![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16713 closed defect (can't reproduce)
Crash in QDockWidget event handling
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000386473000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001e66d3840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, 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.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 93)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
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"modelCode" : "Mac15,6",
"coalitionID" : 117814,
"osVersion" : {
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"build" : "24B91",
"releaseType" : "User"
},
"captureTime" : "2025-01-28 13:12:27.1946 -0500",
"codeSigningMonitor" : 1,
"incident" : "B4A7E697-0C29-4578-9C20-2845A6AC39EC",
"pid" : 91072,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-23 12:52:51.5307 -0500",
"procStartAbsTime" : 31906380340508,
"procExitAbsTime" : 39676052231651,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7503EB96-D773-5265-A406-C0BEADC4D8DE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BC3038C0-1F54-A1BB-0351-D0C706068E0C",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 98743,
"sleepWakeUUID" : "FEFDFC9C-8129-44BC-85E1-990EE74E6FF0",
"sip" : "enabled",
"vmRegionInfo" : "0x40 is not in any region. Bytes before following region: 4343513024\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102e4c000-102e50000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000040","rawCodes":[1,64],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000040"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":91072},
"vmregioninfo" : "0x40 is not in any region. Bytes before following region: 4343513024\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102e4c000-102e50000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jabarro/Documents/collin/set2/1654.xyz format xyz
opened 1654.xyz as an XYZ coordinate file
> style ball
Changed 70 atom styles
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting flat
> lighting simple
> lighting shadows true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> view
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow sticks
Using preset: SEQCROW / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> ui tool show "Buried Volume"
> ui mousemode right "select fragment"
> ui mousemode right select
> select add /a:1@C4
61 atoms, 60 bonds, 1 residue, 1 model selected
> select add /a:1@C1
62 atoms, 60 bonds, 1 residue, 1 model selected
> select add /a:1@N1
63 atoms, 60 bonds, 1 residue, 1 model selected
> select add /a:1@C3
64 atoms, 61 bonds, 1 residue, 1 model selected
> select add /a:1@C2
65 atoms, 62 bonds, 1 residue, 1 model selected
> select clear
> select /a:1@N2
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 8.3327,7.4627,9.5307 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
1654 /a:1@N2 83.0
> ui mousemode right "color key"
> ui mousemode right select
> ui mousemode right "color key"
> key delete
> ui mousemode right select
> ui mousemode right "contour level"
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> view sel
> view
> transparency 0
> volume hide
No volumes specified
> volume style surface
No volumes specified
> transparency 0
> transparecy 9
Unknown command: transparecy 9
> transparency 9
> transparency 20
> transparency 100
> transparency 50
> transparency 60
> open /Users/jabarro/Documents/collin/set2/1654.xyz
opened 1654.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select add #1/a:1@C2
85 atoms, 84 bonds, 2 residues, 2 models selected
> select add #1/a:1@C4
86 atoms, 84 bonds, 2 residues, 2 models selected
> select add #3/a:1@H3
87 atoms, 84 bonds, 2 residues, 2 models selected
> open /Users/jabarro/Documents/collin/set2/1654.xyz
opened 1654.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select clear
> ui mousemode right "select similar fragments"
> ui mousemode right select
> select add #1/a:1@C2
205 atoms, 204 bonds, 3 residues, 3 models selected
> select add #4/a:1@H4
206 atoms, 204 bonds, 3 residues, 3 models selected
> select add #1/a:1@C3
207 atoms, 205 bonds, 3 residues, 3 models selected
> select add #1/a:1@N1
208 atoms, 205 bonds, 3 residues, 3 models selected
> select add #1/a:1@C1
209 atoms, 205 bonds, 3 residues, 3 models selected
> select add #1/a:1@C4
210 atoms, 206 bonds, 3 residues, 3 models selected
Traceback (most recent call last):
File "/Users/jabarro/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/percent_Vbur.py", line 655, in calc_vbur
info = percent_vbur_cmd(
^^^^^^^^^^^^^^^^^
File "/Users/jabarro/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/commands/percent_Vbur.py", line 314, in percent_vbur
targets = rescol.find([AtomSpec(a.atomspec) for a in ligand_atoms])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not iterable
TypeError: 'NoneType' object is not iterable
File "/Users/jabarro/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/commands/percent_Vbur.py", line 314, in percent_vbur
targets = rescol.find([AtomSpec(a.atomspec) for a in ligand_atoms])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select clear
> select #1/a:1@N2
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 8.3327,7.4627,9.5307 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
1654 #1/a:1@N2 83.0
> transparency 60
> select clear
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> transparency 80
> save /Users/jabarro/Documents/collin/set2/sp/image3d.png width 1024 height
> 665 supersample 3
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> lighting soft
> lighting flat
> lighting full
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> save /Users/jabarro/Documents/collin/set2/sp/3d-1654.png width 1024 height
> 665 supersample 3
> ui mousemode right "select similar fragments"
> ui mousemode right select
> select #4/a:1@H4
1 atom, 1 residue, 1 model selected
> ui mousemode right "select similar fragments"
> ui mousemode right select
> select add #1/a:1@C2
206 atoms, 204 bonds, 3 residues, 3 models selected
> select add #1/a:1@C3
207 atoms, 204 bonds, 3 residues, 3 models selected
> select add #3/a:1@H2
208 atoms, 204 bonds, 3 residues, 3 models selected
> select add #1/a:1@N1
209 atoms, 204 bonds, 3 residues, 3 models selected
> select add #1/a:1@C4
210 atoms, 204 bonds, 3 residues, 3 models selected
> select add #3/a:1@H3
211 atoms, 204 bonds, 3 residues, 3 models selected
> select add #3/a:1@H1
212 atoms, 205 bonds, 3 residues, 3 models selected
> select clear
> select #1/a:1@N2
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 8.3327,7.4627,9.5307 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
1654 #1/a:1@N2 81.2
> transparency 80
> select clear
> open /Users/jabarro/Documents/collin/set2/1528a.xyz
opened 1528a.xyz as an XYZ coordinate file
Drag select of 3 atoms
> select clear
> hide #4 models
> hide #3 models
> hide #1 models
> ui mousemode right translate
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> ui mousemode right "select fragment"
> ui mousemode right select
> select add #5/a:1@C5
39 atoms, 38 bonds, 1 residue, 1 model selected
> select add #5/a:1@H5
40 atoms, 38 bonds, 1 residue, 1 model selected
> select add #5/a:1@H6
41 atoms, 38 bonds, 1 residue, 1 model selected
> select add #5/a:1@H4
42 atoms, 41 bonds, 1 residue, 1 model selected
> select add #5/a:1@C1
43 atoms, 41 bonds, 1 residue, 1 model selected
> select add #5/a:1@C2
44 atoms, 43 bonds, 1 residue, 1 model selected
> select add #5/a:1@H1
45 atoms, 44 bonds, 1 residue, 1 model selected
> select add #5/a:1@N2
46 atoms, 45 bonds, 1 residue, 1 model selected
> select add #5/a:1@C3
47 atoms, 46 bonds, 1 residue, 1 model selected
> select add #5/a:1@H2
48 atoms, 47 bonds, 1 residue, 1 model selected
> select add #5/a:1@C4
49 atoms, 48 bonds, 1 residue, 1 model selected
> select add #5/a:1@H3
50 atoms, 48 bonds, 1 residue, 1 model selected
> select clear
> select add #5/a:1@N1
1 atom, 1 residue, 1 model selected
> color radial #5.1 center 4.0327,20.3203,17.5553 palette rainbow range 0,3.50
> coordinateSystem #5
> transparency #5.1 30
model center %Vbur
1528a #5/a:1@N1 88.0
> transparency 80
> save /Users/jabarro/Documents/collin/set2/sp/3d-1528a.png width 1024 height
> 665 supersample 3
> color radial #5.2 center 4.0327,20.3203,17.5553 palette rainbow range 0,3.50
> coordinateSystem #5
> transparency #5.2 30
model center %Vbur
1528a #5/a:1@N1 88.0
> hide #5 models
> select add #1
71 atoms, 70 bonds, 2 residues, 2 models selected
> close
> open /Users/jabarro/Documents/collin/set2/1528b.xyz
opened 1528b.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> ui mousemode right "select fragment"
> ui mousemode right select
> select /a:1@H14
1 atom, 1 residue, 1 model selected
> select add /a:1@C14
2 atoms, 1 bond, 1 residue, 1 model selected
> select add /a:1@C13
3 atoms, 1 bond, 1 residue, 1 model selected
> select add /a:1@H13
4 atoms, 1 bond, 1 residue, 1 model selected
> select add /a:1@N6
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /a:1@C12
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /a:1@H18
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /a:1@C11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /a:1@C15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /a:1@H17
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add /a:1@H15
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /a:1@H16
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right "select fragment"
> ui mousemode right select
> select subtract /a:1@N5
12 atoms, 11 bonds, 1 residue, 1 model selected
> color radial #1.1 center 4.4826,8.4268,15.9536 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
> color radial #1.2 center 3.8680,7.5177,18.0786 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.2 30
> color radial #1.3 center 4.0928,8.5865,17.2102 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.3 30
> color radial #1.4 center 4.6473,7.1598,15.5569 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.4 30
> color radial #1.5 center 4.9406,6.9931,14.6692 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.5 30
> color radial #1.6 center 4.4065,6.0957,16.3879 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.6 30
> color radial #1.7 center 4.5130,5.2136,16.0504 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.7 30
> color radial #1.8 center 3.4754,7.7454,19.4843 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.8 30
> color radial #1.9 center 4.1829,8.2428,19.9447 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.9 30
> color radial #1.10 center 2.6425,8.2612,19.5112 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.10 30
> color radial #1.11 center 3.3397,6.8827,19.9291 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.11 30
> color radial #1.12 center 3.9421,9.5903,17.5791 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.12 30
model center %Vbur
1528b /a:1@N6 61.5
1528b /a:1@C11 82.3
1528b /a:1@C12 67.8
1528b /a:1@C13 66.3
1528b /a:1@H13 50.9
1528b /a:1@C14 74.8
1528b /a:1@H14 59.7
1528b /a:1@C15 59.5
1528b /a:1@H15 45.8
1528b /a:1@H16 52.7
1528b /a:1@H17 60.7
1528b /a:1@H18 47.7
> select clear
> ui mousemode right "select fragment"
> ui mousemode right select
> select subtract /a:1@N5
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select /a:1@N5
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 4.0272,6.2629,17.6591 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
1528b /a:1@N5 87.0
> transparency 80
> select clear
> save /Users/jabarro/Documents/collin/set2/sp/3d-1528b.png width 1024 height
> 665 supersample 3
> select clear
> ui mousemode right "select fragment"
> ui mousemode right select
> select subtract /a:1@N5
50 atoms, 49 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right "select fragment"
> ui mousemode right select
> select /a:1@N5
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select add /a:1@N5
39 atoms, 38 bonds, 1 residue, 1 model selected
> color radial #1.1 center 3.5530,3.8159,19.2383 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
> color radial #1.2 center 1.9472,0.6868,24.2120 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.2 30
> color radial #1.3 center 3.9867,0.8261,18.3503 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.3 30
> color radial #1.4 center 2.5437,3.0927,22.1901 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.4 30
> color radial #1.5 center 0.4085,7.8598,17.5553 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.5 30
> color radial #1.6 center 7.6569,7.8598,17.5553 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.6 30
> color radial #1.7 center 0.9491,5.8417,15.7080 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.7 30
> color radial #1.8 center 8.1975,5.8417,15.7080 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.8 30
> color radial #1.9 center 4.0272,6.2629,17.6591 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.9 30
> color radial #1.10 center 0.3453,6.5909,17.8955 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.10 30
> color radial #1.11 center 7.5937,6.5909,17.8955 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.11 30
> color radial #1.12 center 0.6160,5.5823,16.9688 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.12 30
> color radial #1.13 center 7.8644,5.5823,16.9688 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.13 30
> color radial #1.14 center 0.5604,4.6768,17.2497 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.14 30
> color radial #1.15 center 7.8088,4.6768,17.2497 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.15 30
> color radial #1.16 center 1.0164,7.1324,15.3885 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.16 30
> color radial #1.17 center 8.2648,7.1324,15.3885 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.17 30
> color radial #1.18 center 1.2568,7.3672,14.5001 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.18 30
> color radial #1.19 center 8.5052,7.3672,14.5001 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.19 30
> color radial #1.20 center 0.7535,8.1367,16.2857 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.20 30
> color radial #1.21 center 8.0019,8.1367,16.2857 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.21 30
> color radial #1.22 center 0.8172,9.0430,16.0053 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.22 30
> color radial #1.23 center 8.0656,9.0430,16.0053 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.23 30
> color radial #1.24 center -0.0378,6.2402,19.3259 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.24 30
> color radial #1.25 center 7.2106,6.2402,19.3259 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.25 30
> color radial #1.26 center -0.9114,5.7960,19.3306 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.26 30
> color radial #1.27 center 6.3370,5.7960,19.3306 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.27 30
> color radial #1.28 center 0.6362,5.6394,19.7066 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.28 30
> color radial #1.29 center 7.8846,5.6394,19.7066 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.29 30
> color radial #1.30 center -0.0851,7.0595,19.8615 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.30 30
> color radial #1.31 center 7.1633,7.0595,19.8615 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.31 30
> color radial #1.32 center 3.5155,0.7982,19.6078 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.32 30
> color radial #1.33 center 3.2687,2.0009,20.2457 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.33 30
> color radial #1.34 center 2.8110,1.9384,21.5500 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.34 30
> color radial #1.35 center 2.5893,0.7511,22.2097 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.35 30
> color radial #1.36 center 2.5595,-1.5890,22.1031 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.36 30
> color radial #1.37 center 3.2809,-0.4309,20.2033 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.37 30
> color radial #1.38 center 2.8198,-0.4127,21.4992 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.38 30
> color radial #1.39 center 3.5745,-2.2150,19.1488 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.39 30
model center %Vbur
1528b /a:1@I1 53.9
1528b /a:1@I2 44.6
1528b /a:1@F1 49.3
1528b /a:1@F2 49.5
1528b /a:1@N1 49.6
1528b /a:1@N2 49.2
1528b /a:1@N3 45.4
1528b /a:1@N4 43.3
1528b /a:1@N5 42.8
1528b /a:1@C1 58.8
1528b /a:1@C2 56.1
1528b /a:1@C3 56.1
1528b /a:1@C4 50.9
1528b /a:1@H1 47.9
1528b /a:1@H2 41.1
1528b /a:1@C5 44.5
1528b /a:1@C6 44.5
1528b /a:1@H3 33.5
1528b /a:1@H4 33.5
1528b /a:1@C7 44.8
1528b /a:1@C8 44.8
1528b /a:1@H5 33.3
1528b /a:1@H6 33.3
1528b /a:1@C9 42.9
1528b /a:1@C10 42.6
1528b /a:1@H7 34.5
1528b /a:1@H8 44.2
1528b /a:1@H9 46.0
1528b /a:1@H10 35.5
1528b /a:1@H11 33.7
1528b /a:1@H12 33.8
1528b /a:1@C16 64.6
1528b /a:1@C17 68.0
1528b /a:1@C18 64.3
1528b /a:1@C19 67.8
1528b /a:1@F3 49.1
1528b /a:1@C20 67.8
1528b /a:1@C21 64.5
1528b /a:1@I3 44.6
> select clear
> ui mousemode right "select fragment"
> ui mousemode right select
> select add /a:1@N5
39 atoms, 38 bonds, 1 residue, 1 model selected
> color radial #1.1 center 3.5530,3.8159,19.2383 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
> color radial #1.2 center 1.9472,0.6868,24.2120 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.2 30
> color radial #1.3 center 3.9867,0.8261,18.3503 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.3 30
> color radial #1.4 center 2.5437,3.0927,22.1901 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.4 30
> color radial #1.5 center 0.4085,7.8598,17.5553 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.5 30
> color radial #1.6 center 7.6569,7.8598,17.5553 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.6 30
> color radial #1.7 center 0.9491,5.8417,15.7080 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.7 30
> color radial #1.8 center 8.1975,5.8417,15.7080 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.8 30
> color radial #1.9 center 4.0272,6.2629,17.6591 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.9 30
> color radial #1.10 center 0.3453,6.5909,17.8955 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.10 30
> color radial #1.11 center 7.5937,6.5909,17.8955 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.11 30
> color radial #1.12 center 0.6160,5.5823,16.9688 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.12 30
> color radial #1.13 center 7.8644,5.5823,16.9688 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.13 30
> color radial #1.14 center 0.5604,4.6768,17.2497 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.14 30
> color radial #1.15 center 7.8088,4.6768,17.2497 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.15 30
> color radial #1.16 center 1.0164,7.1324,15.3885 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.16 30
> color radial #1.17 center 8.2648,7.1324,15.3885 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.17 30
> color radial #1.18 center 1.2568,7.3672,14.5001 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.18 30
> color radial #1.19 center 8.5052,7.3672,14.5001 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.19 30
> color radial #1.20 center 0.7535,8.1367,16.2857 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.20 30
> color radial #1.21 center 8.0019,8.1367,16.2857 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.21 30
> color radial #1.22 center 0.8172,9.0430,16.0053 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.22 30
> color radial #1.23 center 8.0656,9.0430,16.0053 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.23 30
> color radial #1.24 center -0.0378,6.2402,19.3259 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.24 30
> color radial #1.25 center 7.2106,6.2402,19.3259 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.25 30
> color radial #1.26 center -0.9114,5.7960,19.3306 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.26 30
> color radial #1.27 center 6.3370,5.7960,19.3306 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.27 30
> color radial #1.28 center 0.6362,5.6394,19.7066 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.28 30
> color radial #1.29 center 7.8846,5.6394,19.7066 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.29 30
> color radial #1.30 center -0.0851,7.0595,19.8615 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.30 30
> color radial #1.31 center 7.1633,7.0595,19.8615 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.31 30
> color radial #1.32 center 3.5155,0.7982,19.6078 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.32 30
> color radial #1.33 center 3.2687,2.0009,20.2457 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.33 30
> color radial #1.34 center 2.8110,1.9384,21.5500 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.34 30
> color radial #1.35 center 2.5893,0.7511,22.2097 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.35 30
> color radial #1.36 center 2.5595,-1.5890,22.1031 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.36 30
> color radial #1.37 center 3.2809,-0.4309,20.2033 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.37 30
> color radial #1.38 center 2.8198,-0.4127,21.4992 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.38 30
> color radial #1.39 center 3.5745,-2.2150,19.1488 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.39 30
model center %Vbur
1528b /a:1@I1 53.9
1528b /a:1@I2 44.6
1528b /a:1@F1 49.3
1528b /a:1@F2 49.5
1528b /a:1@N1 49.6
1528b /a:1@N2 49.2
1528b /a:1@N3 45.4
1528b /a:1@N4 43.3
1528b /a:1@N5 42.8
1528b /a:1@C1 58.8
1528b /a:1@C2 56.1
1528b /a:1@C3 56.1
1528b /a:1@C4 50.9
1528b /a:1@H1 47.9
1528b /a:1@H2 41.1
1528b /a:1@C5 44.5
1528b /a:1@C6 44.5
1528b /a:1@H3 33.5
1528b /a:1@H4 33.5
1528b /a:1@C7 44.8
1528b /a:1@C8 44.8
1528b /a:1@H5 33.3
1528b /a:1@H6 33.3
1528b /a:1@C9 42.9
1528b /a:1@C10 42.6
1528b /a:1@H7 34.5
1528b /a:1@H8 44.2
1528b /a:1@H9 46.0
1528b /a:1@H10 35.5
1528b /a:1@H11 33.7
1528b /a:1@H12 33.8
1528b /a:1@C16 64.6
1528b /a:1@C17 68.0
1528b /a:1@C18 64.3
1528b /a:1@C19 67.8
1528b /a:1@F3 49.1
1528b /a:1@C20 67.8
1528b /a:1@C21 64.5
1528b /a:1@I3 44.6
> select clear
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select add /a:1@N5
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 4.0272,6.2629,17.6591 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
1528b /a:1@N5 42.7
> transparency 80
> save /Users/jabarro/Documents/collin/set2/sp/3d-1528b.png width 1024 height
> 665 supersample 3
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/3d-1528b.png width 1024 height
> 665 supersample 3
> close #1
> open /Users/jabarro/Documents/collin/set2/1528a.xyz format xyz
opened 1528a.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> ui mousemode right "select fragment"
> ui mousemode right select
> select clear
> select /a:1@N1
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 4.0327,20.3203,17.5553 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
1528a /a:1@N1 43.9
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/3d-1528a.png width 1024 height
> 665 supersample 3
> open /Users/jabarro/Documents/collin/set2/1654.xyz
opened 1654.xyz as an XYZ coordinate file
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> hide #!1 models
> show #!1 models
> hide #2 models
> hide #!1 models
> select add #1
51 atoms, 51 bonds, 1 residue, 3 models selected
> select add #1
51 atoms, 51 bonds, 1 residue, 3 models selected
> show #!1 models
> close
> open /Users/jabarro/Documents/collin/set2/1654.xyz
opened 1654.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> select clear
> ui mousemode right translate
> ui mousemode right "select fragment"
> ui mousemode right select
> select add /a:1@N2
61 atoms, 60 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select clear
> select add /a:1@N2
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 0.0000,-0.0000,0.0000 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
1654 /a:1@N2 46.6
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/3d-1654.png width 1024 height
> 665 supersample 3
> close
> open /Users/jabarro/Documents/collin/set2/6677a.xyz
opened 6677a.xyz as an XYZ coordinate file
> ui mousemode right translate
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select /a:1@N3
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 0.0000,-0.0000,0.0000 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6677a /a:1@N3 44.6
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/3d-6677a.png width 1024 height
> 665 supersample 3
> close
> open /Users/jabarro/Documents/collin/set2/6677b.xyz
opened 6677b.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> ui mousemode right "select fragment"
> ui mousemode right select
> select clear
> select /a:1@N6
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 0.0000,-0.0000,0.0000 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6677b /a:1@N6 44.7
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/3d-6677b.png width 1024 height
> 665 supersample 3
> close
> open /Users/jabarro/Documents/collin/set2/6647a.xyz
opened 6647a.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> ui mousemode right translate
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select /a:1@N6
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 0.0000,-0.0000,0.0000 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6647a /a:1@N6 41.9
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/3d-6647b.png width 1024 height
> 665 supersample 3
> close
> open /Users/jabarro/Documents/collin/set2/6647b.xyz
opened 6647b.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select /a:1@N3
1 atom, 1 residue, 1 model selected
> color radial #1.1 center -0.0000,-0.0000,0.0000 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6647b /a:1@N3 43.0
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/3d-6647b.png width 1024 height
> 665 supersample 3
> close
> open /Users/jabarro/Documents/collin/set2/sp/6680a.xyz
opened 6680a.xyz as an XYZ coordinate file
> select clear
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
Drag select of 1 atoms, 1 bonds
> select clear
> ui mousemode right "select fragment"
> ui mousemode right select
> select clear
> select /a:1@N6
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right "select fragment"
> ui mousemode right select
> select clear
> select /a:1@N6
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 15.1339,17.1707,20.0486 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6680a /a:1@N6 40.7
> transparency 60
> select clear
> save /Users/jabarro/Documents/collin/set2/sp/3d-6680a.png width 1024 height
> 665 supersample 3
> save /Users/jabarro/Documents/collin/set2/sp/2d-6680a.png width 1024 height
> 665 supersample 3
> close
> open /Users/jabarro/Documents/collin/set2/sp/6680b.xyz
opened 6680b.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select clear
> ui mousemode right "select fragment"
> lighting full
> graphics silhouettes false
> select clear
> ui mousemode right select
> select /a:1@N5
1 atom, 1 residue, 1 model selected
> select clear
> select /a:1@N5
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 10.6213,10.3164,14.2871 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6680b /a:1@N5 42.7
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/2d-6680b.png width 1024 height
> 665 supersample 3
> save /Users/jabarro/Documents/collin/set2/sp/3d-6680b.png width 1024 height
> 665 supersample 3
> close
> open /Users/jabarro/Documents/collin/set2/sp/6680c.xyz
opened 6680c.xyz as an XYZ coordinate file
> lighting full
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select /a:1@N1
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 14.0278,11.5147,13.0069 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6680c /a:1@N1 42.7
> transparency 60
> color radial #1.2 center 14.0278,11.5147,13.0069 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.2 30
model center %Vbur
6680c /a:1@N1 42.7
> save /Users/jabarro/Documents/collin/set2/sp/2d-6680c.png width 1024 height
> 665 supersample 3
> transparency 60
> color radial #1.1 center 14.0278,11.5147,13.0069 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6680c /a:1@N1 42.7
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/3d-6680c.png width 1024 height
> 665 supersample 3
> close
> open /Users/jabarro/Documents/collin/set2/sp/6680d.xyz
opened 6680d.xyz as an XYZ coordinate file
> lighting full
> graphics silhouettes true
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select /a:1@N2
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 14.7711,8.8695,13.4615 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6680d /a:1@N2 41.7
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/3d-6680d.png width 1024 height
> 665 supersample 3
> close
> open /Users/jabarro/Documents/collin/set2/sp/6679a.xyz
opened 6679a.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> select clear
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select /a:1@N1
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 8.5347,32.6077,4.5766 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6679a /a:1@N1 44.0
> transparency 60
> select clear
Drag select of %Vbur for 6679a, 15 of 5539 triangles
> select clear
> save /Users/jabarro/Documents/collin/set2/sp/3d-6679a.png width 1024 height
> 665 supersample 3
> close
> open /Users/jabarro/Documents/collin/set2/sp/6679b.xyz
opened 6679b.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> select clear
> select /a:1@I3
1 atom, 1 residue, 1 model selected
> select /a:1@N5
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select /a:1@N4
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 6.6301,30.5894,4.3823 palette rainbow range 0,3.50
> coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6679b /a:1@N4 40.1
> transparency 60
> save /Users/jabarro/Documents/collin/set2/sp/3d-6679b.png width 1024 height
> 665 supersample 3
> ui windowfill toggle
> show target m
> close
> open /Users/jabarro/Documents/collin/set2/sp/6680a.xyz format xyz
opened 6680a.xyz as an XYZ coordinate file
> preset seqcrow "ball-stick-endcap (displayed only)"
Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting full
> graphics silhouettes false
> ui mousemode right "select fragment"
> select clear
> ui mousemode right select
> select add /a:1@H18
45 atoms, 44 bonds, 1 residue, 1 model selected
> select add /a:1@C15
46 atoms, 44 bonds, 1 residue, 1 model selected
> select add /a:1@C14
47 atoms, 44 bonds, 1 residue, 1 model selected
> select add /a:1@H17
48 atoms, 44 bonds, 1 residue, 1 model selected
> select clear
> select /a:1@N6
1 atom, 1 residue, 1 model selected
> color radial #1.1 center 15.1339,17.1707,20.0486 palette rainbow range
> 0,3.50 coordinateSystem #1
> transparency #1.1 30
model center %Vbur
6680a /a:1@N6 71.5
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX33LL/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 25 days, 6 hours, 1 minute
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2723QE:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.8.17
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 9 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in QDockWidget event handling |
comment:2 by , 9 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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