id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
19548	Crash on Mac waking from sleep	croal939@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.7.1-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 0x000000020c7fe140 (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, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)


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

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/New Folder/PCH45_Gp25_ModelChecking.cxs""

Opened PCH45_Neck_C6_3_40A_map_sharp.mrc as #1, grid size 416,416,416, pixel
1.37, shown at level 0.496, step 1, values float32  
Log from Tue Dec 30 21:54:50 2025UCSF 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/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/PCH45 Gen 2Maps/PCH45
> Neck/PCH45_neck_RawData/PCH45_Neck_C6_3_40A_map_sharp.mrc""

Opened PCH45_Neck_C6_3_40A_map_sharp.mrc as #1, grid size 416,416,416, pixel
1.37, shown at level 0.496, step 2, values float32  

> surface dust #1 size 13.7

> volume #1 step 1

> open ""/Users/croal939/Downloads/Output for PCH45_NonbulbRingoutput_output
> (3).cif""

Summary of feedback from opening /Users/croal939/Downloads/Output for
PCH45_NonbulbRingoutput_output (3).cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for Output for PCH45_NonbulbRingoutput_output (3).cif #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
3 | No description available  
5 8 | No description available  
7 | No description available  
A | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
AA | No description available  
AB | No description available  
AD | No description available  
AK | No description available  
AL | No description available  
Ad | No description available  
B | No description available  
BA | No description available  
BB | No description available  
BC | No description available  
BD | No description available  
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BH | No description available  
BI | No description available  
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BO | No description available  
BP | No description available  
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BR | No description available  
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BT | No description available  
BU | No description available  
BV | No description available  
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Ba | No description available  
Bb | No description available  
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Bd | No description available  
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Bf | No description available  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
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X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
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f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
r | No description available  
s | No description available  
u | No description available  
z | No description available  
  

> color #2 #929292ff

> hide atoms

> show cartoons

Computing secondary structure  

> select add #2

11623 atoms, 12413 bonds, 1475 residues, 1 model selected  

> show sel cartoons

> select add #1

11623 atoms, 12413 bonds, 1475 residues, 3 models selected  

> transparency sel 50

> select clear

> open ""/Users/croal939/Downloads/output_output (2).cif""

Summary of feedback from opening /Users/croal939/Downloads/output_output
(2).cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for output_output (2).cif #3  
---  
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49 55 | No description available  
4C Gc | No description available  
4E | No description available  
4F 5t Mo yM zL | No description available  
4H Ho | No description available  
4I Agx | No description available  
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AMl | No description available  
AMm | No description available  
AMn | No description available  
AMo | No description available  
AMp | No description available  
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AMr | No description available  
AMs | No description available  
AMt | No description available  
AMu | No description available  
AMv | No description available  
AMw | No description available  
AMx | No description available  
AMy | No description available  
AMz | No description available  
AN | No description available  
AN0 | No description available  
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ANC | No description available  
AND | No description available  
ANE | No description available  
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ANI | No description available  
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ANN | No description available  
ANO | No description available  
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ANT | No description available  
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ANa | No description available  
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ANs | No description available  
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ANv | No description available  
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APf | No description available  
APg | No description available  
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APn | No description available  
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AQN | No description available  
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AQa | No description available  
AQb | No description available  
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AQd | No description available  
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AQn | No description available  
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AQp | No description available  
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AQr | No description available  
AQs | No description available  
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AQu | No description available  
AQv | No description available  
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AR0 | No description available  
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ARD | No description available  
ARE | No description available  
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ARG | No description available  
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ARM | No description available  
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ARS | No description available  
ART | No description available  
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ARV | No description available  
ARW | No description available  
ARX | No description available  
ARY | No description available  
ARZ | No description available  
ARa | No description available  
ARb | No description available  
ARc | No description available  
ARd | No description available  
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ARf | No description available  
ARg | No description available  
ARh | No description available  
ARi | No description available  
ARj T9 | No description available  
ARk | No description available  
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ARm | No description available  
ARn | No description available  
ARo | No description available  
ARp | No description available  
ARq | No description available  
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ARs | No description available  
ARt | No description available  
ARu | No description available  
ARv | No description available  
ARw | No description available  
ARx | No description available  
ARy | No description available  
ARz | No description available  
AS | No description available  
AS0 | No description available  
AS1 | No description available  
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AS4 | No description available  
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ASA | No description available  
ASB | No description available  
ASC | No description available  
ASD | No description available  
ASE | No description available  
ASF | No description available  
ASG | No description available  
ASH | No description available  
ASI | No description available  
ASJ | No description available  
ASK | No description available  
ASL | No description available  
ASM | No description available  
ASN | No description available  
ASO | No description available  
ASP | No description available  
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ASR | No description available  
ASS | No description available  
AST | No description available  
ASU | No description available  
ASV | No description available  
ASW | No description available  
ASX | No description available  
ASY | No description available  
ASZ | No description available  
ASa | No description available  
ASb | No description available  
ASc | No description available  
ASd | No description available  
ASe | No description available  
ASf | No description available  
ASg | No description available  
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ASi | No description available  
ASj | No description available  
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ASl | No description available  
ASm | No description available  
ASn | No description available  
ASo | No description available  
ASp | No description available  
ASq | No description available  
ASr | No description available  
ASs | No description available  
ASt | No description available  
ASu | No description available  
ASv | No description available  
ASw | No description available  
ASx | No description available  
ASy | No description available  
ASz | No description available  
AT0 | No description available  
AT1 | No description available  
AT2 | No description available  
AT3 | No description available  
AT4 | No description available  
AT5 | No description available  
AT6 | No description available  
AT7 | No description available  
AT8 | No description available  
AT9 | No description available  
ATA | No description available  
ATB | No description available  
ATC | No description available  
ATD | No description available  
ATE | No description available  
ATF | No description available  
ATG | No description available  
ATH | No description available  
ATI | No description available  
ATJ | No description available  
ATK | No description available  
ATL | No description available  
ATM | No description available  
ATN | No description available  
ATO | No description available  
ATP | No description available  
ATQ | No description available  
ATR | No description available  
ATS | No description available  
ATT | No description available  
ATU | No description available  
ATV | No description available  
ATW | No description available  
ATX | No description available  
ATY | No description available  
ATZ | No description available  
ATa | No description available  
ATb | No description available  
ATc | No description available  
ATd | No description available  
ATe | No description available  
ATf | No description available  
ATg | No description available  
ATh | No description available  
ATi | No description available  
ATj | No description available  
ATk | No description available  
ATl | No description available  
ATm | No description available  
ATn | No description available  
ATo | No description available  
ATp | No description available  
ATq | No description available  
ATr | No description available  
ATs | No description available  
ATt | No description available  
ATu | No description available  
ATv | No description available  
ATw | No description available  
[deleted to fit within ticket limits]


> show #!9 models

> hide #!9 models

> show #!9 models

> hide #5 models

> show #5 models

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/New Folder/PCH45_Gp25_BetaBulbFitted-coot-3.pdb""

Chain information for PCH45_Gp25_BetaBulbFitted-coot-3.pdb #13  
---  
Chain | Description  
A | No description available  
  

> select add #13

3715 atoms, 3815 bonds, 462 residues, 1 model selected  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 4 maps.  

> select add #1

3715 atoms, 3815 bonds, 462 residues, 3 models selected  

> fitmap #13 inMap #1

Fit molecule PCH45_Gp25_BetaBulbFitted-coot-3.pdb (#13) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 3715 atoms  
average map value = 0.7437, steps = 48  
shifted from previous position = 0.23  
rotated from previous position = 0.258 degrees  
atoms outside contour = 1733, contour level = 0.66964  
  
Position of PCH45_Gp25_BetaBulbFitted-coot-3.pdb (#13) relative to
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998985 0.00390379 -0.00224966 -0.43402769  
-0.00390336 0.99999236 0.00019712 1.28620271  
0.00225041 -0.00018834 0.99999745 -0.63077562  
Axis -0.04273630 -0.49892866 -0.86558870  
Axis point 319.42544666 112.85651605 0.00000000  
Rotation angle (degrees) 0.25838968  
Shift along axis -0.07718241  
  

> select clear

> rename #13 Gp25BetaNotBulb-1-333AA

> select add #13

3715 atoms, 3815 bonds, 462 residues, 1 model selected  
Alignment identifier is 13/A  

> select #13/A:1

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

> select #13/A:1-169

1350 atoms, 1383 bonds, 169 residues, 1 model selected  

> select #13/A:333

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

> select #13/A:333-462

1061 atoms, 1093 bonds, 130 residues, 1 model selected  

> delete sel

> select clear

> hide #5 models

> measure center #1

Center of mass grid index for PCH45_Neck_C6_3_40A_map_sharp.mrc = (208.00,
208.00, 140.90)  
Center of mass xyz scene coordinates for PCH45_Neck_C6_3_40A_map_sharp.mrc =
(284.19, 284.19, 192.51)  

> sym #13 C6 center 284.19, 284.19, 192.51

Made 6 copies for Gp25BetaNotBulb-1-333AA symmetry C6  

> select add #1

2 models selected  

> ui mousemode right ""crop volume""

> volume sel showOutlineBox true

> volume #6 region 0,0,0,415,415,415

> select clear

> volume #!1,6,9,12 showOutlineBox false

> close #14

> show #13 models

> select #13/A:1

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

> select #13/A:1-31

244 atoms, 248 bonds, 31 residues, 1 model selected  

> hide #!9 models

> delete sel

> sym #13 C6 center 284.19, 284.19, 192.51

Made 6 copies for Gp25BetaNotBulb-1-333AA symmetry C6  

> volume zone #1 nearAtoms #14 newMap true range 4

Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #15, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32  

> surface dust #6 size 13.7

> surface dust #12 size 13.7

> surface dust #15 size 13.7

> rename #15 Gp25Beta_NotBulb_33-333AA_VZr4

> hide #!15 models

> show #!15 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!12 models

> hide #!14 models

> hide #!6 models

> show #!6 models

> volume #* level .65

> show #!9 models

> hide #!9 models

> show #!1 models

> vop subtract #1 #15

Opened volume difference as #16, grid size 416,416,416, pixel 1.37, shown at
step 1, values float32  

> surface dust #6 size 13.7

> surface dust #16 size 13.7

> transparency #6.1#16.1 0

> transparency #6.1#16.1 50

> hide #!6 models

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_GP25alpha/PCH45_Gp25alpha_1-200AA fit-coot-2.pdb""

Chain information for PCH45_Gp25alpha_1-200AA fit-coot-2.pdb #17  
---  
Chain | Description  
A | No description available  
  

> sym #17 C6 center 284.19, 284.19, 192.51

Made 6 copies for PCH45_Gp25alpha_1-200AA fit-coot-2.pdb symmetry C6  

> volume zone #1 nearAtoms #18 newMap true range 4

Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #19, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32  

> surface dust #16 size 13.7

> surface dust #19 size 13.7

> vop subtract #16 #19

Opened volume difference as #20, grid size 416,416,416, pixel 1.37, shown at
step 1, values float32  

> surface dust #20 size 13.7

> hide #!18 models

> show #10 models

> rename #20 BulbconfirmationsDensity_Subtractions

> show #!6 models

> hide #!6 models

> show #!6 models

> transparency #6.1#20.1 0

> transparency #6.1#20.1 50

> show #5 models

> volume #6 level 0.65

> hide #!6 models

> show #!1 models

> volume #1 level 0.5963

> volume #1 level 0.556

> volume #1 level 0.6433

> hide #5 models

> show #5 models

> hide #5 models

> hide #10 models

> transparency #1.1#20.1 0

> transparency #1.1#20.1 50

> show #5 models

> select #5/A:387

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

> select #5/A:328-387

474 atoms, 486 bonds, 60 residues, 1 model selected  

> select #5/A:434

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

> select #5/A:434

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

> select #5/A:387

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

> select #5/A:387-390

30 atoms, 30 bonds, 4 residues, 1 model selected  

> select #5/A:398

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

> select #5/A:398-400

25 atoms, 25 bonds, 3 residues, 1 model selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #5/A:322

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

> select #5/A:322-328

61 atoms, 63 bonds, 7 residues, 1 model selected  

> select #5/A:333

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

> select #5/A:333-384

402 atoms, 412 bonds, 52 residues, 1 model selected  

> select #5/A:385

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

> select #5/A:333-385

414 atoms, 425 bonds, 53 residues, 1 model selected  

> color sel lime

> select clear

> select #5/A:386

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

> select #5/A:386-397

100 atoms, 103 bonds, 12 residues, 1 model selected  

> select #5/A:386-387

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

> select #5/A:386-407

188 atoms, 194 bonds, 22 residues, 1 model selected  

> select #5/A:386

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

> select #5/A:386-410

211 atoms, 217 bonds, 25 residues, 1 model selected  

> color sel cyan

> select clear

> show #!1 models

> select #5/A:411-412

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

> select #5/A:411-462

436 atoms, 449 bonds, 52 residues, 1 model selected  

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25_411_462/fold_pch45_gp25_411_462_model_0.cif""

Chain information for fold_pch45_gp25_411_462_model_0.cif #21  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> select add #21

872 atoms, 898 bonds, 104 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #21 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PCH45_Gp25_BetaBulbFitted-coot-3.pdb, chain A (#5) with
fold_pch45_gp25_411_462_model_0.cif, chain A (#21), sequence alignment score =
271.8  
RMSD between 34 pruned atom pairs is 0.624 angstroms; (across all 52 pairs:
5.646)  
  

> select clear

> select add #21

436 atoms, 449 bonds, 52 residues, 1 model selected  

> select add #1

436 atoms, 449 bonds, 52 residues, 3 models selected  

> fitmap #21 inMap #1

Fit molecule fold_pch45_gp25_411_462_model_0.cif (#21) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 436 atoms  
average map value = 0.7079, steps = 68  
shifted from previous position = 1.05  
rotated from previous position = 4.89 degrees  
atoms outside contour = 216, contour level = 0.64329  
  
Position of fold_pch45_gp25_411_462_model_0.cif (#21) relative to
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.89277032 0.01270563 -0.45033290 358.86819646  
-0.29285807 0.74321667 0.60155061 305.50715641  
0.34233799 0.66893015 -0.65980084 233.72255583  
Axis 0.07906588 -0.93015201 -0.35856077  
Axis point 178.95533192 0.00000000 104.36154798  
Rotation angle (degrees) 154.77984855  
Shift along axis -339.59760619  
  

> select clear

> hide #!1 models

> hide #!20 models

> select add #21

436 atoms, 449 bonds, 52 residues, 1 model selected  

> select clear

> show #!1 models

> hide #!1 models

> show #!6 models

> select add #6

2 models selected  

> select add #21

436 atoms, 449 bonds, 52 residues, 3 models selected  

> fitmap #21 inMap #6

Fit molecule fold_pch45_gp25_411_462_model_0.cif (#21) to map
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) using 436 atoms  
average map value = 0.708, steps = 60  
shifted from previous position = 0.00659  
rotated from previous position = 0.0789 degrees  
atoms outside contour = 216, contour level = 0.65  
  
Position of fold_pch45_gp25_411_462_model_0.cif (#21) relative to
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.89309837 0.01155333 -0.44971304 358.87465433  
-0.29329821 0.74303671 0.60155849 305.50641600  
0.34110330 0.66915093 -0.66021630 233.72486139  
Axis 0.07949887 -0.93011879 -0.35855119  
Axis point 179.05599943 0.00000000 104.26268979  
Rotation angle (degrees) 154.84200817  
Shift along axis -339.42945811  
  

> select clear

> select add #21

436 atoms, 449 bonds, 52 residues, 1 model selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #21,-0.87033,-0.041317,-0.49074,358.7,-0.40491,0.62723,0.6653,305.5,0.28032,0.77774,-0.56263,234.11

> view matrix models
> #21,-0.83765,0.014748,-0.546,358.72,-0.43034,0.59779,0.67635,305.5,0.33637,0.80152,-0.49439,234.11

> view matrix models
> #21,-0.83765,0.014748,-0.546,357.9,-0.43034,0.59779,0.67635,306.2,0.33637,0.80152,-0.49439,233.78

> view matrix models
> #21,-0.82144,0.051881,-0.56794,357.93,-0.42967,0.59852,0.67613,306.2,0.375,0.79943,-0.46935,233.73

> view matrix models
> #21,-0.82144,0.051881,-0.56794,357.52,-0.42967,0.59852,0.67613,307.9,0.375,0.79943,-0.46935,233.56

> fitmap #21 inMap #6

Fit molecule fold_pch45_gp25_411_462_model_0.cif (#21) to map
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) using 436 atoms  
average map value = 0.708, steps = 132  
shifted from previous position = 2.55  
rotated from previous position = 14.1 degrees  
atoms outside contour = 216, contour level = 0.65  
  
Position of fold_pch45_gp25_411_462_model_0.cif (#21) relative to
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.89298122 0.01168575 -0.44994220 358.87161135  
-0.29333815 0.74308848 0.60147505 305.50321627  
0.34137555 0.66909114 -0.66013618 233.72537056  
Axis 0.07947713 -0.93012867 -0.35853041  
Axis point 179.04075764 0.00000000 104.29777173  
Rotation angle (degrees) 154.82523086  
Shift along axis -339.43286569  
  

> view matrix models
> #21,-0.62342,-0.11768,-0.77298,357.85,-0.70758,0.50556,0.4937,305.72,0.33269,0.85473,-0.39844,234.57

> fitmap #21 inMap #6

Fit molecule fold_pch45_gp25_411_462_model_0.cif (#21) to map
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) using 436 atoms  
average map value = 0.7081, steps = 120  
shifted from previous position = 0.778  
rotated from previous position = 30 degrees  
atoms outside contour = 215, contour level = 0.65  
  
Position of fold_pch45_gp25_411_462_model_0.cif (#21) relative to
PCH45_Gp25Beta_NotBulb_Segmap5.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.89235317 0.01274596 -0.45115781 358.86164988  
-0.29340057 0.74319042 0.60131864 305.51334753  
0.34296054 0.66895855 -0.65944865 233.70326901  
Axis 0.07922489 -0.93013046 -0.35858158  
Axis point 178.95150405 0.00000000 104.44700249  
Rotation angle (degrees) 154.72993418  
Shift along axis -339.53818078  
  

> select clear

> select add #21

436 atoms, 449 bonds, 52 residues, 1 model selected  

> sym #21 C12 center 284.19, 284.19, 192.51

Made 12 copies for fold_pch45_gp25_411_462_model_0.cif symmetry C12  

> show #!1 models

> show #21 models

> hide #21 models

> hide #!22 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!1 models

> vop subtract #20 #22

volume subtract operation requires exactly two volumes  

> volume zone #1 nearAtoms #22 newMap true range 4

Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #23, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32  

> surface dust #6 size 13.7

> surface dust #20 size 13.7

> surface dust #23 size 13.7

> vop subtract #20 #23

Opened volume difference as #24, grid size 416,416,416, pixel 1.37, shown at
step 1, values float32  

> surface dust #6 size 13.7

> surface dust #24 size 13.7

> show #!23 models

> hide #!23 models

> show #!23 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> show #!19 models

> hide #!19 models

> show #!19 models

> show #17 models

> hide #17 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #5 models

> show #5 models

> transparency #6.1#15.1#19.1#20.1#23.1#24.1 0

> transparency #6.1#15.1#19.1#20.1#23.1#24.1 50

> hide #!23 models

> hide #!20 models

> show #7 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> show #!22 models

> hide #!22 models

> show #!22 models

> hide #7 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!23 models

> hide #!9 models

> show #!1 models

> volume #1 level 0.5963

> volume #1 level 0.5292

> show #!18 models

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_0.cif""

Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_0.cif #25  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> select #5/A:201

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

> select #5/A:201-462

2120 atoms, 2182 bonds, 262 residues, 1 model selected  

> select clear

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25_201_462/fold_pch45_gp25_201_462_model_0.cif""

Chain information for fold_pch45_gp25_201_462_model_0.cif #26  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #26 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PCH45_Gp25_BetaBulbFitted-coot-3.pdb, chain A (#5) with
fold_pch45_gp25_201_462_model_0.cif, chain A (#26), sequence alignment score =
1199.3  
RMSD between 205 pruned atom pairs is 0.779 angstroms; (across all 262 pairs:
3.618)  
  

> hide #5 models

> select add #26

2120 atoms, 2182 bonds, 262 residues, 1 model selected  

> select add #1

2120 atoms, 2182 bonds, 262 residues, 3 models selected  

> fitmap #26 inMap #1

Fit molecule fold_pch45_gp25_201_462_model_0.cif (#26) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 2120 atoms  
average map value = 0.6306, steps = 52  
shifted from previous position = 0.301  
rotated from previous position = 2.29 degrees  
atoms outside contour = 921, contour level = 0.52919  
  
Position of fold_pch45_gp25_201_462_model_0.cif (#26) relative to
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.60407289 -0.55734931 0.56961188 355.41912124  
-0.29798826 -0.50493974 -0.81008571 307.08307748  
0.73912038 -0.65908847 0.13893686 246.20306853  
Axis 0.43808475 -0.49179104 0.75247812  
Axis point 82.93716909 249.69918501 0.00000000  
Rotation angle (degrees) 170.07622060  
Shift along axis 189.94541365  
  

> select clear

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> hide #!22 models

> select add #1

2 models selected  

> volume #1 level 0.348

> volume #1 level 0.5091

> hide #!1 models

> hide #26 models

> show #26 models

> hide #!15 models

> hide #!18 models

> show #!18 models

> hide #!6 models

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #1 level 0.6567

> volume #1 level 0.8044

> select clear

> hide #26 models

> show #26 models

> select add #26

2120 atoms, 2182 bonds, 262 residues, 1 model selected  

> ui tool show ""Model Loops""

Populating font family aliases took 78 ms. Replace uses of missing font family
""Times"" with one that exists to avoid this cost.  

> modeller refine 5/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard

No Modeller license key provided. Get a license key by registering at the
Modeller web site.  

> select clear

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp025/fold_pch45_gp025_model_0.cif""

Chain information for fold_pch45_gp025_model_0.cif #27  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> select add #27

3715 atoms, 3815 bonds, 462 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #27 to #17

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PCH45_Gp25alpha_1-200AA fit-coot-2.pdb, chain A (#17) with
fold_pch45_gp025_model_0.cif, chain A (#27), sequence alignment score = 879.3  
RMSD between 107 pruned atom pairs is 0.766 angstroms; (across all 200 pairs:
25.924)  
  

> select clear

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!1 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!24 models

> show #!1 models

> select add #27

3715 atoms, 3815 bonds, 462 residues, 1 model selected  

> select clear

> select add #27

3715 atoms, 3815 bonds, 462 residues, 1 model selected  

> select clear

> select #13/A:32-132

794 atoms, 811 bonds, 101 residues, 1 model selected  

> select clear

> select #13/A:32-230

1615 atoms, 1656 bonds, 199 residues, 1 model selected  

> select add #27

5330 atoms, 5471 bonds, 661 residues, 2 models selected  

> select clear

> select #13/A:201-332

1059 atoms, 1088 bonds, 132 residues, 1 model selected  

> select add #27

4774 atoms, 4903 bonds, 594 residues, 2 models selected  

> select clear

> select add #27

3715 atoms, 3815 bonds, 462 residues, 1 model selected  
Alignment identifier is 27/A  

> select #27/A:462

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

> select #27/A:201-462

2120 atoms, 2182 bonds, 262 residues, 1 model selected  

> volume gaussian #1 sDev 2

Opened PCH45_Neck_C6_3_40A_map_sharp.mrc gaussian as #28, grid size
416,416,416, pixel 1.37, shown at step 1, values float32  

> surface dust #6 size 13.7

> surface dust #19 size 13.7

> surface dust #28 size 13.7

> transparency #6.1#19.1#28.1 0

> lighting simple

> help fit in map

> ui tool show ""Fit in Map""

> fitmap sel inMap #28 moveWholeMolecules false

Fit molecule fold_pch45_gp025_model_0.cif (#27) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc gaussian (#28) using 2120 atoms  
average map value = 0.3277, steps = 328  
shifted from previous position = 39  
rotated from previous position = 54.7 degrees  
atoms outside contour = 1095, contour level = 0.34651  
  

> hide #!28 models

> hide #27 models

> show #27 models

> hide #27 models

> show #27 models

> show #!28 models

> hide #!28 models

> show #!28 models

> hide #!28 models

> hide #27 models

> show #27 models

> hide #27 models

> show #27 models

> hide #!19 models

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp025/fold_pch45_gp025_model_0.cif""

Chain information for fold_pch45_gp025_model_0.cif #29  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #27 models

> ui tool show Matchmaker

> matchmaker #29 to #17

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PCH45_Gp25alpha_1-200AA fit-coot-2.pdb, chain A (#17) with
fold_pch45_gp025_model_0.cif, chain A (#29), sequence alignment score = 879.3  
RMSD between 107 pruned atom pairs is 0.766 angstroms; (across all 200 pairs:
25.924)  
  

> select add #29

5835 atoms, 5997 bonds, 724 residues, 2 models selected  
Alignment identifier is 1  

> select #27/A:76-77 #29/A:76-77

40 atoms, 38 bonds, 4 residues, 2 models selected  

> select #27/A:76-90 #29/A:76-90

270 atoms, 272 bonds, 30 residues, 2 models selected  
. [ID: 1] region 2 chains [76-90] RMSD: 0.000  
  

> select #27/A:462 #29/A:462

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

> select #27/A:196-462 #29/A:196-462

4316 atoms, 4440 bonds, 534 residues, 2 models selected  
. [ID: 1] region 2 chains [196-462] RMSD: 41.732  
  

> fitmap sel inMap #1 moveWholeMolecules false

Fit molecules fold_pch45_gp025_model_0.cif (#27), fold_pch45_gp025_model_0.cif
(#29) to map PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 4316 atoms  
average map value = 0.2734, steps = 68  
shifted from previous position = 2.4  
rotated from previous position = 9.53 degrees  
atoms outside contour = 3724, contour level = 0.80437  
  

> show #4 models

> hide #4 models

> show #!1 models

> select clear

> hide #29 models

> show #29 models

> hide #29 models

> show #29 models

> hide #29 models

> hide #!1 models

> show #!1 models

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25_201_462/fold_pch45_gp25_201_462_model_0.cif""

Chain information for fold_pch45_gp25_201_462_model_0.cif #30  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #30 to #21

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_pch45_gp25_411_462_model_0.cif, chain A (#21) with
fold_pch45_gp25_201_462_model_0.cif, chain A (#30), sequence alignment score =
271.8  
RMSD between 34 pruned atom pairs is 0.677 angstroms; (across all 52 pairs:
5.408)  
  

> transparency #1.1#6.1 0

> transparency #1.1#6.1 50

> hide #30 models

> show #30 models

> hide #30 models

> show #30 models

> hide #30 models

> show #30 models

> hide #30 models

> show #30 models

> select add #30

2120 atoms, 2182 bonds, 262 residues, 1 model selected  

> select add #1

2120 atoms, 2182 bonds, 262 residues, 3 models selected  

> fitmap #30 inMap #1

Fit molecule fold_pch45_gp25_201_462_model_0.cif (#30) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 2120 atoms  
average map value = 0.6307, steps = 68  
shifted from previous position = 0.628  
rotated from previous position = 3.48 degrees  
atoms outside contour = 1304, contour level = 0.80437  
  
Position of fold_pch45_gp25_201_462_model_0.cif (#30) relative to
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.60384333 -0.55765393 0.56955714 355.42581166  
-0.29831444 -0.50450676 -0.81023541 307.07191066  
0.73917639 -0.65916237 0.13828682 246.21080457  
Axis 0.43821382 -0.49201033 0.75225959  
Axis point 82.88471712 249.76377171 0.00000000  
Rotation angle (degrees) 170.07414215  
Shift along axis 189.88438816  
  

> hide #30 models

> show #30 models

> fitmap #30 inMap #1

Fit molecule fold_pch45_gp25_201_462_model_0.cif (#30) to map
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) using 2120 atoms  
average map value = 0.6307, steps = 48  
shifted from previous position = 0.0112  
rotated from previous position = 0.0145 degrees  
atoms outside contour = 1304, contour level = 0.80437  
  
Position of fold_pch45_gp25_201_462_model_0.cif (#30) relative to
PCH45_Neck_C6_3_40A_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.60383134 -0.55768962 0.56953490 355.41865279  
-0.29811090 -0.50465267 -0.81021946 307.07448850  
0.73926829 -0.65902047 0.13847174 246.20239156  
Axis 0.43820887 -0.49192573 0.75231780  
Axis point 82.87189607 249.75343465 0.00000000  
Rotation angle (degrees) 170.06566978  
Shift along axis 189.91220412  
  

> select clear

> hide #30 models

> show #30 models

> hide #30 models

> hide #26 models

> show #30 models

> hide #30 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> show #30 models

> sym #30 C12 center 284.19, 284.19, 192.51

Made 12 copies for fold_pch45_gp25_201_462_model_0.cif symmetry C12  

> hide #31.2 models

> show #31.2 models

> hide #31.1 models

> show #31.1 models

> hide #31.1 models

> show #31.1 models

> hide #31.2 models

> show #31.2 models

> hide #31.3 models

> hide #31.4 models

> hide #31.1 models

> hide #31.5 models

> hide #31.6 models

> hide #31.7 models

> hide #31.8 models

> hide #31.9 models

> hide #31.10 models

> hide #31.11 models

> hide #31.12 models

> hide #31.2 models

> show #31.2 models

> help combine

> volume zone #1 nearAtoms 31.2 newMap true range 4

Invalid ""nearAtoms"" argument: invalid atoms specifier  

> volume zone #1 nearAtoms #31.2 newMap true range 4

Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #32, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32  

> surface dust #6 size 13.7

> surface dust #32 size 13.7

> save ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_Gp25AlphaCombine201-462SegmapTest.mrc"" models #32

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_Gp25AlphaCombine201-462SegmapTest.mrc""

Opened PCH45_Gp25AlphaCombine201-462SegmapTest.mrc as #33, grid size
416,416,416, pixel 1.37, shown at level 7.63e-05, step 2, values float32  

> save ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_GP25Alpha_CombineFitted200-462Test.pdb"" models #31.2
> relModel #33

> hide #18.4 models

> show #18.4 models

> hide #18.4 models

> hide #18.3 models

> hide #18.2 models

> hide #18.1 models

> hide #18.6 models

> show #18.6 models

> hide #18.5 models

> volume zone #1 nearAtoms #18.6 newMap true range 4

Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #34, grid size 416,416,416,
pixel 1.37, shown at step 1, values float32  

> surface dust #6 size 13.7

> surface dust #32 size 13.7

> surface dust #33 size 13.7

> surface dust #34 size 13.7

> hide #!33 models

> show #!33 models

> hide #!33 models

> show #!33 models

> hide #!34 models

> show #!34 models

> hide #!34 models

> show #!34 models

> vop add #33 #34

Opened volume sum as #35, grid size 416,416,416, pixel 1.37, shown at step 1,
values float32  

> select add #35

2 models selected  

> volume #35 level 0.4228

> surface dust #35 size 13.7

> volume #35 level 0.4705

> save ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_GP25AlphaWHoleMapCombineTestCOot.mrc"" models #35

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_GP25AlphaWHoleMapCombineTestCOot.mrc""

Opened PCH45_GP25AlphaWHoleMapCombineTestCOot.mrc as #36, grid size
416,416,416, pixel 1.37, shown at level 0.000214, step 2, values float32  

> volume #36 step 1

> select add #31.2

2120 atoms, 2182 bonds, 262 residues, 3 models selected  

> save ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/GP25AlphaCootFitPt200-462.pdb"" models #31.2 relModel #36

> save ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45Alpha1-200fit.pdb"" relModel #36

> save ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_Gp25Alpha1-200TestCoot2.pdb"" models #18.6 relModel #36

> hide #!36 models

> hide #35.1 models

> hide #!32 models

> select clear

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp025/fold_pch45_gp025_model_0.cif""

Chain information for fold_pch45_gp025_model_0.cif #37  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #37 models

> show #37 models

> ui tool show Matchmaker

> matchmaker #37 to #31.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_pch45_gp25_201_462_model_0.cif, chain A (#31.2) with
fold_pch45_gp025_model_0.cif, chain A (#37), sequence alignment score = 1282.7  
RMSD between 223 pruned atom pairs is 0.453 angstroms; (across all 262 pairs:
2.831)  
  

> help match

> matchmaker

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

> select add #37

3715 atoms, 3815 bonds, 462 residues, 1 model selected  
Alignment identifier is 37/A  

> select #37/A:264

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

> select #37/A:1-264

2117 atoms, 2173 bonds, 264 residues, 1 model selected  

> select #37/A:199

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

> select #37/A:1-199

1587 atoms, 1624 bonds, 199 residues, 1 model selected  

> select #37/A:200

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

> select #37/A:1-200

1595 atoms, 1632 bonds, 200 residues, 1 model selected  

> matchAtoms sel #18.6

Unknown command: matchAtoms sel #18.6  

> matchAtoms

Unknown command: matchAtoms  

> matchatom

Unknown command: matchatom  

> matchmaker

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

> matchAtoms #37/A:1-200 #18.6

Unknown command: matchAtoms #37/A:1-200 #18.6  

> matchmaker #37/A:1-200 #18.6

Missing required ""to"" argument  

> matchmaker #37/A:1-200 to #18.6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PCH45_Gp25alpha_1-200AA fit-coot-2.pdb, chain A (#18.6) with
fold_pch45_gp025_model_0.cif, chain A (#37), sequence alignment score = 879.3  
RMSD between 107 pruned atom pairs is 0.766 angstroms; (across all 200 pairs:
25.924)  
  

> select clear

> hide #!35 models

> show #!35 models

> show #!36 models

> hide #!36 models

> show #!36 models

> volume #36 level 0.4161

> surface dust #6 size 13.7

> surface dust #36 size 13.7

> volume gaussian #36 sDev 2

Opened PCH45_GP25AlphaWHoleMapCombineTestCOot.mrc gaussian as #38, grid size
416,416,416, pixel 1.37, shown at step 1, values float32  

> volume #38 level 0.2722

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp025/fold_pch45_gp025_model_0.cif""

Chain information for fold_pch45_gp025_model_0.cif #39  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #39 to #31.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_pch45_gp25_201_462_model_0.cif, chain A (#31.2) with
fold_pch45_gp025_model_0.cif, chain A (#39), sequence alignment score = 1282.7  
RMSD between 223 pruned atom pairs is 0.453 angstroms; (across all 262 pairs:
2.831)  
  

> ui tool show ""Fit in Map""

> select clear

> select add #39

3715 atoms, 3815 bonds, 462 residues, 1 model selected  
Alignment identifier is 39/A  

> select #39/A:1

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

> select #39/A:1-207

1661 atoms, 1702 bonds, 207 residues, 1 model selected  

> select #39/A:200

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

> select #39/A:1-200

1595 atoms, 1632 bonds, 200 residues, 1 model selected  

> fitmap #39 inMap #38 moveWholeMolecules false

Fit molecule fold_pch45_gp025_model_0.cif (#39) to map
PCH45_GP25AlphaWHoleMapCombineTestCOot.mrc gaussian (#38) using 3715 atoms  
average map value = 0.2251, steps = 240  
shifted from previous position = 8.84  
rotated from previous position = 33.7 degrees  
atoms outside contour = 2261, contour level = 0.27224  
  

> hide #!38 models

> hide #37 models

> show #37 models

> hide #37 models

> select add #39

3715 atoms, 3815 bonds, 462 residues, 1 model selected  

> select subtract #39

Nothing selected  

> hide #39 models

> show #39 models

> hide #39 models

> show #39 models

> combine #31.2 #18.6

Remapping chain ID 'A' in PCH45_Gp25alpha_1-200AA fit-coot-2.pdb #18.6 to 'B'  

> hide #18.6 models

> show #18.6 models

> hide #18.6 models

> show #18.6 models

> hide #18.6 models

> show #18.6 models

> hide #40 models

> show #40 models

> hide #40 models

> hide #31.2 models

> hide #18.6 models

> show #40 models

> hide #40 models

> show #40 models

> bone

Unknown command: bone  

> bond

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

> help bond

> helpbond

Unknown command: helpbond  

> hide #40 models

> show #40 models

> ui tool show ""Model Panel""

> view #40 clip false

> ui tool show ""Build Structure""

No atoms selected  

> show #31.2 models

> hide #31.2 models

> select add #40

3716 atoms, 3815 bonds, 462 residues, 1 model selected  
FYI: command is replacing existing command: ""build invert""  
FYI: command is replacing existing command: ""build join peptide""  
FYI: command is replacing existing command: ""build join bond""  
FYI: command is replacing existing command: ""build modify""  
FYI: command is replacing existing command: ""build replace""  
FYI: command is replacing existing command: ""build start""  
FYI: command is replacing existing command: ""bond""  
FYI: command is replacing existing command: ""~bond""  
FYI: command is replacing existing command: ""bond length""  

> build join peptide sel length 1.33 omega 180 phi -120 move small

Multiple N- and C-terminii in atoms  

> select clear

> select add #40

3716 atoms, 3815 bonds, 462 residues, 1 model selected  

> select subtract #40

Nothing selected  

> select #40/A:1

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

> select #40/B:200

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

> select add #40/A:1

23 atoms, 23 bonds, 2 residues, 1 model selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

Atoms must be in different models  

> select add #40

3717 atoms, 3816 bonds, 462 residues, 1 model selected  

> hide #40 models

> show #40 models

> hide #40 models

> select subtract #40

Nothing selected  

> show #31.2 models

> show #18.6 models

> select #31.2/A:1

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

> select add #18.6/A:200

23 atoms, 23 bonds, 2 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

> open ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/New Folder/GP25AlphaCootFitPt200-462-coot-0[True Test].pdb""

Chain information for GP25AlphaCootFitPt200-462-coot-0[True Test].pdb #41  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!18 models

> hide #!31 models

> show #!31 models

> hide #!31 models

> hide #41 models

> show #41 models

> select clear

> select #41/A:1

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

> view matrix models
> #41,0.99998,0.0044456,-0.0043127,-0.53243,-0.0044611,0.99998,-0.0035795,2.3082,0.0042967,0.0035987,0.99998,-2.6602

Drag select of 2 residues  

> build join peptide sel length 1.33 omega 180 phi -120 move small

Atoms must be in different models  

> save ""/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for
> Distribution!/PCH45_GP25alpha/FucksSake.cxs"" includeMaps true


===== 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.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
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: Mac15,3
      Model Number: Z1C80004VX/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.1 (24G231)
      Kernel Version: Darwin 24.6.0
      Time since boot: 3 hours, 2 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        VN2410C:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 144.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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-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