id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18414	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-13.3-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000001fad9db40 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.segment._segment, PIL._imagingmath, chimerax.mlp._mlp, chimerax.coulombic._esp (total: 66)


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        ""SIRI_FIND_MY_CONFIGURATION_FILES"" : ""652805151bce5442b8d752e1""
      },
      ""deploymentId"" : 240000031
    }
  ],
  ""experiments"" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v03-RON2.cxs""

Opened CS_J2730_003_map_sharp_zflip_resam.mrc as #1, grid size 600,600,600,
pixel 0.823, shown at level 0.118, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc as #4, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #2.2, grid size
600,600,600, pixel 0.823, shown at level 0.968, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #6.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #8.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #9.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #7.1, grid size
600,600,600, pixel 0.823, shown at level 0.395, step 1, values float32  
Log from Thu Aug 7 18:38:59 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v03-RON2.cxs""

Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #13.1, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #13.2, grid size
600,600,600, pixel 0.823, shown at level 0.0952, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #15, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #16.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #16.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #18.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #18.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #19.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #19.2, grid size
600,600,600, pixel 0.823, shown at level 0.136, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 0 as #20.1, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 1 as #20.2, grid
size 600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2386_005_volume_map.mrc as #21, grid size 600,600,600,
pixel 0.823, shown at level 0.0115, step 4, values float32  
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip as #22, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32  
Opened CS_J2730_003_map_sharp_zflip_resam.mrc as #1, grid size 600,600,600,
pixel 0.823, shown at level 0.118, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc as #4, grid size
600,600,600, pixel 0.823, shown at step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #2.2, grid size
600,600,600, pixel 0.823, shown at level 0.968, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #6.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #8.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #9.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  
Log from Wed Aug 6 11:59:41 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v01.cxs""

Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip as #5, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #7, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #13.1, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #13.2, grid size
600,600,600, pixel 0.823, shown at level 0.0952, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #15, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #16.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #16.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #18.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #18.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #19.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #19.2, grid size
600,600,600, pixel 0.823, shown at level 0.136, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 0 as #20.1, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 1 as #20.2, grid
size 600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2386_005_volume_map.mrc as #21, grid size 600,600,600,
pixel 0.823, shown at level 0.0115, step 4, values float32  
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip as #22, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32  
Opened CS_J2730_003_map_sharp_zflip_resam.mrc as #1, grid size 600,600,600,
pixel 0.823, shown at level 0.118, step 1, values float32  
Log from Wed Jul 16 16:11:23 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> set bgColor #ffffff00

Log from Tue Jun 3 19:59:46 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Map_model_figs_v02.cxs

Opened cryosparc_P4_J2606_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.823, shown at level 0.103, step 1, values float32  
Opened cryosparc_P4_J2602_004_volume_map_sharp.mrc as #2, grid size
600,600,600, pixel 0.823, shown at level 0.172, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc as #3, grid size
600,600,600, pixel 0.823, shown at level 0.176, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip as #5, grid size
600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc as #6, grid size 600,600,600,
pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #7, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc as #9, grid size 600,600,600,
pixel 0.823, shown at level 0.0652, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip as #10, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #13.1, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #13.2, grid size
600,600,600, pixel 0.823, shown at level 0.0952, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #15, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #16.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #16.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #18.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #18.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #19.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #19.2, grid size
600,600,600, pixel 0.823, shown at level 0.136, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 0 as #20.1, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 1 as #20.2, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32  
Opened cryosparc_P4_J2386_005_volume_map.mrc as #21, grid size 600,600,600,
pixel 0.823, shown at level 0.0115, step 4, values float32  
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip as #22, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32  
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip 0 as #23.1, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32  
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip 1 as #23.2, grid size
600,600,600, pixel 0.823, shown at level 0.107, step 1, values float32  
Log from Sat May 31 21:34:44 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Figs/Figures_v03.cxs

Opened cryosparc_P4_J2606_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.823, shown at level 0.103, step 1, values float32  
Opened cryosparc_P4_J2602_004_volume_map_sharp.mrc as #2, grid size
600,600,600, pixel 0.823, shown at level 0.172, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc as #3, grid size
600,600,600, pixel 0.823, shown at level 0.176, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip as #5, grid size
600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc as #6, grid size 600,600,600,
pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #7, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc as #9, grid size 600,600,600,
pixel 0.823, shown at level 0.0652, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip as #10, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #13.1, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #13.2, grid size
600,600,600, pixel 0.823, shown at level 0.0952, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #15, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #16.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #16.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #18.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #18.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #19.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #19.2, grid size
600,600,600, pixel 0.823, shown at level 0.136, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 0 as #20.1, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 1 as #20.2, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32  
Log from Mon May 26 07:46:14 2025 Startup Messages  
---  
warning | Registration file '/Users/meserethaile/Library/Application Support/ChimeraX/registration' has expired  
note | available bundle cache has not been initialized yet  
  

> ui tool hide ""command line interface""

> ui tool show clix

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/meserethaile/Downloads/cryosparc_P4_J2606_003_volume_map_sharp.mrc

Opened cryosparc_P4_J2606_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.823, shown at level 0.0517, step 2, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #1 step 1

> volume #1 level 0.1032

> open
> /Users/meserethaile/Downloads/cryosparc_P4_J2602_004_volume_map_sharp.mrc

Opened cryosparc_P4_J2602_004_volume_map_sharp.mrc as #2, grid size
600,600,600, pixel 0.823, shown at level 0.0141, step 4, values float32  

> open
> /Users/meserethaile/Downloads/cryosparc_P4_J2614_003_volume_map_sharp.mrc

Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc as #3, grid size
600,600,600, pixel 0.823, shown at level 0.0176, step 4, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #2 step 1

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #3 step 1

> volume #2 level 0.04849

> volume #3 level 0.06161

> volume #2 level 0.1218

> volume #2 level 0.186

> volume #2 level 0.1722

> volume #3 level 0.1757

> open 3zwz fromDatabase pdb format mmcif

3zwz title:  
Crystal structure of Plasmodium falciparum AMA1 in complex with a 39aa PfRON2
peptide [more info...]  
  
Chain information for 3zwz #4  
---  
Chain | Description | UniProt  
A | APICAL MEMBRANE ANTIGEN 1, AMA1 | Q7KQK5_PLAF7 103-441  
B | RHOPTRY NECK PROTEIN 2 | Q8IKV6_PLAF7 2021-2059  
  
Non-standard residues in 3zwz #4  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  

> select add #4

2892 atoms, 2731 bonds, 1 pseudobond, 564 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #4,1,0,0,150.77,0,1,0,-101.07,0,0,1,505.95

> view matrix models #4,1,0,0,256.23,0,1,0,273.07,0,0,1,143.04

> view matrix models #4,1,0,0,222.62,0,1,0,292.97,0,0,1,161.57

> volume flip #3

Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip as #5, grid size
600,600,600, pixel 0.823, shown at step 1, values float32  

> view matrix models #4,1,0,0,259.12,0,1,0,329.33,0,0,1,277.73

> view matrix models #4,1,0,0,254.66,0,1,0,319.52,0,0,1,298.54

> ui mousemode right ""rotate selected models""

> view matrix models
> #4,0.0052801,0.089762,0.99595,237.42,0.92241,0.38418,-0.039516,314.48,-0.38617,0.91888,-0.080769,325.77

> view matrix models
> #4,-0.64059,-0.42716,0.63811,246.1,-0.0063165,0.8339,0.55188,307.43,-0.76786,0.3495,-0.53688,335.13

> view matrix models
> #4,0.17142,-0.9826,0.071492,252.99,-0.21167,0.03414,0.97674,296.72,-0.96219,-0.18256,-0.20214,327.12

> view matrix models
> #4,-0.060486,-0.99228,-0.10831,257.6,-0.30748,-0.084709,0.94778,297.35,-0.94963,0.09063,-0.29998,329.93

> ui mousemode right ""translate selected models""

> view matrix models
> #4,-0.060486,-0.99228,-0.10831,253.1,-0.30748,-0.084709,0.94778,301.11,-0.94963,0.09063,-0.29998,332.09

> ui tool show ""Fit in Map""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> fitmap #4 inMap #5

Fit molecule 3zwz (#4) to map cryosparc_P4_J2614_003_volume_map_sharp.mrc z
flip (#5) using 2892 atoms  
average map value = 0.07416, steps = 208  
shifted from previous position = 26.6  
rotated from previous position = 9.94 degrees  
atoms outside contour = 2377, contour level = 0.17568  
  
Position of 3zwz (#4) relative to cryosparc_P4_J2614_003_volume_map_sharp.mrc
z flip (#5) coordinates:  
Matrix rotation and translation  
0.05293533 -0.99853692 0.01103978 231.31013513  
-0.35796158 -0.00865367 0.93369621 287.44663572  
-0.93223460 -0.05337734 -0.35789594 320.36343888  
Axis -0.65450719 0.62546490 0.42475169  
Axis point 0.00000000 341.34388986 171.06253126  
Rotation angle (degrees) 131.05681941  
Shift along axis 164.46854871  
  

> select subtract #4

Nothing selected  

> hide #!4 models

> volume #5 level 0.2183

> show #!4 models

> select add #4

2892 atoms, 2731 bonds, 1 pseudobond, 564 residues, 2 models selected  

> view matrix models
> #4,0.052935,-0.99854,0.01104,229.69,-0.35796,-0.0086537,0.9337,285.99,-0.93223,-0.053377,-0.3579,323.84

> view matrix models
> #4,0.052935,-0.99854,0.01104,228.73,-0.35796,-0.0086537,0.9337,285.96,-0.93223,-0.053377,-0.3579,323.53

> ui mousemode right ""rotate selected models""

> view matrix models
> #4,-0.0547,-0.98937,0.13473,226.63,-0.33782,0.14531,0.92993,286.43,-0.93962,0.0053534,-0.34218,323.42

> view matrix models
> #4,0.39287,-0.91501,-0.091711,229.84,-0.61421,-0.33531,0.71436,290.68,-0.6844,-0.22432,-0.69374,329.13

> view matrix models
> #4,0.25263,-0.9345,0.25078,223.38,-0.44053,0.11967,0.88973,287.62,-0.86146,-0.33525,-0.38144,322.8

> view matrix models
> #4,0.38852,-0.91614,0.098708,226.06,-0.44983,-0.095083,0.88804,287.03,-0.80418,-0.38942,-0.44904,323.79

> view matrix models
> #4,0.51294,-0.85793,-0.029166,228.46,-0.35492,-0.24289,0.90279,285.86,-0.78162,-0.45273,-0.42908,323.08

> view matrix models
> #4,0.5206,-0.85156,-0.061848,229.15,-0.25126,-0.22203,0.94211,284.66,-0.81599,-0.47492,-0.32955,321.02

> view matrix models
> #4,0.71686,-0.68356,0.13731,224.61,-0.28789,-0.11083,0.95123,284.96,-0.63501,-0.72143,-0.27624,318.38

> fitmap #4 inMap #5

Fit molecule 3zwz (#4) to map cryosparc_P4_J2614_003_volume_map_sharp.mrc z
flip (#5) using 2892 atoms  
average map value = 0.1527, steps = 188  
shifted from previous position = 3.62  
rotated from previous position = 34.8 degrees  
atoms outside contour = 2079, contour level = 0.2183  
  
Position of 3zwz (#4) relative to cryosparc_P4_J2614_003_volume_map_sharp.mrc
z flip (#5) coordinates:  
Matrix rotation and translation  
0.27882958 -0.95722043 -0.07735055 228.32568023  
-0.45677008 -0.20304060 0.86610369 287.32033700  
-0.84475745 -0.20616391 -0.49384338 324.58692754  
Axis -0.76027814 0.54412042 0.35483816  
Axis point 0.00000000 304.01666654 152.06635633  
Rotation angle (degrees) 135.15582083  
Shift along axis 97.92166563  
  

> fitmap #4 inMap #5

Fit molecule 3zwz (#4) to map cryosparc_P4_J2614_003_volume_map_sharp.mrc z
flip (#5) using 2892 atoms  
average map value = 0.1527, steps = 44  
shifted from previous position = 0.00249  
rotated from previous position = 0.00333 degrees  
atoms outside contour = 2080, contour level = 0.2183  
  
Position of 3zwz (#4) relative to cryosparc_P4_J2614_003_volume_map_sharp.mrc
z flip (#5) coordinates:  
Matrix rotation and translation  
0.27881318 -0.95722143 -0.07739731 228.32597888  
-0.45673538 -0.20306577 0.86611609 287.32176523  
-0.84478163 -0.20613450 -0.49381431 324.58774291  
Axis -0.76027285 0.54410925 0.35486663  
Axis point 0.00000000 304.01462600 152.07234351  
Rotation angle (degrees) 135.15632817  
Shift along axis 97.92974526  
  

> volume #5 level 0.1672

> volume #5 color #b2af69

> volume #5 color #b2af6980

> select subtract #4

Nothing selected  

> color #4 #906f90ff

> color #4 #907190ff

> select add #4

2892 atoms, 2731 bonds, 1 pseudobond, 564 residues, 2 models selected  

> hide (#!4 & sel) target a

> volume #5 color #b2af4e80

> volume #5 color #97af4e80

> volume #5 color #974d4e80

> select subtract #4

Nothing selected  

> ui tool show ""Show Sequence Viewer""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> sequence chain /B

Alignment identifier is 4/B  

> select clear

> select /B:2023-2058

259 atoms, 263 bonds, 36 residues, 1 model selected  

> color sel yellow

> open /Users/meserethaile/Downloads/cryosparc_P4_J2546_009_volume_map.mrc

Opened cryosparc_P4_J2546_009_volume_map.mrc as #6, grid size 600,600,600,
pixel 0.823, shown at level 0.0188, step 4, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #6 step 1

> volume #6 level 0.1093

> volume #6 level 0.166

> view matrix models
> #4,0.36407,-0.87396,0.32196,219.7,-0.92177,-0.28861,0.25892,301.94,-0.13336,-0.39103,-0.91066,330.01

> view matrix models
> #4,0.16705,-0.86529,0.47262,217.32,-0.94349,-0.0011332,0.3314,301.37,-0.28622,-0.50127,-0.81658,328.28

> view matrix models
> #4,0.07023,-0.98771,0.13961,224.45,-0.51618,0.083782,0.85237,288.75,-0.8536,-0.13193,-0.50395,325.07

> fitmap #4 inMap #5

Fit molecule 3zwz (#4) to map cryosparc_P4_J2614_003_volume_map_sharp.mrc z
flip (#5) using 2892 atoms  
average map value = 0.1527, steps = 92  
shifted from previous position = 0.44  
rotated from previous position = 17.4 degrees  
atoms outside contour = 1601, contour level = 0.16716  
  
Position of 3zwz (#4) relative to cryosparc_P4_J2614_003_volume_map_sharp.mrc
z flip (#5) coordinates:  
Matrix rotation and translation  
0.27889580 -0.95720965 -0.07724516 228.32390022  
-0.45685548 -0.20300112 0.86606790 287.31926264  
-0.84468941 -0.20625282 -0.49392264 324.58696998  
Axis -0.76030148 0.54413664 0.35476328  
Axis point 0.00000000 304.01942783 152.05049424  
Rotation angle (degrees) 135.15474655  
Shift along axis 97.89747611  
  

> fitmap #4 inMap #5

Fit molecule 3zwz (#4) to map cryosparc_P4_J2614_003_volume_map_sharp.mrc z
flip (#5) using 2892 atoms  
average map value = 0.1527, steps = 40  
shifted from previous position = 0.0056  
rotated from previous position = 0.0178 degrees  
atoms outside contour = 1600, contour level = 0.16716  
  
Position of 3zwz (#4) relative to cryosparc_P4_J2614_003_volume_map_sharp.mrc
z flip (#5) coordinates:  
Matrix rotation and translation  
0.27870107 -0.95724887 -0.07746165 228.32828427  
-0.45674437 -0.20306688 0.86611109 287.31956721  
-0.84481376 -0.20600591 -0.49381299 324.59072368  
Axis -0.76023879 0.54412983 0.35490803  
Axis point 0.00000000 304.01305348 152.09214800  
Rotation angle (degrees) 135.16087469  
Shift along axis 97.95498318  
  

> select add #4

2892 atoms, 2731 bonds, 1 pseudobond, 564 residues, 2 models selected  

> select subtract #4

Nothing selected  

> volume #5 color #974d6b80

> volume flip #6

Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #7, grid size
600,600,600, pixel 0.823, shown at step 1, values float32  

> volume #7 color #974d6b80

> select add #7

2 models selected  

> volume #7 level 0.1394

> volume #5 level 0.2524

> select subtract #7

Nothing selected  

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting full

> lighting soft

> lighting simple

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> set bgColor white

> volume #5 level 0.1899

> volume #5 level 0.187

> volume #7 level 0.1394

> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/J1332_R2seq_coot.pdb

Chain information for J1332_R2seq_coot.pdb #8  
---  
Chain | Description  
A | No description available  
  

> fitmap #8 inMap #7

Fit molecule J1332_R2seq_coot.pdb (#8) to map
cryosparc_P4_J2546_009_volume_map.mrc z flip (#7) using 9230 atoms  
average map value = 0.2458, steps = 72  
shifted from previous position = 3.27  
rotated from previous position = 2.51 degrees  
atoms outside contour = 2295, contour level = 0.13942  
  
Position of J1332_R2seq_coot.pdb (#8) relative to
cryosparc_P4_J2546_009_volume_map.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
0.99955761 -0.02952277 -0.00360310 7.28628788  
0.02939182 0.99905011 -0.03217133 2.98774955  
0.00454947 0.03205119 0.99947587 -7.84771483  
Axis 0.73369975 -0.09313775 0.67306021  
Axis point -0.00000000 241.74080827 85.11189816  
Rotation angle (degrees) 2.50842052  
Shift along axis -0.21430926  
  

> volume #5 level 0.2108

> save
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Figs/Figures_v01.cxs

> volume #5 level 0.1752

> volume #5 level 0.1942

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui tool show ""Hide Dust""

> surface dust #5 size 4.94

> volume #7 level 0.1136

> surface dust #7 size 4.94

> volume #7 level 0.08787

> surface dust #7 size 4.91

> surface dust #7 size 7.26

> open ""/Users/meserethaile/Desktop/HoLab/Lab Meeting
> PPTs/Figs/250519_figs/cryosparc_P4_J1996_004_volume_map.mrc""

Opened cryosparc_P4_J1996_004_volume_map.mrc as #9, grid size 600,600,600,
pixel 0.823, shown at level 0.0124, step 4, values float32  

> volume #9 step 1

> volume #9 level 0.06524

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> volume flip #9

Opened cryosparc_P4_J1996_004_volume_map.mrc z flip as #10, grid size
600,600,600, pixel 0.823, shown at step 1, values float32  

> volume #10 level 0.1445

> surface dust #10 size 4.94

> volume #10 level 0.1638

> volume #10 color #974d6b80

> volume #10 level 0.1339

> surface dust #10 size 5.11

> surface dust #10 size 13.92

> hide #!4 models

> hide #!8 models

> show #!8 models

> color #8 #9d8420ff

> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/J1332_R4seq_coot.pdb

Chain information for J1332_R4seq_coot.pdb #11  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/J1332_R5seq_coot.pdb

Chain information for J1332_R5seq_coot.pdb #12  
---  
Chain | Description  
A | No description available  
  

> hide #!12 models

> show #!12 models

> color #12 #7d6f86ff

> color #11 #90a583ff

> hide #!10 models

> hide #!7 models

> hide #!5 models

> color #11 #1f2041ff

> color #11 #94b9afff

> show #!4 models

> color #4 #edbfb7ff

> color #4 #273c2cff

> color #4 #114b5fff

> color #4 #f79d84ff

> color #4 #002e2cff

> show #!10 models

> hide #!10 models

> show #!7 models

> hide #!7 models

> save
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Figs/Figures_v01.cxs

> show #!10 models

> hide #!10 models

> show #!7 models

> ui tool show ""Surface Color""

> ui tool show ""Surface Zone""

> surface zone #7 nearAtoms #8 distance 4.94

[Repeated 1 time(s)]

> surface zone #7 nearAtoms #8 distance 5.09

> surface zone #7 nearAtoms #8 distance 2.84

[Repeated 1 time(s)]

> ui tool show ""Segment Map""

> ui tool show ""Color Zone""

> color zone #7 near #8 distance 4.94

> volume splitbyzone #7

Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #13.1, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #13.2, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32  

> volume #13.2 level 0.1012

> surface dust #13.2 size 4.94

> volume #13.2 level 0.09233

> color zone #7 near #11 distance 4.94

[Repeated 1 time(s)]

> color zone #7 near #12 distance 4.94

[Repeated 2 time(s)]

> color zone #7 near #12 distance 4.88

> color zone #7 near #12 distance 6.23

[Repeated 1 time(s)]

> help help:user/tools/colorzone.html

> color zone #5 near #4 distance 4.94

> show #!5 models

> color zone #5 near #4 distance 5.15

> color zone #5 near #4 distance 5.23

> hide #!4 models

> show #!7 models

> color zone #7 near #11 distance 6.23

[Repeated 1 time(s)]

> color zone #7 near #12 distance 6.23

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!5 models

> color zone #7 near #12 distance 6.23

> color zone #7 near #12 distance 5.82

[Repeated 1 time(s)]

> color single #7

> color zone #7 near #12 distance 5.82

> color zone #10 near #12 distance 4.94

> show #!10 models

> volume splitbyzone #10

Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #14.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #14.2, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32  

> close #14.2

> close #14.1

> hide #!8 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> show #!10 models

> hide #!10 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> volume flip #6

Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #15, grid size
600,600,600, pixel 0.823, shown at step 1, values float32  

> color zone #15 near #12 distance 4.94

> color zone #15 near #12 distance 4.96

> color zone #15 near #12 distance 5.9

> volume splitbyzone #15

Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #16.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #16.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  

> color zone #16.1 near #11 distance 4.94

> color zone #16.1 near #11 distance 4.7

> color zone #16.1 near #11 distance 6.39

> color zone #16.1 near #11 distance 6.48

> color zone #16.1 near #11 distance 6.82

> color zone #16.1 near #11 distance 6.91

> color zone #16.1 near #11 distance 5.55

> color zone #16.1 near #11 distance 5.63

> color zone #16.1 near #11 distance 2.78

[Repeated 2 time(s)]

> volume splitbyzone #16.1

Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #17.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #17.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  

> close #17.2

> close #17.1

> color zone #16.1 near #11 distance 2.75

> color zone #16.1 near #11 distance 3.78

> color zone #16.1 near #11 distance 3.83

> color zone #16.1 near #11 distance 4.47

> volume splitbyzone #16.1

Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #18.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #18.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32  

> volume #13.2 level 0.09516

> color zone #10 near #12 distance 4.94

> color zone #10 near #12 distance 5.01

> color zone #10 near #12 distance 32.15

> color zone #10 near #12 distance 34.28

> color zone #10 near #12 distance 28.65

> color zone #10 near #12 distance 26.87

> volume splitbyzone #10

Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #19.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32  
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #19.2, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32  

> volume #19.2 level 0.1306

> volume #19.2 level 0.1355

> ui tool show ""Hide Dust""

> surface dust #19.2 size 4.94

> surface dust #19.2 size 5.15

> surface dust #19.2 size 12.08

> save
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Figs/Figures_v02.cxs

> lighting flat

> show #!4 models

> hide #!4 models

> lighting full

> lighting simple

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> color zone #5 near #4 distance 5.23

> show #!5 models

> color zone #5 near #4 distance 5.41

> color zone #5 near #4 distance 14.34

> color zone #5 near #4 distance 15.49

> color zone #5 near #4 distance 9.52

> color zone #5 near #4 distance 9.27

> color zone #5 near #4 distance 8.48

> hide #!13.2 models

> show #!13.2 models

> hide #!13.2 models

> show #!13.2 models

> hide #!13.2 models

> show #!13.2 models

> hide #!13.2 models

> show #!13.2 models

> hide #!13.2 models

> volume splitbyzone #5

Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 0 as #20.1, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32  
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 1 as #20.2, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32  

> surface dust #20.2 size 4.94

> save
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Figs/Figures_v02.cxs

——— End of log from Mon May 26 07:46:14 2025 ———

opened ChimeraX session  

> hide #!19.2 models

> show #!19.2 models

> color #19.2 #f1a805ff models

> color #19.2 #e0ac70ff models

> color #19.2 #d8a768ff models

> hide #!16.2 models

> show #!16.2 models

> color #16.2 #d8a768ff models

> hide #!13.2 models

> show #!13.2 models

> color #13.2 #9d7982ff models

> hide #!20.2 models

> show #!20.2 models

> hide #!20.2 models

> open /Users/meserethaile/Downloads/cryosparc_P4_J2386_005_volume_map.mrc

Opened cryosparc_P4_J2386_005_volume_map.mrc as #21, grid size 600,600,600,
pixel 0.823, shown at level 0.0115, step 4, values float32  

> ui tool show CliX

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> volume flip #21

Opened cryosparc_P4_J2386_005_volume_map.mrc z flip as #22, grid size
600,600,600, pixel 0.823, shown at step 1, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #22 level 0.09923

> ui tool show ""Color Zone""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> color zone #22 near #4 distance 4.94

> color zone #22 near #4 distance 5.04

> color zone #22 near #4 distance 9.82

> color zone #22 near #4 distance 9.49

> volume splitbyzone #22

Opened cryosparc_P4_J2386_005_volume_map.mrc z flip 0 as #23.1, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32  
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip 1 as #23.2, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32  

> color #23.2 #5e718bff models

> hide #!18.2 models

> show #!18.2 models

> color #18.2 #c2754cff models

> volume #23.2 level 0.1074

> hide #11 models

> hide #!12 models

> color #18.2 #99a99aff models

> lighting flat

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Cart01.png width
> 1320 height 877 supersample 3 transparentBackground true

> turn x -90

> save /Users/meserethaile/Desktop/image18.png supersample 3

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Cart02.png width
> 1320 height 877 supersample 3 transparentBackground true

> turn x 90

> turn y 180

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Cart03.png width
> 1320 height 877 supersample 3 transparentBackground true

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting soft

> lighting simple

> lighting flat

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting full

[Repeated 1 time(s)]

> lighting shadows false

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Fig01.png width
> 1320 height 877 supersample 3 transparentBackground true

> turn y -180

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Fig02.png width
> 1320 height 877 supersample 3 transparentBackground true

> turn x -90

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Fig03.png width
> 1320 height 877 supersample 3 transparentBackground true

> show #!4 models

> hide #!4 models

> show #!12 models

> show #11 models

> color #12 #d8a768ff

> color #11 #99a99aff

> color #8 #9d7982ff

> show #!8 models

> hide #!18.2 models

> hide #!19.2 models

> hide #!16.2 models

> hide #!13.2 models

> hide #!23.2 models

> show #!23.2 models

> hide #!23.2 models

> ui tool show ""Side View""

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Fig04.png width
> 1320 height 877 supersample 3 transparentBackground true

> turn x 90

> show #!4 models

> color #4 grey

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Fig05.png width
> 1320 height 877 supersample 3 transparentBackground true

> save
> /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Map_model_figs_v02.cxs

——— End of log from Sat May 31 21:34:44 2025 ———

opened ChimeraX session  

> hide #11 models

> show #11 models

> color #11 #7da99aff

> color #11 #7ca99aff

> color #11 #78a99aff

> color #11 #70a99aff

> color #11 #6da99aff

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./newgreen1.png
> width 1984 height 1296 supersample 3

> ui tool show CliX

> turn x -90

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./newgreen2.png
> width 1984 height 1237 supersample 3

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> ui tool show ""Side View""

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./newgreen3.png
> width 1984 height 1237 supersample 3

> turn x 90

> lighting shadows true

> lighting shadows false

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./newgreen4.png
> width 1984 height 1237 supersample 3

[Repeated 1 time(s)]

> color #4 #bfbfbfff

> color #4 grey

> color #4 #acacacff

> color #4 #aaaaaaff

> color #4 #abababff

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./newgrey1.png
> width 1984 height 1237 supersample 3

> hide #11 models

> hide #!12 models

> show #!19.2 models

> show #!16.2 models

> show #!18.2 models

> show #11 models

> color #11 #9c9c9cff

> color #18.2 #a3dfceff models

> hide #11 models

> show #11 models

> color #11 #a3dfceff

> hide #11 models

> show #11 models

> hide #11 models

> save
> /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Map_model_figs_v03_newcolors.cxs

> hide #!16.2 models

> hide #!19.2 models

> show #!12 models

> show #11 models

> hide #!18.2 models

> color #11 #99a99aff

> color #11 #67a99aff

> color #11 #5ea99aff

> color #11 #60a99aff

> color #11 #61a99aff

> color #11 #65a99aff

> color #11 #66a99aff

> color #11 #69a99aff

> color #11 #68a99aff

> color #11 #64a99aff

> hide #11 models

> color #18.2 #64a99aff models

> show #!18.2 models

> show #!13.2 models

> show #!16.2 models

> hide #!12 models

> show #!23.2 models

> hide #!4 models

> show #!19.2 models

> hide #!19.2 models

> show #!19.2 models

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./mapnew1.png
> width 1984 height 1237 supersample 3

> turn x -90

> hide #!8 models

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./mapnew2png.png
> width 1984 height 1237 supersample 3

> turn x 90

> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./mapnew1.png
> width 1984 height 1237 supersample 3

> save
> /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Map_model_figs_v03_newcolors.cxs

——— End of log from Tue Jun 3 19:59:46 2025 ———

opened ChimeraX session  

> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/July2025/AMA1-RON_coot17-branch2a.pdb

Summary of feedback from opening
/Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/July2025/AMA1-RON_coot17-branch2a.pdb  
---  
warning | PDB SEQRES record for chain B is incomplete. Ignoring input sequence records as basis for sequence.  
  
Chain information for AMA1-RON_coot17-branch2a.pdb #24  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> close #24

> close #1

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> close #2

> show #!3 models

> hide #!3 models

> close #3

> close #4

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> close #6

> show #!7 models

> hide #!7 models

> close #9

> show #!10 models

> hide #!10 models

> close #10

> show #!12 models

> hide #!12 models

> show #11 models

> hide #11 models

> show #!8 models

> hide #!8 models

> hide #!23.2 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!16.2 models

> show #!16.2 models

> hide #!16.2 models

> show #!16.2 models

> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/June2025/CS_J2730_003_map_sharp_zflip_resam.mrc

Opened CS_J2730_003_map_sharp_zflip_resam.mrc as #1, grid size 600,600,600,
pixel 0.823, shown at level 0.00632, step 4, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #1 step 1

> close #23

> volume #1 level 0.07624

> volume #1 level 0.07974

> hide #!19.2 models

> ui tool show ""Hide Dust""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> surface dust #1 size 4.94

> volume #1 level 0.09722

> color #22 #d8a768ff models

> show #!22 models

> hide #!22 models

> color #1 #d8a768ff models

> volume #1 level 0.1532

> volume #1 level 0.1182

> show #!5 models

> hide #!5 models

> show #!5 models

> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/July2025/AMA1-RON_coot17-2a.pdb

Summary of feedback from opening
/Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/July2025/AMA1-RON_coot17-2a.pdb  
---  
warning | PDB SEQRES record for chain B is incomplete. Ignoring input sequence records as basis for sequence.  
  
Chain information for AMA1-RON_coot17-2a.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> show #!2 target m

> hide #!20 models

> hide #!19 models

> hide #!18.2 models

> hide #!18 models

> hide #17 models

> hide #!16.2 models

> hide #!16 models

> hide #14 models

> hide #!13.2 models

> hide #!13 models

> hide #!5 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #11 models

> hide #11 models

> show #!18.2 models

> hide #!18.2 models

> show #!5 models

> ui tool show ""Color Zone""

Drag select of 2464 residues, 6 pseudobonds  

> select up

20536 atoms, 20917 bonds, 6 pseudobonds, 2508 residues, 2 models selected  

> select up

21149 atoms, 21545 bonds, 6 pseudobonds, 2592 residues, 2 models selected  

> select up

24379 atoms, 24851 bonds, 7 pseudobonds, 2993 residues, 2 models selected  

> select down

21149 atoms, 21545 bonds, 6 pseudobonds, 2592 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> save
> /Users/meserethaile/Desktop/AMA1-RON2/Manuscript/Figures_v01/AMA1-RON_coot17-2a-AMA1.pdb
> models #2

> color zone #5 near #2 distance 8.37

> color zone #5 near #2 distance 8.51

> color zone #5 near #2 distance 9.49

> color single #5

> color zone #5 near #2 distance 9.49

> color zone #5 near #2 distance 9.38

> color zone #5 near #2 distance 764.89

> color zone #5 near #2 distance 823

> color zone #5 near #2 distance 6.11

> hide #!18 models

> hide #!5 models

> show #!5 models

> volume #20.2 level 0.09497

> volume #20.2 level 0.1661

> hide #!20.2 models

> volume #5 level 0.1657

> color zone #5 near #2 distance 6.11

> ui tool show ""Fit in Map""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> fitmap #2 inMap #5

Fit molecule AMA1-RON_coot17-2a.pdb (#2) to map
cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip (#5) using 3230 atoms  
average map value = 0.1745, steps = 92  
shifted from previous position = 4.59  
rotated from previous position = 4.84 degrees  
atoms outside contour = 1589, contour level = 0.16572  
  
Position of AMA1-RON_coot17-2a.pdb (#2) relative to
cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.99722033 -0.05751848 0.04736287 1.36165169  
0.05934502 0.99750995 -0.03810588 -2.20762168  
-0.04505314 0.04081071 0.99815064 2.71122437  
Axis 0.46807268 0.54814092 0.69314465  
Axis point 49.71397994 10.63849155 0.00000000  
Rotation angle (degrees) 4.83574496  
Shift along axis 1.30653483  
  

> color single #5

> color zone #5 near #2 distance 6.11

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> open /Users/meserethaile/Downloads/cryosparc_P4_J3019_019_volume_map.mrc

Opened cryosparc_P4_J3019_019_volume_map.mrc as #3, grid size 600,600,600,
pixel 0.823, shown at level 0.00748, step 4, values float32  

> hide #!3 models

> close #3

> save
> /Users/meserethaile/Desktop/AMA1-RON2/Manuscript/Figures_v01/Fig1_v02.cxs

——— End of log from Wed Jul 16 16:11:23 2025 ———

opened ChimeraX session  

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> open ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb""

Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/composite_J2546-J2730-J2902-J2614 copy.mrc""

Opened composite_J2546-J2730-J2902-J2614 copy.mrc as #4, grid size
600,600,600, pixel 0.823, shown at level 0.162, step 4, values float32  

> show #!15 models

> hide #!15 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #4 step 1

> volume #4 level 0.7613

> volume #4 level 0.8394

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> show #!3 models

> ui tool show CliX

> split #3 chains

Split AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb (#3) into 4 models  
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A
#3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb B
#3.2  
---  
Chain | Description  
B | No description available  
  
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb C
#3.3  
---  
Chain | Description  
C | No description available  
  
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb D
#3.4  
---  
Chain | Description  
D | No description available  
  

> hide #!4 models

> select add #3.4

3230 atoms, 3313 bonds, 1 pseudobond, 401 residues, 2 models selected  

> select subtract #3.4

Nothing selected  

> hide #!3.4 models

> hide #!3.3 models

> hide #3.2 models

> hide #!3.1 models

> show #!3.1 models

> close #2

> hide #!3 models

> show #!3 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> color #3.1 #9d7982ff

> show #3.2 models

> hide #3.2 models

> show #3.2 models

> color #3.2 #64a99aff

> show #!3.3 models

> color #3.3 #f1a805ff

> color #3.3 #d8a768ff

> show #!3.4 models

> color #3.4 #6699ffff

> color #3.4 #788ba9ff

> ui tool show ""Side View""

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v01.cxs""

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-1.png"" width 1686 height 1098 supersample 3

> close #11#8,12

> show #!4 models

> hide #!4 models

> show #!4 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui tool show ""Color Zone""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color zone #4 near #3.1 distance 4.94

> color zone #4 near #3.1 distance 5.1

> color zone #4 near #3.1 distance 7.23

> color zone #4 near #3.1 distance 7.3

> color zone #4 near #3.1 distance 5.87

> color zone #4 near #3.1 distance 5

[Repeated 1 time(s)]

> volume splitbyzone #4

Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #2.1, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #2.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  

> hide #!2.1 models

> volume #2.2 level 0.9678

> color zone #4 near #3.2 distance 5

> show #!2.1 models

> hide #!2.2 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #!2.1 models

> hide #!2 models

> show #!4 models

> volume splitbyzone #4

Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #6.1, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #6.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  

> color zone #4 near #3.3 distance 5

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!6.1 models

> hide #!6 models

> show #!6 models

> color zone #4 near #3.3 distance 5.16

> color zone #4 near #3.3 distance 5.67

> color zone #4 near #3.3 distance 5.77

> color zone #4 near #3.3 distance 6.78

> color zone #4 near #3.3 distance 6.84

> color zone #4 near #3.3 distance 6.52

> hide #!3.4 models

> hide #3.2 models

> hide #!3.1 models

> hide #!3 models

> show #!3.1 models

> hide #!3.1 models

> hide #!6 models

> hide #!6.2 models

> color single #4

> color zone #4 near #3.3 distance 6.52

> color zone #4 near #3.3 distance 7

[Repeated 1 time(s)]

> volume splitbyzone #4

Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #8.1, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #8.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  

> hide #!8.1 models

> hide #!8 models

> hide #!3.3 models

> color zone #4 near #3.4 distance 7

> show #!4 models

> color zone #4 near #3.4 distance 6

[Repeated 1 time(s)]

> color zone #4 near #3.4 distance 5

[Repeated 3 time(s)]

> volume splitbyzone #4

Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #9.1, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #9.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32  

> hide #!9.1 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> close #8.1

> close #9.1

> close #6.1

> show #!8 models

> show #!7 models

> hide #!7 models

> close #7

> show #!6.2 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> hide #4.1 models

> show #!4 models

> show #!2.2 models

> close #2.1

> show #4.1 models

> hide #4.1 models

> hide #!4 models

> close #5

> ui tool show ""Hide Dust""

> surface dust #2.2 size 4.94

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> surface dust #6.2 size 4.94

> surface dust #8.2 size 4.94

> surface dust #9.2 size 4.94

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-1.png"" width 1470 height 1098 supersample 3

> hide #!9.2 models

> hide #!8.2 models

> hide #!6.2 models

> hide #!2.2 models

> show #!3.1 models

> show #3.2 models

> show #!3.3 models

> show #!3.4 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-2.png"" width 1470 height 1098 supersample 3

> hide #!3 models

> show #!3 models

> turn x -90

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-2-1.png"" width 1470 height 1098 supersample 3

> show #!6.2 models

> hide #!3.4 models

> hide #!3.3 models

> hide #3.2 models

> hide #!3.1 models

> hide #!3 models

> show #!8.2 models

> show #!9.2 models

> show #!2.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-1-1.png"" width 1470 height 1098 supersample 3

> turn y -90

> turn y 90

> turn x 90

> turn y 180

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-3-1.png"" width 1470 height 1098 supersample 3

> hide #!2.2 models

> show #!3.4 models

> show #!3.3 models

> show #3.2 models

> show #!3.1 models

> hide #!6.2 models

> hide #!8.2 models

> hide #!9.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-3.png"" width 1470 height 1098 supersample 3

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v01.cxs""

——— End of log from Wed Aug 6 11:59:41 2025 ———

opened ChimeraX session  

> close #14,17#13,15-16,18-22

> show #!9.2 models

> hide #!9.2 models

> show #!9.2 models

> hide #!9.2 models

> hide #!3.3 models

> hide #3.2 models

> hide #!3.4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> volume #4 change surface color #6699ff

> hide #!3.1 models

> hide #!4 models

> show #!4 models

> show #4.1 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> color #4 grey models

> color #4 #404040ff models

> color #4 grey models

> volume #4 level 0.3966

> ui tool show ""Color Zone""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> open ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb""

Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> color zone #4 near #5 distance 4.94

> color zone #4 near #5 distance 5.05

> color zone #4 near #5 distance 7.87

> color zone #4 near #5 distance 11.07

> color zone #4 near #5 distance 11.71

> color zone #4 near #5 distance 20.07

> color zone #4 near #5 distance 12.39

> color zone #4 near #5 distance 24.93

> color zone #4 near #5 distance 20.85

> color zone #4 near #5 distance 39.26

> color zone #4 near #5 distance 39

> color zone #4 near #5 distance 3

> color zone #4 near #5 distance 1

> color zone #4 near #5 distance 18

> color zone #4 near #5 distance 189

> color zone #4 near #5 distance 18

> color zone #4 near #5 distance 1

> color zone #4 near #5 distance 19

> color zone #4 near #5 distance 1

> color zone #4 near #5 distance 17

> volume #4 level 0.4677

> volume #4 level 0.5388

> color zone #4 near #5 distance 1

> color zone #4 near #5 distance 12

> color zone #4 near #5 distance 1

> color zone #4 near #5 distance 8

> color zone #4 near #5 distance 6

> ui tool show ""Hide Dust""

> surface dust #4 size 4.94

> surface dust #4 size 4.93

> surface dust #4 size 2.98

> volume #4 level 0.4045

> color zone #4 near #5 distance 7

> color zone #4 near #5 distance 9

> volume splitbyzone #4

Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #7.1, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #7.2, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 2 as #7.3, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 3 as #7.4, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32  
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 4 as #7.5, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32  

> hide #!7.1 models

> show #!7.1 models

> hide #!7.1 models

> show #!7.1 models

> close #7.2-5

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #!7.1 models

> show #!7.1 models

> volume #7.1 level 0.4377

> surface dust #7.1 size 4.94

> volume #7.1 level 0.3952

> surface dust #7.1 size 4.97

> surface dust #7.1 size 7.19

> hide #!5 models

> ui tool show ""Map Eraser""

> volume erase #7.1 center 241.98,202.77,305.6 radius 20.333

> volume erase #7.1 center 280.23,164.5,268.59 radius 20.333

> volume erase #7.1 center 217.03,293.11,207.92 radius 20.333

> hide #!7.1 models

> show #!7.1 models

> color #7.1 #bfbfbfff models

> color #7.1 #404040ff models

> color #7.1 grey models

> color #7.1 #80808080 models

> volume erase #7.1 center 198.09,236.21,234.68 radius 20.246

> volume erase #7.1 center 197.72,249.34,219 radius 20.246

> show #3.2 models

> show #!3.3 models

> show #!3.4 models

> show #!3.1 models

> ui tool show ""Side View""

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v03-RON2.cxs""

> hide #!3.4 models

> hide #3.2 models

> hide #!3.3 models

> hide #!7.1 models

> ui tool show CliX

> setattr m autochain false

Assigning autochain attribute to 29 items  
Traceback (most recent call last):  
File ""/Users/meserethaile/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py"", line 514, in event  
done = self._keypress_event(event)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/meserethaile/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py"", line 388, in _keypress_event  
done = self._event_return(event)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File ""/Users/meserethaile/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py"", line 493, in _event_return  
self.run_command()  
File ""/Users/meserethaile/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py"", line 72, in run_command  
run(self._session, line)  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py"", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py"", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/setattr.py"", line 148, in set_attr  
if attr_name not in type_attrs(class_):  
^^^^^^^^^^^^^^^^^^  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py"", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
AttributeError: type object 'Volume' has no attribute '_attr_registration'  
  
AttributeError: type object 'Volume' has no attribute '_attr_registration'  
  
File
""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py"", line 69, in type_attrs  
attrs.extend(t._attr_registration.reg_attr_info.keys())  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> setattr #3.1 autochain false

Missing or invalid ""attrValue"" argument: Expected a text string  

> select clear

[Repeated 1 time(s)]

> hide #!3.1 atoms

> hide #!3.1 cartoons

> show #!3.1 cartoons

> ui tool show ""Selection Inspector""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> setattr =sel p display false

Assigning display attribute to 1 item  

> select clear

[Repeated 6 time(s)]

> ui tool show ""Selection Inspector""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> setattr =sel p display false

Assigning display attribute to 1 item  

> show #3.2 models

> hide #3.2 models

> show #3.2 models

> hide #3.2 models

> hide #!3.1 models

> select add #3.1

10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 2 models selected  

> select subtract #3.1

Nothing selected  

> show #!7.1 models

> vop gaussian #7.1 sdev 2.47

Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 gaussian as #10, grid size
600,600,600, pixel 0.823, shown at step 1, values float32  

> close #10

> show #!7.1 models

> hide #!7.1 models

> show #!3.1 models

> show #3.2 models

> hide #3.2 models

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> lighting full

> lighting simple

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows false

> graphics silhouettes true

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting full

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting simple

> view orient

Drag select of 366 residues  

> select up

3848 atoms, 3927 bonds, 461 residues, 1 model selected  

> select up

10058 atoms, 10274 bonds, 1228 residues, 1 model selected  

> select down

3848 atoms, 3927 bonds, 461 residues, 1 model selected  

> select clear

Drag select of 578 residues  

> select up

5000 atoms, 5106 bonds, 604 residues, 1 model selected  

> select down

4794 atoms, 578 residues, 1 model selected  

> select add #3.1/A:1176

4805 atoms, 11 bonds, 579 residues, 1 model selected  

> select add #3.1/A:1175

4813 atoms, 18 bonds, 580 residues, 1 model selected  

> color sel 550C18

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select clear

Alignment identifier is 3.1/A  
Alignment identifier is 3.2/B  
Alignment identifier is 3.3/C  
Alignment identifier is 3.4/D  
Alignment identifier is 5/A  
Alignment identifier is 5/B  
Alignment identifier is 5/C  
Alignment identifier is 5/D  

> select #3.1/A:821

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3.1/A:821-1217

2738 atoms, 2799 bonds, 1 pseudobond, 331 residues, 2 models selected  

> select #3.1/A:1237-1238

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #3.1/A:821-1238

2903 atoms, 2966 bonds, 1 pseudobond, 352 residues, 2 models selected  

> select #3.1/A:1349

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3.1/A:821-1349

3822 atoms, 3909 bonds, 1 pseudobond, 463 residues, 2 models selected  

> select #3.1/A:1489

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3.1/A:821-1489

4641 atoms, 4742 bonds, 2 pseudobonds, 560 residues, 2 models selected  

> select
> #3.1/A:828-846,926-930,934-946,951-964,973-996,1009-1020,1034-1039,1048-1066,1073-1086,1089-1094,1098-1100,1108-1112,1117-1131,1133-1137,1147-1153,1156-1166,1185-1187,1198-1227,1239-1250,1264-1266,1279-1307,1312-1318,1325-1332,1345-1347,1358-1366,1415-1450,1454-1459,1461-1472,1476-1487,1493-1503,1507-1512,1521-1531,1534-1551,1555-1563,1570-1575,1581-1585,1595-1601,1606-1621,1623-1647,1658-1686,1689-1707,1711-1715,1717-1732,1750-1765,1785-1800,1806-1826,1829-1831,1850-1852,1855-1887,1890-1898,1902-1907,1913-1915,1917-1921,1925-1933,1936-1944,1949-1966,1970-1978,1980-2027,2056-2058,2063-2068,2070-2072,2075-2078,2080-2082,2085-2098,2100-2123,2127-2155

6847 atoms, 6923 bonds, 825 residues, 1 model selected  

> select #3.1/A:1492

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3.1/A:821-1492

4663 atoms, 4765 bonds, 2 pseudobonds, 563 residues, 2 models selected  

> select #3.1/A:1507-1508

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3.1/A:1507-1513

55 atoms, 55 bonds, 7 residues, 1 model selected  

> select #3.1/A:1503

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3.1/A:1494-1503

93 atoms, 94 bonds, 10 residues, 1 model selected  

> select #3.1/A:1492

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3.1/A:821-1492

4663 atoms, 4765 bonds, 2 pseudobonds, 563 residues, 2 models selected  

> select #3.1/A:1578

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3.1/A:1578

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #3.1

10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 2 models selected  

> select subtract #3.1

Nothing selected  

> select add #3

24900 atoms, 25398 bonds, 7 pseudobonds, 3059 residues, 8 models selected  

> select subtract #3

Nothing selected  

> show #!7.1 models

> hide #!7.1 models

> coulombic #!3.1

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic #!3.1

Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> show #!3.1 atoms

[Repeated 1 time(s)]

> color #!3.1 bychain

> color #!3.1 byhetero

[Repeated 1 time(s)]

> color #!3.1 bychain

> hide #!3.1 cartoons

> show #!3.1 cartoons

> hide #!3.1 surfaces

> hide #!3.1 atoms

> show #!3.1 cartoons

> color #3.1 #9d7982ff

> select clear

> select #3.1/A:1411

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3.1/A:1493

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3.1/A:1493-1831

2795 atoms, 2847 bonds, 339 residues, 1 model selected  

> select #3.1/A:1493-1494

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3.1/A:1493-1863

3055 atoms, 3113 bonds, 371 residues, 1 model selected  

> select #3.1/A:1948

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3.1/A:1493-1948

3738 atoms, 3815 bonds, 456 residues, 1 model selected  

> select #3.1/A:1968-1969

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3.1/A:1493-1969

3903 atoms, 3982 bonds, 477 residues, 1 model selected  

> select #3.1/A:2027-2028

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3.1/A:1992-2028

295 atoms, 297 bonds, 37 residues, 1 model selected  

> select #3.1/A:1978-1979

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3.1/A:1493-1979

3993 atoms, 4076 bonds, 487 residues, 1 model selected  

> select
> #3.1/A:828-846,926-930,934-946,951-964,973-996,1009-1020,1034-1039,1048-1066,1073-1086,1089-1094,1098-1100,1108-1112,1117-1131,1133-1137,1147-1153,1156-1166,1185-1187,1198-1227,1239-1250,1264-1266,1279-1307,1312-1318,1325-1332,1345-1347,1358-1366,1415-1450,1454-1459,1461-1472,1476-1487,1493-1503,1507-1512,1521-1531,1534-1551,1555-1563,1570-1575,1581-1585,1595-1601,1606-1621,1623-1647,1658-1686,1689-1707,1711-1715,1717-1732,1750-1765,1785-1800,1806-1826,1829-1831,1850-1852,1855-1887,1890-1898,1902-1907,1913-1915,1917-1921,1925-1933,1936-1944,1949-1966,1970-1978,1980-2027,2056-2058,2063-2068,2070-2072,2075-2078,2080-2082,2085-2098,2100-2123,2127-2155

6847 atoms, 6923 bonds, 825 residues, 1 model selected  

> select #3.1/A:2059-2060

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #3.1/A:2059-2061

19 atoms, 18 bonds, 3 residues, 1 model selected  

> mlp sel

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  
To also show corresponding color key, enter the above mlp command and add key
true  

> select clear

> mlp #!3.1

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic #!3.1

Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> rainbow #!3.1

> mlp #!3.1

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  
To also show corresponding color key, enter the above mlp command and add key
true  

> rainbow #!3.1

> mlp #!3.1

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!3.1 surfaces

> select add #3.1

10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 2 models selected  

> color #3.1 #d8a768ff

> color #3.1 #9d7982ff

> select subtract #3.1

1 model selected  

> select add #3.1

10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 2 models selected  

> select subtract #3.1

1 model selected  

> select
> #3.1/A:828-846,926-930,934-946,951-964,973-996,1009-1020,1034-1039,1048-1066,1073-1086,1089-1094,1098-1100,1108-1112,1117-1131,1133-1137,1147-1153,1156-1166,1185-1187,1198-1227,1239-1250,1264-1266,1279-1307,1312-1318,1325-1332,1345-1347,1358-1366,1415-1450,1454-1459,1461-1472,1476-1487,1493-1503,1507-1512,1521-1531,1534-1551,1555-1563,1570-1575,1581-1585,1595-1601,1606-1621,1623-1647,1658-1686,1689-1707,1711-1715,1717-1732,1750-1765,1785-1800,1806-1826,1829-1831,1850-1852,1855-1887,1890-1898,1902-1907,1913-1915,1917-1921,1925-1933,1936-1944,1949-1966,1970-1978,1980-2027,2056-2058,2063-2068,2070-2072,2075-2078,2080-2082,2085-2098,2100-2123,2127-2155

6847 atoms, 6923 bonds, 825 residues, 1 model selected  

> select #3.1/A:1980

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3.1/A:1980-2027

391 atoms, 400 bonds, 48 residues, 1 model selected  

> select #3.1/A:2092

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

106 atoms, 108 bonds, 14 residues, 2 models selected  

> select up

6076 atoms, 6202 bonds, 747 residues, 2 models selected  

> select down

106 atoms, 108 bonds, 14 residues, 2 models selected  

> select add #3.1/A:2081

118 atoms, 120 bonds, 15 residues, 2 models selected  

> select add #3.1/A:2083

129 atoms, 131 bonds, 16 residues, 2 models selected  

> select up

149 atoms, 154 bonds, 19 residues, 2 models selected  

> select add #3.1/A:2077

155 atoms, 159 bonds, 20 residues, 2 models selected  

> select add #3.1/A:2079

159 atoms, 162 bonds, 21 residues, 2 models selected  

> select up

183 atoms, 189 bonds, 24 residues, 2 models selected  

> show #!7.1 models

> hide #!7.1 models

> show #!7.1 models

> hide #!7.1 models

> show #!7.1 models

> hide #!7.1 models

> show #!3.4 models

> hide #!3.4 models

> show #!7.1 models

> coulombic sel

Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select #3.1/A:2118

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select
> #3.1/A:828-846,926-930,934-946,951-964,973-996,1009-1020,1034-1039,1048-1066,1073-1086,1089-1094,1098-1100,1108-1112,1117-1131,1133-1137,1147-1153,1156-1166,1185-1187,1198-1227,1239-1250,1264-1266,1279-1307,1312-1318,1325-1332,1345-1347,1358-1366,1415-1450,1454-1459,1461-1472,1476-1487,1493-1503,1507-1512,1521-1531,1534-1551,1555-1563,1570-1575,1581-1585,1595-1601,1606-1621,1623-1647,1658-1686,1689-1707,1711-1715,1717-1732,1750-1765,1785-1800,1806-1826,1829-1831,1850-1852,1855-1887,1890-1898,1902-1907,1913-1915,1917-1921,1925-1933,1936-1944,1949-1966,1970-1978,1980-2027,2056-2058,2063-2068,2070-2072,2075-2078,2080-2082,2085-2098,2100-2123,2127-2155

6847 atoms, 6923 bonds, 825 residues, 1 model selected  

> select #3.1/A:2123

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3.1/A:2100-2123

206 atoms, 210 bonds, 24 residues, 1 model selected  

> select #3.1/A:1763

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3.1/A 949-1272

Expected a keyword  

> select #3.1/949-1272

Nothing selected  

> select #3.1:949-1272

2654 atoms, 2714 bonds, 324 residues, 1 model selected  

> select #3.1:1857-2062

1639 atoms, 1678 bonds, 206 residues, 1 model selected  

> hide #!7.1 models

> hide sel surfaces

> select clear

> hide #!3.1 surfaces

> mlp #!3.1

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!3.1 surfaces

> select #3.1/A:1761

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #3.1/A:2101

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select up

341 atoms, 347 bonds, 40 residues, 2 models selected  

> mlp sel

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp sel key true

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  

> key lipophilicity :-20 :0 :20 showTool true

> ui mousemode right ""color key""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select #3.1/A:2077

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #3.1/A:2064

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select add #3.1/A:2072

19 atoms, 16 bonds, 3 residues, 2 models selected  

> select add #3.1/A:2070

30 atoms, 27 bonds, 4 residues, 2 models selected  

> select add #3.1/A:2074

38 atoms, 34 bonds, 5 residues, 2 models selected  

> select up

109 atoms, 109 bonds, 15 residues, 2 models selected  

> select up

6076 atoms, 6202 bonds, 747 residues, 2 models selected  

> select down

109 atoms, 109 bonds, 15 residues, 2 models selected  

> select add #3.1/A:2069

116 atoms, 115 bonds, 16 residues, 2 models selected  

> mlp sel

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> select clear

> select #3.1/A:2028

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3.1/A:2061

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #3.1/A:2028

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select up

86 atoms, 85 bonds, 14 residues, 2 models selected  

> select clear

Drag select of 26 residues  

> select up

220 atoms, 224 bonds, 31 residues, 2 models selected  

> select up

6076 atoms, 6202 bonds, 747 residues, 2 models selected  

> select down

220 atoms, 224 bonds, 31 residues, 2 models selected  

> select add #3.1/A:2059

226 atoms, 229 bonds, 32 residues, 2 models selected  

> select add #3.1/A:2060

233 atoms, 235 bonds, 33 residues, 2 models selected  

> select add #3.1/A:2061

239 atoms, 240 bonds, 34 residues, 2 models selected  

> ui mousemode right ""map eraser""

> mlp sel key true

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  

> key lipophilicity :-20 :0 :20 showTool true

> ui mousemode right ""color key""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> key delete

> ui mousemode right ""map eraser""

> select #3.1/A:1850

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3.1/A:1850

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3.1/A:1802

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3.1/A:1802-1878

624 atoms, 638 bonds, 77 residues, 1 model selected  

> show #!3.3 models

> hide #!3.3 models

> show #!3.3 models

> open /Users/meserethaile/Downloads/cryosparc_P4_J3693_004_volume_map.mrc

Opened cryosparc_P4_J3693_004_volume_map.mrc as #10, grid size 600,600,600,
pixel 0.823, shown at level 0.0115, step 4, values float32  

> close #10

> hide sel surfaces

> select add #3.1

10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 3 models selected  

> hide sel surfaces

> select clear

> show #!7.1 models

> hide #!7.1 models

> show #!7.1 models

> show #!3.4 models

> hide #!7.1 models

> show #!7.1 models

> hide #!7.1 models

> hide #!3.4 models

Drag select of 42 residues  

> select up

680 atoms, 694 bonds, 89 residues, 2 models selected  

> select down

299 atoms, 42 residues, 2 models selected  
Drag select of 56 residues  
[Repeated 1 time(s)]

> select #3.1/A:2058-2059

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #3.1/A:2058-2073

112 atoms, 112 bonds, 16 residues, 1 model selected  
Drag select of 5 residues  

> show sel atoms

> coulombic sel

Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> select clear

Drag select of 4 atoms, 20 residues, 2 bonds  

> select subtract #3.1/A:2019

140 atoms, 2 bonds, 19 residues, 2 models selected  

> select subtract #3.1/A:2020

132 atoms, 2 bonds, 18 residues, 2 models selected  

> select subtract #3.1/A:2021

124 atoms, 2 bonds, 17 residues, 2 models selected  

> select subtract #3.1/A:2018

118 atoms, 2 bonds, 16 residues, 2 models selected  

> show sel atoms

> coulombic sel

Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> hide sel atoms

> select clear

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v03-RON2.cxs""

——— End of log from Thu Aug 7 18:38:59 2025 ———

opened ChimeraX session  

> hide #!3.3 models

> hide #!3.1 models

> ui tool show ""Command Line Interface""

> ui tool show CliX

> show #!7.1 models

> hide #!7.1 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> open ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/composite_J2546-J2730-J2902-J2614 copy.mrc""

Opened composite_J2546-J2730-J2902-J2614 copy.mrc as #10, grid size
600,600,600, pixel 0.823, shown at level 0.162, step 4, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #10 step 1

> volume #10 level 0.9566

> volume #10 level 1.009

> show #!6.2 models

> hide #!6.2 models

> show #!6.2 models

> hide #!6.2 models

> show #!9.2 models

> show #!8.2 models

> show #!6.2 models

> hide #!6.2 models

> hide #!8.2 models

> hide #!9.2 models

> view #6.2 #8.2 #9.2 #2.2

No displayed objects specified.  

> rock y 15

> rock y 50

> rock y 80

> rock y 15 4

> rock y 15 10

> rock y 15 1

> stop

> rock y 15 4 frames 200

Repeated keyword argument ""frames""  

> rock y 15 frames 200

> rock y 80 frames 200

> stop

> rock y 80 frames 1000

> stop

> show #!9.2 models

> show #!8.2 models

> show #!2.2 models

> show #!6.2 models

> rock y 30

> stop

> hide #!6.2 models

> hide #!8.2 models

> hide #!9.2 models

> hide #!2.2 models

> rock y 30

> view #2.2

No displayed objects specified.  

> stop

> rock y 30

> open #2.2

Unrecognized file suffix '.2'  

> stop

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> volume #10 level 1.048

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /1.png"" width 1339 height 769 supersample 3
> transparentBackground true

> show #!2.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /2.png"" width 1339 height 769 supersample 3
> transparentBackground true

> show #!6.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /3.png"" width 1339 height 769 supersample 3
> transparentBackground true

> show #!8.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /4.png"" width 1339 height 769 supersample 3
> transparentBackground true

> show #!9.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /5.png"" width 1339 height 769 supersample 3
> transparentBackground true

> turn x -90

> ui tool show ""Side View""

> turn x -90

> show #!3.1 models

> show #3.2 models

> hide #3.2 models

> show #!3.3 models

> show #3.2 models

> show #!3.4 models

> hide #!2.2 models

> hide #!10 models

> hide #!9.2 models

> hide #!8.2 models

> hide #!6.2 models

> hide #3.2 models

> hide #!3.3 models

> hide #!3.4 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.png"" width 1339 height 769 supersample 3

> show #!2.2 models

> show #!7.1 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.1.png"" width 1339 height 769 supersample 3

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.1.png"" width 1339 height 769 supersample 3
> transparentBackground true

> hide #!7.1 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.2.png"" width 1339 height 769 supersample 3
> transparentBackground true

> hide #!2.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.3.png"" width 1339 height 769 supersample 3
> transparentBackground true

> show #!2.2 models

> hide #!3.1 models

> show #3.2 models

> hide #3.2 models

> show #!9.2 models

> show #!6.2 models

> show #!8.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.4.png"" width 1339 height 769 supersample 3
> transparentBackground true

> hide #!8.2 models

> hide #!9.2 models

> hide #!6.2 models

> hide #!2.2 models

> show #3.2 models

> select #3.2:740-899

1283 atoms, 1297 bonds, 160 residues, 1 model selected  

> transparency sel 40

> transparency #3.1 sel 40

Missing or invalid ""percent"" argument: Expected a number  

> transparency 40 #3.1 sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> select clear

> color #3.2:740-899 #72c1af

> transparency 30 #3.2:740-899

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #3.2:740-899 #72c1af

> transparency 30 #3.2/740-899

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color #3.2:740-899 #72c1af

> transparency 30 cartoons #3.2/740-899

Expected ',' or a keyword  

> color #3.2:740-899 #72c1af

> transparency 30 cartoons #3.2/740-899

Expected ',' or a keyword  

> colordef domaincol ffcc00

> color name domaincol ffcc00

Missing or invalid ""color"" argument: Invalid color name or specifier  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color #3.2:740-899 #72c1af

> transparency 30 cartoons #3.2:740-899

Expected ',' or a keyword  

> select #3.2:740-899

1283 atoms, 1297 bonds, 160 residues, 1 model selected  

> transparency 30 ribbons sel

Expected ',' or a keyword  

> colordef domaincol ffcc00

> color name domaincol ffcc00

Missing or invalid ""color"" argument: Invalid color name or specifier  

> namecolor domaincol ffcc00

Unknown command: namecolor domaincol ffcc00  

> color #ffcc00 #3:740-899

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> select #3.2:740-899

1283 atoms, 1297 bonds, 160 residues, 1 model selected  

> color #ffcc00 sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> select #3.2:740-899

1283 atoms, 1297 bonds, 160 residues, 1 model selected  

> color ribbons #ffcc00 sel

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color ffcc00 #3.2:740-899 target r

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select clear

> show #!6.2 models

> hide #!6.2 models

> show #!6.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /7.png"" width 1339 height 718 supersample 3
> transparentBackground true

> hide #!6.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /7.1.png"" width 1339 height 718 supersample 3
> transparentBackground true

> show #!2.2 models

> hide #!2.2 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> turn x -90

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /7.2.png"" width 1339 height 718 supersample 3
> transparentBackground true

> show #!2.2 models

> hide #!2.2 models

> show #!2.2 models

> hide #!2.2 models

> show #!2.2 models

> color #2.2 #9d798280 models

> show #!3.1 models

> hide #!2.2 models

> hide #!3.1 models

> show #!2.2 models

> color #2.2 #9d7982ff models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /7.3.png"" width 1339 height 718 supersample 3
> transparentBackground true

> color #2.2 #9d798280 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /7.4.png"" width 1339 height 718 supersample 3
> transparentBackground true

> hide #!2.2 models

> show #!3.1 models

> select add #3.1

10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 2 models selected  

> show sel surfaces

> mlp sel

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> style sel sphere

Changed 10058 atom styles  

> show sel surfaces

> color sel bypolymer

> color sel bychain

> color sel byhetero

> mlp sel

Map values for surface ""AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface"": minimum -28.48, mean -4.09, maximum 23.02  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic sel

Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> color #2.2 #9d7982ff models

> color #3.1 #9d7982ff

> select clear

> turn y 50

> turn y -50

> turn y 20

> turn y -20

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /RON4.cxs""

> hide #3.2 models

> hide #!3.1 models

> show #!3.3 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.1.png"" width 1339 height 718 supersample 3
> transparentBackground true

> turn y 90

> turn y -90

> turn x 90

> turn x -90

> turn x 40

> turn x 10

> turn x -10

> turn x 10

> turn x 40

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.2.png"" width 1339 height 718 supersample 3
> transparentBackground true

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> turn x 40

> turn x -40

> show #!3.1 models

> turn x -40

> turn x 40

> turn x -50

> turn x 50

> turn x -70

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.3.png"" width 1339 height 718 supersample 3
> transparentBackground true

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> turn x 70

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> turn x -70

> turn x 90

> hide #!3.1 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.4.png"" width 1339 height 718 supersample 3
> transparentBackground true

> show #!3.1 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.5.png"" width 1339 height 718 supersample 3
> transparentBackground true

> show #!2.2 models

> hide #!3.1 models

> show #!8.2 models

> hide #!3.3 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.6.png"" width 1339 height 718 supersample 3
> transparentBackground true

> show #!3.3 models

> hide #!2.2 models

> hide #!8.2 models

> save ""/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /RON5.cxs""

> show #!3.4 models

> hide #!3.3 models


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | Registration file '/Users/meserethaile/Library/Application Support/ChimeraX/registration' has expired  
note | available bundle cache has not been initialized yet  
  

> ui tool hide ""command line interface""

> ui tool show clix

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/August2025/AMA1-RON_coot21_recombine_rsr8_isolde_delh.pdb
> format pdb

Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> set bgColor white

Drag select of 216 residues, 1 pseudobonds  

> select up

2087 atoms, 2137 bonds, 1 pseudobond, 259 residues, 2 models selected  

> select up

3230 atoms, 3313 bonds, 1 pseudobond, 401 residues, 2 models selected  

> select up

24900 atoms, 25398 bonds, 7 pseudobonds, 3059 residues, 2 models selected  

> select down

3230 atoms, 3313 bonds, 1 pseudobond, 401 residues, 2 models selected  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16R0005ZLL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3 (22E252)
      Kernel Version: Darwin 22.4.0
      Time since boot: 2 days, 7 hours, 13 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP M27fe FHD:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    annotated-types: 0.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.5.0
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-clix: 0.1.9
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    pandas: 2.2.3
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pyarrow: 18.0.0
    pycollada: 0.8
    pydantic: 2.9.2
    pydantic-core: 2.23.4
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    starfile: 0.5.10
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX