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Opened 3 hours ago
#20082 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 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 0x00000001fed6f100 (most recent call first):
File "/Applications/ChimeraX-1.10.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.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.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, cython.cimports.libc.math, scipy._lib._ccallback_c, _cyutility, scipy._cyutility, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_schur_sqrtm, scipy.linalg._matfuncs_expm, scipy.linalg._linalg_pythran, scipy.linalg.cython_blas, scipy.linalg._decomp_update, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.special._ufuncs_cxx, scipy.special._ellip_harm_2, scipy.special._special_ufuncs, scipy.special._gufuncs, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.spatial._hausdorff, scipy.spatial._distance_wrap, scipy.spatial.transform._rotation, scipy.spatial.transform._rigid_transform, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, 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, torch._C, torch._C._dynamo.autograd_compiler, torch._C._dynamo.eval_frame, torch._C._dynamo.guards, torch._C._dynamo.utils, torch._C._fft, torch._C._linalg, torch._C._nested, torch._C._nn, torch._C._sparse, torch._C._special, PIL._imaging, PIL._imagingft, yaml._yaml, scipy.ndimage._nd_image, scipy.ndimage._rank_filter_1d, _ni_label, scipy.ndimage._ni_label, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath, chimerax.connect_structure._cs, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, kiwisolver._cext, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._slsqplib, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy._lib._uarray._uarray, scipy.linalg._decomp_interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.interpolate._dierckx, scipy.interpolate._ppoly, scipy.interpolate._interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree (total: 144)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 1011626602,
"deployVersion" : 210,
"modelCode" : "Mac16,8",
"coalitionID" : 1622,
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"build" : "25D2128",
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"captureTime" : "2026-03-26 13:58:04.3249 +0200",
"codeSigningMonitor" : 2,
"incident" : "D5C21842-F967-49AA-945A-00F67E009331",
"pid" : 6487,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-03-24 10:27:07.8808 +0200",
"procStartAbsTime" : 17775801296,
"procExitAbsTime" : 3028005451169,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 102557,
"sleepWakeUUID" : "1C07AD76-506F-4B78-8A2B-BFF8BB7E84A6",
"sip" : "enabled",
"vmRegionInfo" : "0xffffe44778eafe50 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":6487},
"vmregioninfo" : "0xffffe44778eafe50 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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===== Log before crash start =====
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot 7,0.25
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000
> alias map_unsphere volume unzone ~##num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ~##num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias open_vseries "open browse vseries true"
> alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask
> #10000 spacing 1 border -0.5
> alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr;
> sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001
> minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001;
> close sel; show $2
> alias centersel cofr sel; clip near 10 position cofr; clip far -10 position
> cofr; cofr centerOfView showpivot true; view sel
> alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine
> $1.* close true
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr
> radius 1"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> buttonpanel Shortcuts add reset_mouse_and_help command "mousemode alt right
> contour ; mousemode right clip ; mousemode alt left 'translate selected
> models' ; mousemode shift left 'rotate selected models' ; mousemode alt
> control left 'pick blobs'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md"
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> runscript /Users/avenka/Chimera/chimera_startup.py
> phenix location /Applications/Phenix/phenix-1.21.2-5419
Using Phenix installation /Applications/Phenix/phenix-1.21.2-5419
> open /Users/avenka/Downloads/cryosparc_P1_J574_012_volume_map.mrc format mrc
Opened cryosparc_P1_J574_012_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.828, shown at level 0.00417, step 1, values float32
> volume flip #1
Opened cryosparc_P1_J574_012_volume_map.mrc z flip as #2, grid size
512,512,512, pixel 0.828, shown at step 1, values float32
> close #1
> color #2 #7a81ffff models
> color #2 #ff85ffff models
> color #2 #ff8ad8ff models
> color #2 #ffcefaff models
> volume #2 level 0.005756
> ui tool show LocScale-SURFER
LocScale-SURFER tool initialized.
Segment and hide micelle densities in cryo-EM maps.
Use unsharpened halfmaps as input, and optionally a mask map to speed up
computation. Recommended to use GPUs
Window position QRect(1934,920 626x398) outside any known screen, using
primary screen
Segmenting map with the following inputs:
Input map: cryosparc_P1_J574_012_volume_map.mrc z flip
No mask map provided.
Starting segmentation...
Using Apple Silicon GPU (MPS).
Prediction done. Shape: (512, 512, 512)
Segmentation complete.
Opened Predicted detergent micelle as #1, grid size 512,512,512, pixel 0.828,
shown at step 1, values float64
> color #1 #b2ffff71 models
> hide #!2 models
> hide #!1 models
> close #1
> show #!2 models
> volume #2 level 0.01013
Segment largest component set to: False
Segmenting map with the following inputs:
Input map: cryosparc_P1_J574_012_volume_map.mrc z flip
No mask map provided.
Starting segmentation...
Using Apple Silicon GPU (MPS).
Prediction done. Shape: (512, 512, 512)
Segmentation complete.
Opened Predicted detergent micelle as #1, grid size 512,512,512, pixel 0.828,
shown at step 1, values float64
> hide #!2 models
> volume #1 level 0.02161
> open
> /Users/avenka/Phenix/RealSpaceRefine_38/placed_model_real_space_refined_034_real_space_refined_037_real_space_refined_038.pdb
> format pdb
Chain information for
placed_model_real_space_refined_034_real_space_refined_037_real_space_refined_038.pdb
#3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> close #1
> show #!2 models
> close #3
> open /Users/avenka/Downloads/8dnw.pdb format pdb
8dnw.pdb title:
Cryo-em structure of the human SEC61 complex In A partially-open apo state
(class 2) [more info...]
Chain information for 8dnw.pdb #1
---
Chain | Description | UniProt
A | SEC61 α-1 | S61A1_HUMAN 1-476
B | protein transport protein SEC61 subunit γ | SC61G_HUMAN 1-68
C | protein transport protein SEC61 subunit β | SC61B_HUMAN 1-96
> ui tool show LocScale-SURFER
LocScale-SURFER tool initialized.
Segment and hide micelle densities in cryo-EM maps.
Use unsharpened halfmaps as input, and optionally a mask map to speed up
computation. Recommended to use GPUs
Window position QRect(1934,920 626x398) outside any known screen, using
primary screen
> close #1
Segmenting map with the following inputs:
Input map: cryosparc_P1_J574_012_volume_map.mrc z flip
No mask map provided.
Starting segmentation...
Using Apple Silicon GPU (MPS).
Prediction done. Shape: (512, 512, 512)
Segmentation complete.
Opened Predicted detergent micelle as #1, grid size 512,512,512, pixel 0.828,
shown at step 1, values float64
> color #1 #7b64ffff models
No target map selected for detergent removal.
Largest component selected.
Binarised segmented map smoothed with filter size 5.
Creating binarised segmented volume.
Opened Binarised Segmentation as #3, grid size 512,512,512, pixel 0.828, shown
at step 1, values float64
Binarised segmented volume created: Binarised Segmentation
> hide #!1 models
Largest component selected.
Binarised segmented map smoothed with filter size 5.
Opened cryosparc_P1_J574_012_volume_map.mrc z flip_without_micelle as #4, grid
size 512,512,512, pixel 0.828, shown at step 1, values float64
Micelle removal complete.
> vop hide
> volume #4 close image
> volume #4 level 0.01013
> hide #!4 models
> show #!2 models
> show #!3 models
> volume #3 level 0.2365
> close #4
Largest component selected.
Binarised segmented map smoothed with filter size 5.
Opened cryosparc_P1_J574_012_volume_map.mrc z flip_without_micelle as #4, grid
size 512,512,512, pixel 0.828, shown at step 1, values float64
Micelle removal complete.
> vop hide
> close #4
Largest component selected.
Binarised segmented map smoothed with filter size 5.
Opened cryosparc_P1_J574_012_volume_map.mrc z flip_without_micelle as #4, grid
size 512,512,512, pixel 0.828, shown at step 1, values float64
Micelle removal complete.
> vop hide
> volume #4 close image
> volume #4 level 0.04362
> volume #4 level 0.04607
> show #!2 models
> volume #2 style mesh
> volume #2 level 0.0375
> open /Users/avenka/Downloads/8dnw.pdb format pdb
8dnw.pdb title:
Cryo-em structure of the human SEC61 complex In A partially-open apo state
(class 2) [more info...]
Chain information for 8dnw.pdb #5
---
Chain | Description | UniProt
A | SEC61 α-1 | S61A1_HUMAN 1-476
B | protein transport protein SEC61 subunit γ | SC61G_HUMAN 1-68
C | protein transport protein SEC61 subunit β | SC61B_HUMAN 1-96
> ui mousemode right select
> select /A:178
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #5
4060 atoms, 4146 bonds, 4 pseudobonds, 528 residues, 3 models selected
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,43.695,0,1,0,-0.27973,0,0,1,56.146
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.16695,-0.95991,-0.22516,303.77,-0.9584,-0.10437,-0.26566,299.71,0.23151,0.26015,-0.9374,220.06
> view matrix models
> #5,0.15497,-0.97238,0.17451,259.92,-0.97352,-0.12025,0.19443,249.61,-0.16807,-0.20002,-0.96527,335.34
> view matrix models
> #5,0.1175,-0.9853,-0.12404,301.58,0.99117,0.10863,0.075995,-20.148,-0.061402,-0.13187,0.98936,82.639
> view matrix models
> #5,-0.7049,0.49655,-0.50652,258.2,-0.46501,-0.86274,-0.19862,327.69,-0.53562,0.095527,0.83904,131.69
> ui mousemode right "move picked models"
> view matrix models
> #5,-0.7049,0.49655,-0.50652,334.37,-0.46501,-0.86274,-0.19862,355.69,-0.53562,0.095527,0.83904,148.8
> view matrix models
> #5,-0.7049,0.49655,-0.50652,295.48,-0.46501,-0.86274,-0.19862,408.56,-0.53562,0.095527,0.83904,150.4
> view matrix models
> #5,-0.7049,0.49655,-0.50652,310.48,-0.46501,-0.86274,-0.19862,410.74,-0.53562,0.095527,0.83904,160.17
> ui mousemode right select
> select subtract #5
Nothing selected
> ui tool show "Fit in Map"
> fitmap #5 inMap #4
Fit molecule 8dnw.pdb (#5) to map cryosparc_P1_J574_012_volume_map.mrc z
flip_without_micelle (#4) using 4060 atoms
average map value = 0.05148, steps = 128
shifted from previous position = 9.02
rotated from previous position = 18.5 degrees
atoms outside contour = 1797, contour level = 0.046075
Position of 8dnw.pdb (#5) relative to cryosparc_P1_J574_012_volume_map.mrc z
flip_without_micelle (#4) coordinates:
Matrix rotation and translation
-0.81179900 0.32273297 -0.48664753 341.40704976
-0.18355470 -0.93218087 -0.31200400 405.58049446
-0.55433750 -0.16395809 0.81598265 199.99269904
Axis 0.27837882 0.12728114 -0.95200039
Axis point 229.17995517 191.01701701 0.00000000
Rotation angle (degrees) 164.57912950
Shift along axis -43.72988892
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> color #4 #99bfe5b8 models
> color #4 #99bfe5b3 models
> color #4 #99bfe592 models
> color #4 #99bfe595 models
> color #4 #99bfe599 models
> color #4 #99bfe580 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> save "/Users/avenka/OneDrive - University of Helsinki/Ville Paavilainen
> lab/Chimera Sessions/Sec61_NatCba.cxs"
> show atoms
> hide cartoons
> open /Users/avenka/Downloads/output_see_alpha_output_see_alpha_output_p.cif
Summary of feedback from opening
/Users/avenka/Downloads/output_see_alpha_output_see_alpha_output_p.cif
---
warning | No mmCIF models found.
> open /Users/avenka/Downloads/output/output_raw.cif
Summary of feedback from opening /Users/avenka/Downloads/output/output_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for output_raw.cif #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | 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
V | No description available
W | No description available
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
> hide #!5 models
> hide #6 surfaces
> hide #6 cartoons
> show #6 cartoons
Computing secondary structure
> hide #6 atoms
> select add #6
11921 atoms, 12368 bonds, 1507 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,65.479,0,1,0,-49.195,0,0,1,5.6331
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.9305,-0.06227,0.36096,13.008,0.15404,0.96059,-0.23137,-21.172,-0.33233,0.2709,0.90342,37.652
> view matrix models
> #6,-0.21564,0.78621,-0.57912,277.73,-0.85818,-0.43553,-0.27173,504.55,-0.46586,0.43839,0.76863,59.152
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.21564,0.78621,-0.57912,222.68,-0.85818,-0.43553,-0.27173,544.79,-0.46586,0.43839,0.76863,57.995
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.23739,0.83724,-0.49262,196.78,-0.83061,-0.43791,-0.34398,555.67,-0.50372,0.32752,0.79937,83.259
> view matrix models
> #6,-0.16502,0.84221,-0.51327,185.15,-0.80309,-0.41684,-0.42577,563.58,-0.57254,0.34194,0.74516,106.63
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.16502,0.84221,-0.51327,180.65,-0.80309,-0.41684,-0.42577,556.57,-0.57254,0.34194,0.74516,105.61
> view matrix models
> #6,-0.16502,0.84221,-0.51327,176.25,-0.80309,-0.41684,-0.42577,557.86,-0.57254,0.34194,0.74516,103.2
> select subtract #6
Nothing selected
> ui tool show "Fit in Map"
> show #!2 models
> hide #!2 models
> fitmap #6 inMap #2
Fit molecule output_raw.cif (#6) to map cryosparc_P1_J574_012_volume_map.mrc z
flip (#2) using 11921 atoms
average map value = 0.05749, steps = 88
shifted from previous position = 0.662
rotated from previous position = 5.95 degrees
atoms outside contour = 3532, contour level = 0.037497
Position of output_raw.cif (#6) relative to
cryosparc_P1_J574_012_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
-0.25586859 0.83936045 -0.47958865 188.42985948
-0.76910678 -0.47730590 -0.42503390 563.78167634
-0.58566715 0.26010206 0.76768541 118.03489102
Axis 0.39116597 0.06056360 -0.91832524
Axis point 300.66682651 225.11900096 -0.00000000
Rotation angle (degrees) 118.86480660
Shift along axis -0.54242435
> show #!2 models
> hide #!2 models
> save "/Users/avenka/OneDrive - University of Helsinki/Ville Paavilainen
> lab/Chimera Sessions/Sec61_NatCba.cxs"
> show #!2 models
> hide #!4 models
> color #2 #ffcefaa7 models
> color #2 #ffcefa9f models
> color #2 #ffcefa99 models
> show #6 atoms
> hide #6 atoms
> style #6 stick
Changed 11921 atom styles
> show #6 atoms
> hide #6 cartoons
> show #!4 models
> save /Users/avenka/Downloads/placed_model.pdb models #6 relModel #6
Alignment identifier is 5/B
Alignment identifier is 5/C
Alignment identifier is 5/A
Alignment identifier is 6/A
Alignment identifier is 6/B
Alignment identifier is 6/C
Alignment identifier is 6/D
Alignment identifier is 6/E
Alignment identifier is 6/F
Alignment identifier is 6/G
Alignment identifier is 6/H
Alignment identifier is 6/I
Alignment identifier is 6/J
Alignment identifier is 6/K
Alignment identifier is 6/L
Alignment identifier is 6/M
Alignment identifier is 6/N
Alignment identifier is 6/O
Alignment identifier is 6/P
Alignment identifier is 6/Q
Alignment identifier is 6/R
Alignment identifier is 6/S
Alignment identifier is 6/T
Alignment identifier is 6/U
Alignment identifier is 6/V
Alignment identifier is 6/W
Alignment identifier is 6/X
Alignment identifier is 6/Y
Alignment identifier is 6/Z
Alignment identifier is 6/a
Alignment identifier is 6/b
Alignment identifier is 6/c
Alignment identifier is 6/d
Alignment identifier is 5/B
Alignment identifier is 5/C
Alignment identifier is 5/A
Destroying pre-existing alignment with identifier 6/A
Alignment identifier is 6/A
Destroying pre-existing alignment with identifier 6/B
Alignment identifier is 6/B
Destroying pre-existing alignment with identifier 6/C
Alignment identifier is 6/C
Destroying pre-existing alignment with identifier 6/D
Alignment identifier is 6/D
Destroying pre-existing alignment with identifier 6/E
Alignment identifier is 6/E
Destroying pre-existing alignment with identifier 6/F
Alignment identifier is 6/F
Destroying pre-existing alignment with identifier 6/G
Alignment identifier is 6/G
Destroying pre-existing alignment with identifier 6/H
Alignment identifier is 6/H
Destroying pre-existing alignment with identifier 6/I
Alignment identifier is 6/I
Destroying pre-existing alignment with identifier 6/J
Alignment identifier is 6/J
Destroying pre-existing alignment with identifier 6/K
Alignment identifier is 6/K
Destroying pre-existing alignment with identifier 6/L
Alignment identifier is 6/L
Destroying pre-existing alignment with identifier 6/M
Alignment identifier is 6/M
Destroying pre-existing alignment with identifier 6/N
Alignment identifier is 6/N
Destroying pre-existing alignment with identifier 6/O
Alignment identifier is 6/O
Destroying pre-existing alignment with identifier 6/P
Alignment identifier is 6/P
Destroying pre-existing alignment with identifier 6/Q
Alignment identifier is 6/Q
Destroying pre-existing alignment with identifier 6/R
Alignment identifier is 6/R
Destroying pre-existing alignment with identifier 6/S
Alignment identifier is 6/S
Destroying pre-existing alignment with identifier 6/T
Alignment identifier is 6/T
Destroying pre-existing alignment with identifier 6/U
Alignment identifier is 6/U
Destroying pre-existing alignment with identifier 6/V
Alignment identifier is 6/V
Destroying pre-existing alignment with identifier 6/W
Alignment identifier is 6/W
Destroying pre-existing alignment with identifier 6/X
Alignment identifier is 6/X
Destroying pre-existing alignment with identifier 6/Y
Alignment identifier is 6/Y
Destroying pre-existing alignment with identifier 6/Z
Alignment identifier is 6/Z
Destroying pre-existing alignment with identifier 6/a
Alignment identifier is 6/a
Destroying pre-existing alignment with identifier 6/b
Alignment identifier is 6/b
Destroying pre-existing alignment with identifier 6/c
Alignment identifier is 6/c
Destroying pre-existing alignment with identifier 6/d
Alignment identifier is 6/d
Destroying pre-existing alignment with identifier 5/B
Alignment identifier is 5/B
Destroying pre-existing alignment with identifier 5/C
Alignment identifier is 5/C
Destroying pre-existing alignment with identifier 5/A
Alignment identifier is 5/A
Destroying pre-existing alignment with identifier 6/A
Alignment identifier is 6/A
Destroying pre-existing alignment with identifier 6/B
Alignment identifier is 6/B
Destroying pre-existing alignment with identifier 6/C
Alignment identifier is 6/C
Destroying pre-existing alignment with identifier 6/D
Alignment identifier is 6/D
Destroying pre-existing alignment with identifier 6/E
Alignment identifier is 6/E
Destroying pre-existing alignment with identifier 6/F
Alignment identifier is 6/F
Destroying pre-existing alignment with identifier 6/G
Alignment identifier is 6/G
Destroying pre-existing alignment with identifier 6/H
Alignment identifier is 6/H
Destroying pre-existing alignment with identifier 6/I
Alignment identifier is 6/I
Destroying pre-existing alignment with identifier 6/J
Alignment identifier is 6/J
Destroying pre-existing alignment with identifier 6/K
Alignment identifier is 6/K
Destroying pre-existing alignment with identifier 6/L
Alignment identifier is 6/L
Destroying pre-existing alignment with identifier 6/M
Alignment identifier is 6/M
Destroying pre-existing alignment with identifier 6/N
Alignment identifier is 6/N
Destroying pre-existing alignment with identifier 6/O
Alignment identifier is 6/O
Destroying pre-existing alignment with identifier 6/P
Alignment identifier is 6/P
Destroying pre-existing alignment with identifier 6/Q
Alignment identifier is 6/Q
Destroying pre-existing alignment with identifier 6/R
Alignment identifier is 6/R
Destroying pre-existing alignment with identifier 6/S
Alignment identifier is 6/S
Destroying pre-existing alignment with identifier 6/T
Alignment identifier is 6/T
Destroying pre-existing alignment with identifier 6/U
Alignment identifier is 6/U
Destroying pre-existing alignment with identifier 6/V
Alignment identifier is 6/V
Destroying pre-existing alignment with identifier 6/W
Alignment identifier is 6/W
Destroying pre-existing alignment with identifier 6/X
Alignment identifier is 6/X
Destroying pre-existing alignment with identifier 6/Y
Alignment identifier is 6/Y
Destroying pre-existing alignment with identifier 6/Z
Alignment identifier is 6/Z
Destroying pre-existing alignment with identifier 6/a
Alignment identifier is 6/a
Destroying pre-existing alignment with identifier 6/b
Alignment identifier is 6/b
Destroying pre-existing alignment with identifier 6/c
Alignment identifier is 6/c
Destroying pre-existing alignment with identifier 6/d
Alignment identifier is 6/d
> close #5
> cootmode
> surface cap false
Changed 11921 atom styles
Changed 0 atom styles
Changed 1 ball scales
Changed 12368 bond radii
Window position QRect(1906,305 654x62) outside any known screen, using primary
screen
Window position QRect(1906,310 654x62) outside any known screen, using primary
screen
Window position QRect(1906,315 654x62) outside any known screen, using primary
screen
Window position QRect(1906,321 654x62) outside any known screen, using primary
screen
Window position QRect(1906,327 654x62) outside any known screen, using primary
screen
> hide #!3 models
> hide #!2 models
> hide #!1 models
> ui tool show "Side View"
Window position QRect(1906,1331 654x206) outside any known screen, using
primary screen
> ui tool show "Side View"
Window position QRect(1906,517 654x94) outside any known screen, using primary
screen
> volume #4 level 0.04151
> volume #4 level 0.03391
> view #4 clip false
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume #2 level 0.03788
> volume #2 style mesh
> show #!4 models
> hide #!2 models
> volume #2
> volume #2 style surface
> hide #!2 models
> volume #4 style mesh
> volume #4 level 0.04531
> close #3
> ui tool show "Side View"
> ui mousemode right select
> show atoms
> hide atoms
> show atoms
> style stick
Changed 11921 atom styles
> style sphere
Changed 11921 atom styles
> style stick
Changed 11921 atom styles
> style ball
Changed 11921 atom styles
> style stick
Changed 11921 atom styles
> hide atoms
> show cartoons
> show #!2 models
> color bychain
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> color #4 #f1c4bf4c models
> color #4 #f0b2f14c models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides fill
> style nucleic stick
Changed 0 atom styles
> hide #6 models
> show #6 models
> hide #!4 models
> nucleotides fill
> style nucleic stick
Changed 0 atom styles
> nucleotides fill
> style nucleic stick
Changed 0 atom styles
> nucleotides tube/slab shape box
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> show #!4 models
> show #!2 models
> hide #!4 models
> volume #2 style mesh
> volume #4 style surface
> show #!4 models
Window position QRect(1906,1051 654x267) outside any known screen, using
primary screen
> ui favorite true Toolbar
Traceback (most recent call last):
File "/Users/avenka/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/chopchop_mf/chopalignment.py", line 457, in save
distutils.dir_util.copy_tree(output_dir, str(download_dir))
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/setuptools/_distutils/dir_util.py", line 127, in copy_tree
raise DistutilsFileError(f"cannot copy tree '{src}': not a directory")
distutils.errors.DistutilsFileError: cannot copy tree
'/Users/avenka/ChopChop_output': not a directory
distutils.errors.DistutilsFileError: cannot copy tree
'/Users/avenka/ChopChop_output': not a directory
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/setuptools/_distutils/dir_util.py", line 127, in copy_tree
raise DistutilsFileError(f"cannot copy tree '{src}': not a directory")
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/avenka/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/chopchop_mf/chopalignment.py", line 457, in save
distutils.dir_util.copy_tree(output_dir, str(download_dir))
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/setuptools/_distutils/dir_util.py", line 127, in copy_tree
raise DistutilsFileError(f"cannot copy tree '{src}': not a directory")
distutils.errors.DistutilsFileError: cannot copy tree
'/Users/avenka/ChopChop_output': not a directory
distutils.errors.DistutilsFileError: cannot copy tree
'/Users/avenka/ChopChop_output': not a directory
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/setuptools/_distutils/dir_util.py", line 127, in copy_tree
raise DistutilsFileError(f"cannot copy tree '{src}': not a directory")
See log for complete Python traceback.
> ui dockable false Toolbar
> ui dockable true Toolbar
Alignment identifier is 6/A
Alignment identifier is 6/B
Alignment identifier is 6/C
Alignment identifier is 6/D
Alignment identifier is 6/E
Alignment identifier is 6/F
Alignment identifier is 6/G
Alignment identifier is 6/H
Alignment identifier is 6/I
Alignment identifier is 6/J
Alignment identifier is 6/K
Alignment identifier is 6/L
Alignment identifier is 6/M
Alignment identifier is 6/N
Alignment identifier is 6/O
Alignment identifier is 6/P
Alignment identifier is 6/Q
Alignment identifier is 6/R
Alignment identifier is 6/S
Alignment identifier is 6/T
Alignment identifier is 6/U
Alignment identifier is 6/V
Alignment identifier is 6/W
Alignment identifier is 6/X
Alignment identifier is 6/Y
Alignment identifier is 6/Z
Alignment identifier is 6/a
Alignment identifier is 6/b
Alignment identifier is 6/c
Alignment identifier is 6/d
Destroying pre-existing alignment with identifier 6/A
Alignment identifier is 6/A
Destroying pre-existing alignment with identifier 6/B
Alignment identifier is 6/B
Destroying pre-existing alignment with identifier 6/C
Alignment identifier is 6/C
Destroying pre-existing alignment with identifier 6/D
Alignment identifier is 6/D
Destroying pre-existing alignment with identifier 6/E
Alignment identifier is 6/E
Destroying pre-existing alignment with identifier 6/F
Alignment identifier is 6/F
Destroying pre-existing alignment with identifier 6/G
Alignment identifier is 6/G
Destroying pre-existing alignment with identifier 6/H
Alignment identifier is 6/H
Destroying pre-existing alignment with identifier 6/I
Alignment identifier is 6/I
Destroying pre-existing alignment with identifier 6/J
Alignment identifier is 6/J
Destroying pre-existing alignment with identifier 6/K
Alignment identifier is 6/K
Destroying pre-existing alignment with identifier 6/L
Alignment identifier is 6/L
Destroying pre-existing alignment with identifier 6/M
Alignment identifier is 6/M
Destroying pre-existing alignment with identifier 6/N
Alignment identifier is 6/N
Destroying pre-existing alignment with identifier 6/O
Alignment identifier is 6/O
Destroying pre-existing alignment with identifier 6/P
Alignment identifier is 6/P
Destroying pre-existing alignment with identifier 6/Q
Alignment identifier is 6/Q
Destroying pre-existing alignment with identifier 6/R
Alignment identifier is 6/R
Destroying pre-existing alignment with identifier 6/S
Alignment identifier is 6/S
Destroying pre-existing alignment with identifier 6/T
Alignment identifier is 6/T
Destroying pre-existing alignment with identifier 6/U
Alignment identifier is 6/U
Destroying pre-existing alignment with identifier 6/V
Alignment identifier is 6/V
Destroying pre-existing alignment with identifier 6/W
Alignment identifier is 6/W
Destroying pre-existing alignment with identifier 6/X
Alignment identifier is 6/X
Destroying pre-existing alignment with identifier 6/Y
Alignment identifier is 6/Y
Destroying pre-existing alignment with identifier 6/Z
Alignment identifier is 6/Z
Destroying pre-existing alignment with identifier 6/a
Alignment identifier is 6/a
Destroying pre-existing alignment with identifier 6/b
Alignment identifier is 6/b
Destroying pre-existing alignment with identifier 6/c
Alignment identifier is 6/c
Destroying pre-existing alignment with identifier 6/d
Alignment identifier is 6/d
> interfaces ~solvent
27 buried areas: Y U 2974, G B 2754, X V 2096, A C 2093, Y W 1406, Y V 1136, G
D 780, N M 725, A F 626, C F 584, A H 530, Y X 528, B F 490, Y F 490, C E 483,
A B 472, V D 436, X T 409, G F 399, Y C 388, B D 384, G P 372, Y O 333, Y D
318, C G 307, A G 304, C I 301
> ui tool show "Selection Inspector"
> select add #6
11921 atoms, 12368 bonds, 1507 residues, 1 model selected
> redock
Unknown command: redock
> ui tool show Toolbar
> ui tool show "Side View"
Window position QRect(1906,1090 654x207) outside any known screen, using
primary screen
Window position QRect(1906,684 654x613) outside any known screen, using
primary screen
Window position QRect(1906,1140 654x178) outside any known screen, using
primary screen
> lighting simple
> hide #!4 models
> show sel atoms
> hide sel cartoons
> select subtract #6
Nothing selected
> select add #6
11921 atoms, 12368 bonds, 1507 residues, 1 model selected
> select subtract #6
Nothing selected
> ui tool show "Hide Dust"
> surface dust #2 size 12
> show #!4 models
> hide #!2 models
> surface dust #4 size 8
> show #!2 models
> toolshed show
Downloading bundle chimerax_daqplugin-0.13.51-py3-none-any.whl
Malformed ChimeraX :: Tool line in AlphaFold2 skipped.
Expected 5 fields and got 4.
Installed ChimeraX-DAQplugin (0.13.51)
Downloading bundle ChimeraX_AllMetal3D-0.8-py3-none-any.whl
Malformed ChimeraX :: Tool line in AlphaFold2 skipped.
Expected 5 fields and got 4.
Installed ChimeraX-AllMetal3D (0.8)
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 70 residues in model #6 to IUPAC-IUB
standards.
Chain information for output_raw.cif
---
Chain | Description
3.2/A | No description available
3.2/B | No description available
3.2/C | No description available
3.2/D | No description available
3.2/E | No description available
3.2/F | No description available
3.2/G | No description available
3.2/H | No description available
3.2/I | No description available
3.2/J | No description available
3.2/K | No description available
3.2/L | No description available
3.2/M | No description available
3.2/N | No description available
3.2/O | No description available
3.2/P | No description available
3.2/Q | No description available
3.2/R | No description available
3.2/S | No description available
3.2/T | No description available
3.2/U | No description available
3.2/V | No description available
3.2/W | No description available
3.2/X | No description available
3.2/Y | No description available
3.2/Z | No description available
3.2/a | No description available
3.2/b | No description available
3.2/c | No description available
3.2/d | No description available
> isolde tutorial
> clipper associate #2 toModel #3
Opened cryosparc_P1_J574_012_volume_map.mrc z flip as #3.1.1.1, grid size
512,512,512, pixel 0.828, shown at step 1, values float32
> clipper associate #2 toModel #1
Invalid "toModel" argument: must specify 1 structure, got 0 for "#1"
> clipper associate #3.1 toModel #3.2
> hide #!3.2 models
> hide #!3.1 models
> hide #3.3 models
> show #!3.2 models
> show #!3.1 models
> show #3.3 models
Drag select of 4 cryosparc_P1_J574_012_volume_map.mrc z flip_without_micelle
> select clear
> hide #!4 models
> show #!4 models
> select clear
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> isolde sim start /A-d
Sim termination reason: None
ISOLDE: stopped sim
> addh #3.2
Summary of feedback from adding hydrogens to output_raw.cif #3.2
---
warnings | Unknown hybridization for atoms (OE1, O) of residue type GLN; not adding hydrogens to them
Unknown hybridization for atoms (N, O) of residue type THR; not adding
hydrogens to them
Unknown hybridization for atoms (OH, O) of residue type TYR; not adding
hydrogens to them
Unknown hybridization for atom (OD1) of residue type ASN; not adding hydrogens
to it
Unknown hybridization for atom (O) of residue type SER; not adding hydrogens
to it
8 messages similar to the above omitted
Skipped 19 atom(s) with bad connectivities; see log for details
notes | No usable SEQRES records for output_raw.cif (#3.2) chain A; guessing termini instead
No usable SEQRES records for output_raw.cif (#3.2) chain B; guessing termini
instead
No usable SEQRES records for output_raw.cif (#3.2) chain C; guessing termini
instead
No usable SEQRES records for output_raw.cif (#3.2) chain D; guessing termini
instead
No usable SEQRES records for output_raw.cif (#3.2) chain E; guessing termini
instead
25 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A ASN 1, /B GLY 1, /D ARG
1, /E GLY 1, /F LEU 1, /G GLN 1, /H LEU 1, /I GLY 1, /J LEU 1, /K MET 1, /L
GLY 1, /M THR 1, /O THR 1, /P LEU 1, /Q ARG 1, /R LEU 1, /T GLU 1, /W SER 1,
/Y THR 1, /Z THR 1, /a ARG 1, /b GLY 1, /c THR 1
Chain-initial residues that are not actual N termini: /C GLY 1, /N LEU 1, /S
SER 1, /U TYR 1, /V VAL 1, /X GLY 1, /d GLY 1
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A MET 122, /B GLY 102, /C
LEU 99, /D ARG 32, /E GLY 15, /F GLY 66, /G THR 97, /H THR 11, /I GLY 16, /J
THR 3, /K GLY 3, /L ARG 3, /M PHE 31, /N GLU 33, /O GLU 7, /P LEU 5, /Q PRO 6,
/R LEU 5, /S GLY 9, /T GLY 10, /U SER 51, /V GLY 180, /W LEU 40, /X TYR 185,
/Y GLU 366, /Z GLY 2, /a LEU 2, /b THR 2, /c SER 2, /d GLY 2
Skipping possible acceptor with bad geometry: /R ASP 3 O
Wrong number of grandchild atoms for phi/psi acceptor /R ASP 3 O
Skipping possible acceptor with bad geometry: /R ALA 2 O
Wrong number of grandchild atoms for phi/psi acceptor /R ALA 2 O
Skipping possible acceptor with bad geometry: /R ASP 3 O
Wrong number of grandchild atoms for phi/psi acceptor /R ASP 3 O
Skipping possible acceptor with bad geometry: /R ASP 3 O
Wrong number of grandchild atoms for phi/psi acceptor /R ASP 3 O
Skipping possible acceptor with bad geometry: /R ALA 2 O
Wrong number of grandchild atoms for phi/psi acceptor /R ALA 2 O
14 messages similar to the above omitted
1117 hydrogen bonds
Adding 'H' to /S SER 1
Adding 'H' to /U TYR 1
Adding 'H' to /X GLY 1
Adding 'H' to /d GLY 1
/A MET 122 is not terminus, removing H atom from 'C'
/B GLY 102 is not terminus, removing H atom from 'C'
/C LEU 99 is not terminus, removing H atom from 'C'
/D ARG 32 is not terminus, removing H atom from 'C'
/F GLY 66 is not terminus, removing H atom from 'C'
20 messages similar to the above omitted
12166 hydrogens added
Fetching CCD AAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/AAC/AAC.cif
> isolde sim start /A:3
Sim termination reason: None
ISOLDE: stopped sim
Fetching CCD ORN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ORN/ORN.cif
Fetching CCD NLQ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/NLQ/NLQ.cif
> clipper associate #3.1 toModel #3.2
> close session
> open "/Users/avenka/Library/CloudStorage/OneDrive-UniversityofHelsinki/Ville
> Paavilainen lab/Chimera Sessions/Sec61_NatCba.cxs"
> surface cap true
Opened cryosparc_P1_J574_012_volume_map.mrc z flip as #2, grid size
512,512,512, pixel 0.828, shown at level 0.0375, step 1, values float32
Opened Predicted detergent micelle as #1, grid size 512,512,512, pixel 0.828,
shown at level 0.00404, step 1, values float64
Opened Binarised Segmentation as #3, grid size 512,512,512, pixel 0.828, shown
at level 0.236, step 1, values float64
Opened cryosparc_P1_J574_012_volume_map.mrc z flip_without_micelle as #4, grid
size 512,512,512, pixel 0.828, shown at level 0.0461, step 1, values float64
> view name session-start
opened ChimeraX session
> show #!5 models
> hide #!5 models
> hide #6 models
> show #!5 models
> hide #!5 models
> show #6 models
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!4 models
> show #!4 models
> ui tool show "Hide Dust"
> surface dust #2 size 12
> surface dust #4 size 12
> hide #!4 models
> volume #2 level 0.0356
> volume #2 level 0.035
> show #!4 models
> hide #!2 models
> volume #4 level 0.035
> volume #4 level 0.032
> volume #4 level 0.036
> ui tool show "Hide Dust"
> surface dust #4 size 1
> surface dust #4 size 15
> volume #4 level 0.032
> ui tool show "Hide Dust"
> surface dust #4 size 25
> surface dust #4 size 5
> surface dust #4 size 45
> surface dust #4 size 5
> surface dust #4 size 15
> surface dust #4 size 115
> surface dust #4 size 15
> surface dust #4 size 5
> show #!2 models
> runscript /Users/avenka/Chimera/chimera_startup.py
FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> phenix location /Applications/Phenix/phenix-1.21.2-5419
Using Phenix installation /Applications/Phenix/phenix-1.21.2-5419
> cootmode
> surface cap false
Changed 15981 atom styles
Changed 0 atom styles
Changed 2 ball scales
Changed 16514 bond radii
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #6 models
> show #6 models
> show #!2 models
> show #!4 models
> color #4 #e3cbf14c models
> color #4 #deb9f14c models
> color #4 #e6c7f14c models
> color #4 #f0aef14c models
> color #4 #f1b1f14c models
> volume #2 style mesh
> hide #!4 models
> show #!4 models
> clipper associate #2 toModel #6
Opened cryosparc_P1_J574_012_volume_map.mrc z flip as #2.1.1.1, grid size
512,512,512, pixel 0.828, shown at level 0.0604, step 1, values float32
> hide #!4 models
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 70 residues in model #2.2 to IUPAC-IUB
standards.
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> show #!4 models
> clipper associate #4 toModel #2
Opened cryosparc_P1_J574_012_volume_map.mrc z flip_without_micelle as
#2.1.1.2, grid size 512,512,512, pixel 0.828, shown at step 1, values float64
Expected fewer arguments
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to 8dnw.pdb #5/B GLN 6 CB because it is missing heavy-atom bond partners
Not adding hydrogens to 8dnw.pdb #5/B PHE 7 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 8dnw.pdb #5/B VAL 8 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 8dnw.pdb #5/B GLU 9 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 8dnw.pdb #5/B SER 11 CB because it is missing heavy-
atom bond partners
9 messages similar to the above omitted
Unknown hybridization for atoms (OE1, O) of residue type GLN; not adding
hydrogens to them
Unknown hybridization for atoms (N, O) of residue type THR; not adding
hydrogens to them
Unknown hybridization for atoms (OH, O) of residue type TYR; not adding
hydrogens to them
Unknown hybridization for atom (OD1) of residue type ASN; not adding hydrogens
to it
Unknown hybridization for atom (O) of residue type SER; not adding hydrogens
to it
8 messages similar to the above omitted
Skipped 19 atom(s) with bad connectivities; see log for details
notes | Termini for 8dnw.pdb (#5) chain A determined from SEQRES records
Termini for 8dnw.pdb (#5) chain B determined from SEQRES records
Termini for 8dnw.pdb (#5) chain C determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 8dnw.pdb #5/A ILE 9,
8dnw.pdb #5/A ARG 109, 8dnw.pdb #5/A VAL 227, 8dnw.pdb #5/A ASN 315, 8dnw.pdb
#5/A ALA 335, 8dnw.pdb #5/B GLN 6, 8dnw.pdb #5/C GLY 65
Chain-final residues that are actual C termini: 8dnw.pdb #5/C SER 96
Chain-final residues that are not actual C termini: 8dnw.pdb #5/A LYS 98,
8dnw.pdb #5/A ARG 223, 8dnw.pdb #5/A PHE 312, 8dnw.pdb #5/A SER 325, 8dnw.pdb
#5/A GLU 467, 8dnw.pdb #5/B VAL 66
474 hydrogen bonds
Adding 'H' to 8dnw.pdb #5/A ILE 9
Adding 'H' to 8dnw.pdb #5/A ARG 109
Adding 'H' to 8dnw.pdb #5/A VAL 227
Adding 'H' to 8dnw.pdb #5/A ASN 315
Adding 'H' to 8dnw.pdb #5/A ALA 335
2 messages similar to the above omitted
8dnw.pdb #5/A GLU 467 is not terminus, removing H atom from 'C'
8dnw.pdb #5/B VAL 66 is not terminus, removing H atom from 'C'
No usable SEQRES records for output_raw.cif (#2.2) chain A; guessing termini
instead
No usable SEQRES records for output_raw.cif (#2.2) chain B; guessing termini
instead
No usable SEQRES records for output_raw.cif (#2.2) chain C; guessing termini
instead
No usable SEQRES records for output_raw.cif (#2.2) chain D; guessing termini
instead
No usable SEQRES records for output_raw.cif (#2.2) chain E; guessing termini
instead
25 messages similar to the above omitted
Chain-initial residues that are actual N termini: output_raw.cif #2.2/A ASN 1,
output_raw.cif #2.2/B GLY 1, output_raw.cif #2.2/D ARG 1, output_raw.cif
#2.2/E GLY 1, output_raw.cif #2.2/F LEU 1, output_raw.cif #2.2/G GLN 1,
output_raw.cif #2.2/H LEU 1, output_raw.cif #2.2/I GLY 1, output_raw.cif
#2.2/J LEU 1, output_raw.cif #2.2/K MET 1, output_raw.cif #2.2/L GLY 1,
output_raw.cif #2.2/M THR 1, output_raw.cif #2.2/O THR 1, output_raw.cif
#2.2/P LEU 1, output_raw.cif #2.2/Q ARG 1, output_raw.cif #2.2/R LEU 1,
output_raw.cif #2.2/T GLU 1, output_raw.cif #2.2/W SER 1, output_raw.cif
#2.2/Y THR 1, output_raw.cif #2.2/Z THR 1, output_raw.cif #2.2/a ARG 1,
output_raw.cif #2.2/b GLY 1, output_raw.cif #2.2/c THR 1
Chain-initial residues that are not actual N termini: output_raw.cif #2.2/C
GLY 1, output_raw.cif #2.2/N LEU 1, output_raw.cif #2.2/S SER 1,
output_raw.cif #2.2/U TYR 1, output_raw.cif #2.2/V VAL 1, output_raw.cif
#2.2/X GLY 1, output_raw.cif #2.2/d GLY 1
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: output_raw.cif #2.2/A MET
122, output_raw.cif #2.2/B GLY 102, output_raw.cif #2.2/C LEU 99,
output_raw.cif #2.2/D ARG 32, output_raw.cif #2.2/E GLY 15, output_raw.cif
#2.2/F GLY 66, output_raw.cif #2.2/G THR 97, output_raw.cif #2.2/H THR 11,
output_raw.cif #2.2/I GLY 16, output_raw.cif #2.2/J THR 3, output_raw.cif
#2.2/K GLY 3, output_raw.cif #2.2/L ARG 3, output_raw.cif #2.2/M PHE 31,
output_raw.cif #2.2/N GLU 33, output_raw.cif #2.2/O GLU 7, output_raw.cif
#2.2/P LEU 5, output_raw.cif #2.2/Q PRO 6, output_raw.cif #2.2/R LEU 5,
output_raw.cif #2.2/S GLY 9, output_raw.cif #2.2/T GLY 10, output_raw.cif
#2.2/U SER 51, output_raw.cif #2.2/V GLY 180, output_raw.cif #2.2/W LEU 40,
output_raw.cif #2.2/X TYR 185, output_raw.cif #2.2/Y GLU 366, output_raw.cif
#2.2/Z GLY 2, output_raw.cif #2.2/a LEU 2, output_raw.cif #2.2/b THR 2,
output_raw.cif #2.2/c SER 2, output_raw.cif #2.2/d GLY 2
Skipping possible acceptor with bad geometry: output_raw.cif #2.2/R ASP 3 O
Wrong number of grandchild atoms for phi/psi acceptor output_raw.cif #2.2/R
ASP 3 O
Skipping possible acceptor with bad geometry: output_raw.cif #2.2/R ALA 2 O
Wrong number of grandchild atoms for phi/psi acceptor output_raw.cif #2.2/R
ALA 2 O
Skipping possible acceptor with bad geometry: output_raw.cif #2.2/R ASP 3 O
Wrong number of grandchild atoms for phi/psi acceptor output_raw.cif #2.2/R
ASP 3 O
Skipping possible acceptor with bad geometry: output_raw.cif #2.2/R ASP 3 O
Wrong number of grandchild atoms for phi/psi acceptor output_raw.cif #2.2/R
ASP 3 O
Skipping possible acceptor with bad geometry: output_raw.cif #2.2/R ALA 2 O
Wrong number of grandchild atoms for phi/psi acceptor output_raw.cif #2.2/R
ALA 2 O
14 messages similar to the above omitted
1117 hydrogen bonds
Adding 'H' to output_raw.cif #2.2/S SER 1
Adding 'H' to output_raw.cif #2.2/U TYR 1
Adding 'H' to output_raw.cif #2.2/X GLY 1
Adding 'H' to output_raw.cif #2.2/d GLY 1
output_raw.cif #2.2/A MET 122 is not terminus, removing H atom from 'C'
output_raw.cif #2.2/B GLY 102 is not terminus, removing H atom from 'C'
output_raw.cif #2.2/C LEU 99 is not terminus, removing H atom from 'C'
output_raw.cif #2.2/D ARG 32 is not terminus, removing H atom from 'C'
output_raw.cif #2.2/F GLY 66 is not terminus, removing H atom from 'C'
20 messages similar to the above omitted
16374 hydrogens added
> isolde restrain ligands #2.2
> ui tool show "Ramachandran Plot"
> ui mousemode right pivot
> ui mousemode right "translate selected atoms"
> ui mousemode right select
> select #2.2
24087 atoms, 24534 bonds, 1507 residues, 11 models selected
> isolde sim start sel
Sim termination reason: None
ISOLDE: stopped sim
> ui mousemode right pivot
Deleted the following atoms from residue GLN A48: HN, H
Fetching CCD FME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FME/FME.cif
Fetching CCD AME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/AME/AME.cif
Deleted the following atoms from residue MET Y364: HE
Deleted the following atoms from residue MET K1: HN3, H, HN2, HN1
Deleted the following atoms from residue MET G45: H, HN
Deleted the following atoms from residue MET C85: HE
Deleted the following atoms from residue MET B41: HN, H
Deleted the following atoms from residue MET A54: H, HN
Deleted the following atoms from residue GLY d1: HA
Deleted the following atoms from residue GLY X112: HA
Deleted the following atoms from residue GLY X8: H
Deleted the following atoms from residue GLY T10: HN2, HN3
Deleted the following atoms from residue GLY S9: HA
Deleted the following atoms from residue GLY S7: HN, H
Deleted the following atoms from residue GLY K3: HN2, HN3
Deleted the following atoms from residue GLY I16: HA
Deleted the following atoms from residue GLY I13: HN, H
Deleted the following atoms from residue GLY I8: H
Deleted the following atoms from residue GLY I7: H
Deleted the following atoms from residue GLY I1: H, HN1, HN3, HN2
Deleted the following atoms from residue GLY E1: H, HN3, HN2, HN1
Deleted the following atoms from residue GLY B102: HA
Deleted the following atoms from residue GLY B72: HA
Deleted the following atoms from residue GLY B1: H, HN1, HN2, HN3
Fetching CCD THC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/THC/THC.cif
Deleted the following atoms from residue THR c1: HN3, HN2, HN1, H
Deleted the following atoms from residue THR Z1: HN1, HN2, HN3, H
Deleted the following atoms from residue THR Y2: HN, H
Deleted the following atoms from residue THR Y1: H1, H2, H3
Deleted the following atoms from residue THR T7: HN, H
Deleted the following atoms from residue THR M1: HN1, H, HN2, HN3
Deleted the following atoms from residue THR I15: H, HN
Deleted the following atoms from residue THR I2: H
Deleted the following atoms from residue THR D31: HN, H
Deleted the following atoms from residue THR D3: HN, H
Deleted the following atoms from residue THR B101: H
Deleted the following atoms from residue THR B2: H
Fetching CCD LAY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/LAY/LAY.cif
Deleted the following atoms from residue LEU R1: HN3, H, HN1, HN2
Deleted the following atoms from residue LEU Q3: H
Deleted the following atoms from residue LEU P1: HN3, H, HN1, HN2
Deleted the following atoms from residue LEU K2: H
Deleted the following atoms from residue LEU J1: H1, H3, H2
Deleted the following atoms from residue LEU G71: H
Deleted the following atoms from residue LEU G6: HB
Deleted the following atoms from residue LEU G3: H, HN
Deleted the following atoms from residue LEU C17: HB
Deleted the following atoms from residue LEU B73: H, HN
Fetching CCD LYZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/LYZ/LYZ.cif
Fetching CCD MLZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/MLZ/MLZ.cif
Deleted the following atoms from residue LYS Y170: HZ, HE
Deleted the following atoms from residue LYS Y130: HZ
Deleted the following atoms from residue LYS U7: HZ
Deleted the following atoms from residue LYS F26: HE
Deleted the following atoms from residue LYS D29: HZ
Deleted the following atoms from residue LYS D4: HB
Deleted the following atoms from residue LYS B32: HE
Deleted the following atoms from residue GLN Y279: H, HN
Deleted the following atoms from residue GLN P4: H
Deleted the following atoms from residue GLN C72: HE2
Deleted the following atoms from residue GLN B13: HB
Fetching CCD SAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/SAC/SAC.cif
Deleted the following atoms from residue SER T3: HN, H
Deleted the following atoms from residue SER N30: HN, H
Deleted the following atoms from residue SER G94: H2, H3
Deleted the following atoms from residue SER G49: HN, H
Deleted the following atoms from residue SER G47: HN, H
Deleted the following atoms from residue SER B75: HN, H
Fetching CCD 5CR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/5CR/5CR.cif
Deleted the following atoms from residue PHE G93: HN, H
Deleted the following atoms from residue PHE G42: H, HN
Deleted the following atoms from residue PHE B94: HN, H
Fetching CCD DAH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/DAH/DAH.cif
Fetching CCD 3NF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/3NF/3NF.cif
Deleted the following atoms from residue TYR U1: H
Deleted the following atoms from residue TYR B71: H, HN
Deleted the following atoms from residue ASP X7: H, HN
Deleted the following atoms from residue ASP V132: H
Deleted the following atoms from residue ASP V131: H
Deleted the following atoms from residue ASP C3: H
Fetching CCD NMM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/NMM/NMM.cif
Fetching CCD DA2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/DA2/DA2.cif
Fetching CCD 2MR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/2MR/2MR.cif
Fetching CCD AAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/AAG/AAG.cif
Deleted the following atoms from residue ARG a1: H, HN2, HN3, HN1
Deleted the following atoms from residue ARG Y309: HH2, HH13
Deleted the following atoms from residue ARG W28: H, HH1, HN
Deleted the following atoms from residue ARG U48: H, HN
Deleted the following atoms from residue ARG Q1: HG, H2, H1, H3
Deleted the following atoms from residue ARG P2: HH2, H
Deleted the following atoms from residue ARG O2: HN, H
Deleted the following atoms from residue ARG M5: HH13
Deleted the following atoms from residue ARG J2: H, HN
Deleted the following atoms from residue ARG I11: HN, H
Deleted the following atoms from residue ARG H10: H
Deleted the following atoms from residue ARG D1: H, HN1, HN2, HN3
Deleted the following atoms from residue ARG C89: HH23, HH13, HE3, HE2
Deleted the following atoms from residue ASN Y269: HB
Deleted the following atoms from residue ASN G72: H2, H3
Deleted the following atoms from residue ASN B100: H, HN
Fetching CCD AYA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/AYA/AYA.cif
Deleted the following atoms from residue ALA E14: H
Fetching CCD NLG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NLG/NLG.cif
Fetching CCD CGU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/CGU/CGU.cif
Deleted the following atoms from residue GLU N31: H
Deleted the following atoms from residue GLU H9: HN, H
Deleted the following atoms from residue GLU G70: H, HN
Fetching CCD HY3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/HY3/HY3.cif
Fetching CCD N7P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/N7P/N7P.cif
Deleted the following atoms from residue PRO Y245: H
Deleted the following atoms from residue PRO Y238: H
Deleted the following atoms from residue PRO Y10: HG
Deleted the following atoms from residue PRO X164: H
Deleted the following atoms from residue PRO X10: HD
Deleted the following atoms from residue PRO Q6: HD
Deleted the following atoms from residue PRO N4: HD
Deleted the following atoms from residue VAL V179: HN, H
Deleted the following atoms from residue VAL D5: HN, H
Deleted the following atoms from residue ILE V99: H, HN
Fetching CCD 0AF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/0AF/0AF.cif
Fetching CCD 4PQ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/4PQ/4PQ.cif
> select #2.2
24212 atoms, 24659 bonds, 1507 residues, 14 models selected
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> view /S:3
> select clear
> isolde pepflip #2.2/S:3
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #2.2/S:3
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde cisflip #2.2/S:3
> isolde cisflip #2.2/G:72
> isolde cisflip #2.2/C:3
> isolde pepflip #2.2/C:3
> isolde pepflip #2.2/X:33
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #2.2/G:94
> isolde cisflip #2.2/G:94
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde cisflip #2.2/G:94
> isolde pepflip #2.2/G:94
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #2.2/G:71
> isolde cisflip #2.2/G:71
> isolde pepflip #2.2/G:71
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #2.2/E:14
> isolde pepflip #2.2/B:3
> isolde pepflip #2.2/W:3
> isolde pepflip #2.2/I:14
> isolde cisflip #2.2/B:3
> isolde cisflip #2.2/E:14
> isolde pepflip #2.2/G:72
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde cisflip #2.2/G:71
> isolde pepflip #2.2/P:3
> isolde cisflip #2.2/P:3
> isolde pepflip #2.2/G:4
> isolde pepflip #2.2/I:15
> isolde cisflip #2.2/I:15
> isolde pepflip #2.2/I:15
> isolde cisflip #2.2/I:15
> isolde pepflip #2.2/R:4
> isolde cisflip #2.2/R:4
> isolde cisflip #2.2/G:93
> isolde pepflip #2.2/G:93
> isolde pepflip #2.2/V:131
> isolde cisflip #2.2/V:131
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #2.2/V:131
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #2.2/L:2
> isolde cisflip #2.2/L:2
> isolde pepflip #2.2/L:2
> isolde cisflip #2.2/L:2
> isolde cisflip #2.2/G:87
> isolde pepflip #2.2/V:135
> isolde cisflip #2.2/V:135
> isolde cisflip #2.2/I:5
> isolde pepflip #2.2/I:5
> isolde pepflip #2.2/G:90
> isolde cisflip #2.2/G:90
> isolde pepflip #2.2/P:3
> isolde cisflip #2.2/P:3
> isolde pepflip #2.2/P:3
> isolde cisflip #2.2/P:3
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde cisflip #2.2/P:3
> isolde pepflip #2.2/L:2
> isolde cisflip #2.2/L:2
> isolde pepflip #2.2/N:13
> isolde cisflip #2.2/N:13
> isolde pepflip #2.2/G:89
> isolde cisflip #2.2/G:89
> isolde pepflip #2.2/G:89
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #2.2/G:87
> isolde cisflip #2.2/G:87
> isolde pepflip #2.2/G:87
> isolde cisflip #2.2/G:87
> isolde pepflip #2.2/G:93
> isolde pepflip #2.2/P:2
> isolde cisflip #2.2/P:2
> isolde pepflip #2.2/P:4
> isolde pepflip #2.2/V:126
> isolde cisflip #2.2/V:126
> isolde pepflip #2.2/V:126
> isolde pepflip #2.2/Y:337
> isolde cisflip #2.2/Y:337
> isolde pepflip #2.2/Y:337
> isolde cisflip #2.2/V:127
> isolde sim pause
> isolde pepflip #2.2/A:28
> isolde sim resume
> isolde pepflip #2.2/A:28
> isolde cisflip #2.2/A:28
> isolde pepflip #2.2/A:28
> isolde pepflip #2.2/A:24
> isolde pepflip #2.2/A:28
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde cisflip #2.2/A:28
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #2.2/A:28
> isolde pepflip #2.2/A:24
> isolde pepflip #2.2/A:27
> isolde sim pause
===== Log before crash end =====
Log:
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot 7,0.25
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000
> alias map_unsphere volume unzone ~##num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ~##num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias open_vseries "open browse vseries true"
> alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask
> #10000 spacing 1 border -0.5
> alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr;
> sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001
> minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001;
> close sel; show $2
> alias centersel cofr sel; clip near 10 position cofr; clip far -10 position
> cofr; cofr centerOfView showpivot true; view sel
> alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine
> $1.* close true
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr
> radius 1"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> buttonpanel Shortcuts add reset_mouse_and_help command "mousemode alt right
> contour ; mousemode right clip ; mousemode alt left 'translate selected
> models' ; mousemode shift left 'rotate selected models' ; mousemode alt
> control left 'pick blobs'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md"
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 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: Mac16,8
Model Number: Z1FF000KKKS/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 Performance and 4 Efficiency)
Memory: 48 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (25D2128)
Kernel Version: Darwin 25.3.0
Time since boot: 2 days, 23 hours, 8 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
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
P27h-20:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
LEN P27h-10:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
annotated-doc: 0.0.4
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 3.5.0
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-AllMetal3D: 0.8
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: 14.1.18
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-ChopChopMF: 1.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-clix: 0.2.5
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
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-crai: 0.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DAQplugin: 0.13.51
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-EMalign: 0.1.3
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-LigandRecognizer: 0.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-locscalesurfer: 0.1.3
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-PhenixUI: 1.4.12
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
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-RMF: 0.16
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
click: 8.3.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cripser: 0.0.22
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
DiffFit: 0.7.0
docutils: 0.21.2
einops: 0.8.2
executing: 2.2.0
filelock: 3.18.0
finufft: 2.4.1
flatbuffers: 25.12.19
fonttools: 4.58.4
fsspec: 2025.7.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
gradio_client: 0.11.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.14.0
hf-xet: 1.3.2
html2text: 2024.2.26
httpcore: 1.0.9
httpx: 0.28.1
huggingface_hub: 1.5.0
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: 4.4.4
markdown-it-py: 4.0.0
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
mdurl: 0.1.2
MolecularDynamicsViewer: 1.6
mpmath: 1.3.0
mrcfile: 1.5.4
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
onnxruntime: 1.24.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
pandas: 2.3.3
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: 26.0.1
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
protobuf: 7.34.1
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
pyelftools: 0.32
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
PyQt5: 5.15.11
PyQt5-Qt5: 5.15.18
PyQt5_sip: 12.17.2
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
PyYAML: 6.0.3
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
rich: 14.3.3
roman-numerals-py: 3.1.0
safetensors: 0.7.0
scipy: 1.16.3
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.9.7
setuptools: 78.1.0
sfftk-rw: 0.8.1
shellingham: 1.5.4
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
sympy: 1.14.0
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
timm: 1.0.25
tinyarray: 1.2.4
torch: 2.9.1
torchvision: 0.24.1
tornado: 6.5.1
tqdm: 4.67.3
traitlets: 5.14.3
typer: 0.24.1
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
websockets: 11.0.3
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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