2 level 0.06008
> volume #2 level 0.07439
> volume #2 level 0.08028
> volume #2 level 0.07439
> volume #2 level 0.1142
> open /Users/colinmuir/Downloads/cryosparc_P33_J447_010_volume_map.mrc
Opened cryosparc_P33_J447_010_volume_map.mrc as #3, grid size 320,320,320,
pixel 0.86, shown at level 0.0434, step 2, values float32
> ui tool show "Fit in Map"
> fitmap #1 inMap #3
Fit map cryosparc_P36_J252_009_volume_map_sharp.mrc in map
cryosparc_P33_J447_010_volume_map.mrc using 27778 points
correlation = 0.4909, correlation about mean = 0.133, overlap = 537.5
steps = 248, shift = 5.86, angle = 14.5 degrees
Position of cryosparc_P36_J252_009_volume_map_sharp.mrc (#1) relative to
cryosparc_P33_J447_010_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.97299994 -0.22646590 0.04454563 30.81230509
0.22087206 0.96962906 0.10504771 -47.40265504
-0.06698246 -0.09237253 0.99346901 20.50963257
Axis -0.39364209 0.22237917 0.89196043
Axis point 224.19644734 101.72027326 0.00000000
Rotation angle (degrees) 14.52255453
Shift along axis -4.37660255
> volume #1 level 0.2508
> fitmap #2 inMap #3
Fit map cryosparc_P36_J252_009_volume_map.mrc in map
cryosparc_P33_J447_010_volume_map.mrc using 38073 points
correlation = 0.5009, correlation about mean = 0.2777, overlap = 352.6
steps = 140, shift = 10.2, angle = 5.77 degrees
Position of cryosparc_P36_J252_009_volume_map.mrc (#2) relative to
cryosparc_P33_J447_010_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99675591 0.04955250 0.06342093 -19.19200642
-0.04563575 0.99704569 -0.06178414 10.07330266
-0.06629512 0.05868945 0.99607254 -4.95882203
Axis 0.59937153 0.64535393 -0.47357373
Axis point -109.86594214 0.00000000 271.91185174
Rotation angle (degrees) 5.76795924
Shift along axis -2.65392885
> volume #3 level 0.09285
> hide #!1 models
> select #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.049691,0.9956,-0.079422,4.8363,0.99731,-0.053745,-0.049753,9.2765,-0.053803,-0.076736,-0.9956,346.91
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.049691,0.9956,-0.079422,0.21484,0.99731,-0.053745,-0.049753,4.7202,-0.053803,-0.076736,-0.9956,303.9
> view matrix models
> #2,0.049691,0.9956,-0.079422,-9.2559,0.99731,-0.053745,-0.049753,-3.1061,-0.053803,-0.076736,-0.9956,305.95
> view matrix models
> #2,0.049691,0.9956,-0.079422,-10.445,0.99731,-0.053745,-0.049753,-2.1416,-0.053803,-0.076736,-0.9956,305.24
> fitmap #2 inMap #3
Fit map cryosparc_P36_J252_009_volume_map.mrc in map
cryosparc_P33_J447_010_volume_map.mrc using 38073 points
correlation = 0.9472, correlation about mean = 0.7393, overlap = 1292
steps = 148, shift = 3.45, angle = 12.5 degrees
Position of cryosparc_P36_J252_009_volume_map.mrc (#2) relative to
cryosparc_P33_J447_010_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.24673047 0.96908414 0.00010384 -50.62573244
0.96908413 -0.24673048 0.00014336 25.75388873
0.00016455 0.00006526 -0.99999999 288.55337215
Axis -0.78953261 -0.61370861 -0.00008531
Axis point 0.00000000 32.55731200 144.27878563
Rotation angle (degrees) 179.99716603
Shift along axis 24.14066824
> view matrix models
> #2,0.24673,0.96908,0.00010384,-47.434,0.96908,-0.24673,0.00014336,22.53,0.00016455,6.526e-05,-1,283.2
> ui mousemode right zoom
> volume #2 level 0.09951
> transparency sel 50
> select clear
> volume #3 level 0.1836
> volume #2 level 0.1367
> volume #3 level 0.1848
> volume #3 level 0.1176
> volume #2 level 0.08373
> volume #3 level 0.09168
> volume #2 level 0.08034
> volume #3 level 0.1058
> volume #2 level 0.09951
> volume #2 level 0.05329
> volume #3 level 0.06221
> hide #!2 models
> volume #3 level 0.09875
> open /Users/colinmuir/Downloads/cryosparc_P33_J447_010_volume_map_sharp.mrc
Opened cryosparc_P33_J447_010_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.86, shown at level 0.0478, step 2, values float32
> volume #3 step 1
> hide #!4 models
> show #!2 models
> volume #2 level 0.08147
> hide #!2 models
> open
> /Users/colinmuir/Documents/phenix/CM25/RealSpaceRefine_13/RSR9_dockedJ442_real_space_refined_010_real_space_refined_013.pdb
Chain information for
RSR9_dockedJ442_real_space_refined_010_real_space_refined_013.pdb #5
---
Chain | Description
A B D | No description available
C | No description available
> hide #!3 models
> select /A:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> select up
5652 atoms, 5768 bonds, 681 residues, 1 model selected
> select clear
> select /A:231
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> select up
5652 atoms, 5768 bonds, 681 residues, 1 model selected
> select down
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel light sea green
> select clear
[Repeated 1 time(s)]Drag select of 5 residues
> select up
727 atoms, 738 bonds, 89 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel light sea green
> select clear
> select /B:270
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
216 atoms, 224 bonds, 26 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> select /C:276
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /B:230
21 atoms, 21 bonds, 2 residues, 1 model selected
> select up
943 atoms, 962 bonds, 115 residues, 1 model selected
> select up
2830 atoms, 2888 bonds, 341 residues, 1 model selected
> color sel orange
> select clear
> show #!3 models
> color zone #3 near #5 distance 5.16
> surface dust #3 size 8.6
> ui tool show "Hide Dust"
> surface dust #3 size 8.36
> surface dust #3 size 2.07
> volume #3 level 0.06185
> ui tool show "Segment Map"
Segmenting cryosparc_P33_J447_010_volume_map.mrc, density threshold 0.061847
Only showing 60 of 98 regions.
Showing 60 of 98 region surfaces
1267 watershed regions, grouped to 98 regions
Showing cryosparc_P33_J447_010_volume_map.seg - 98 regions, 60 surfaces
> hide #!6 models
> show #!6 models
> hide #!6 models
> ui tool show "Surface Zone"
> surface zone #3 nearAtoms #5 distance 5.16
> surface zone #3 nearAtoms #5 distance 4.93
> surface zone #3 nearAtoms #5 distance 3.24
> surface zone #3 nearAtoms #5 distance 3.08
> surface zone #3 nearAtoms #5 distance 3.9
> surface zone #3 nearAtoms #5 distance 4
> surface zone #3 nearAtoms #5 distance 5.32
> volume #3 level 0.07629
> surface dust #3 size 8.6
[Repeated 1 time(s)]
> ui tool show "Color Zone"
> surface unzone #3
> volume #3 level 0.11
> color zone #3 near #5 distance 5.13
> color zone #3 near #5 distance 4.94
> volume #3 level 0.05898
> color zone #3 near #5 distance 5.13
> color zone #3 near #5 distance 7.19
> volume #3 level 0.09361
> volume splitbyzone #3
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #7.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #7.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #7.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0936, step 1, values float32
> surface dust #7.2 size 8.6
> surface dust #7.3 size 8.6
> hide #5 models
> volume #3 level 0.06667
> volume #7.2 level 0.0667
> volume #7.3 level 0.0667
> volume #7.3 level 0.0936
> volume #7.2 level 0.06766
> volume #7.2 level 0.0936
> ui tool show "Side View"
> set bgColor white
> set bgColor #ffffff00
> save "/Users/colinmuir/Desktop/MCU alone
> map/Figures/MCU_alone_DimerDimerColor.cxs"
——— End of log from Fri Sep 6 18:02:51 2024 ———
opened ChimeraX session
Showing cryosparc_P33_J447_010_volume_map.seg - 98 regions, 60 surfaces
> hide #!7.2 models
> show #!7.2 models
> hide #!7.3 models
> show #!7.3 models
> hide #!6 models
> show #5 models
> hide #!7.2 models
> hide #!7.3 models
> select /B:277
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
216 atoms, 224 bonds, 26 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel forest green
> select clear
[Repeated 2 time(s)]Drag select of 9 residues
> select clear
Drag select of 4 residues
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel hot pink
> color sel orange red
> show #!7.2 models
> hide #!7.2 models
> show #!7.3 models
> hide #!7.3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7.1 models
> show #!7.2 models
> show #!7.3 models
> show #!6 models
> hide #!6 models
> hide #5 models
> show #5 models
> show #!3 models
> hide #!3 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 3 maps.
> select clear
> hide #!7 models
> hide #!7.1 models
> hide #!7.2 models
> hide #!7.3 models
> show #!3 models
> hide #5 models
> show #5 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> color zone #3 near #5 distance 5.16
> ui tool show "Segment Map"
> ui tool show "Color Zone"
> color zone #3 near #5 distance 5.18
> color zone #3 near #5 distance 4.91
> color zone #3 near #5 distance 4.83
> color zone #3 near #5 distance 3.72
> volume splitbyzone #3
Opened cryosparc_P33_J447_010_volume_map.mrc 0 as #1.1, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 1 as #1.2, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 2 as #1.3, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 3 as #1.4, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
Opened cryosparc_P33_J447_010_volume_map.mrc 4 as #1.5, grid size 320,320,320,
pixel 0.86, shown at level 0.0667, step 1, values float32
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> surface dust #1.2 size 8.6
> surface dust #1.3 size 8.6
> surface dust #1.4 size 8.6
> surface dust #1.5 size 8.6
> show #!1.1 models
> hide #!1.5 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> transparency #1.1.1 50
> volume #1.1 level 0.04526
> volume #1.1 color #ebebeb
> volume #1.1 color white
> transparency #1.1.1 50
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> lighting soft
[Repeated 1 time(s)]
> graphics silhouettes true
> graphics silhouettes false
> show #!1.2 models
> hide #!1.2 models
> lighting simple
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> surface dust #1.1 size 8.6
> surface dust #1.2 size 8.6
> surface dust #1.3 size 8.6
> surface dust #1.4 size 8.6
> surface dust #1.5 size 8.6
> hide #5 models
> hide #!1.1 models
> ui tool show "Side View"
> volume #1.1 level 0.04312
> hide #!1.1 models
> lighting soft
> volume #1.1 color #ebebeb
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> transparency #1.1.1 50
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> graphics silhouettes true
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> select #1.1
4 models selected
> graphics selection color black
> graphics silhouettes false
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> select clear
> graphics selection color green
> color #1.1 silver models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> lighting soft
> color #1.1 #ebebebff models
> color #1.1 #ebebeb42 models
> color #1.1 #ebebeb3e models
> color #1.1 #ebebeb3d models
> color #1.1 #ebebeb34 models
> graphics silhouettes true
> color #1.1 #ebebeb36 models
> graphics silhouettes width 1
> graphics silhouettes width 0.5
> graphics silhouettes width 0.75
> graphics silhouettes width 1
> graphics silhouettes depthJump 0.01
> graphics silhouettes depthJump 0.03
> graphics silhouettes depthJump 0.05
> graphics silhouettes depthJump 0.07
> graphics silhouettes depthJump 0.05
> graphics silhouettes depthJump 0.03
> color #1.1 #ebebeb1f models
> color #1.1 #ebebeb00 models
> graphics silhouettes depthJump 0.01
> graphics silhouettes false
> color #1.1 #ebebeb34 models
> color #1.1 #d6d6d6ff models
> transparency #1.1.1#1.2.1#1.3.1#1.4.1#1.5.1 50
> transparency #1.1.1#1.2.1#1.3.1#1.4.1#1.5.1 0
> color #1.1 #ebebebff models
> color #1.1 #ebebeb00 models
> graphics silhouettes true
> volume #1.1 level 0.04269
> graphics silhouettes depthJump 0.03
> color #1.5 #76d6ffff models
> color #1.5 #73fdffff models
> color #1.5 #76d6ffff models
> color #1.2 #ff7e79ff models
> volume #1.4 color #ffd479
> volume #1.4 color #ffbe3d
> volume #1.4 color #ffbf27
> volume #1.1 level 0.05382
> volume #1.1 level 0.04526
> volume #1.1 level 0.06667
> volume #1.1 level 0.04526
> color zone #3 near #5 distance 2.9
> color zone #3 near #5 distance 2.87
> color zone #3 near #5 distance 3.17
> color #1.5 #3fb3ffff models
> color #1.5 #0096ffff models
> color #1.5 #00a8ffff models
> color #1.5 #00aaffff models
> surface dust #1.1 size 8.6
> surface dust #1.2 size 8.6
> surface dust #1.3 size 8.6
> surface dust #1.4 size 8.6
> surface dust #1.5 size 8.6
> surface dust #1.1 size 8.6
> surface dust #1.2 size 8.6
> surface dust #1.3 size 8.6
> surface dust #1.4 size 8.6
> surface dust #1.5 size 8.6
> surface dust #1.1 size 8.6
> surface dust #1.2 size 8.6
> surface dust #1.3 size 8.6
> surface dust #1.4 size 8.6
> surface dust #1.5 size 8.6
> surface dust #1.1 size 8.6
> surface dust #1.2 size 8.6
> surface dust #1.3 size 8.6
> surface dust #1.4 size 8.6
> surface dust #1.5 size 8.6
> ui tool show "Hide Dust"
> surface undust #1.1
> color zone #3 near #5 distance 3.2
> color zone #3 near #5 distance 3.47
[Repeated 1 time(s)]
> color zone #3 near #5 distance 3.37
> color zone #3 near #5 distance 5.57
> surface undust #1.1
> surface dust #1.1 size 5.43
> surface dust #1.1 size 5.24
> surface dust #1.1 size 4.86
> surface dust #1.1 size 5.11
> surface dust #1.1 size 3.7
> surface dust #1.1 size 3.93
> surface dust #1.1 size 2.25
> surface dust #1.1 size 2.27
> surface dust #1.1 size 1.95
> surface dust #1.1 size 2.02
> surface dust #1.1 size 2.63
> surface dust #1.1 size 2.65
> surface dust #1.1 size 3.79
> surface dust #1.1 size 3.86
> surface dust #1.1 size 5.16
> surface dust #1.1 size 4.86
> surface dust #1.1 size 4.9
> surface dust #1.1 size 4.24
> surface dust #1.1 size 4.31
> surface dust #1.1 size 6.33
> save "/Users/colinmuir/Desktop/MCU Paper Figures/MCU Y289S alone.cxs"
> includeMaps true
——— End of log from Sat Nov 9 12:42:50 2024 ———
opened ChimeraX session
Showing cryosparc_P33_J447_010_volume_map.seg - 98 regions, 60 surfaces
> hide #!6 models
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_micelleSilhouette_Fig1A.png" width 1500 height 1696
> supersample 3 transparentBackground true
> show #5 models
> hide #!1 models
> dssp
> save "/Users/colinmuir/Desktop/MCU Paper Figures/Y289S_cartoon_Fig1A.png"
> width 1500 height 1696 supersample 3 transparentBackground true
> color #1.4 #ffcc33ff models
> color #1.4 #0066ffff models
> color #1.3 #00ccffff models
> show #!1 models
> hide #5 models
> color #1.2 blue models
> ui mousemode right zoom
> color #1.3 #99ccffff models
> color #1.3 #5ac8f5ff models
> color #1.3 #76d6ffff models
> color #1.3 #5ac8f5ff models
> color #1.3 #63e6e2ff models
Unsupported scale factor (0.000000) detected on Display1
[Repeated 1 time(s)]
> open /Users/colinmuir/Downloads/cryosparc_P33_J463_map_sharp.mrc
Opened cryosparc_P33_J463_map_sharp.mrc as #2, grid size 320,320,320, pixel
0.86, shown at level 0.000232, step 2, values float32
> hide #!1 models
> volume #2 step 1
> volume #2 level 0.1118
> ui tool show "Hide Dust"
> surface dust #2 size 5.16
> surface dust #2 size 4.98
> surface dust #2 size 11.03
> volume #2 level 0.01103
> show #5 models
> ui tool show "Color Zone"
> color zone #2 near #5 distance 5.16
> color zone #2 near #5 distance 5.34
> color zone #2 near #5 distance 4.46
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> color zone #2 near #5 distance 4.59
> color zone #2 near #5 distance 5.98
> volume #2 level 0.1155
> hide #5 models
> volume #2 level 0.02212
> volume #2 level 0.009062
> volume splitbyzone #2
Opened cryosparc_P33_J463_map_sharp.mrc 0 as #8.1, grid size 320,320,320,
pixel 0.86, shown at level 0.00906, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 1 as #8.2, grid size 320,320,320,
pixel 0.86, shown at level 0.00906, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 2 as #8.3, grid size 320,320,320,
pixel 0.86, shown at level 0.00906, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 3 as #8.4, grid size 320,320,320,
pixel 0.86, shown at level 0.00906, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 4 as #8.5, grid size 320,320,320,
pixel 0.86, shown at level 0.00906, step 1, values float32
> surface dust #8.2 size 8.6
> surface dust #8.3 size 8.6
> surface dust #8.4 size 8.6
> surface dust #8.5 size 8.6
> surface dust #8.2 size 8.52
> surface dust #8.2 size 10.76
> surface dust #8.2 size 10.29
> surface dust #8.2 size 17.14
> surface dust #8.3 size 8.91
> surface dust #8.3 size 35.12
> volume #8.3 level 0.03698
> volume #8.2 level 0.037
> surface dust #8.4 size 9.07
> surface dust #8.4 size 11.05
> volume #8.4 level 0.0037
> volume #8.4 level 0.037
> volume #8.5 level 0.037
> volume #8.5 level 0.0283
> volume #8.5 level 0.037
> surface dust #8.2 size 17.45
> surface dust #8.2 size 6.51
> volume #8.2 level 0.03142
> volume #8.2 level 0.03973
> color zone #2 near #5 distance 4.55
[Repeated 1 time(s)]
> color zone #2 near #5 distance 4.64
> color zone #2 near #5 distance 3.95
> color zone #2 near #5 distance 4.06
> color zone #2 near #5 distance 3.6
[Repeated 1 time(s)]
> surface dust #8.2 size 6.63
> surface dust #8.2 size 6.81
> volume #8.2 level 0.008568
> ui tool show "Map Eraser"
> ui tool show "Side View"
> ui mousemode right zoom
[Repeated 1 time(s)]
Can only have one displayed volume when erasing
> ui mousemode right translate
[Repeated 1 time(s)]
> ui tool show "Map Eraser"
[Repeated 1 time(s)]
> select #9
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,132.68,0,1,0,107.5,0,0,1,151.85
> view matrix models #9,1,0,0,131.63,0,1,0,105.38,0,0,1,151.71
> view matrix models #9,1,0,0,132.69,0,1,0,107.39,0,0,1,160.44
> view matrix models #9,1,0,0,130.59,0,1,0,105.08,0,0,1,163.71
> view matrix models #9,1,0,0,130.72,0,1,0,106.27,0,0,1,170.27
> view matrix models #9,1,0,0,133.16,0,1,0,109.99,0,0,1,177.66
> close #8
> hide #9 models
> select subtract #9
Nothing selected
> show #!2 models
> ui mousemode right zoom
> volume #2 level 0.02212
> volume #2 level 0.037
> color zone #2 near #5 distance 3.63
> color zone #2 near #5 distance 5
> color zone #2 near #5 distance 5.19
> color zone #2 near #5 distance 5
> volume splitbyzone #2
Opened cryosparc_P33_J463_map_sharp.mrc 0 as #8.1, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 1 as #8.2, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 2 as #8.3, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 3 as #8.4, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
Opened cryosparc_P33_J463_map_sharp.mrc 4 as #8.5, grid size 320,320,320,
pixel 0.86, shown at level 0.037, step 1, values float32
> hide #!8.1 models
> surface dust #8.4 size 5.16
> surface dust #8.4 size 4.98
> surface dust #8.4 size 7
> volume #8.4 level 0.0855
> volume #8.2 level 0.01623
> volume #8.2 level 0.02661
> surface dust #8.3 size 5.16
> surface dust #8.2 size 5.16
> surface dust #8.2 size 5.45
> surface dust #8.2 size 11.98
> surface dust #8.2 size 8.6
> surface dust #8.3 size 8.6
> surface dust #8.4 size 8.6
> surface dust #8.5 size 8.6
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> show #!2 models
> hide #!1.5 models
> hide #!2 models
> select add #8
13 models selected
Can only have one displayed volume when erasing
> select clear
Can only have one displayed volume when erasing
[Repeated 4 time(s)]
> select add #9
1 model selected
> select subtract #9
Nothing selected
Can only have one displayed volume when erasing
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
[Repeated 2 time(s)]
> hide #!8.2 models
> hide #!8.4 models
> hide #!8.5 models
> volume erase #8.3 center 105.29,144.16,156.06 radius 8.6688
> volume erase #8.3 center 122.67,128.33,150.95 radius 2.4768
> volume erase #8.3 center 122.62,127.46,153.84 radius 2.4768
> volume erase #8.3 center 122.91,127.03,156.63 radius 2.4768
> show #!8.2 models
> show #!8.4 models
> show #!8.5 models
> hide #!8.5 models
> hide #!8.4 models
> hide #!8.3 models
> volume erase #8.2 center 141.03,110.99,156.13 radius 2.4768
> volume erase #8.2 center 136.73,109.57,154.38 radius 2.4768
> show #!8.1 models
> hide #!8.1 models
> show #!8.1 models
> hide #!8.1 models
> show #!8.3 models
> show #!8.4 models
> show #!8.5 models
> hide #!8.4 models
> hide #!8.3 models
> hide #!8.2 models
> volume erase #8.5 center 127.24,152.88,154.09 radius 2.4768
> show #!8.4 models
> show #!8.3 models
> show #!8.2 models
> ui mousemode right zoom
> color #8.2 #0433ffff models
> color #8.2 #011993ff models
> color #8.2 #0433ffff models
> color #8.3 #73fdffff models
> color #8.4 #00fdffff models
> color #8.5 #005493ff models
> color #8.2 #005493ff models
> color #8.5 #0433ffff models
> volume #8.2 level 0.037
> volume #8.4 level 0.037
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_deepEMhancer_blue_Fig1A.png" width 1500 height 1788
> supersample 3 transparentBackground true
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
> hide #!8.5 models
> hide #!8.4 models
> hide #!8.3 models
> volume erase #8.2 center 151.89,108.02,124.59 radius 7.7056
> hide #9 models
> show #9 models
> hide #9 models
> ui mousemode right zoom
> show #!8.3 models
> show #!8.4 models
> show #!8.5 models
> volume #8.3 level 0.036
> volume #8.3 level 0.035
> volume #8.3 level 0.036
> volume #8.4 level 0.036
> volume #8.5 level 0.036
> volume #8.2 level 0.036
> volume #8.2 level 0.008996
> volume #8.3 level 0.09
> volume #8.3 level 0.009
> volume #8.3 level 0.01
> show #!8.1 models
> hide #!8.1 models
> hide #!8.2 models
> show #!8.1 models
> hide #!8 models
> show #!8 models
> hide #!8.1 models
> hide #!8.5 models
> hide #!8.4 models
> hide #!8.3 models
> show #!2 models
> surface dust #2 size 8.6
[Repeated 4 time(s)]
> surface dust #2 size 8.52
> surface dust #2 size 33.57
> surface dust #2 size 37.7
[Repeated 1 time(s)]
> surface dust #2 size 38.39
> surface dust #2 size 87.58
> color zone #2 near #5 distance 4.72
> color zone #2 near #5 distance 5.81
> hide #!2 models
> show #5 models
> select /A:237
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
128 atoms, 132 bonds, 15 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> select up
5652 atoms, 5768 bonds, 681 residues, 1 model selected
> select down
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cyan
> select /B:267
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
171 atoms, 177 bonds, 21 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel dark blue
> color sel navy
> color sel blue
> color sel teal
> color sel blue
> select /C:296
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select /C:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
141 atoms, 144 bonds, 16 residues, 1 model selected
> select up
1419 atoms, 1448 bonds, 171 residues, 1 model selected
> color sel midnight blue
> color sel steel blue
> color sel cornflower blue
> color sel dodger blue
> select /D:228
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
84 atoms, 85 bonds, 10 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel dark cyan
> show #!2 models
> color zone #2 near #5 distance 5.81
> hide #!2 models
> select /C:301
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
141 atoms, 144 bonds, 16 residues, 1 model selected
> select up
1419 atoms, 1448 bonds, 171 residues, 1 model selected
> color sel cyan
> select /A:237
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
128 atoms, 132 bonds, 15 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel dark cyan
> color sel teal
> color sel steel blue
> color sel cadet blue
> color sel royal blue
> color sel light sea green
> color sel dodger blue
> color sel dark turquoise
> color sel dodger blue
> show #!2 models
> color zone #2 near #5 distance 5.81
> color zone #2 near #5 distance 5.7
> color zone #2 near #5 distance 7.63
> hide #!2 models
> select /C:300
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
141 atoms, 144 bonds, 16 residues, 1 model selected
> select up
1419 atoms, 1448 bonds, 171 residues, 1 model selected
> color sel aquamarine
> color sel light cyan
> show #!2 models
> color zone #2 near #5 distance 7.63
> hide #!2 models
> color sel deep sky blue
> show #!2 models
> color zone #2 near #5 distance 7.63
> color sel azure
> color zone #2 near #5 distance 7.63
> color sel light sky blue
> color zone #2 near #5 distance 7.63
> hide #!2 models
> select /A:237
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /D:239
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
105 atoms, 107 bonds, 13 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel dodger blue
> select /A:241
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
128 atoms, 132 bonds, 15 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel dark blue
> color sel medium blue
> color sel dark blue
> color sel midnight blue
> show #!2 models
> color zone #2 near #5 distance 7.63
> hide #!2 models
> select /C:300
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
141 atoms, 144 bonds, 16 residues, 1 model selected
> select up
1419 atoms, 1448 bonds, 171 residues, 1 model selected
> show #!2 models
> color sel pale turquoise
> color zone #2 near #5 distance 7.63
> color sel light blue
[Repeated 1 time(s)]
> color zone #2 near #5 distance 7.63
> color sel powder blue
[Repeated 1 time(s)]
> color zone #2 near #5 distance 7.63
> color sel light steel blue
[Repeated 1 time(s)]
> color zone #2 near #5 distance 7.63
> color sel powder blue
[Repeated 1 time(s)]
> color zone #2 near #5 distance 7.63
> hide #!2 models
> select /D:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
84 atoms, 85 bonds, 10 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel blue
> select /B:234
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
213 atoms, 216 bonds, 27 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel dodger blue
> select /A:240
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
128 atoms, 132 bonds, 15 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel slate blue
> show #!2 models
> color zone #2 near #5 distance 7.63
> hide #!2 models
> show #!2 models
> color sel steel blue
> color zone #2 near #5 distance 7.63
> color sel dark blue
> color zone #2 near #5 distance 7.63
> color sel sky blue
> color zone #2 near #5 distance 7.63
> color sel steel blue
> color zone #2 near #5 distance 7.63
> color sel royal blue
[Repeated 1 time(s)]
> color zone #2 near #5 distance 7.63
> hide #!2 models
> select /C:301
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
141 atoms, 144 bonds, 16 residues, 1 model selected
> select up
1419 atoms, 1448 bonds, 171 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #fffcfdff
> color sel #fffdfeff
[Repeated 2 time(s)]
> color sel #fffefeff
[Repeated 2 time(s)]
> color sel #ffffffff
> color sel #fefffeff
> color sel #fdfffeff
[Repeated 1 time(s)]
> color sel #fcfffeff
> color sel #fbfffeff
> color sel #fafffeff
[Repeated 1 time(s)]
> color sel #f7fffeff
[Repeated 2 time(s)]
> color sel #f5fffeff
> color sel #f4ffffff
[Repeated 3 time(s)]
> color sel #f5ffffff
> color sel #f7ffffff
> color sel #f8ffffff
> color sel #f9ffffff
> color sel #fcffffff
> color sel #fdffffff
> color sel #ffffffff
[Repeated 1 time(s)]
> color sel #fffefeff
> color sel #fffdfeff
[Repeated 2 time(s)]
> color sel #fffdffff
[Repeated 1 time(s)]
> color sel #fbfbffff
> color sel #f9fbffff
[Repeated 1 time(s)]
> color sel #f3fbffff
> color sel #f1faffff
> color sel #effaffff
> color sel #ebf9ffff
> color sel #e9f9ffff
[Repeated 1 time(s)]
> color sel #e5f9ffff
> color sel #e2f9ffff
> color sel #e1f9ffff
> color sel #e0f9ffff
> color sel #def9ffff
[Repeated 1 time(s)]
> color sel #ddf8ffff
[Repeated 2 time(s)]
> color sel #dcf8ffff
[Repeated 2 time(s)]
> color sel #dbf8ffff
> color sel #dcf8ffff
[Repeated 2 time(s)]
> color sel #ddf8ffff
[Repeated 1 time(s)]
> color sel #def8ffff
> color sel #dff8ffff
[Repeated 1 time(s)]
> color sel #e2f8ffff
[Repeated 1 time(s)]
> color sel #e3f9ffff
> color sel #e4f9ffff
[Repeated 1 time(s)]
> color sel #e3f9ffff
[Repeated 1 time(s)]
> color sel #e2f9ffff
> color sel #e1f9ffff
[Repeated 1 time(s)]
> color sel #dff9ffff
[Repeated 1 time(s)]
> color sel #def9ffff
[Repeated 1 time(s)]
> color sel #ddfaffff
> color sel #dafbffff
> color sel #d9fcffff
> color sel #d8fcffff
[Repeated 1 time(s)]
> color sel #d8fdffff
> color sel #d7fdffff
> color sel #d5feffff
> color sel #d4ffffff
[Repeated 3 time(s)]
> color sel #d3fffeff
[Repeated 1 time(s)]
> color sel #d3fffdff
> color sel #d2fffdff
[Repeated 2 time(s)]
> color sel #d2fffcff
[Repeated 2 time(s)]
> color sel #d2fffbff
[Repeated 2 time(s)]
> color sel #d3fffbff
> color sel #d3fffaff
> color sel #d2fff9ff
> color sel #d3fff8ff
> color sel #d3fff7ff
[Repeated 2 time(s)]
> color sel #d3fff6ff
[Repeated 3 time(s)]
> color sel #d3fff4ff
> color sel #d3fff2ff
[Repeated 1 time(s)]
> color sel #d3fff1ff
[Repeated 1 time(s)]
> color sel #d4fff2ff
> color sel #d3fff2ff
[Repeated 1 time(s)]
> color sel #d4fff4ff
[Repeated 1 time(s)]
> color sel #d4fff6ff
> color sel #d5fff9ff
[Repeated 1 time(s)]
> color sel #d5fffaff
> color sel #d5fffcff
> color sel #d5fffdff
[Repeated 1 time(s)]
> color sel #d5feffff
[Repeated 1 time(s)]
> color sel #d5fdffff
> color sel #d6fcffff
> color sel #d6fbffff
> color sel #d6faffff
> color sel #d7f8ffff
[Repeated 1 time(s)]
> color sel #d7f7ffff
> color sel #d7f6ffff
> color sel #d7f5ffff
> color sel #d7f0ffff
> color sel #d7edffff
> color sel #d7ecffff
> color sel #d6ebffff
> color sel #d6eaffff
[Repeated 1 time(s)]
> color sel #d5e8ffff
> color sel #d5e7ffff
[Repeated 1 time(s)]
> color sel #d4e6ffff
> color sel #d4e5ffff
> color sel #d3e5ffff
> color sel #d2e4ffff
> color sel #d2e3ffff
[Repeated 1 time(s)]
> color sel #d1e3ffff
> color sel #d0e2ffff
> color sel #cee1ffff
> color sel #cde1ffff
> color sel #c8dfffff
> color sel #c4dfffff
[Repeated 1 time(s)]
> color sel #c3e0ffff
> color sel #c2e0ffff
[Repeated 1 time(s)]
> color sel #c1e0ffff
> color sel #bfe2ffff
[Repeated 1 time(s)]
> color sel #bee4ffff
[Repeated 1 time(s)]
> color sel #bee5ffff
> color sel #bee8ffff
> color sel #bee9ffff
[Repeated 1 time(s)]
> color sel #beebffff
[Repeated 1 time(s)]
> color sel #beecffff
[Repeated 2 time(s)]
> color sel #beedffff
> color sel #bdedffff
[Repeated 1 time(s)]
> color sel #bcedffff
> color sel #bcecffff
[Repeated 1 time(s)]
> color sel #bbecffff
[Repeated 1 time(s)]
> color sel #baecffff
> color sel #b9ebffff
[Repeated 1 time(s)]
> color sel #b6ebffff
> color sel #b6eaffff
> color sel #b5eaffff
> color sel #b2e8ffff
[Repeated 1 time(s)]
> color sel #b1e8ffff
> color sel #b0e7ffff
[Repeated 1 time(s)]
> color sel #afe6ffff
[Repeated 1 time(s)]
> color sel #ace4ffff
[Repeated 1 time(s)]
> color sel #abe4ffff
> color sel #aae3ffff
> color sel #a9e2ffff
[Repeated 2 time(s)]
> color sel #a8e2ffff
> color sel #a7e2ffff
> color sel #a7e1ffff
> color sel #a5e0ffff
> color sel #a4e0ffff
[Repeated 1 time(s)]
> color sel #a1deffff
> color sel #a0deffff
> color sel #9fddffff
> color sel #9bdbffff
> color sel #9adbffff
> color sel #99dbffff
> color sel #96daffff
> color sel #91daffff
> color sel #87d9ffff
> color sel #82d9ffff
> color sel #80d9ffff
> color sel #7fd9ffff
> color sel #7ed9ffff
[Repeated 1 time(s)]
> color sel #7ad9ffff
> color sel #79d9ffff
[Repeated 1 time(s)]
> color sel #78d9ffff
[Repeated 1 time(s)]
> color sel #77daffff
> color sel #77d9ffff
[Repeated 1 time(s)]
> color sel #76d9ffff
> color sel #74daffff
[Repeated 1 time(s)]
> color sel #73daffff
> color sel #72dbffff
[Repeated 1 time(s)]
> color sel #71dcffff
> color sel #71ddffff
[Repeated 1 time(s)]
> color sel #71deffff
> color sel #72dfffff
[Repeated 2 time(s)]
> color sel #75e0ffff
> color sel #7ce1ffff
> color sel #87e1ffff
> color sel #9cdfffff
> color sel #9fdfffff
> color sel #a3dfffff
> color sel #a4dfffff
> color sel #a5dfffff
[Repeated 1 time(s)]
> color sel #a7dfffff
[Repeated 1 time(s)]
> color sel #a8dfffff
> color sel #aae0ffff
[Repeated 1 time(s)]
> color sel #abe0ffff
[Repeated 1 time(s)]
> color sel #ace0ffff
[Repeated 1 time(s)]
> color sel #ade0ffff
> color sel #aee1ffff
> color sel #afe1ffff
[Repeated 1 time(s)]
> color sel #b0e0ffff
> color sel #b1e0ffff
> color sel #b2e0ffff
> color sel #b3e1ffff
[Repeated 1 time(s)]
> color sel #b4e1ffff
[Repeated 1 time(s)]
> color sel #b6e0ffff
[Repeated 2 time(s)]
> color sel #b7dfffff
[Repeated 2 time(s)]
> color sel #b7e0ffff
> color sel #b8e2ffff
> color sel #b8e4ffff
[Repeated 2 time(s)]
> color sel #b7e5ffff
[Repeated 1 time(s)]
> color sel #b7e7ffff
> color sel #b7e8ffff
> color sel #b6e9ffff
[Repeated 1 time(s)]
> color sel #b6eaffff
> color sel #b6ebffff
[Repeated 1 time(s)]
> color sel #b6ecffff
> color sel #b6edffff
> color sel #b5f0ffff
> color sel #b4f3ffff
> color sel #b4f4ffff
> color sel #b4f5ffff
> color sel #b3f8ffff
> color sel #b2f9ffff
> color sel #b3faffff
> color sel #b2feffff
> color sel #b1feffff
> color sel #b1fffcff
> color sel #b1fffaff
> color sel #b1fff9ff
> color sel #b0fff7ff
> color sel #b1fff6ff
[Repeated 1 time(s)]
> color sel #b1fff4ff
> color sel #b1fff3ff
> color sel #b1fff2ff
> color sel #b1fff0ff
> color sel #b2ffefff
[Repeated 1 time(s)]
> color sel #b2ffeeff
[Repeated 1 time(s)]
> color sel #b2ffedff
> color sel #b3ffedff
> color sel #b3ffecff
[Repeated 1 time(s)]
> color sel #b4ffebff
[Repeated 2 time(s)]
> color sel #b5ffebff
> color sel #b5ffeaff
> color sel #b6ffe9ff
> color sel #b7ffe9ff
[Repeated 1 time(s)]
> color sel #b8ffe9ff
[Repeated 1 time(s)]
> color sel #baffe8ff
[Repeated 2 time(s)]
> color sel #bbffe8ff
> color sel #bfffe7ff
> color sel #c0ffe7ff
[Repeated 2 time(s)]
> color sel #c1ffe7ff
> color sel #c2ffe7ff
[Repeated 1 time(s)]
> color sel #c2ffe6ff
> color sel #c3ffe6ff
> color sel #c3ffe5ff
> color sel #c3ffe4ff
> color sel #c3ffe3ff
> color sel #c2ffe1ff
> color sel #c2ffdfff
> color sel #c1ffdfff
> color sel #c1ffdeff
> color sel #c1ffddff
[Repeated 1 time(s)]
> color sel #c0ffdcff
[Repeated 2 time(s)]
> color sel #c0ffdbff
> color sel #bfffdbff
[Repeated 2 time(s)]
> color sel #bdffdbff
> color sel #bcffdbff
[Repeated 2 time(s)]
> color sel #baffdbff
> color sel #baffdcff
> color sel #b5ffddff
[Repeated 1 time(s)]
> color sel #b4ffddff
[Repeated 1 time(s)]
> color sel #b3ffddff
[Repeated 1 time(s)]
> color sel #b1ffddff
> color sel #afffddff
> color sel #aeffddff
> color sel #abffddff
> color sel #aaffddff
[Repeated 1 time(s)]
> color sel #a9ffddff
[Repeated 1 time(s)]
> color sel #a8ffddff
> color sel #a7ffddff
[Repeated 3 time(s)]
> color sel #a7ffdeff
[Repeated 1 time(s)]
> color sel #a6ffdfff
> color sel #a6ffe1ff
> color sel #a6ffe2ff
[Repeated 2 time(s)]
> color sel #a7ffe3ff
> color sel #a7ffe4ff
> color sel #a8ffe5ff
> color sel #a9ffe6ff
> color sel #aaffe7ff
> color sel #acffeaff
[Repeated 1 time(s)]
> color sel #adffebff
> color sel #b0ffeeff
> color sel #b1ffefff
> color sel #b1fff0ff
> color sel #b6fff5ff
> color sel #b7fff6ff
> color sel #b9fff8ff
> color sel #bcfffaff
> color sel #bdfffbff
> color sel #c1fffeff
> color sel #c2ffffff
> color sel #c2feffff
> color sel #c3fdffff
> color sel #c4fdffff
[Repeated 3 time(s)]
> color sel #c5fcffff
[Repeated 2 time(s)]
> color sel #c5fbffff
> color sel #c6fbffff
[Repeated 1 time(s)]
> color sel #c5fbffff
[Repeated 1 time(s)]
> color sel #c4fbffff
[Repeated 2 time(s)]
> color sel #c4fcffff
> color sel #c3fcffff
> color sel #c2fcffff
[Repeated 1 time(s)]
> color sel #c1fcffff
[Repeated 1 time(s)]
> color sel #c1fbffff
> color sel #c0fbffff
[Repeated 2 time(s)]
> color sel #bffbffff
> color sel #befaffff
[Repeated 2 time(s)]
> color sel #bdfaffff
[Repeated 1 time(s)]
> color sel #bcf9ffff
[Repeated 1 time(s)]
> color sel #bcf8ffff
> color sel #bbf8ffff
> color sel #bbf7ffff
> color sel #baf7ffff
[Repeated 1 time(s)]
> color sel #b9f6ffff
[Repeated 1 time(s)]
> color sel #b8f5ffff
[Repeated 2 time(s)]
> color sel #b7f4ffff
[Repeated 1 time(s)]
> color sel #b7f3ffff
> color sel #b7f2ffff
> color sel #b6f1ffff
[Repeated 1 time(s)]
> color sel #b7f0ffff
> color sel #b6f0ffff
> color sel #b7efffff
> color sel #b7eeffff
[Repeated 1 time(s)]
> color sel #b8edffff
> color sel #b8ecffff
> color sel #b9ebffff
> color sel #bae9ffff
[Repeated 1 time(s)]
> color sel #bbe8ffff
> color sel #bce7ffff
> color sel #bde7ffff
[Repeated 1 time(s)]
> color sel #bee6ffff
> color sel #bee5ffff
> color sel #bfe5ffff
> color sel #bfe4ffff
[Repeated 1 time(s)]
> color sel #c0e4ffff
> color sel #c0e3ffff
[Repeated 2 time(s)]
> color sel #c0e2ffff
[Repeated 1 time(s)]
> color sel #c0e1ffff
> color sel #c0e0ffff
> color sel #c1dfffff
> color sel #c1deffff
[Repeated 2 time(s)]
> color sel #c1ddffff
> color sel #c1daffff
> color sel #bed4ffff
> color sel #bed3ffff
> color sel #bdd2ffff
> color sel #bbcfffff
> color sel #baceffff
> color sel #b9cdffff
> color sel #b8ccffff
> color sel #b7caffff
> color sel #b6c9ffff
> color sel #b6c8ffff
> color sel #b4c6ffff
> color sel #b2c4ffff
> color sel #b2c3ffff
> color sel #b1c3ffff
> color sel #afc1ffff
> color sel #aec0ffff
> color sel #adbfffff
> color sel #abbeffff
> color sel #aabdffff
> color sel #a9bcffff
> color sel #a4baffff
> color sel #a3baffff
> color sel #a2b9ffff
> color sel #9db8ffff
> color sel #9cb7ffff
> color sel #9ab7ffff
> color sel #98b8ffff
> color sel #98b7ffff
> color sel #97b7ffff
[Repeated 1 time(s)]
> color sel #96b7ffff
[Repeated 1 time(s)]
> color sel #96b6ffff
> color sel #95b6ffff
> color sel #93b2ffff
> color sel #91aeffff
> color sel #90acffff
> color sel #8fa9ffff
> color sel #8ea6ffff
> color sel #8ea5ffff
> color sel #8da2ffff
> color sel #8da1ffff
> color sel #8da0ffff
> color sel #8d9fffff
> color sel #8c9fffff
> color sel #8c9effff
> color sel #8c9dffff
> color sel #8b9bffff
> color sel #8b9affff
> color sel #8a98ffff
> color sel #8997ffff
> color sel #8897ffff
> color sel #8699ffff
> color sel #82a0ffff
> color sel #80a2ffff
> color sel #7ba9ffff
> color sel #79afffff
> color sel #79b0ffff
> color sel #79b1ffff
> color sel #79b3ffff
> color sel #79b4ffff
[Repeated 1 time(s)]
> color sel #79b5ffff
> color sel #79b6ffff
> color sel #79b7ffff
> color sel #7ab8ffff
> color sel #7bbbffff
> color sel #7cbdffff
> color sel #7dc0ffff
> color sel #7ec1ffff
> color sel #7ec3ffff
> color sel #80c5ffff
[Repeated 1 time(s)]
> color sel #81c7ffff
> color sel #82c8ffff
> color sel #82c9ffff
> color sel #83c9ffff
> color sel #83cbffff
> color sel #84ccffff
[Repeated 1 time(s)]
> color sel #85cdffff
[Repeated 1 time(s)]
> color sel #85ceffff
> color sel #86d0ffff
[Repeated 1 time(s)]
> color sel #86d1ffff
> color sel #87d4ffff
[Repeated 1 time(s)]
> color sel #87d5ffff
[Repeated 1 time(s)]
> color sel #88d6ffff
> color sel #88d7ffff
> color sel #88d8ffff
> color sel #89ddffff
[Repeated 1 time(s)]
> color sel #8addffff
> color sel #8adeffff
> color sel #8adfffff
[Repeated 1 time(s)]
> color sel #8ae0ffff
[Repeated 1 time(s)]
> color sel #8be1ffff
> color sel #8be3ffff
> color sel #8ce4ffff
> color sel #8ee6ffff
[Repeated 1 time(s)]
> color sel #8ee7ffff
> color sel #8fe7ffff
> color sel #90e8ffff
[Repeated 1 time(s)]
> color sel #91eaffff
> color sel #92eaffff
> color sel #93ebffff
> color sel #94ecffff
> color sel #95edffff
[Repeated 1 time(s)]
> color sel #97eeffff
[Repeated 2 time(s)]
> color sel #98efffff
[Repeated 1 time(s)]
> color sel #99f0ffff
[Repeated 1 time(s)]
> color sel #99f1ffff
> color sel #9af1ffff
> color sel #9af2ffff
> color sel #9bf3ffff
[Repeated 1 time(s)]
> color sel #9cf4ffff
[Repeated 1 time(s)]
> color sel #9cf5ffff
[Repeated 1 time(s)]
> color sel #9df5ffff
> color sel #9df6ffff
> color sel #9ef6ffff
> color sel #9ef7ffff
> color sel #9ff7ffff
[Repeated 1 time(s)]
> color sel #a2f7ffff
> color sel #a4f7ffff
> color sel #a5f7ffff
> color sel #a7f7ffff
> color sel #a8f7ffff
[Repeated 1 time(s)]
> color sel #a9f7ffff
[Repeated 1 time(s)]
> color sel #aaf7ffff
[Repeated 1 time(s)]
> color sel #abf7ffff
> color sel #acf6ffff
[Repeated 1 time(s)]
> color sel #b0f5ffff
> color sel #b1f5ffff
> color sel #b2f5ffff
> color sel #b2f4ffff
[Repeated 2 time(s)]
> color sel #b3f4ffff
> color sel #b3f3ffff
> color sel #b4f3ffff
> color sel #b4f2ffff
> color sel #b4f1ffff
[Repeated 2 time(s)]
> color sel #b3efffff
[Repeated 2 time(s)]
> color sel #b3eeffff
> color sel #b2edffff
> color sel #b1ecffff
> color sel #b0ecffff
> color sel #b0ebffff
> color sel #afebffff
> color sel #aeebffff
> color sel #adebffff
> color sel #adecffff
> color sel #abedffff
> color sel #aaedffff
> color sel #a8eeffff
> color sel #a4efffff
> color sel #a1f0ffff
> color sel #a0f0ffff
> color sel #9ff0ffff
[Repeated 1 time(s)]
> color sel #99f2ffff
> color sel #94f2ffff
> color sel #93f2ffff
> color sel #8df3ffff
[Repeated 1 time(s)]
> color sel #8bf3ffff
> color sel #89f3ffff
> color sel #88f3ffff
> color sel #86f3ffff
> color sel #78f3ffff
> color sel #75f3ffff
> color sel #72f3ffff
> color sel #6af3ffff
> color sel #65f2ffff
> color sel #64f2ffff
> color sel #62f2ffff
> color sel #61f2ffff
> color sel #5af2ffff
> color sel #57f2ffff
> color sel #56f2ffff
> color sel #54f1ffff
> color sel #4df0ffff
> color sel #4bf0ffff
> color sel #48f0ffff
> color sel #40f0ffff
> color sel #3bf0ffff
> color sel #36f0ffff
> color sel #25f1ffff
> color sel #22f1ffff
> color sel #1ff1ffff
> color sel #1bf1ffff
> color sel #19f0ffff
> color sel #18f0ffff
> color sel #17efffff
> color sel #16efffff
> color sel #15efffff
> color sel #11efffff
[Repeated 1 time(s)]
> color sel #10efffff
> color sel #0fefffff
> color sel #0eefffff
> color sel #0defffff
[Repeated 2 time(s)]
> color sel #0cefffff
[Repeated 1 time(s)]
> color sel #09efffff
[Repeated 2 time(s)]
> color sel #08efffff
[Repeated 1 time(s)]
> color sel #07efffff
[Repeated 2 time(s)]
> color sel #08efffff
> color sel #09f0ffff
> color sel #0cf0ffff
> color sel #23f1ffff
> color sel #2ff1ffff
> color sel #33f1ffff
> color sel #40f1ffff
> color sel #45f1ffff
> color sel #49f0ffff
> color sel #53efffff
> color sel #57efffff
> color sel #5aefffff
> color sel #67f0ffff
> color sel #69f0ffff
[Repeated 1 time(s)]
> color sel #6bf1ffff
> color sel #6cf1ffff
> color sel #6df2ffff
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[Repeated 1 time(s)]
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[Repeated 2 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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> color sel #aaeaffff
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> color sel #ade9ffff
> color sel #aee9ffff
> color sel #b0e9ffff
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[Repeated 1 time(s)]
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[Repeated 2 time(s)]
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[Repeated 2 time(s)]
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[Repeated 2 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 2 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 2 time(s)]
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[Repeated 2 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 2 time(s)]
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[Repeated 2 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 3 time(s)]
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> color sel #c3ffeeff
[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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> color sel #c5ffecff
[Repeated 1 time(s)]
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> color sel #c6ffeaff
[Repeated 1 time(s)]
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> color sel #c7ffe8ff
> color sel #c8ffe8ff
> color sel #c7ffe8ff
> color sel #c8ffe7ff
> color sel #c9ffe6ff
> color sel #c9ffe5ff
[Repeated 1 time(s)]
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> color sel #c9ffe3ff
> color sel #caffe3ff
> color sel #caffe2ff
> color sel #caffe1ff
[Repeated 2 time(s)]
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> color sel #cbffe2ff
[Repeated 1 time(s)]
> color sel #cbffe3ff
> color sel #cbffe4ff
> color sel #cbffe6ff
[Repeated 1 time(s)]
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> color sel #caffe8ff
> color sel #caffe9ff
> color sel #caffebff
> color sel #cbffebff
> color sel #caffecff
[Repeated 1 time(s)]
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> color sel #caffeeff
> color sel #c9fff1ff
[Repeated 1 time(s)]
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> color sel #c8fff4ff
[Repeated 1 time(s)]
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> color sel #c6fff7ff
> color sel #c5fff8ff
[Repeated 1 time(s)]
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> color sel #c4fff9ff
[Repeated 1 time(s)]
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> color sel #c3fffaff
> color sel #c3fffbff
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[Repeated 1 time(s)]
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> color sel #c2fffdff
> color sel #c2fffeff
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> color sel #c2feffff
> color sel #c2fdffff
> color sel #c2faffff
[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 2 time(s)]
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> color sel #c2f5ffff
[Repeated 2 time(s)]
> color sel #c2f4ffff
[Repeated 2 time(s)]
> color sel #c1f3ffff
> show #!2 models
> color zone #2 near #5 distance 7.63
> hide #!2 models
> select /A:230
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
87 atoms, 88 bonds, 11 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel medium blue
> color sel #c2f7ffff
> color sel #c1f5ffff
> color sel #c1f3ffff
> color sel #c1f2ffff
> color sel #c0f0ffff
> color sel #bce9ffff
> color sel #b9e3ffff
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> color sel #acceffff
> color sel #a7c4ffff
> color sel #a3beffff
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> color sel #91a3ffff
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> color sel #7f8bffff
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> color sel #7076ffff
> color sel #6d72ffff
> color sel #676bffff
> color sel #5c5dffff
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> color sel #5756ffff
> color sel #4c48ffff
> color sel #4b47ffff
> color sel #4a45ffff
> color sel #403affff
> color sel #3f38ffff
> color sel #3931ffff
> color sel #2c21ffff
> color sel #271bffff
> color sel #2216ffff
> color sel #2114ffff
> color sel #1d11ffff
> color sel #1c10ffff
> color sel #170bffff
> color sel #160affff
[Repeated 1 time(s)]
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> color sel #1305ffff
> color sel #1204ffff
> color sel #0f00ffff
> color sel #1100ffff
> color sel #1200ffff
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[Repeated 1 time(s)]
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> color sel #1900ffff
> color sel #1a00ffff
> color sel #1c00ffff
> color sel #1d00ffff
> color sel #1f00ffff
> color sel #2000ffff
> color sel #2100ffff
> color sel #2200ffff
> color sel #2300ffff
> color sel #2400ffff
> color sel #2600ffff
[Repeated 1 time(s)]
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> color sel #2900ffff
[Repeated 1 time(s)]
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> color sel #2c00ffff
> color sel #2e00ffff
> color sel #3000ffff
> color sel #3300ffff
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> color sel #3600ffff
> color sel #3a00ffff
> color sel #3c00ffff
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[Repeated 1 time(s)]
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> color sel #4900ffff
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> color sel #5a00ffff
> color sel #5b00ffff
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[Repeated 1 time(s)]
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[Repeated 2 time(s)]
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> color sel #1500d2ff
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> color sel #1400c4ff
> color sel #1400c3ff
> color sel #1400c2ff
[Repeated 1 time(s)]
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> color sel #1300bcff
[Repeated 2 time(s)]
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> color sel #1300baff
> color sel #1300b9ff
[Repeated 1 time(s)]
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[Repeated 2 time(s)]
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> color sel #1200b3ff
> color sel #1100a8ff
> color sel #1100a6ff
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[Repeated 2 time(s)]
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[Repeated 2 time(s)]
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> color sel #0f0092ff
> color sel #0e008fff
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[Repeated 1 time(s)]
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> color sel #13038eff
[Repeated 1 time(s)]
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> color sel #180a8eff
[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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> color sel #2e258eff
> color sel #2f268eff
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> color sel #362e8eff
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> color sel #7b658eff
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[Repeated 1 time(s)]
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> color sel #7d678eff
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 2 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 3 time(s)]
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[Repeated 6 time(s)]
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[Repeated 4 time(s)]
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[Repeated 4 time(s)]
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[Repeated 5 time(s)]
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[Repeated 1 time(s)]
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> color sel #25158eff
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> color sel #271a8eff
> color sel #281b8eff
> color sel #291e8eff
[Repeated 1 time(s)]
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> color sel #2c258eff
> color sel #2d268eff
[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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> color sel #302b8eff
> color sel #302c8eff
> color sel #302d8eff
[Repeated 1 time(s)]
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> color sel #34338eff
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[Repeated 1 time(s)]
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> color sel #37388eff
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> color sel #3a3c8eff
> color sel #3a3d8eff
[Repeated 1 time(s)]
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> color sel #3b3e8eff
[Repeated 2 time(s)]
> color sel #3b3f8eff
> color sel #3c3f8eff
[Repeated 1 time(s)]
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> color sel #40448eff
> color sel #41458eff
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[Repeated 3 time(s)]
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> color sel #3e418eff
> color sel #3d408eff
> color sel #3a3c8eff
> color sel #38398eff
> color sel #37388eff
> color sel #34348eff
> color sel #33328eff
> color sel #32328eff
> color sel #302f8eff
> color sel #2f2e8eff
[Repeated 1 time(s)]
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> color sel #25258eff
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[Repeated 1 time(s)]
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[Repeated 1 time(s)]
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> color sel #26268eff
> color sel #28278eff
> color sel #28288eff
> color sel #2a298eff
> color sel #2a2a8eff
[Repeated 2 time(s)]
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> color sel #2c2c8eff
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> color sel #2d2f8eff
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> color sel #353e8eff
> color sel #363f8eff
> color sel #36408eff
[Repeated 1 time(s)]
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> color sel #383f8eff
> color sel #383e8eff
[Repeated 1 time(s)]
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> color sel #393d8eff
[Repeated 1 time(s)]
> color sel #393b8eff
[Repeated 2 time(s)]
> color sel #393a8eff
[Repeated 1 time(s)]
> color sel #3a398eff
> color sel #3b398eff
> color sel #3d398eff
> color sel #3d388eff
> color sel #3d398eff
> color sel #3e388eff
> color sel #3f388eff
[Repeated 2 time(s)]
> color sel #40388eff
[Repeated 1 time(s)]
> color sel #40378eff
> color sel #41378eff
[Repeated 1 time(s)]
> color sel #42378eff
[Repeated 1 time(s)]
> color sel #43378eff
[Repeated 1 time(s)]
> color sel #44378eff
[Repeated 1 time(s)]
> color sel #45368eff
> color sel #45378eff
> color sel #45368eff
> color sel #46368eff
> color sel #47368eff
[Repeated 4 time(s)]
> color sel #46368eff
[Repeated 2 time(s)]
> color sel #43358eff
[Repeated 1 time(s)]
> color sel #41358eff
> color sel #3f348eff
> color sel #3e348eff
> color sel #3d348eff
> color sel #36328eff
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> color sel #2f318eff
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> color sel #2d338eff
> color sel #2c338eff
> color sel #2a348eff
[Repeated 4 time(s)]
> color sel #29358eff
> color sel #29348eff
[Repeated 1 time(s)]
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> color sel #27358eff
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> color sel #22348eff
> color sel #1e328eff
> color sel #1d318eff
> color sel #1c308eff
> color sel #1a2f8eff
> color sel #1a2e8eff
> color sel #192e8eff
> color sel #192d8eff
[Repeated 1 time(s)]
> color sel #182d8eff
> color sel #182c8eff
[Repeated 2 time(s)]
> color sel #172c8eff
[Repeated 1 time(s)]
> color sel #152a8eff
[Repeated 1 time(s)]
> color sel #14298eff
[Repeated 1 time(s)]
> color sel #13298eff
> color sel #13288eff
[Repeated 1 time(s)]
> color sel #12288eff
> color sel #13288eff
> color sel #13298eff
> color sel #142a8eff
> color sel #142b8eff
> color sel #182f8eff
> color sel #19318eff
> color sel #1a328eff
> color sel #1a338eff
> show #!2 models
> color zone #2 near #5 distance 7.63
> select clear
> hide #5 models
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_deepEMhancer_blue_Fig1A_v2.png" width 1500 height 2189
> supersample 3 transparentBackground true
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_deepEMhancer_blue_v2.cxs"
——— End of log from Mon Dec 16 12:03:21 2024 ———
opened ChimeraX session
Showing cryosparc_P33_J447_010_volume_map.seg - 98 regions, 60 surfaces
> hide #!6 models
> close #6
> open
> /Users/colinmuir/Documents/phenix/CM25/RealSpaceRefine_15/CM25_deepEMhancerJ463docked_real_space_refined_015_coot1.pdb
Chain information for
CM25_deepEMhancerJ463docked_real_space_refined_015_coot1.pdb #6
---
Chain | Description
A B D | No description available
C | No description available
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #5 models
> hide #6 models
> hide #5 models
> show #6 models
> dssp
Computing secondary structure
> select #6/C:216
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
58 atoms, 57 bonds, 7 residues, 1 model selected
> select up
1422 atoms, 1451 bonds, 171 residues, 1 model selected
> color sel dodger blue
> select #6/A:224
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
84 atoms, 85 bonds, 10 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel blue
> select #6/D:237
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
117 atoms, 120 bonds, 14 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel #243897ff
> select #6/B:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
122 atoms, 125 bonds, 14 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel #defefeff
> color sel #d3fffdff
> color sel #d2fffdff
> color sel #d1fffdff
[Repeated 1 time(s)]
> color sel #cffffdff
> color sel #cefffdff
[Repeated 1 time(s)]
> color sel #cdfffdff
> color sel #ccfffdff
> color sel #ccfffcff
> color sel #cafffcff
> color sel #c8fffcff
> color sel #c6fffcff
> color sel #c4fffcff
> color sel #c3fffcff
> color sel #c1fffcff
> color sel #bbfffcff
[Repeated 1 time(s)]
> color sel #bafffcff
[Repeated 2 time(s)]
> color sel #b9fffcff
[Repeated 1 time(s)]
> color sel #b9fffdff
> color sel #b8fffdff
> color sel #b6fffdff
> color sel #b5fffdff
> color sel #b2ffffff
> color sel #b1ffffff
[Repeated 1 time(s)]
> color sel #b2ffffff
[Repeated 1 time(s)]
> color sel #b5ffffff
> color sel #b6ffffff
> color sel #b6feffff
> color sel #b6fdffff
> color sel #b5fdffff
> color sel #b4fdffff
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> setattr /D:190-248 res ss_type 1
Assigning ss_type attribute to 118 items
> setattr /D:190-248 res ss_id 130
Assigning ss_id attribute to 118 items
> setattr /A:190-248 res ss_type 1
Assigning ss_type attribute to 118 items
> setattr /A:190-248 res ss_id 131
Assigning ss_id attribute to 118 items
> setattr /A:190-250 res ss_id 131
Assigning ss_id attribute to 122 items
> setattr /D:190-250 res ss_id 132
Assigning ss_id attribute to 122 items
> setattr /D:190-250 res ss_type 1
Assigning ss_type attribute to 122 items
> setattr /D:250 res ss_type 0
Assigning ss_type attribute to 2 items
> setattr /C:190-248 res ss_type 1
Assigning ss_type attribute to 118 items
> setattr /C:190-248 res ss_id 133
Assigning ss_id attribute to 118 items
> setattr /B:190-248 res ss_type 1
Assigning ss_type attribute to 118 items
> setattr /B:190-248 res ss_id 134
Assigning ss_id attribute to 118 items
> setattr /a:255-277 res ss_type 1
Assigning ss_type attribute to 46 items
> setattr /a:255-277 res ss_id 135
Assigning ss_id attribute to 46 items
> setattr /a:254 res ss_type 0
Assigning ss_type attribute to 2 items
> setattr /a:255 res ss_type 0
Assigning ss_type attribute to 2 items
> setattr /a:255 res ss_type 1
Assigning ss_type attribute to 2 items
> setattr /A:289-301 res ss_type 1
Assigning ss_type attribute to 26 items
> setattr /A:289-301 res ss_id 136
Assigning ss_id attribute to 26 items
> setattr /D:289-301 res ss_type 1
Assigning ss_type attribute to 26 items
> setattr /D:289-301 res ss_id 137
Assigning ss_id attribute to 26 items
> select #6/B:164
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #6/B:165
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #6/B:166
19 atoms, 16 bonds, 3 residues, 1 model selected
> select subtract #6/B:166
12 atoms, 10 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> setattr /B:167-181 res ss_id 138
Assigning ss_id attribute to 30 items
> setattr /B:167-181 res ss_type 1
Assigning ss_type attribute to 30 items
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_cartoon_blue_Fig1A_v1.png" width 1500 height 1735 supersample
> 3 transparentBackground true
> setattr /A:185-249 res ss_type 1
Assigning ss_type attribute to 130 items
> setattr /A:185-249 res ss_id 140
Assigning ss_id attribute to 130 items
> setattr /C:255-285 res ss_id 141
Assigning ss_id attribute to 62 items
> setattr /C:255-285 res ss_type 1
Assigning ss_type attribute to 62 items
> setattr /C:255-277 res ss_type 1
Assigning ss_type attribute to 46 items
> setattr /C:255-277 res ss_id 141
Assigning ss_id attribute to 46 items
> setattr /C:278 285 res ss_id 142
Expected a keyword
> setattr /C:278-285 res ss_id 142
Assigning ss_id attribute to 16 items
> setattr /C:278-285 res ss_type 0
Assigning ss_type attribute to 16 items
> setattr /C:254 res ss_type 0
Assigning ss_type attribute to 2 items
> setattr /C:255 res ss_type 0
Assigning ss_type attribute to 2 items
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_cartoon_blue_Fig1A_v2.png" width 1500 height 1735 supersample
> 3 transparentBackground true
> setattr /B:287-303 res ss_type 1
Assigning ss_type attribute to 34 items
> setattr /B:287-303 res ss_id 143
Assigning ss_id attribute to 34 items
> ui tool show "Side View"
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_cartoon_blue_Fig1A_v2.png" width 1500 height 1735 supersample
> 3 transparentBackground true
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!2 models
> show #!8 models
> hide #!8 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> cartoon style protein modeHelix tube radius 2 sides 24
> setattr /C:185-248 res ss_id 145
Assigning ss_id attribute to 128 items
> setattr /D:254-277 res ss_id 146
Assigning ss_id attribute to 48 items
> setattr /D:254 res ss_type 0
Assigning ss_type attribute to 2 items
> setattr /B:185-248 res ss_id 147
Assigning ss_id attribute to 128 items
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_cartoon_blue_Fig1A_cylinders.png" width 1500 height 2189
> supersample 3 transparentBackground true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> lighting soft
> lighting flat
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_cartoon_blue_Fig1A_cylinders_flat.png" width 1500 height 2189
> supersample 3 transparentBackground true
> save "/Users/colinmuir/Desktop/MCU Paper Figures/289S_cylinder_model.cxs"
——— End of log from Mon Dec 16 14:31:03 2024 ———
opened ChimeraX session
> cartoon style protein modeHelix default
> lighting soft
> select #6/C:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> select subtract #6/C:226
Nothing selected
> select #6/C:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #6/C:229
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
527 atoms, 534 bonds, 64 residues, 1 model selected
> select down
15 atoms, 13 bonds, 2 residues, 1 model selected
> graphics selection color green width 3
> select #6/C:230
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #6/C:229
22 atoms, 22 bonds, 2 residues, 1 model selected
> select add #6/C:226
29 atoms, 28 bonds, 3 residues, 1 model selected
> graphics selection color green width 5
> graphics selection color springgreen width 5
> graphics selection color springgreen width 3
> select clear
[Repeated 1 time(s)]
> select #6/C:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/Y289S_deepEMhancer_cartoon_blue.cxs"
> select #6/C:230
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #6/D:225
21 atoms, 21 bonds, 2 residues, 1 model selected
> select up
1023 atoms, 1038 bonds, 124 residues, 1 model selected
> select up
2833 atoms, 2891 bonds, 341 residues, 1 model selected
> hide sel target a
> hide sel cartoons
> show sel cartoons
> select clear
> ui tool show "Side View"
> select #6/B:295
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #6/B:291
20 atoms, 19 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #6/B:297
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/B:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/B:297
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/B:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/B:292
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #6/B:297
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #6/B:290
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> select clear
> select #6/B:292
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/colinmuir/Desktop/MCU Paper Figures/Y289S_lateralhelix.png"
> width 826 height 602 supersample 3 transparentBackground true
> select #6/A:221
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix_v2.png" width 826 height 602
> supersample 3 transparentBackground true
> hide #6 atoms
> select add #6/B:295
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #6/B:291
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #6/B:290
31 atoms, 29 bonds, 3 residues, 1 model selected
> select add #6/B:297
41 atoms, 39 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> graphics silhouettes false
> graphics silhouettes true
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix_v2.png" width 826 height 602
> supersample 3 transparentBackground true
> select #6/A:289
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> hide #6 atoms
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix_v2_zoomOut.png" width 359 height
> 603 supersample 3 transparentBackground true
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix_v2_zoomOut.png" width 800 height
> 1344 supersample 3 transparentBackground true
> select #6/B:297
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/B:295
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/B:291
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/B:290
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #6/B:291
20 atoms, 18 bonds, 2 residues, 1 model selected
> select add #6/B:295
31 atoms, 29 bonds, 3 residues, 1 model selected
> select add #6/B:297
41 atoms, 39 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix_v2.png" width 800 height 893
> supersample 3 transparentBackground true
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix.cxs"
——— End of log from Thu Dec 19 14:59:01 2024 ———
opened ChimeraX session
> select #6/B:297
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/B:291
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/B:297
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add #6/B:290
30 atoms, 28 bonds, 3 residues, 1 model selected
> hide sel atoms
> select clear
> select add #6/A:221
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #6/B:301
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #6/B:287
19 atoms, 16 bonds, 3 residues, 1 model selected
> select add #6/B:294
27 atoms, 23 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix_crosslinkResidues.png" width
> 1000 height 1402 supersample 3 transparentBackground true
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure/Y289S_lateralhelix_crosslinkResidues.cxs"
——— End of log from Thu Dec 19 15:55:09 2024 ———
opened ChimeraX session
> ui tool show "Side View"
> open
> /Users/colinmuir/Documents/phenix/CM25/RealSpaceRefine_15/CM25_deepEMhancerJ463docked_real_space_refined_015_coot3-2.pdb
Chain information for
CM25_deepEMhancerJ463docked_real_space_refined_015_coot3-2.pdb #9
---
Chain | Description
A B D | No description available
C | No description available
> hide #6 models
> dssp
Computing secondary structure
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.02899
> volume #2 level 0.01187
> hide #!2 models
> select #9/A:316
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
208 atoms, 209 bonds, 25 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> select clear
> select #9/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
80 atoms, 80 bonds, 10 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> select down
80 atoms, 80 bonds, 10 residues, 1 model selected
> select add #9/A:297
90 atoms, 90 bonds, 11 residues, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 1 model selected
> select add #9/A:293
120 atoms, 122 bonds, 14 residues, 1 model selected
> select add #9/A:287
125 atoms, 126 bonds, 15 residues, 1 model selected
> select add #9/A:285
132 atoms, 133 bonds, 16 residues, 1 model selected
> select up
260 atoms, 266 bonds, 30 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #9/D:306
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #9/D:299
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #9/D:295
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #9/D:291
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add #9/D:285
39 atoms, 36 bonds, 5 residues, 1 model selected
> select up
244 atoms, 249 bonds, 28 residues, 1 model selected
> select add #9/D:293
252 atoms, 256 bonds, 29 residues, 1 model selected
> undo
[Repeated 9 time(s)]
> close #9
> open
> /Users/colinmuir/Documents/phenix/CM25/RealSpaceRefine_15/CM25_deepEMhancerJ463docked_real_space_refined_015_coot3-2.pdb
Chain information for
CM25_deepEMhancerJ463docked_real_space_refined_015_coot3-2.pdb #9
---
Chain | Description
A B D | No description available
C | No description available
> dssp
Computing secondary structure
> open
> /Users/colinmuir/Documents/phenix/CM25/RealSpaceRefine_15/CM25_deepEMhancerJ463docked_real_space_refined_015_coot4.pdb
Chain information for
CM25_deepEMhancerJ463docked_real_space_refined_015_coot4.pdb #10
---
Chain | Description
A B D | No description available
C | No description available
> close #9
> dssp
Computing secondary structure
> select #10/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> transparency #2.1 50
> hide #!2 models
> show #!8 models
> show #!8.5 models
> hide #!8.5 models
> show #!8.4 models
> hide #!8.4 models
> show #!8.3 models
> show #!8.2 models
> transparency #8.2.1#8.3.1 50
> hide #!8.3 models
> hide #!8.2 models
> select up
38 atoms, 38 bonds, 4 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cyan
> show #!8.3 models
> show #!8.2 models
> color sel medium blue
> select clear
> select #8.3
4 models selected
> hide #!8.3 models
> hide #!8.2 models
> select #10/B:288
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
122 atoms, 125 bonds, 14 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel deep sky blue
> select clear
> select #10/C:301
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!8.5 models
> hide #!8.5 models
> show #!8.4 models
> hide #!8.4 models
> select up
143 atoms, 146 bonds, 16 residues, 1 model selected
> select up
1422 atoms, 1451 bonds, 171 residues, 1 model selected
> color sel dark blue
[Repeated 1 time(s)]
> select clear
> select add #10/D:228
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
88 atoms, 89 bonds, 11 residues, 1 model selected
> select up
1411 atoms, 1440 bonds, 170 residues, 1 model selected
> color sel dodger blue
> select clear
> show #!8.3 models
> show #!8.2 models
> color #8.3 #76d6ffff models
> transparency #8.2.1#8.3.1 0
> transparency #8.2.1#8.3.1 50
> ui tool show "Side View"
> select #8.3
4 models selected
> hide #!8.3 models
> hide #!8.2 models
> select add #10/B:274
12 atoms, 12 bonds, 1 residue, 3 models selected
> select up
171 atoms, 177 bonds, 21 residues, 3 models selected
> select up
1411 atoms, 1440 bonds, 170 residues, 3 models selected
> show sel atoms
> color sel byhetero
> select clear
> select #10/A:308
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
38 atoms, 38 bonds, 4 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #10/B:209
7 atoms, 7 bonds, 1 residue, 1 model selected
> setattr /B:187-249 res ss_type 1
Assigning ss_type attribute to 189 items
> setattr /B:187-249 res ss_id 200
Assigning ss_id attribute to 189 items
> setattr /B:187-250 res ss_id 200
Assigning ss_id attribute to 192 items
> select #10/A:299
4 atoms, 3 bonds, 1 residue, 1 model selected
> setattr /A:187-250 res ss_id 201
Assigning ss_id attribute to 192 items
> setattr /A:187-250 res ss_type 1
Assigning ss_type attribute to 192 items
> setattr /A:287-299 res ss_type 1
Assigning ss_type attribute to 39 items
> setattr /A:287-299 res ss_id 202
Assigning ss_id attribute to 39 items
> show #!8.3 models
> select clear
> select #10/A:208
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
533 atoms, 542 bonds, 64 residues, 1 model selected
> style sel stick
Changed 533 atom styles
> show sel atoms
> color sel byhetero
> show #!8.2 models
> color #8.2 #0433ffff models
> transparency #8.2.1#8.3.1 0
> transparency #8.2.1#8.3.1 50
> select clear
> hide #10 atoms
> save "/Users/colinmuir/Desktop/MCU Paper
> Figures/DomainSwapFigure2/Y289S_showDomainSwapDensity.cxs"
——— End of log from Fri Dec 20 10:08:48 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
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 Air
Model Identifier: MacBookAir10,1
Model Number: Z124000FLLL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.60.44
OS Loader Version: 8419.60.44
Software:
System Software Overview:
System Version: macOS 13.1 (22C65)
Kernel Version: Darwin 22.2.0
Time since boot: 29 days, 22 hours, 5 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP 24mh:
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 , 10 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Same crash, same reporter as #16504