id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
19378	Crash on Mac waking from sleep	yaohe@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x00000001fdb62080 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)


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===== Log before crash start =====
> set bgColor white

> lighting soft

> graphics silhouettes true

> ui mousemode right zoom

UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/heyao/My Drive/RaiA_2024/NAR_revision/Structural_comparison/Ca-
> raiA_flip2base_isolde_real_space_refine.pdb""

Chain information for Ca-raiA_flip2base_isolde_real_space_refine.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open ""/Users/heyao/My
> Drive/RaiA_2024/NAR_revision/Structural_comparison/Ca_raiA_structural_comparison.cxs""

Opened D_1000289662_em-volume-annotate_P1.map as #5, grid size 256,256,256,
pixel 0.856, shown at level 0.111, step 1, values float32  
Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 0.856, shown at level 0.56, step 1, values float32  

> view name session-start

opened ChimeraX session  

> show #!7 models

> close #7

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!4.1 models

> hide #!4 models

> hide #!2 models

> hide #1 models

> volume #6 level 0.2048

> close #6

> show #!5 models

> close #5

> close #1

> open ""/Users/heyao/My Drive/RaiA_2024/NAR_revision/Structural_comparison/Ca-
> raiA_flip2base_isolde_real_space_refine.pdb""

Chain information for Ca-raiA_flip2base_isolde_real_space_refine.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> show #!2 models

> show #!3 models

> show #!4 models

> cartoon style xsection oval width 1.6 thickness 1.6

> select clear

> nucleotides #1#!2-3 atoms

> style nucleic & #1#!2-3 stick

Changed 13010 atom styles  

> select clear

> hide #2.1 models

> hide #3.1 models

> hide #3.2 models

> select Mg

22 atoms, 22 residues, 1 model selected  

> hide sel atoms

> select clear

> ui tool show Matchmaker

> matchmaker #!2-3#!4.1 to #1

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8  
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9CXF_Toor_NatComm.cif, chain A (#3), sequence alignment score = 811.2  
RMSD between 180 pruned atom pairs is 0.564 angstroms; (across all 200 pairs:
1.510)  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 562.4  
RMSD between 130 pruned atom pairs is 1.210 angstroms; (across all 204 pairs:
6.174)  
  

> nucleotides #1#!2-3 tube/slab shape box

> nucleotides #1#!2-3 ladder

> nucleotides #1#!2-3 fill

> style nucleic & #1#!2-3 stick

Changed 13010 atom styles  

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> hide #1 models

> show #1 models

> hide #!3 models

> select add #1

4380 atoms, 4907 bonds, 204 residues, 1 model selected  

> color sel silver

> select clear

> show #!2 models

> select add #2

4334 atoms, 4856 bonds, 189 pseudobonds, 202 residues, 2 models selected  

> color sel cyan

> select clear

> show #!3 models

> hide #!2 models

> select add #3

4318 atoms, 4813 bonds, 200 pseudobonds, 222 residues, 3 models selected  

> color #3 #ffb2ffff

> select clear

> show #!4 models

> hide #!3 models

> show #!4.1 models

> select add #4

4826 atoms, 5406 bonds, 167 pseudobonds, 224 residues, 3 models selected  

> color sel lime green

> select clear

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #1 models

> select add #4

4826 atoms, 5406 bonds, 167 pseudobonds, 224 residues, 3 models selected  

> ui tool show ""Color Actions""

> color sel medium spring green

> select clear

> show #!2 models

> hide #!2 models

> select add #4

4826 atoms, 5406 bonds, 167 pseudobonds, 224 residues, 3 models selected  

> hide #!4 models

> show #!2 models

> select add #2

9160 atoms, 10262 bonds, 356 pseudobonds, 426 residues, 5 models selected  

> select clear

> select add #2

4334 atoms, 4856 bonds, 189 pseudobonds, 202 residues, 2 models selected  

> color sel deep sky blue

> select clear

> show #1 models

> show #!4 models

> show #!3 models

> select clear

> save ""/Users/heyao/My
> Drive/RaiA_2024/NAR_revision/Structural_comparison/Ca_raiA_structural_comparison.cxs""

> select clear

> view

> select clear

> nucleotides fill

> style nucleic stick

Changed 17836 atom styles  

> select clear

> nucleotides atoms

> style nucleic stick

Changed 17836 atom styles  

> nucleotides fill

> style nucleic stick

Changed 17836 atom styles  

> hide atoms

> select clear

> view

> view name p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p1

> view name p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> view name p2

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> nucleotides tube/slab shape box

> nucleotides fill

> style nucleic stick

Changed 17836 atom styles  

> nucleotides fill

> style nucleic stick

Changed 17836 atom styles  

> show atoms

> select clear

> select Mg

22 atoms, 22 residues, 1 model selected  

> delete sel

> select clear

> select add #1

4380 atoms, 4907 bonds, 204 residues, 1 model selected  
Alignment identifier is 1/A  

> select clear

> select #1/A:23-24

45 atoms, 50 bonds, 2 residues, 1 model selected  

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> view

> ui tool show ""Side View""

> select clear

> hide cartoons

> select clear

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:23-24

45 atoms, 50 bonds, 2 residues, 1 model selected  

> select #1/A:28

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:28

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> color byhetero

> select clear

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #1 cartoons

> cartoon style xsection oval width 1.2 thickness 1.2

> cartoon style xsection oval width 1 thickness 1

> cartoon style xsection oval width 0.6 thickness 0.6

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> open /Users/heyao/Desktop/raiA_model_refinement_20251112/Ca-
> raiA/cryosparc_P44_J306_007_volume_map_sharp.mrc

Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 0.856, shown at level 0.0348, step 1, values float32  

> volume #5 level 0.2898

> volume #5 color #b2b2b281

> volume #5 level 0.4

> volume #5 level 0.3

> select clear

> select add #1

4380 atoms, 4907 bonds, 204 residues, 1 model selected  

> show #!2 models

> hide #!2 models

> color #1 #d6d6d6ff

> color #1 #76d6ffff

> color sel byhetero

> select clear

> show #2.1 models

> hide #1 models

> show #1 models

> hide #!2 models

> select add #1

4380 atoms, 4907 bonds, 204 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel dodger blue

> color sel deep sky blue

> color sel byhetero

> select add #2

8714 atoms, 9763 bonds, 189 pseudobonds, 406 residues, 3 models selected  

> show #!2 models

> select clear

> select add #2

4334 atoms, 4856 bonds, 189 pseudobonds, 202 residues, 2 models selected  

> color sel silver

> color sel byhetero

> select clear

> hide #2.1 models

> show #2.1 models

> hide #!2 models

> select clear

> surface dust #5 size 5

> select clear

> hide #1 cartoons

> select clear

> show #!4 models

> hide #!5 models

> hide #2.1 models

> show #2.1 models

> hide #1 models

> show #1 models

> hide #2.1 models

> hide #!2 models

> hide #!4 models

> show #!5 models

> view name p3

> save ""/Users/heyao/My
> Drive/RaiA_2024/NAR_revision/Structural_comparison/Ca_raiA_structural_comparison.cxs""

> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #1 models

> show #!2 models

> hide #!5 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!2 models

> show #!5 models

> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true

> view name p3

> hide #!5 models

> hide #1 models

> show #!2 models

> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!2 models

> show #!3 models

> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!3 models

> show #!4 models

> hide #4.1.1 models

> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #1 models

> hide #!4 models

> show #!5 models

> fitmap #1 inMap #5

Fit molecule Ca-raiA_flip2base_isolde_real_space_refine.pdb (#1) to map
cryosparc_P44_J306_007_volume_map_sharp.mrc (#5) using 4380 atoms  
average map value = 0.3516, steps = 44  
shifted from previous position = 0.00487  
rotated from previous position = 0.0222 degrees  
atoms outside contour = 2228, contour level = 0.3  
  
Position of Ca-raiA_flip2base_isolde_real_space_refine.pdb (#1) relative to
cryosparc_P44_J306_007_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999994 0.00013628 -0.00032600 0.02175851  
-0.00013623 0.99999998 0.00015937 -0.00309180  
0.00032602 -0.00015933 0.99999993 -0.01345924  
Axis -0.41111243 -0.84108259 -0.35152047  
Axis point 43.03571144 0.00000000 64.70033062  
Rotation angle (degrees) 0.02220852  
Shift along axis -0.00161353  
  

> fitmap #1 inMap #5

Fit molecule Ca-raiA_flip2base_isolde_real_space_refine.pdb (#1) to map
cryosparc_P44_J306_007_volume_map_sharp.mrc (#5) using 4380 atoms  
average map value = 0.3516, steps = 28  
shifted from previous position = 0.0083  
rotated from previous position = 0.00946 degrees  
atoms outside contour = 2226, contour level = 0.3  
  
Position of Ca-raiA_flip2base_isolde_real_space_refine.pdb (#1) relative to
cryosparc_P44_J306_007_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999998 0.00008865 -0.00020163 0.00844154  
-0.00008864 0.99999999 0.00006177 -0.00169879  
0.00020164 -0.00006175 0.99999998 -0.01585479  
Axis -0.26996742 -0.88144339 -0.38752437  
Axis point 68.32965835 0.00000000 49.03806337  
Rotation angle (degrees) 0.01310664  
Shift along axis 0.00536256  
  

> hide #!5 models

> view list

Named views: p1, p2, p3, session-start  

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> view list

Named views: p1, p2, p3, session-start  

> view name p4

> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #1 models

> hide #!5 models

> show #!2 models

> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!2 models

> show #!3 models

> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!3 models

> show #!4 models

> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #!5 models

> hide #!5 models

> save /Users/heyao/Desktop/14.png width 1000 height 1000 supersample 3
> transparentBackground true

> show #1 models

> hide #!4.1 models

> hide #!4 models

> show #!5 models

> save /Users/heyao/Desktop/11.png width 1000 height 1000 supersample 3
> transparentBackground true

> hide #1 models

> hide #!5 models

> show #!2 models

> save /Users/heyao/Desktop/12.png width 1000 height 1000 supersample 3
> transparentBackground true

> hide #!2 models

> show #!3 models

> save /Users/heyao/Desktop/13.png width 1000 height 1000 supersample 3
> transparentBackground true

> hide #!3 models

> show #!4 models

> show #!4.1 models

> save /Users/heyao/Desktop/14.png width 1000 height 1000 supersample 3
> transparentBackground true

> hide #!4 models

> show #1 models

> select #1/A:80

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:80-81

42 atoms, 46 bonds, 2 residues, 1 model selected  

> view sel

> select #1/A80,81,192,183,184

Nothing selected  

> select #1/A:80,81,192,183,184

106 atoms, 116 bonds, 5 residues, 1 model selected  

> view sel

> select #1/A:80,81,182,183,184

108 atoms, 120 bonds, 5 residues, 1 model selected  

> view sel

> show #!5 models

> select clear

> hide #!5 models

> show #!2 models

> hide #!2 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #4.1.1 models

> hide #4.1.1 models

> show #4.1.1 models

> hide #4.1.1 models

> hide #!4.1 models

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!5 models

> show #4.1.1 models

> hide #4.1.1 models

> show #3.2 models

> hide #3.2 models

> show #3.2 models

> hide #3.2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!5 models

> view list

Named views: p1, p2, p3, p4, session-start  

> view name p5

> save /Users/heyao/Desktop/11.png width 1000 height 1000 supersample 3
> transparentBackground true

> hide #1 models

> hide #!5 models

> show #!2 models

> save /Users/heyao/Desktop/12.png width 1000 height 1000 supersample 3
> transparentBackground true

> hide #!2 models

> show #!3 models

> save /Users/heyao/Desktop/13.png width 1000 height 1000 supersample 3
> transparentBackground true

> hide #!3 models

> show #!4 models

> save /Users/heyao/Desktop/14.png width 1000 height 1000 supersample 3
> transparentBackground true

> hide #!4 models

> show #1 models

> show #!5 models

> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true

> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #1 models

> hide #!5 models

> show #!2 models

> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!2 models

> show #!3 models

> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!3 models

> show #!4 models

> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #1 models

> hide #!4 models

> view p5

> show #!4 models

> hide #1 models

> view

> hide #!4.1 models

> show #1 models

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> show #!2 models

> show #!3 models

> show #!4.1 models

> hide #!2 models

> show #2.1 models

> hide #2.1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #1 models

> show #1 models

> hide #!4 models

> select #1/A:28

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> show #2.1 models

> hide #2.1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #1 models

> show #1 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #1 models

> show #1 models

> select #1/A:43

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> hide #!4 models

> hide #1 models

> show #1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> select #1/A:78

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #1 models

> show #1 models

> hide #!4.1 models

> select #1/A:80

20 atoms, 21 bonds, 1 residue, 1 model selected  

> view sel

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select #1/A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4.1 models

> hide #!4.1 models

> select #1/A:97

23 atoms, 25 bonds, 1 residue, 1 model selected  

> view sel

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4.1 models

> select #1/A119

Nothing selected  

> select #1/A:119

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!4 models

> select #1/A:154

23 atoms, 25 bonds, 1 residue, 1 model selected  

> view sel

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> select #1/A:171

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> select #1/A:182

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> select #1/A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> select #1/A:184

22 atoms, 24 bonds, 1 residue, 1 model selected  

> view sel

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> view

> ui tool show Matchmaker

> matchmaker #!2-3#!4.1 to #1

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8  
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9CXF_Toor_NatComm.cif, chain A (#3), sequence alignment score = 811.2  
RMSD between 180 pruned atom pairs is 0.564 angstroms; (across all 200 pairs:
1.510)  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 562.4  
RMSD between 130 pruned atom pairs is 1.210 angstroms; (across all 204 pairs:
6.174)  
  

> show sel cartoons

> select clear

> show #1#!4.1 cartoons

> select clear

> show #2.1 models

> hide #2.1 models

> show #!3 models

Drag select of 14974 atoms, 16668 bonds, 2104 shapes, 411 residues  

> select up

17460 atoms, 16668 bonds, 813 residues, 4 models selected  

> select up

17474 atoms, 16685 bonds, 813 residues, 4 models selected  

> select up

17836 atoms, 18555 bonds, 830 residues, 4 models selected  

> select down

17474 atoms, 16685 bonds, 813 residues, 4 models selected  

> ui tool show Matchmaker

> matchmaker #!2-3#!4.1 & sel to #1 & sel

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8  
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9CXF_Toor_NatComm.cif, chain A (#3), sequence alignment score = 811.2  
RMSD between 180 pruned atom pairs is 0.564 angstroms; (across all 200 pairs:
1.510)  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 556.2  
RMSD between 129 pruned atom pairs is 1.205 angstroms; (across all 200 pairs:
3.390)  
  

Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.  

Alignment identifier is 2/A  
Alignment identifier is 3/A  
Alignment identifier is 4.1/A  
Alignment identifier is 1/A  

> ui tool show ""Show Sequence Viewer""

> ui tool show Matchmaker

> matchmaker #!2-3#!4.1 to #1

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8  
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9CXF_Toor_NatComm.cif, chain A (#3), sequence alignment score = 811.2  
RMSD between 180 pruned atom pairs is 0.564 angstroms; (across all 200 pairs:
1.510)  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 562.4  
RMSD between 130 pruned atom pairs is 1.210 angstroms; (across all 204 pairs:
6.174)  
  

> ui tool show ""Modeller Comparative""

Populating font family aliases took 123 ms. Replace uses of missing font
family ""Times"" with one that exists to avoid this cost.  

> showseqalignment

Unknown command: showseqalignment  

> matchmaker

Missing or invalid ""matchAtoms"" argument: empty atom specifier  

> matchmaker #2 to #1 showAlignment true

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8  
Alignment identifier is 1  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, 9ELY_Chiu_Nature.cif #2/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)  
  

> matchmaker #2 #3 to #1 showAlignment true

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8  
Alignment identifier is 1  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, 9ELY_Chiu_Nature.cif #2/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9CXF_Toor_NatComm.cif, chain A (#3), sequence alignment score = 811.2  
Alignment identifier is 2  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, 9CXF_Toor_NatComm.cif #3/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  
RMSD between 180 pruned atom pairs is 0.564 angstroms; (across all 200 pairs:
1.510)  
  

> matchmaker #4.1 to #1 showAlignment true

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 562.4  
Alignment identifier is 1  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, 9G7C_Bujnicki_JMB.cif #4.1/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 130 pruned atom pairs is 1.210 angstroms; (across all 204 pairs:
6.174)  
  

> select add #2

17474 atoms, 16685 bonds, 189 pseudobonds, 813 residues, 5 models selected  

> select subtract #2

13140 atoms, 11829 bonds, 611 residues, 3 models selected  

> hide #!2 models

> hide #!3 models

> select subtract #3.2

13140 atoms, 11829 bonds, 611 residues, 3 models selected  

> nucleotides sel & #1#!4.1 ladder

> nucleotides sel & #1#!4.1 slab

> style nucleic & sel & #1#!4.1 stick

Changed 8844 atom styles  

> nucleotides sel & #1#!4.1 tube/slab shape box

> select clear

> select #4.1/A:53

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #4.1/A:53-54

42 atoms, 46 bonds, 2 residues, 1 model selected  

> color sel red

> select #4.1/A:61

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #4.1/A:61-77

367 atoms, 410 bonds, 7 pseudobonds, 17 residues, 2 models selected  

> color (#!4.1 & sel) red

> select #1/A:93

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:93-99

154 atoms, 173 bonds, 7 residues, 1 model selected  

> color sel red

> select #1/A:102

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:102-104

60 atoms, 65 bonds, 3 residues, 1 model selected  

> select #1/A:105

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:105-113

186 atoms, 205 bonds, 9 residues, 1 model selected  

> select #4.1/A:110

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #4.1/A:110-118

191 atoms, 212 bonds, 9 residues, 1 model selected  

> select #4.1/A:157

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #4.1/A:157-159

66 atoms, 73 bonds, 3 residues, 1 model selected  

> color sel red

> hide #!4 models

> open /Users/heyao/Desktop/raiA_model_refinement_20251112/Ns-raiA/Ns-
> raiA_flip2base_isolde_real_space_refine.pdb

Chain information for Ns-raiA_flip2base_isolde_real_space_refine.pdb #6  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #!6 models

> open /Users/heyao/Desktop/raiA_model_refinement_20251112/Mp-raiA/Mp-
> raiA_flip2base_isolde_real_space_refinement.pdb

Chain information for Mp-raiA_flip2base_isolde_real_space_refinement.pdb #7  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> matchmaker #7 to #1 showAlignment true

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
Mp-raiA_flip2base_isolde_real_space_refinement.pdb, chain A (#7), sequence
alignment score = 328.1  
Alignment identifier is 1  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Mp-
raiA_flip2base_isolde_real_space_refinement.pdb #7/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 113 pruned atom pairs is 0.894 angstroms; (across all 153 pairs:
13.905)  
  

> select #7/A:60

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #7/A:60-71

259 atoms, 289 bonds, 12 residues, 1 model selected  

> select #7/A:99

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #7/A:99-109

230 atoms, 255 bonds, 11 residues, 1 model selected  

> select #7/A:110

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #7/A:110-121

264 atoms, 296 bonds, 12 residues, 1 model selected  

> color #7 #76d6ffff

> color #7 #b2b2b2ff

> select #1/A:2-59,70-86,88-92,169-201 #7/A:2-59,72-88,90-94,128-160

4858 atoms, 5435 bonds, 226 residues, 2 models selected  

> select #7/A:163

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A #7/A

7716 atoms, 8641 bonds, 2 pseudobonds, 359 residues, 3 models selected  
MatchMaker Alignment [ID: 1] region chain A..chain A [1-206] RMSD: 13.905  
  

> save /Users/heyao/Desktop/raiA_model_refinement_20251112/Mp-raiA/ca2mp
> format aln alignment 1

> matchmaker #7,#6 to #1 show true

Missing or invalid ""matchAtoms"" argument: only initial part ""#7"" of atom
specifier valid  

> matchmaker #7 #6 to #1 showAlignment true

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
Mp-raiA_flip2base_isolde_real_space_refinement.pdb, chain A (#7), sequence
alignment score = 328.1  
Alignment identifier is 2  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Mp-
raiA_flip2base_isolde_real_space_refinement.pdb #7/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  
RMSD between 113 pruned atom pairs is 0.894 angstroms; (across all 153 pairs:
13.905)  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
Ns-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#6), sequence
alignment score = 412.4  
Alignment identifier is 3  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Ns-
raiA_flip2base_isolde_real_space_refine.pdb #6/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3  
RMSD between 106 pruned atom pairs is 0.722 angstroms; (across all 193 pairs:
29.026)  
  

> show #!6 models

> hide #!7 models

> select #6/A:1

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #6/A:1-25

530 atoms, 589 bonds, 25 residues, 1 model selected  

> select #1/A:1

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:1-22

471 atoms, 526 bonds, 22 residues, 1 model selected  

> matchmaker #6 to #1 showAlignment true

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
Ns-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#6), sequence
alignment score = 412.4  
Alignment identifier is 1  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Ns-
raiA_flip2base_isolde_real_space_refine.pdb #6/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 106 pruned atom pairs is 0.722 angstroms; (across all 193 pairs:
29.026)  
  

> hide #!6 models

> show #!7 models

> matchmaker #7 to #1 showAlignment true

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
Mp-raiA_flip2base_isolde_real_space_refinement.pdb, chain A (#7), sequence
alignment score = 328.1  
Alignment identifier is 1  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Mp-
raiA_flip2base_isolde_real_space_refinement.pdb #7/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 113 pruned atom pairs is 0.894 angstroms; (across all 153 pairs:
13.905)  
  

> select #7/A:119

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #7/A:119-121

69 atoms, 77 bonds, 3 residues, 1 model selected  

> select #1/A:164

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:164-166

65 atoms, 72 bonds, 3 residues, 1 model selected  

> select #7/A:110

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #7/A:110-121

264 atoms, 296 bonds, 12 residues, 1 model selected  

> select #7/A:108

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #7/A:108-109

40 atoms, 43 bonds, 2 residues, 1 model selected  

> show #!6 models

> hide #!7 models

> matchmaker #1 to #6 showAlignment true

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ns-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#6) with
Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1), sequence
alignment score = 412.4  
Alignment identifier is 1  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Ns-
raiA_flip2base_isolde_real_space_refine.pdb #6/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 106 pruned atom pairs is 0.722 angstroms; (across all 193 pairs:
29.026)  
  

> save /Users/heyao/Desktop/Ns2ca format aln alignment 1

> hide #!6 models

> show #!6 models

> select #6/A:60

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:60-72

278 atoms, 310 bonds, 13 residues, 1 model selected  

> select #6/A:60-101,107-124,131-144,211-242 #1/A:23-64,74-91,98-111,162-193

4553 atoms, 5090 bonds, 212 residues, 2 models selected  

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:23-37

321 atoms, 358 bonds, 15 residues, 1 model selected  
No sequence chosen for copying  

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:23-37

321 atoms, 358 bonds, 15 residues, 1 model selected  

> color sel red

> select #1/A:70

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:70-73

80 atoms, 87 bonds, 4 residues, 1 model selected  

> color sel yellow

> select #6/A:108

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:107

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/A:74

45 atoms, 49 bonds, 2 residues, 2 models selected  

> select #1/A:93

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:93-96

89 atoms, 100 bonds, 4 residues, 1 model selected  

> color sel lime

> select #1/A:113

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:113-114

42 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> color #6 #b2b2b2ff

> select #1/A:113

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:113-114

42 atoms, 46 bonds, 2 residues, 1 model selected  

> color sel purple

> select clear

> select #1/A:115

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:144

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/A:111

43 atoms, 46 bonds, 2 residues, 2 models selected  

> select #6/A:159

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #6/A:159-202

959 atoms, 1076 bonds, 44 residues, 1 model selected  

> select #1/A:113

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:113-126

303 atoms, 339 bonds, 14 residues, 1 model selected  

> select clear

> select #1/A:115

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:171

43 atoms, 46 bonds, 2 residues, 2 models selected  

> select #6/A:172

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:185 #6/A:234

46 atoms, 50 bonds, 2 residues, 2 models selected  

> select add #6/A:172

69 atoms, 75 bonds, 3 residues, 2 models selected  

> select add #1/A:117

89 atoms, 96 bonds, 4 residues, 2 models selected  

> select subtract #1/A:117

69 atoms, 75 bonds, 3 residues, 2 models selected  

> select add #1/A:116

92 atoms, 100 bonds, 4 residues, 2 models selected  

> select #6/A:171

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #6/A:172

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/A:116

46 atoms, 50 bonds, 2 residues, 2 models selected  

> select #6/A:172

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:172-178

158 atoms, 178 bonds, 7 residues, 1 model selected  

> select add #1/A:116

181 atoms, 203 bonds, 8 residues, 2 models selected  

> select #1/A:111

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:111

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:112

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:112-115

85 atoms, 94 bonds, 4 residues, 1 model selected  

> select #6/A:159

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #6/A:159-167

193 atoms, 215 bonds, 9 residues, 1 model selected  

> select #1/A:128

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:128-130

65 atoms, 72 bonds, 3 residues, 1 model selected  

> matchmaker #1 to #6 matrix Nucleic showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ns-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#6) with
Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1), sequence
alignment score = 412.4  
Alignment identifier is 2  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Ns-
raiA_flip2base_isolde_real_space_refine.pdb #6/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  
RMSD between 106 pruned atom pairs is 0.722 angstroms; (across all 193 pairs:
29.026)  
  

> select add #1/A:65

85 atoms, 93 bonds, 4 residues, 1 model selected  

> select #6/A:197

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:189

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:190

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:133

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:134

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:191

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> hide #!6 models

> show #!4 models

> matchmaker #4.1 to #1 matrix Nucleic showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 562.4  
Alignment identifier is 1  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, 9G7C_Bujnicki_JMB.cif #4.1/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 130 pruned atom pairs is 1.210 angstroms; (across all 204 pairs:
6.174)  
  

> select #1/A:105

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:105-111

146 atoms, 161 bonds, 7 residues, 1 model selected  

> select #1/A:112

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:112-113

40 atoms, 43 bonds, 2 residues, 1 model selected  

> select #1/A:105

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:105-113

186 atoms, 205 bonds, 9 residues, 1 model selected  

> select clear

> select #4.1/A:159

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #4.1/A:159-166

172 atoms, 192 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select #4.1/A:133

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #4.1/A:133-137

109 atoms, 121 bonds, 5 residues, 1 model selected  

> select #1/A:114

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:114-120

156 atoms, 175 bonds, 7 residues, 1 model selected  

> select #4.1/A:158

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #4.1/A:158

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel black

> select add #4.1/A:121

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #4.1/A:122

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select add #4.1/A:123

87 atoms, 94 bonds, 4 residues, 1 model selected  

> hide #1 models

> show #!6 models

> matchmaker #4.1 to #6 matrix Nucleic showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Ns-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#6) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 476.2  
Alignment identifier is 1  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 9G7C_Bujnicki_JMB.cif #4.1/A,
Ns-raiA_flip2base_isolde_real_space_refine.pdb #6/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 101 pruned atom pairs is 1.063 angstroms; (across all 207 pairs:
23.093)  
  
Drag select of 236 atoms, 35 residues, 258 bonds, 79 shapes  

> select clear

Drag select of 260 atoms, 59 residues, 286 bonds, 132 shapes  

> select up

10179 atoms, 11394 bonds, 473 residues, 2 models selected  

> select down

1262 atoms, 286 bonds, 59 residues, 2 models selected  

> select clear

> select add #4.1/A:116

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:149

42 atoms, 45 bonds, 2 residues, 2 models selected  
Drag select of 260 atoms, 50 residues, 286 bonds, 115 shapes  

> select clear

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!6 models

> show #!6 models

> select #6/A:134

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:134-141

166 atoms, 183 bonds, 8 residues, 1 model selected  

> color sel red

> select #6/A:142

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #6/A:142-146

106 atoms, 117 bonds, 5 residues, 1 model selected  

> color sel red

> select #6/A:147

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:147-152

125 atoms, 138 bonds, 6 residues, 1 model selected  

> color sel red

> undo

> select #6/A:146

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:142

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #6/A:142-146

106 atoms, 117 bonds, 5 residues, 1 model selected  

> select add #4.1/A:113

129 atoms, 142 bonds, 6 residues, 2 models selected  

> select clear

> select #4.1/A:113

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #4.1/A:112

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #4.1/A:111

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #4.1/A:110

86 atoms, 92 bonds, 4 residues, 1 model selected  

> select add #6/A:146

109 atoms, 117 bonds, 5 residues, 2 models selected  

> select clear

> select #6/A:146

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #4.1/A:113

46 atoms, 50 bonds, 2 residues, 2 models selected  

> select #6/A:147

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:148

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #6/A:149

63 atoms, 67 bonds, 3 residues, 1 model selected  


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

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open ""/Users/heyao/My Drive/RaiA_2024/Figures/fig1.cxs""

restore_snapshot for ""Volume"" returned None  

restore_snapshot for ""VolumeSurface"" returned None  

restore_snapshot for ""Volume"" returned None  

restore_snapshot for ""VolumeSurface"" returned None  

restore_snapshot for ""Volume"" returned None  

restore_snapshot for ""VolumeSurface"" returned None  

restore_snapshot for ""Volume"" returned None  

restore_snapshot for ""VolumeSurface"" returned None  

restore_snapshot for ""Volume"" returned None  

restore_snapshot for ""VolumeSurface"" returned None  

restore_snapshot for ""Volume"" returned None  

restore_snapshot for ""VolumeSurface"" returned None  

restore_snapshot for ""Volume"" returned None  

restore_snapshot for ""VolumeSurface"" returned None  

restore_snapshot for ""ZoneColor"" returned None  

restore_snapshot for ""Redust"" returned None  

[Repeated 1 time(s)]

restore_snapshot for ""ZoneColor"" returned None  

restore_snapshot for ""Redust"" returned None  

[Repeated 1 time(s)]

restore_snapshot for ""ZoneColor"" returned None  

[Repeated 3 time(s)]

restore_snapshot for ""Redust"" returned None  

Log from Mon Dec 16 22:23:52 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/heyao/Desktop/fig1.cxs

Opened cryosparc_P44_J306_007_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.856, shown at level 0.06, step 1, values float32  
Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.856, shown at level 0.148, step 1, values float32  
Opened cryosparc_P44_J306_007_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.856, shown at level 0.0478, step 1, values float32  
Opened cryosparc_P44_J208_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 0.856, shown at level 0.0521, step 1, values float32  
Opened cryosparc_P44_J208_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 0.856, shown at level 0.0951, step 1, values float32  
Opened cryosparc_P44_J119_007_volume_map.mrc as #8, grid size 256,256,256,
pixel 0.856, shown at level 0.05, step 1, values float32  
Opened cryosparc_P44_J119_007_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 0.856, shown at level 0.0712, step 1, values float32  
Log from Sat Dec 14 18:45:20 2024You can double click a model's Name or ID in
the model panel to edit those fields  
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/heyao/My Drive/RaiA_2024/PDB_deposition/raiA_3.0A/raiA_OD-
> coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb""

Chain information for raiA_OD-
coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb
#1  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> lighting soft

> graphics silhouettes true

> open ""/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc""

Opened cryosparc_P44_J306_007_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.856, shown at level 0.0213, step 1, values float32  

> open ""/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map_sharp.mrc""

Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.856, shown at level 0.0348, step 1, values float32  

> ui mousemode right zoom

> hide #!2 models

> show atoms

> style stick

Changed 6580 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 6575 atom styles  

> select H

2195 atoms, 204 residues, 1 model selected  

> delete sel

> select clear

> show #!2 models

> volume #2 level 0.06175

> view

> select clear

> show #!3 models

> hide #!2 models

> hide #1 models

> volume #3 level 0.1598

> volume #3 level 0.2398

> show #1 models

> hide #!3 models

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

Drag select of 3161 atoms, 204 residues, 3480 bonds  

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

> select #1

4385 atoms, 4907 bonds, 209 residues, 1 model selected  

> select #1/1-14

Nothing selected  

> select #1/A:1-14

298 atoms, 332 bonds, 14 residues, 1 model selected  

> select #1/A:1-14,191-204

593 atoms, 661 bonds, 28 residues, 1 model selected  

> color sel orange red

> select clear

> color #1/A:1-14,191-204 orange red

> select /A:190

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #1/A:15-23,183-190 purple

> select clear

> select add /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select add /A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:184

44 atoms, 48 bonds, 2 residues, 1 model selected  

> color sel gray

> select clear

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #1/A:15-23,185-190 purple

> select clear

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:186

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #1/A:15-23,186-190 purple

> color sel light gray

> select clear

[Repeated 2 time(s)]

> select /A:24

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:25

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:26

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add /A:27

86 atoms, 92 bonds, 4 residues, 1 model selected  

> select add /A:50

106 atoms, 113 bonds, 5 residues, 1 model selected  

> select add /A:49

128 atoms, 137 bonds, 6 residues, 1 model selected  

> select add /A:48

151 atoms, 162 bonds, 7 residues, 1 model selected  

> select add /A:47

171 atoms, 183 bonds, 8 residues, 1 model selected  

> select add /A:46

193 atoms, 207 bonds, 9 residues, 1 model selected  

> select add /A:45

215 atoms, 231 bonds, 10 residues, 1 model selected  

> color #1/A:24-27,45-50 royal blue

> color sel cornflower blue

> select clear

> color #1/A:24-27,45-50 cornflower blue

> select /A:28

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:29

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add /A:30

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select add /A:31

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add /A:32

105 atoms, 112 bonds, 5 residues, 1 model selected  

> color #1/A:28-32,40-44 yellow

> select clear

> color #1/A:33-39 green

> select /A:90

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color #1/A:33-39,85-90 green

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select /A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel gray

> select clear

> select /A:29

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select /A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:35

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select /A:34

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:35

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:36

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add /A:37

86 atoms, 92 bonds, 4 residues, 1 model selected  

> select add /A:38

106 atoms, 113 bonds, 5 residues, 1 model selected  

> select add /A:39

128 atoms, 137 bonds, 6 residues, 1 model selected  

> select /A:85

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /A:34

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> select /A:85

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /A:90

40 atoms, 42 bonds, 2 residues, 1 model selected  

> color #1/A:34-39,85-90 green

> select clear

> select /A:51

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /A:52

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add /A:53

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add /A:54

82 atoms, 87 bonds, 4 residues, 1 model selected  

> color sel cyan

> select clear

> select add /A:51

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /A:52

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add /A:53

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add /A:54

82 atoms, 87 bonds, 4 residues, 1 model selected  

> select /A:177

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:176

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add /A:175

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add /A:174

89 atoms, 96 bonds, 4 residues, 1 model selected  

> select /A:174

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #1/A:51-54, 174-177 cyan

> select clear

> select /A:55

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:79

46 atoms, 50 bonds, 2 residues, 1 model selected  

> color #1/A:55-79 orange

> select clear

> view

[Repeated 1 time(s)]

> color #1/A:55-79 goldenrod rod

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

> color #1/A:55-79 goldenrod

> select /A:80

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /A:81

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select clear

> select /A:82

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /A:83

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:84

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:80

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:83

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:82

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:181

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add /A:182

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add /A:170

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select add /A:121

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select subtract /A:170

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select subtract /A:121

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add /A:81

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select add /A:180

127 atoms, 136 bonds, 6 residues, 1 model selected  

> select add /A:179

150 atoms, 161 bonds, 7 residues, 1 model selected  

> select add /A:178

173 atoms, 186 bonds, 8 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel salmon

> color sel dark salmon

> color sel salmon

> color sel light salmon

> select clear

> select add /A:178

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:179

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add /A:180

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add /A:181

86 atoms, 92 bonds, 4 residues, 1 model selected  

> select add /A:182

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select clear

> select /A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:82

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add /A:83

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select clear

> select add /A:178

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:179

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select /A:180

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /A:181

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add /A:182

62 atoms, 66 bonds, 3 residues, 1 model selected  

> color #1/A:81-83, 178-182 salmon

> select clear

> select add /A:184

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #1/A:81-83, 178-184 salmon

> select clear

> select add /A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:183@C3'

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:173

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /A:172

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> select /A:91

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select /A:99

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /A:100

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /A:101

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:100

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select add /A:99

67 atoms, 73 bonds, 3 residues, 1 model selected  

> select subtract /A:99

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select /A:103

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /A:168

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> color #1/A:119-163 hotpink

> select clear

> select /A:163

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:118

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:106

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select /A:101

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:118

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:108

43 atoms, 46 bonds, 2 residues, 1 model selected  

> color #1/A:108-118 blue

> color #1/A:108-118 royalblue

> color #1/A:108-118 lblue

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

> color #1/A:108-118 blue

> select clear

> color #1/A:108-118 darkblue

> select /A:107

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color #1/A:101-107,164-170 limegreen

> select clear

> color #1/A:101-107,164-170 lime

> select clear

> select add /A:171

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:172

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select add /A:173

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select add /A:100

87 atoms, 94 bonds, 4 residues, 1 model selected  

> select add /A:91

107 atoms, 115 bonds, 5 residues, 1 model selected  

> color #1/A:91-100, 171-173 lightgray

> color #1/A:91-100, 171-173 gray

> color #1/A:91-100, 171-173 darkgray

> select clear

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:183

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:165

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:33

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color #1/A:33, 84, 91-100, 171-173 darkgray

> select clear

> select add /A:29

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select add /A:29

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:183

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color #1/A:33, 84, 91-100, 171-173, 183,185 darkgray

> select clear

> color byhetero

> select clear

[Repeated 1 time(s)]

> undo

[Repeated 4 time(s)]

> select clear

> view

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> volume #2 level 0.06614

> hide #!2 models

> view

[Repeated 1 time(s)]

> show #!2 models

> volume #2 level 0.07928

> volume #2 color #b2b2b283

> view

[Repeated 1 time(s)]

> show #!3 models

> hide #!3 models

> hide #!2 models

> save ""/Users/heyao/Google Drive/My Drive/RaiA_2024/Figures/fig1.cxs""

> show #!2 models

> hide #!2 models

> select Mg

5 atoms, 5 residues, 1 model selected  

> hide sel target a

> select clear

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> ui tool show ""Color Zone""

> color zone #2 near #1 distance 5.14

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> open ""/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc""

Opened cryosparc_P44_J306_007_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.856, shown at level 0.0213, step 1, values float32  

> volume #4 level 0.04781

> volume #4 color #b2b2b27a

> select clear

> view

> hide #!2 models

> show #!2 models

> hide #1 models

> hide #!4 models

> volume #2 level 0.06335

> select clear

> view

> view name p1

> ui tool show ""Side View""

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> surface dust size 3

Missing or invalid ""surfaces"" argument: invalid surfaces specifier  

> surface dust

Missing or invalid ""surfaces"" argument: empty atom specifier  

> surface dust #2 size 3

> select clear

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

[Repeated 2 time(s)]

> color single #2

> show #1 models

> hide #!2 models

> select clear

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!2 models

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

> color zone #2 near sel distance 5.14

> select clear

> hide #1 models

> select clear

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

[Repeated 2 time(s)]

> turn y 90

[Repeated 1 time(s)]

> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3
> transparentBackground true

> view name p2

> view p1

> turn y 90

[Repeated 1 time(s)]

> turn y 190

[Repeated 1 time(s)]

> view p1

> view

> open ""/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map.mrc""

Opened cryosparc_P44_J208_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 0.856, shown at level 0.0194, step 1, values float32  

> volume #5 color #b2b2b2

> volume #5 level 0.04769

> ui mousemode right ""rotate selected models""

> select add #5

2 models selected  

> view matrix models
> #5,0.98908,-0.10981,-0.098248,23.585,0.018638,0.75465,-0.65586,89.971,0.14617,0.64687,0.74846,-68.003

> fitmap #5 inMap #2

Fit map cryosparc_P44_J208_006_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 57510 points  
correlation = 0.6961, correlation about mean = 0.1762, overlap = 166.5  
steps = 160, shift = 7.08, angle = 13.6 degrees  
  
Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99520792 0.09266609 -0.03121206 -1.90478254  
-0.08638041 0.68359534 -0.72473156 121.64881794  
-0.04582162 0.72395470 0.68832403 -45.65379273  
Axis 0.99239916 0.01000804 -0.12265292  
Axis point 0.00000000 113.18746461 118.36999355  
Rotation angle (degrees) 46.87724941  
Shift along axis 4.92673271  
  

> select clear

> select add #5

2 models selected  

> view matrix models
> #5,-0.28863,-0.93163,0.22081,242.43,0.58353,-0.35401,-0.73086,165.17,0.75907,-0.082096,0.64582,-41.296

> view matrix models
> #5,-0.86039,-0.42794,0.27676,244.86,0.12692,-0.70587,-0.69688,256.01,0.49358,-0.56446,0.66164,44.269

> fitmap #5 inMap #2

Fit map cryosparc_P44_J208_006_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 57510 points  
correlation = 0.9304, correlation about mean = 0.7264, overlap = 384.4  
steps = 420, shift = 27.3, angle = 61.9 degrees  
  
Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.82309682 0.56737562 0.02442404 134.59045503  
-0.45808180 -0.63789380 -0.61907396 298.40293952  
-0.33566753 -0.52074601 0.78495280 110.25649577  
Axis 0.09010312 0.32997103 -0.93968109  
Axis point 119.35289183 147.39940598 0.00000000  
Rotation angle (degrees) 146.93150884  
Shift along axis 6.98539970  
  

> select clear

> view p1

> select clear

> hide #!2 models

> open ""/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/KN-
> coot-13_isolde_real_space_refined_065_isolde.pdb""

Chain information for KN-coot-13_isolde_real_space_refined_065_isolde.pdb #6  
---  
Chain | Description  
A | No description available  
  

> select add #6

5353 atoms, 5988 bonds, 1 pseudobond, 249 residues, 2 models selected  

> view matrix models
> #6,-0.90858,0.1578,-0.38676,255.46,0.17715,-0.69294,-0.6989,251.02,-0.37829,-0.70352,0.60164,171.11

> view matrix models
> #6,-0.51182,0.84433,-0.15861,100.53,-0.62781,-0.49363,-0.60182,317.23,-0.58643,-0.20844,0.78272,119.21

> fitmap #6 inMap #5

Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map
cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms  
average map value = 0.01605, steps = 132  
shifted from previous position = 4.23  
rotated from previous position = 9.84 degrees  
atoms outside contour = 4651, contour level = 0.047687  
  
Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative
to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.86772792 -0.39727738 0.29869543 2.06277270  
0.42913695 0.90201861 -0.04694588 -47.94991180  
-0.25077830 0.16891749 0.95319313 19.39883446  
Axis 0.21254395 0.54102425 0.81370623  
Axis point 94.65981773 -21.12486692 0.00000000  
Rotation angle (degrees) 30.51798290  
Shift along axis -9.71868299  
  

> view matrix models
> #6,-0.62963,0.75199,0.19515,92.984,-0.76605,-0.55911,-0.3171,317.86,-0.12935,-0.34915,0.9281,70.549

> ui mousemode right ""translate selected models""

> view matrix models
> #6,-0.62963,0.75199,0.19515,68.108,-0.76605,-0.55911,-0.3171,313.96,-0.12935,-0.34915,0.9281,63.027

> view matrix models
> #6,-0.62963,0.75199,0.19515,68.366,-0.76605,-0.55911,-0.3171,300.24,-0.12935,-0.34915,0.9281,53.164

> fitmap #6 inMap #5

Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map
cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms  
average map value = 0.07683, steps = 172  
shifted from previous position = 10.1  
rotated from previous position = 25.4 degrees  
atoms outside contour = 1263, contour level = 0.047687  
  
Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative
to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999995 0.00001997 0.00032109 -0.03981368  
-0.00001996 1.00000000 -0.00003851 0.01104931  
-0.00032109 0.00003851 0.99999995 0.04171659  
Axis 0.11885500 0.99099744 -0.06162443  
Axis point 130.60221565 0.00000000 125.36760562  
Rotation angle (degrees) 0.01856408  
Shift along axis 0.00364702  
  

> ui mousemode right zoom

> select clear

> view p1

> select clear

> view p1

> hide #!5 models

> hide #!6 models

> show #!6 models

> show #!5 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> select clear

Drag select of 249 residues, 1 pseudobonds, 498 shapes  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 5353 atom styles  

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

> show #1 models

> hide #!6 models

> show #!6 models

> select #6/A:240

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:14

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:240

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:1

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #6/A:253

22 atoms, 24 bonds, 1 residue, 1 model selected  

> P1a and P1b color #6/A:1-14,240-253 orange red

Unknown command: P1a and P1b color #6/A:1-14,240-253 orange red  

> color #6/A:1-14,240-253 orange red

> select clear

[Repeated 1 time(s)]

> select #6/A:15

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:239

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:238

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select #6/A:235

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:239

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select clear

> select #6/A:15

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #6/A:20

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select #6/A:19

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color #6/A:15-19,235-239 purple

> select #6/A:92

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> hide #1 models

> select #6/A:60

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:59

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #6/A:20

65 atoms, 70 bonds, 3 residues, 1 model selected  

> ui tool show ""Color Actions""

> color #6/A:20-60 darkgoldenrod

> select clear

> view

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> color #6/A:20-60 pylegoldenrod

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

> color #6/A:20-60 palegoldenrod

> select clear

> view

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> color #6/A:20-60 tan

> select clear

[Repeated 1 time(s)]

> show #!2 models

> hide #!2 models

> show #1 models

> hide #!6 models

> show #!6 models

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:60

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel purple

> select clear

> select #6/A:20

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color sel purple

> select clear

[Repeated 1 time(s)]

> hide #1 models

> select #6/A:20

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!6 models

> show #!6 models

> select #6/A:60

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:59

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color #6/A:15-20,60,235-239 purple

> select clear

> hide #1 models

> show #!2 models

> show #1 models

> hide #!2 models

> color #6/A:21-59 tan

> hide #1 models

> show #1 models

> select #6/A:61

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:64

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add #1/A:50

66 atoms, 71 bonds, 3 residues, 2 models selected  

> select subtract #1/A:50

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add #6/A:87

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #6/A:82

88 atoms, 95 bonds, 4 residues, 1 model selected  

> color #6/A:61-64,82-87 cornflower blue

> select #6/A:65

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:65

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:69

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #6/A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:65-69,77-81 yellow

> select clear

[Repeated 1 time(s)]

> select #6/A:70

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:71

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:76

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select clear

> select #6/A:71

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:76

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select clear

> select #6/A:123

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #6/A:118

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color #1/A:71-76,118-123 green

> undo

> color #6/A:71-76,118-123 green

> select clear

> hide #1 models

> show #1 models

> select #6/A:88

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #6/A:91

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #6/A:92

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select subtract #6/A:92

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select #6/A:226

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:223

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select subtract #6/A:223

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:223

46 atoms, 50 bonds, 2 residues, 1 model selected  

> color #6/A:88-91,223-226 cyan

> select clear

> select #1/A:55

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:92

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:112

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> select #6/A:92

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:112

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide #1 models

> show #1 models

> hide #!6 models

> select #1/A:80

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color #1/A:33,80,84,91-100,171-173,183,185 darkgray

> select clear

> show #!2 models

> hide #1 models

> show #1 models

> hide #!2 models

> select clear

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> color #2 near 1 distance 5

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

> colorzone #2 near 1 distance 5

Unknown command: colorzone #2 near 1 distance 5  

> color zone #2 near 1 distance 5

Invalid ""near"" argument: invalid atoms specifier  

> color zone #2 near #1 distance 5

> select clear

> hide #!2 models

> hide #1 models

> view p1

> show #1 models

> show #!2 models

> hide #1 models

> show #!6 models

> hide #!2 models

> color #6/A:92-112 goldenrod

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #1 models

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> select #6/A:70

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #1 models

> select #1/A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:114

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:115

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #6/A:116

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select #6/A:227

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:233

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:114-116,227-233 salmon

> hide #1 models

> show #1 models

> hide #!6 models

> show #!6 models

> select #1/A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:232

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #1 models

> show #1 models

> hide #1 models

> select #6/A:234

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #6/A:70,232,234 darkgray

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> select #1/A:170

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:219

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:170

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #1/A:170

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:219

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:213

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select #6/A:140

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #6/A:134

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> color #6/A:134-140,213-219 lime

> select #6/A:141

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #6/A:174

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #6/A:141-174 darkblue

> select clear

> select #6/A:212

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:175

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:175-212 hotpink

> hide #1 models

> view p1

> select clear

> show #1 models

> hide #1 models

> select #6/A:124

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #6/A:133

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #6/A:222

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #6/A:220

42 atoms, 45 bonds, 2 residues, 1 model selected  

> color #6/A:70,113,117,124-133,220-222,232,234 darkgray

> select clear

> view p1

> show #!5 models

> volume #5 level 0.05695

> 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 #5 near #6 distance 5.14

> color zone #5 near #6 distance 5.1

> color zone #5 near #6 distance 5

[Repeated 2 time(s)]

> hide #!5 models

> show #!5 models

> hide #!6 models

> volume #5 level 0.05886

> volume #5 level 0.05504

> show #!2 models

> hide #!2 models

> show #1 models

> show #!6 models

> hide #!6 models

> hide #!5 models

> show #!2 models

> hide #1 models

> save /Users/heyao/Desktop/fig1.cxs

> show #!6 models

> hide #!2 models

> show #!2 models

> hide #!6 models

> show #1 models

> hide #!2 models

> show #!2 models

> hide #1 models

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

[Repeated 1 time(s)]

> turn x 180

[Repeated 1 time(s)]

> turn z 180

> save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #1 models

> hide #1 models

> hide #!2 models

> show #!6 models

> hide #!6 models

> show #!5 models

> ui tool show ""Hide Dust""

> surface dust #5 size 5.14

> surface dust #5 size 4.94

> surface dust #5 size 1.19

> surface dust #5 size 1.74

> surface dust #5 size 1

> surface dust #5 size 3

[Repeated 1 time(s)]

> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn z 180

> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p1

> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true

> view

[Repeated 3 time(s)]

> select clear

> volume #5 level 0.07883

> view p1

> volume #5 level 0.04591

> view p1

> open ""/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map_sharp.mrc""

Opened cryosparc_P44_J208_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 0.856, shown at level 0.0321, step 1, values float32  

> volume #7 level 0.09953

> select add #7

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,-0.76381,0.63589,-0.11064,143.02,-0.52039,-0.70812,-0.47725,309.35,-0.38182,-0.30695,0.87178,93.617

> fitmap #7 inMap #5

Fit map cryosparc_P44_J208_006_volume_map_sharp.mrc in map
cryosparc_P44_J208_006_volume_map.mrc using 33096 points  
correlation = 0.9546, correlation about mean = 0.7783, overlap = 698.7  
steps = 164, shift = 18.4, angle = 13.5 degrees  
  
Position of cryosparc_P44_J208_006_volume_map_sharp.mrc (#7) relative to
cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999995 -0.00009731 0.00030468 -0.02233620  
0.00009737 0.99999998 -0.00018529 0.01126621  
-0.00030466 0.00018532 0.99999994 0.01925316  
Axis 0.50131231 0.82422219 0.26333202  
Axis point 60.44868633 0.00000000 78.51712028  
Rotation angle (degrees) 0.02117924  
Shift along axis 0.00315842  
  

> select clear

> hide #!5 models

> volume #7 level 0.1479

> volume #7 level 0.1142

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

> surface dust #7 size 5.14

> color zone #7 near #6 distance 5.14

> select clear

> volume #7 level 0.09513

> surface dust #7 size 5.17

> surface dust #7 size 2.59

> hide #!7 models

> show #1 models

> hide #1 models

> show #!2 models

> open ""/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map.mrc""

Opened cryosparc_P44_J119_007_volume_map.mrc as #8, grid size 256,256,256,
pixel 0.856, shown at level 0.0109, step 1, values float32  

> volume #8 level 0.05676

> select add #8

2 models selected  

> view matrix models
> #8,-0.7258,0.66222,0.18623,91.252,0.62651,0.52455,0.57647,-87.693,0.28407,0.53508,-0.79561,134.51

> ui mousemode right ""translate selected models""

> view matrix models
> #8,-0.7258,0.66222,0.18623,96.465,0.62651,0.52455,0.57647,-78.886,0.28407,0.53508,-0.79561,111.51

> view matrix models
> #8,-0.7258,0.66222,0.18623,95.693,0.62651,0.52455,0.57647,-77.05,0.28407,0.53508,-0.79561,109.84

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,-0.59361,-0.78521,0.17626,238.98,-0.41119,0.48422,0.77231,14.761,-0.69177,0.38597,-0.61031,208.04

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  
Must specify one map, got 0  

> fitmap #8 inMap #2

Fit map cryosparc_P44_J119_007_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 32003 points  
correlation = 0.7141, correlation about mean = 0.06117, overlap = 96.41  
steps = 120, shift = 7.63, angle = 7.11 degrees  
  
Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67932839 -0.70734554 0.19538482 233.17463966  
-0.32924966 0.53174106 0.78028592 -1.20521285  
-0.65582589 0.46573999 -0.59412007 187.73366128  
Axis -0.31995815 0.86585704 0.38460157  
Axis point 145.04886475 0.00000000 58.92440994  
Rotation angle (degrees) 150.55799757  
Shift along axis -3.44700659  
  

> select clear

> select add #8

2 models selected  

> view matrix models
> #8,0.92597,-0.247,0.28559,-0.62486,-0.33951,-0.87565,0.34347,206.09,0.16524,-0.41501,-0.89469,231.71

> fitmap #8 inMap #2

Fit map cryosparc_P44_J119_007_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 32003 points  
correlation = 0.918, correlation about mean = 0.5232, overlap = 217.2  
steps = 132, shift = 2.14, angle = 21.9 degrees  
  
Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98172391 0.09005861 0.16765326 -29.84294848  
-0.01268335 -0.84802486 0.52980466 149.11768328  
0.18988760 -0.52224830 -0.83138403 232.76992784  
Axis -0.99504515 -0.02102952 -0.09717466  
Axis point 0.00000000 108.37326391 96.40524730  
Rotation angle (degrees) 148.08599472  
Shift along axis 3.93986945  
  

> select clear

> hide #!8 models

> show #!8 models

> hide #!2 models

> show #!2 models

> select clear

> open ""/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/initial_model_AN-
> coot-11_isolde.pdb""

Chain information for initial_model_AN-coot-11_isolde.pdb #9  
---  
Chain | Description  
A | No description available  
  

> select add #9

3336 atoms, 3734 bonds, 2 pseudobonds, 155 residues, 2 models selected  

> hide #!2 models

> view matrix models
> #9,0.92235,0.35553,0.15123,-47.92,0.17678,-0.73639,0.65305,87.261,0.34354,-0.57561,-0.74206,237.51

> ui mousemode right ""translate selected models""

> view matrix models
> #9,0.92235,0.35553,0.15123,-46.908,0.17678,-0.73639,0.65305,102.26,0.34354,-0.57561,-0.74206,218.07

> fitmap #9 inMap #8

Fit molecule initial_model_AN-coot-11_isolde.pdb (#9) to map
cryosparc_P44_J119_007_volume_map.mrc (#8) using 3336 atoms  
average map value = 0.06906, steps = 132  
shifted from previous position = 6.96  
rotated from previous position = 16.8 degrees  
atoms outside contour = 1046, contour level = 0.056762  
  
Position of initial_model_AN-coot-11_isolde.pdb (#9) relative to
cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.99999922 0.00120715 0.00033324 -0.17137916  
-0.00120711 0.99999926 -0.00015796 0.15354463  
-0.00033343 0.00015757 0.99999994 0.01154017  
Axis 0.12499238 0.26409247 -0.95636399  
Axis point 125.34278901 142.88874346 0.00000000  
Rotation angle (degrees) 0.07231914  
Shift along axis 0.00809228  
  

> select clear

> ui mousemode right zoom

> view p1

> select clear

> hide #!8 models

> select clear

Drag select of 155 residues, 2 pseudobonds, 310 shapes  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 3336 atom styles  

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

> show #!8 models

> hide #!8 models

> show #1 models

> select clear

> select #1/A:191

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:150

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:14

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:150

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:163

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #9/A:1-14,150-163 orange red

> select clear

> select #1/A:190

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:15

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #9/A:23

42 atoms, 45 bonds, 2 residues, 2 models selected  

> select #1/A:190

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:149

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:145

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:15-23,145-149 purple

[Repeated 1 time(s)]

> undo

[Repeated 2 time(s)]

> hide #1 models

> hide #!9 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!9 models

> hide #!6 models

> undo

[Repeated 10 time(s)]No undo action is available  

> undo

No undo action is available  

> undo

No undo action is available  

> undo

No undo action is available  

> select clear

[Repeated 1 time(s)]

> color #9/A:15-23,145-149 purple

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> select #1/A:24

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/A:27

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add #1/A:50

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #9/A:45

88 atoms, 95 bonds, 4 residues, 2 models selected  

> color #9/A:24-27,45-50 cornflower blue

> select clear

> hide #!9 models

> show #!9 models

> hide #1 models

> show #1 models

> select #9/A:28

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:32

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #9/A:40

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:44

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color #9/A:28-32,40-44 yellow

> select clear

> select #1/A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:34

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:34

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:39

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select #9/A:92

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #9/A:87

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color #9/A:34-39,87-92 green

> select clear

> hide #1 models

> show #1 models

> hide #1 models

> select #9/A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel darg gray

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

> color sel darkgray

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!9 models

> show #!9 models

> select #1/A:51

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #9/A:51

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #9/A:54

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select clear

> select #9/A:136

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:133

46 atoms, 50 bonds, 2 residues, 1 model selected  

> color #9/A:51-54,133-136 cyan

> select clear

> hide #1 models

> show #1 models

> select #9/A:55

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:81

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide #1 models

> select clear

> select #9/A:81

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show #1 models

> color #9/A:55-81 goldenrod

> select clear

> hide #1 models

> show #1 models

> select #9/A:83

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:85

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select #1/A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:83

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:85

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select #1/A:184

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:143

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:143

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:137

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #9/A:83-85,137-143 salmon

> select clear

> select #1/A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #1/A:185

45 atoms, 49 bonds, 2 residues, 1 model selected  

> hide #1 models

> show #1 models

> hide #1 models

> select add #9/A:142

67 atoms, 73 bonds, 3 residues, 2 models selected  

> select add #9/A:144

89 atoms, 97 bonds, 4 residues, 2 models selected  

> color #9/A:33, 82, 86, 142,144 darkgray

> select clear

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> select #9/A:93

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show #1 models

> select #9/A:121

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #1 models

> select add #9/A:108

43 atoms, 46 bonds, 2 residues, 1 model selected  

> show #1 models

> hide #1 models

> color #9/A:108-121 darkblue

> select clear

> select add #9/A:107

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show #1 models

> select add #1/A:101

43 atoms, 46 bonds, 2 residues, 2 models selected  

> select add #9/A:102

65 atoms, 70 bonds, 3 residues, 2 models selected  

> select #1/A:102

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/A:101

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #!9 models

> show #!9 models

> hide #1 models

> select #9/A:107

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #9/A:128

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #9/A:127

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #9/A:126

66 atoms, 71 bonds, 3 residues, 1 model selected  

> show #1 models

> select add #9/A:129

88 atoms, 95 bonds, 4 residues, 1 model selected  

> select #9/A:103

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:107

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> color #9/A:103-107,126-129 lime

> select clear

> hide #1 models

> select #9/A:102

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:130

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:132

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #9/A:93

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #9/A:102

42 atoms, 45 bonds, 2 residues, 1 model selected  

> color #9/A:33,82,86,93-102,130-132,142,144 darkgray

> select clear

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> save /Users/heyao/Desktop/fig1.cxs

> show #!8 models

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

> color zone #8 near #9 distance 5.14

> color zone #8 near #9 distance 4.96

> color zone #8 near #9 distance 3.98

> surface dust #8 size 5.14

> volume #8 level 0.06701

> open ""/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map_sharp.mrc""

Opened cryosparc_P44_J119_007_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 0.856, shown at level 0.0198, step 1, values float32  

> volume #10 level 0.1802

> select add #10

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,-0.97132,-0.23766,0.0077356,235.93,-0.15228,0.64668,0.7474,-32.131,-0.18263,0.72479,-0.66433,134.13

> volume #10 level 0.08858

> view matrix models
> #10,0.93215,0.020628,0.36147,-38.767,-0.19435,-0.81384,0.54762,154.01,0.30548,-0.58072,-0.75462,233.48

> ui mousemode right ""translate selected models""

> view matrix models
> #10,0.93215,0.020628,0.36147,-35.457,-0.19435,-0.81384,0.54762,162.59,0.30548,-0.58072,-0.75462,224.58

Must specify one map, got 0  

> fitmap #10 inMap #8

Fit map cryosparc_P44_J119_007_volume_map_sharp.mrc in map
cryosparc_P44_J119_007_volume_map.mrc using 27855 points  
correlation = 0.931, correlation about mean = 0.5914, overlap = 393.1  
steps = 120, shift = 6.72, angle = 13 degrees  
  
Position of cryosparc_P44_J119_007_volume_map_sharp.mrc (#10) relative to
cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.99999985 0.00045450 0.00030702 -0.07641814  
-0.00045451 0.99999989 0.00002918 0.05384633  
-0.00030700 -0.00002931 0.99999995 0.03236712  
Axis -0.05324606 0.55895242 -0.82748840  
Axis point 109.35316698 167.30731259 0.00000000  
Rotation angle (degrees) 0.03147028  
Shift along axis 0.00738308  
  

> select clear

> save /Users/heyao/Desktop/fig1.cxs

> surface dust #10 size 5.14

> color zone #10 near #9 distance 5.14

> hide #!8 models

> hide #!9 models

> volume #10 level 0.08349

> view p1

> show #!2 models

> hide #!2 models

> show #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!10 models

> show #!8 models

> hide #!10 models

> show #!10 models

> hide #!8 models

> volume #10 level 0.08172

> volume #10 level 0.07116

> show #!8 models

> volume #8 level 0.05258

> volume #8 level 0.04487

> select #8

2 models selected  

> show #!9 models

> hide #!8 models

> select clear

> show #!8 models

> color #8 #d6d6d6ff models

> color #8 silver models

> color zone #10 near #9 distance 5.14

[Repeated 1 time(s)]

> color zone #8 near #9 distance 5.14

> select clear

> hide #!8 models

> hide #!9 models

> show #1 models

> hide #1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> color #3 #b2b2b2ff models

> color zone #3 near #1 distance 5.14

> view

> view p1

> volume #3 level 0.1706

> volume #3 level 0.19

> volume #3 level 0.2

> volume #3 level 0.1481

> view

> view p1

> show #1 models

> hide #!2 models

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> ui tool show ""Color Zone""

> color zone #2 near sel distance 5

> hide #!2 models

> show #!2 models

> hide #1 models

> view p1

> volume #2 level 0.07

> volume #2 level 0.05

> volume #2 level 0.06

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!4 models

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #!3 models

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

> view p1

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!5 models

> volume #5 level 0.05207

> view p1

> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!5 models

> show #!10 models

> show #!8 models

> hide #!10 models

> view p1

> volume #8 level 0.05187

> volume #8 level 0.04053

> view p1

> view

> view p1

> save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!10 models

> hide #!10 models

> show #!9 models

> hide #!9 models

> show #!8 models

> view p1

> hide #!8 models

> show #!8 models

> hide #!2 models

> volume #8 level 0.05

> view p1

> save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

[Repeated 1 time(s)]

> turn z 180

> save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3
> transparentBackground true

> save /Users/heyao/Desktop/fig1.cxs

——— End of log from Sat Dec 14 18:45:20 2024 ———

opened ChimeraX session  

> ui mousemode right translate

> ui mousemode right zoom

> hide #!8 models

> show #1 models

> view p1

> select clear

> ui tool show ""Side View""

> save /Users/heyao/Desktop/101.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p1

> turn y 180

> save /Users/heyao/Desktop/102.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p1

> save /Users/heyao/Desktop/101.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/102.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #!3 models

> hide #1 models

> show #!2 models

> hide #!3 models

> view p2

> turn z 180

> turn y 180

> turn z 180

> select clear

> save /Users/heyao/Desktop/103.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #1 models

> hide #!2 models

> save /Users/heyao/Desktop/104.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #!2 models

> hide #1 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!6 models

> hide #!5 models

> save /Users/heyao/Desktop/105.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p1

> hide #6.1 models

> save /Users/heyao/Desktop/106.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/107.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #!5 models

> hide #!6 models

> view p1

> turn z 90

[Repeated 3 time(s)]

> turn x 90

[Repeated 2 time(s)]

> view p2

> turn x 90

[Repeated 1 time(s)]

> turn z 90

[Repeated 1 time(s)]

> save /Users/heyao/Desktop/108.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!5 models

> show #!6 models

> save /Users/heyao/Desktop/105.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!6 models

> show #!9 models

> hide #9.1 models

> hide #!9 models

> show #!6 models

> view name p3

> show #!9 models

> hide #!9 models

> hide #!6 models

> show #!9 models

> hide #!9 models

> show #!6 models

> view p1

> show #6.1 models

> hide #6.1 models

> show #6.1 models

> hide #!6 models

Cell requested for row 9 is out of bounds for table with 12 rows! Resizing
table model.  

> show #!9 models

> view p1

> save /Users/heyao/Desktop/111.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/112.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p3

> save /Users/heyao/Desktop/113.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!9 models

> show #!8 models

> save /Users/heyao/Desktop/114.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!8 models

> show #!9 models

> show #9.1 models

> view p1

[Repeated 1 time(s)]

> turn y 180

> view p3

> save /Users/heyao/Desktop/fig1.cxs

——— End of log from Mon Dec 16 22:23:52 2024 ———

> view name session-start

opened ChimeraX session  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.41.1
      OS Loader Version: 13822.41.1

Software:

    System Software Overview:

      System Version: macOS 26.1 (25B78)
      Kernel Version: Darwin 25.1.0
      Time since boot: 10 days, 2 hours, 50 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2717D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL U2417H:
          Resolution: 1080 x 1920
          UI Looks like: 1080 x 1920 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: 270


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.25.2
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.10.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX