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Opened 2 weeks ago
Closed 2 weeks ago
#20464 closed defect (can't reproduce)
Crash in swap_buffers
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000302013000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000301007000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017f63b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017e62f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017d623000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017c617000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017b60b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017a5ff000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000001795f3000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000001785e7000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000001775db000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x00000001ed7a7100 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, PIL._imaging, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 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._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, kiwisolver._cext, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 121)
{"app_name":"ChimeraX","timestamp":"2026-06-05 09:49:21.00 +0200","app_version":"1.11.1","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.3.1 (25D2128)","roots_installed":0,"name":"ChimeraX","incident_id":"773F4277-A842-4A88-8C3A-DB26D23541F0"}
{
"uptime" : 1500000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 516682,
"osVersion" : {
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"build" : "25D2128",
"releaseType" : "User"
},
"captureTime" : "2026-06-05 09:48:48.0847 +0200",
"codeSigningMonitor" : 2,
"incident" : "773F4277-A842-4A88-8C3A-DB26D23541F0",
"pid" : 56719,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-06-01 10:31:11.5992 +0200",
"procStartAbsTime" : 33554379235210,
"procExitAbsTime" : 36088948420838,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3CD89724-BB06-51E5-BC56-C5D26E8407B2","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "76115092-3197-B1C1-2CDC-D4DB48A9BE8D",
"appleIntelligenceStatus" : {"reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage","selectedLanguageDoesNotMatchSelectedSiriLanguageInfo(system: en, siri: en-GB)"],"state":"unavailable"},
"developerMode" : 1,
"bootProgressRegister" : "0x3f000000",
"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=="},
"bootSessionUUID" : "90FCEEF0-3643-41C8-9243-80F4787C3196",
"wakeTime" : 35,
"sleepWakeUUID" : "5D9B6463-44C9-4F53-925A-CFEA5A502E72",
"sip" : "enabled",
"vmRegionInfo" : "0x500001240 is not in any region. Bytes after previous region: 7871042113 Bytes before following region: 704638400
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
Stack 32a594000-32ad98000 [ 8208K] rw-\/rwx SM=PRV thread 49
---> GAP OF 0x1ff268000 BYTES
MALLOC_SMALL 52a000000-52a400000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000000500001240","rawCodes":[1,21474841152],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000500001240"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":56719},
"vmregioninfo" : "0x500001240 is not in any region. Bytes after previous region: 7871042113 Bytes before following region: 704638400
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
Stack 32a594000-32ad98000 [ 8208K] rw-\/rwx SM=PRV thread 49
---> GAP OF 0x1ff268000 BYTES
MALLOC_SMALL 52a000000-52a400000 [ 4096K] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/pz/Downloads/cryosparc_P151_J169_014_volume_map_sharp.mrc
Opened cryosparc_P151_J169_014_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.68, shown at level 0.032, step 2, values float32
> volume #1 step 1
> ui tool show Toolbar
> lighting soft
> surface dust #1 size 6.8
> volume #1 level 0.06324
> volume #1 level 0.05789
> volume #1 level 0.07305
> volume #1 level 0.057
> volume #1 level 0.06652
> volume #1 level 0.06133
> close #1
> open "/Users/pz/Documents/structures/model building/MsbA R497A van
> open/MsbA-R497A-van-open-2.78A_J1407.mrc"
Opened MsbA-R497A-van-open-2.78A_J1407.mrc as #1, grid size 400,400,400, pixel
0.68, shown at level 0.0141, step 2, values float32
> open "/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA
> R497A van open 27.04 A404.pdb"
Chain information for MsbA R497A van open 27.04 A404.pdb #2
---
Chain | Description
A B | No description available
> fitmap #2 inMap #1
Fit molecule MsbA R497A van open 27.04 A404.pdb (#2) to map MsbA-R497A-van-
open-2.78A_J1407.mrc (#1) using 18118 atoms
average map value = 0.06259, steps = 44
shifted from previous position = 0.0281
rotated from previous position = 0.0196 degrees
atoms outside contour = 4275, contour level = 0.014051
Position of MsbA R497A van open 27.04 A404.pdb (#2) relative to
MsbA-R497A-van-open-2.78A_J1407.mrc (#1) coordinates:
Matrix rotation and translation
0.99999995 -0.00028328 0.00015275 0.02138794
0.00028326 0.99999995 0.00011788 -0.04615004
-0.00015279 -0.00011784 0.99999998 0.00954088
Axis -0.34386366 0.44572376 0.82649145
Axis point 131.39825309 51.15161870 0.00000000
Rotation angle (degrees) 0.01963769
Shift along axis -0.02003925
> surface dust #1 size 6.8
> volume #1 step 1
> volume #1 level 0.04068
> 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...
Chain information for MsbA R497A van open 27.04 A404.pdb #2.2
---
Chain | Description
A B | No description available
> clipper associate #1 toModel #2
Opened MsbA-R497A-van-open-2.78A_J1407.mrc as #2.1.1.1, grid size 400,400,400,
pixel 0.68, shown at step 1, values float32
> select clear
> select A:404
Expected an objects specifier or a keyword
> select A?:404
Expected an objects specifier or a keyword
> select A/:404
Expected an objects specifier or a keyword
> select /A:404
7 atoms, 6 bonds, 1 residue, 1 model selected
> view sel
> isolde stepto /A:404
> isolde stepto next
> volume #2.1.1.1 level 0.07958
> isolde stepto next
> volume #2.1.1.1 level 0.08056
> volume #2.1.1.1 level 0.06596
> volume #2.1.1.1 level 0.05526
> isolde stepto next
> isolde stepto prev
> isolde sim stop
No simulation is currently running!
> isolde sim start /A:403
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim start #!2.2/A:417
ISOLDE: started sim
> select clear
> volume #2.1.1.1 level 0.05644
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.0483
> volume #2.1.1.1 level 0.032
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto /A:442
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.02679
> isolde stepto next
> volume #2.1.1.1 level 0.0372
> isolde stepto next
> volume #2.1.1.1 level 0.02011
> volume #2.1.1.1 level 0.0417
> isolde stepto next
> isolde stepto prev
> isolde sim start /A:457
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim start /A:465
ISOLDE: started sim
> volume #2.1.1.1 level 0.02389
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde stepto next
> volume #2.1.1.1 level 0.04643
> isolde stepto next
> volume #2.1.1.1 level 0.03405
> isolde sim start /A:467
ISOLDE: started sim
> volume #2.1.1.1 level 0.03048
> volume #2.1.1.1 level 0.04592
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.06017
> isolde stepto next
> volume #2.1.1.1 level 0.06104
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.03428
> volume #2.1.1.1 level 0.05609
> isolde stepto next
> volume #2.1.1.1 level 0.03685
> volume #2.1.1.1 level 0.05074
> isolde stepto next
> volume #2.1.1.1 level 0.03477
> isolde stepto next
> isolde stepto prev
> isolde sim start /A:517
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start /A:529
ISOLDE: started sim
> volume #2.1.1.1 level 0.01476
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.03214
> isolde stepto next
> volume #2.1.1.1 level 0.0415
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.02462
> volume #2.1.1.1 level 0.03447
> isolde stepto next
> volume #2.1.1.1 level 0.02166
> volume #2.1.1.1 level 0.03447
> isolde stepto next
> volume #2.1.1.1 level 0.01901
> isolde sim start #!2.2/A:553
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde sim start /A:553
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> volume #2.1.1.1 level 0.04278
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.04024
> isolde stepto next
> volume #2.1.1.1 level 0.0246
> isolde sim start #!2.2/A:567
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.02969
> isolde stepto next
> volume #2.1.1.1 level 0.02053
> volume #2.1.1.1 level 0.02786
> isolde stepto next
> volume #2.1.1.1 level 0.01259
> volume #2.1.1.1 level 0.02932
> isolde stepto next
> volume #2.1.1.1 level 0.01631
> isolde sim start /B:5
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.03365
> isolde stepto next
> volume #2.1.1.1 level 0.03043
> volume #2.1.1.1 level 0.03607
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.02665
> isolde sim start /B:24
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.04653
> isolde stepto next
> isolde sim start /B:41
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.03802
> isolde stepto next
> volume #2.1.1.1 level 0.02146
> volume #2.1.1.1 level 0.0392
> isolde stepto next
> volume #2.1.1.1 level 0.018
> volume #2.1.1.1 level 0.03284
> isolde stepto next
> volume #2.1.1.1 level 0.03186
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.01809
> volume #2.1.1.1 level 0.02547
> isolde stepto next
> isolde sim start #!2.2/B:60
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.02173
> volume #2.1.1.1 level 0.0292
> isolde stepto next
> volume #2.1.1.1 level 0.02327
> isolde stepto next
> volume #2.1.1.1 level 0.03082
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim start /B:118
ISOLDE: started sim
> volume #2.1.1.1 level 0.01993
> volume #2.1.1.1 level 0.02114
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.04014
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim start #!2.2/B:131
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.0258
> volume #2.1.1.1 level 0.00941
> volume #2.1.1.1 level 0.03297
> isolde stepto next
> isolde sim start /B:140
ISOLDE: started sim
> isolde pepflip #!2.2/B:140
> isolde stepto next
> isolde pepflip /B:141
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select /A:140
11 atoms, 10 bonds, 1 residue, 1 model selected
> view sel
> select clear
> select /B:140
11 atoms, 10 bonds, 1 residue, 1 model selected
> view sel
> isolde sim start #!2.2/B:140
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:140
ISOLDE: started sim
> isolde stepto prev
> isolde pepflip /B:139
> isolde stepto next
> isolde pepflip /B:140
> isolde stepto next
> isolde pepflip /B:141
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto prev
> isolde sim start /B:140
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:140
ISOLDE: started sim
> select clear
> isolde stepto next
> isolde pepflip /B:141
> isolde stepto next
> isolde pepflip /B:142
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto prev
> isolde sim start #!2.2/B:140
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start #!2.2/B:147
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> volume #2.1.1.1 level 0.03799
> isolde stepto next
> volume #2.1.1.1 level 0.02989
> volume #2.1.1.1 level 0.04314
> isolde stepto next
> isolde stepto prev
> volume #2.1.1.1 level 0.02557
> volume #2.1.1.1 level 0.01717
> volume #2.1.1.1 level 0.04009
> isolde stepto next
> volume #2.1.1.1 level 0.02389
> isolde stepto next
> volume #2.1.1.1 level 0.03525
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.03643
> isolde stepto next
> volume #2.1.1.1 level 0.02829
> volume #2.1.1.1 level 0.03469
> isolde stepto next
> volume #2.1.1.1 level 0.02694
> isolde stepto next
> volume #2.1.1.1 level 0.03451
> isolde stepto next
> volume #2.1.1.1 level 0.02818
> isolde stepto next
> volume #2.1.1.1 level 0.0336
> isolde sim start /B:164
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start #!2.2/B:168
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.03407
> isolde sim start #!2.2/B:169
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save "/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA
> R497A van open 1.06 B169.pdb" relModel #2.1.1.1
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.02581
> volume #2.1.1.1 level 0.03252
> isolde stepto next
> isolde sim start #!2.2/B:180
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.03336
> isolde sim start #!2.2/B:183
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.04343
> isolde stepto next
> volume #2.1.1.1 level 0.03129
> volume #2.1.1.1 level 0.01915
> isolde sim start /B:187
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.03028
> isolde stepto next
> volume #2.1.1.1 level 0.02453
> isolde stepto next
> isolde stepto prev
> isolde sim start /B:279
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.01878
> volume #2.1.1.1 level 0.02289
> isolde stepto next
> volume #2.1.1.1 level 0.0203
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim start /B:299
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.003304
> volume #2.1.1.1 level 0.01059
> volume #2.1.1.1 level 0.02759
> isolde stepto next
> volume #2.1.1.1 level 0.03304
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.04049
> isolde stepto next
> volume #2.1.1.1 level 0.01465
> volume #2.1.1.1 level 0.03016
> isolde stepto next
> isolde stepto /B:340
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.0199
> volume #2.1.1.1 level 0.03669
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.02422
> volume #2.1.1.1 level 0.03573
> isolde stepto next
> volume #2.1.1.1 level 0.02623
> volume #2.1.1.1 level 0.03454
> isolde stepto next
> volume #2.1.1.1 level 0.03335
> isolde sim start #!2.2/B:378
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start /B:403
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim start #!2.2/B:424
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.03573
> isolde stepto prev
> save "/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA
> R497A van open 1.06 B422.pdb" relModel #2.1.1.1
> isolde stepto prev
> isolde stepto next
> isolde sim start #!2.2/B:423
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.02472
> isolde sim start /B:425
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.0345
> isolde stepto prev
> isolde stepto next
> isolde sim start #!2.2/B:424
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.03259
> isolde stepto next
> isolde sim start #!2.2/B:442
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.02399
> volume #2.1.1.1 level 0.03641
> isolde stepto next
> volume #2.1.1.1 level 0.01984
> volume #2.1.1.1 level 0.01302
> isolde sim start /B:448
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto prev
> volume #2.1.1.1 level 0.03205
> isolde stepto next
> volume #2.1.1.1 level 0.0223
> isolde sim start /B:448
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start /B:452
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:449-455
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.02964
> isolde stepto next
> volume #2.1.1.1 level 0.02457
> volume #2.1.1.1 level 0.03471
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> volume #2.1.1.1 level 0.04695
> isolde stepto next
> volume #2.1.1.1 level 0.02345
> isolde stepto next
> volume #2.1.1.1 level 0.03438
> isolde stepto next
> isolde stepto prev
> isolde sim start /B:506
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim start /B:504
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim start /B:514
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> volume #2.1.1.1 level 0.02395
> isolde stepto next
> isolde stepto prev
> isolde sim start /B:525
ISOLDE: started sim
> isolde stepto next
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.01788
> volume #2.1.1.1 level 0.03522
> isolde stepto next
> volume #2.1.1.1 level 0.01988
> isolde sim start #!2.2/B:544
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim start /B:553
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:553
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde sim start /B:551
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto prev
> isolde stepto next
> isolde sim start /B:551
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.02482
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> volume #2.1.1.1 level 0.03325
> isolde stepto next
> isolde stepto prev
> save "/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA
> R497A van open checked.pdb" relModel #2.1.1.1
> isolde sim start #!2.2/A:477
ISOLDE: started sim
> isolde cisflip /A:477
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:477
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:477
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start /B:337
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto /B:337
> volume #2.1.1.1 level 0.01816
> volume #2.1.1.1 level 0.03148
> isolde sim start /B:337
ISOLDE: started sim
> isolde pepflip /B:337
> isolde stepto next
> isolde pepflip /B:338
> isolde stepto prev
> isolde pepflip /B:337
> isolde stepto prev
> isolde pepflip /B:336
> isolde stepto next
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:337
ISOLDE: started sim
> select clear
> isolde stepto prev
> volume #2.1.1.1 level 0.01558
> isolde stepto next
> volume #2.1.1.1 level 0.03392
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:354
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:354
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:441
ISOLDE: started sim
> isolde stepto next
> isolde pepflip /A:442
> isolde stepto prev
> isolde pepflip /A:441
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde pepflip /A:440
> isolde stepto prev
> isolde stepto next
> isolde pepflip /A:441
> isolde stepto prev
> isolde pepflip /A:440
> isolde stepto prev
> isolde pepflip /A:439
> isolde stepto prev
> isolde pepflip /A:438
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde pepflip /A:439
> isolde stepto next
> isolde pepflip /A:440
> isolde stepto next
> isolde cisflip /A:441
> isolde pepflip /A:441
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde pepflip /A:438
> isolde stepto prev
> isolde pepflip /A:436
> isolde stepto next
> isolde pepflip /A:437
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:437
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:514
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:140
ISOLDE: started sim
> isolde pepflip /B:140
> isolde stepto prev
> isolde stepto next
> isolde pepflip /B:141
> isolde stepto prev
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:240
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:551
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:551
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!2.2/B:224
ISOLDE: started sim
> volume #2.1.1.1 level 0.02058
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:424
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:424
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:424
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!2.2/A:501
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:501
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto /A:441
> isolde sim start /A:441
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:441
ISOLDE: started sim
> isolde stepto #!2.2/A:441
> isolde pepflip #!2.2/A:441
> isolde stepto next
> isolde stepto prev
> isolde pepflip /A:439
> isolde stepto next
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select B/:441
Expected an objects specifier or a keyword
> select /B:441
24 atoms, 23 bonds, 1 residue, 1 model selected
> select view
Expected an objects specifier or a keyword
> select view
Expected an objects specifier or a keyword
> view sel
> select clear
> isolde sim start #!2.2/A:441
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select /B:439
21 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> isolde sim start /A:542
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:542
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!2.2/B:542
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
Multiple residues selected! Going to the first...
> isolde sim start /A:442
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:452
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto next
> isolde stepto prev
> isolde sim start #!2.2/A:544
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:74
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!2.2/A:77
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:535
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:544
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:224
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:443
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:542
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.02634
> isolde sim start /B:164
ISOLDE: started sim
> isolde pepflip /B:164
> isolde stepto next
> isolde pepflip /B:165
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto prev
> select ~sel & ##selected
18107 atoms, 18240 bonds, 1151 residues, 1 model selected
> save "/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA
> R497A van open 4.06.pdb" relModel #2.1.1.1
> volume #2.1.1.1 level 0.02953
> isolde sim start /B:164
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:140
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:140
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
Could not find virtual screen for QCocoaScreen(0xc3014c6c0, "PA278CV (1)",
QRect(-2560,-566 2560x1440), dpr=1, displayId=184, )
with displayId 184
> select
> /A-B:9-54,56-58,61-110,113-118,121-123,125-145,147-161,165-212,214-219,223-270,273-278,281-322,382-389,407-409,412-418,433-437,447-456,460-465,469-471,483-496,513-526,539-542,562-568,571-577
12204 atoms, 12244 bonds, 764 residues, 1 model selected
> select /A-B:342-345,371-376,399-402,419-422,501-505,531-535,547-552,555-560
1298 atoms, 1284 bonds, 80 residues, 1 model selected
> select /A-B:5
48 atoms, 46 bonds, 2 residues, 1 model selected
> select /A-B
18118 atoms, 18250 bonds, 1152 residues, 1 model selected
> select /A-B:580
42 atoms, 42 bonds, 2 residues, 1 model selected
> select /A-B
18118 atoms, 18250 bonds, 1152 residues, 1 model selected
> select /A-B:580
42 atoms, 42 bonds, 2 residues, 1 model selected
> select /A-B
18118 atoms, 18250 bonds, 1152 residues, 1 model selected
> select clear
> select /A-B:580
42 atoms, 42 bonds, 2 residues, 1 model selected
> select /A-B
18118 atoms, 18250 bonds, 1152 residues, 1 model selected
> save "/Users/pz/Downloads/msba sequence" format fasta alignment 1
> select /A-B:5
48 atoms, 46 bonds, 2 residues, 1 model selected
> select /A-B:5-49
1456 atoms, 1472 bonds, 90 residues, 1 model selected
> isolde sim start /A:12
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!2.2/A:512
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:512,515
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save "/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA
> R497A van open 4.06.pdb" relModel #2.1.1.1
> isolde sim start /A:509-518
ISOLDE: started sim
> hbonds
1253 hydrogen bonds found
> hide hbonds
> display H
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:390
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:382
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:382
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!2.2/B:382
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:551
ISOLDE: started sim
> select clear
> volume #2.1.1.1 level 0.04054
> isolde pepflip /B:551
> isolde stepto next
> isolde pepflip /B:552
> isolde stepto prev
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:542
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:219
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:390
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!2.2/B:535
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:501
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start /B:382
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:535
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!2.2/B:390
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:421
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:219
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:479,481
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde stepto /A:337
> isolde stepto next
> isolde stepto /A:338
> isolde stepto /A:480
> isolde pepflip /A:480
> isolde stepto next
> isolde stepto prev
> isolde pepflip #!2.2/A:479
> isolde stepto next
> isolde pepflip #!2.2/A:480
> isolde stepto next
> isolde pepflip /A:481
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:480
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:480
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:480
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:506
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:480
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Side View"
> isolde sim start /A:480
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:432
ISOLDE: started sim
> hbonds
1253 hydrogen bonds found
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ~display hbond
> hide hbond
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide hbonds
> isolde sim start /B:439,441
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:382
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:379-385
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!2.2/B:520
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:516
ISOLDE: started sim
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:516
ISOLDE: started sim
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:382
ISOLDE: started sim
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:93
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:541
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save "/Users/pz/Documents/structures/model building/MsbA R497A van open/MsbA
> R497A van open 4.06.pdb" relModel #2.1.1.1
> close session
> open "/Users/pz/Documents/structures/not mine/LMNG-closed.pdb"
Chain information for LMNG-closed.pdb #1
---
Chain | Description
A B | No description available
> open "/Users/pz/Documents/structures/model building/MsbA R497A van
> closed/MsbA-R497A-van-closed-2.79A_J1408.mrc"
Opened MsbA-R497A-van-closed-2.79A_J1408.mrc as #2, grid size 400,400,400,
pixel 0.68, shown at level 0.0137, step 2, values float32
> volume #2 step 1
> surface dust #2 size 6.8
> lighting simple
> lighting soft
> volume #2 level 0.02632
> select add #1
9020 atoms, 9142 bonds, 19 pseudobonds, 1158 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.55027,0.83497,-0.0039043,-51.737,-0.82209,0.54095,-0.17757,187.56,-0.14615,0.10092,0.9841,15.922
> view matrix models
> #1,0.51729,0.84619,0.12794,-60.648,-0.85576,0.50978,0.088352,172.13,0.0095418,-0.15519,0.98784,27.8
> view matrix models
> #1,0.90797,0.41817,0.027123,-43.01,-0.41626,0.89259,0.17322,54.941,0.048224,-0.16857,0.98451,24.948
> view matrix models
> #1,0.90215,0.42068,-0.095662,-28.956,-0.41659,0.9071,0.060236,65.913,0.11211,-0.01449,0.99359,-0.88221
> view matrix models
> #1,0.44133,0.89083,-0.1079,-29.475,-0.88527,0.4519,0.10997,180.21,0.14673,0.046989,0.98806,-12.751
> select subtract #1
Nothing selected
> hide #!1 models
> volume #2 level 0.0339
> vop flip #2
Opened MsbA-R497A-van-closed-2.79A_J1408.mrc z flip as #3, grid size
400,400,400, pixel 0.68, shown at step 1, values float32
> close #2
> surface dust #3 size 6.8
> show #!1 models
> select add #1
9020 atoms, 9142 bonds, 19 pseudobonds, 1158 residues, 2 models selected
> view matrix models
> #1,0.087609,0.98419,-0.15392,9.5708,0.99443,-0.095492,-0.044576,27.32,-0.058569,-0.14916,-0.98708,276.49
> view matrix models
> #1,0.17437,0.97251,-0.1543,-0.076924,0.98402,-0.17783,-0.0088091,35.163,-0.036008,-0.1503,-0.98798,273.83
> view matrix models
> #1,0.17546,0.97547,-0.13291,3.5096,0.98384,-0.17863,-0.012216,34.411,-0.035658,-0.12862,-0.99105,285.84
> view matrix models
> #1,0.17546,0.97547,-0.13291,1.5688,0.98384,-0.17863,-0.012216,34.756,-0.035658,-0.12862,-0.99105,283.67
> view matrix models
> #1,0.17985,0.98272,-0.043812,-10.639,0.98311,-0.1811,-0.026481,36.886,-0.033958,-0.038309,-0.99869,272.53
> view matrix models
> #1,0.33235,0.94261,-0.032125,-25.721,0.943,-0.33272,-0.0066497,57.089,-0.016957,-0.028084,-0.99946,269.39
> fitmap #1 inMap #3
Fit molecule LMNG-closed.pdb (#1) to map MsbA-R497A-van-closed-2.79A_J1408.mrc
z flip (#3) using 9020 atoms
average map value = 0.1008, steps = 104
shifted from previous position = 3.09
rotated from previous position = 9.57 degrees
atoms outside contour = 1737, contour level = 0.033898
Position of LMNG-closed.pdb (#1) relative to MsbA-R497A-van-
closed-2.79A_J1408.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.18356215 0.98298161 0.00721784 -17.78647697
0.98137254 -0.18282840 -0.05900612 38.55300354
-0.05668231 0.01791467 -0.99823153 265.85391199
Axis 0.76910697 0.63891754 -0.01608859
Axis point 0.00000000 22.33851026 133.29861512
Rotation angle (degrees) 177.13363952
Shift along axis 6.67527321
> select subtract #1
Nothing selected
> volume #3 level 0.05158
> hide #!3 models
> select ::name="AOV"::name="MG"
66 atoms, 58 bonds, 14 pseudobonds, 4 residues, 2 models selected
> delete sel
> select add #1
8954 atoms, 9084 bonds, 1154 residues, 1 model selected
> hide sel atoms
> select clear
> show #!3 models
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 87 residues in model #1 to IUPAC-IUB
standards.
Chain information for LMNG-closed.pdb #1.2
---
Chain | Description
A B | No description available
> clipper associate #3 toModel #1
Opened MsbA-R497A-van-closed-2.79A_J1408.mrc z flip as #1.1.1.1, grid size
400,400,400, pixel 0.68, shown at step 1, values float32
> isolde stepto /A:3
3 models selected
> isolde stepto next
> isolde stepto prev
> volume #1.1.1.1 level 0.03554
> isolde stepto next
> isolde sim start /A:4
Sim termination reason: None
ISOLDE: stopped sim
> addh #1.2
Summary of feedback from adding hydrogens to LMNG-closed.pdb #1.2
---
notes | Termini for LMNG-closed.pdb (#1.2) chain A determined from SEQRES records
Termini for LMNG-closed.pdb (#1.2) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A ASN 3, /B ASN 3
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A GLN 579, /B GLN 579
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A GLN 579
Missing OXT added to C-terminal residue /B GLN 579
1105 hydrogen bonds
9202 hydrogens added
> isolde sim start /A:3-7
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:12
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:18
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:22
ISOLDE: started sim
> isolde stepto next
> volume #1.1.1.1 level 0.0296
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:28
ISOLDE: started sim
> select clear
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:34
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:39
ISOLDE: started sim
> isolde stepto next
> volume #1.1.1.1 level 0.02237
> isolde stepto next
> isolde stepto prev
> volume #1.1.1.1 level 0.03592
> isolde stepto next
> isolde stepto prev
> isolde pepflip /A:43
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:44
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:49
ISOLDE: started sim
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:53
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> close session
> open emdb:27545
Summary of feedback from opening 27545 fetched from emdb
---
notes | Fetching compressed map 27545 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-27545/map/emd_27545.map.gz
Fetching map header 27545 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-27545/header/emd-27545.xml
Opened emdb 27545 as #1, grid size 280,280,280, pixel 1.07, shown at level
0.17, step 2, values float32, fit PDB 8dmo
> open emdb:27544
Opened emdb 27544 as #2, grid size 200,200,200, pixel 1.07, shown at level
0.14, step 1, values float32, fit PDB 8dmm
> close #1
> lighting soft
> surface dust #2 size 10.7
> open emdb:44445
Opened emdb 44445 as #1, grid size 270,270,270, pixel 0.832, shown at level
0.04, step 2, values float32, fit PDB 9bd7
> hide #!1 models
> show #!1 models
> hide #!2 models
> open emdb:44444
Opened emdb 44444 as #3, grid size 270,270,270, pixel 0.832, shown at level
0.04, step 2, values float32, fit PDB 9bd6
> hide #!1 models
> volume #1 step 1
> volume #3 step 1
> surface dust #3 size 8.32
> volume #3 level 0.03369
> volume #3 level 0.0298
> volume #3 level 0.03175
> show #!1 models
> hide #!3 models
> surface dust #1 size 8.32
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/pz/Downloads/cryosparc_P77_J1566_013_volume_map_sharp (1).mrc"
Opened cryosparc_P77_J1566_013_volume_map_sharp (1).mrc as #1, grid size
400,400,400, pixel 0.68, shown at level 0.0333, step 2, values float32
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15S000JKD/A
Chip: Apple M2
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 8 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: 90 days, 9 hours
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.26.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ISOLDE: 1.11.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 2 weeks ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in swap_buffers |
comment:2 by , 2 weeks ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Using ISOLDE on a MacBook Air with 8 GB of memory. Probably OpenGL driver ran out of memory.