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Opened 10 months ago
Closed 10 months ago
#16730 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | 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-15.2-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Thread 0x000000044a18f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003470af000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003460a3000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000345097000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034408b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034307f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000342073000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000341067000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034005b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033f04f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033e043000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033d037000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033c02b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033b01f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033a013000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000339007000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f9ce4240 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, openmm._openmm, 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, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.dssp._dssp, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, psutil._psutil_osx, psutil._psutil_posix, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._cdflib, 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._minpack2, 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, cftime._cftime, netCDF4._netCDF4, lxml._elementpath, lxml.etree (total: 132)
{"app_name":"ChimeraX","timestamp":"2025-01-29 18:59:57.00 +0100","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.2 (24C101)","roots_installed":0,"name":"ChimeraX","incident_id":"DE1FE111-C4BF-4321-A0BC-76BC80C57B21"}
{
"uptime" : 390000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,6",
"coalitionID" : 82156,
"osVersion" : {
"train" : "macOS 15.2",
"build" : "24C101",
"releaseType" : "User"
},
"captureTime" : "2025-01-29 18:59:52.5630 +0100",
"codeSigningMonitor" : 1,
"incident" : "DE1FE111-C4BF-4321-A0BC-76BC80C57B21",
"pid" : 44603,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-28 12:15:22.0840 +0100",
"procStartAbsTime" : 8667286744054,
"procExitAbsTime" : 9559693911542,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0B854952-B91C-511E-9D40-67EBCC719858","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4AAB6390-76F2-0A24-A7A7-7A75AB52E181",
"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=="},
"bootSessionUUID" : "EE6025EA-9EDC-4E50-8EED-322C1E5B3419",
"wakeTime" : 28921,
"sleepWakeUUID" : "397551EE-487D-43B4-B06A-7E39CE6734AB",
"sip" : "enabled",
"vmRegionInfo" : "0x727272727272 is not in any region. Bytes after previous region: 20274058293875 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [102.5M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000101, 0x7272727272727272","rawCodes":[257,8246779703540740722],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"UNKNOWN_0x101 at 0x7272727272727272 -> 0x0000727272727272 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":44603},
"vmregioninfo" : "0x727272727272 is not in any region. Bytes after previous region: 20274058293875 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [102.5M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"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,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4832131736},{"value":120},{"value":122},{"value":1153027057749975424},{"value":0},{"value":10715489311225584948},{"value":10715489307899387764},{"value":14757395258967641293},{"value":4294967286},{"value":4832131665},{"value":0},{"value":49},{"value":4294967280},{"value":328},{"value":8626728112},{"value":0},{"value":10},{"value":259},{"value":8486011680,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4362913328,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8449118208,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableViewCellMockElement._tableColumn"},{"value":8449118208,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableViewCellMockElement._tableColumn"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6715096944},"cpsr":{"value":1073745920},"fp":{"value":4832131808},"sp":{"value":4832131776},"esr":{"value":1442840704,"description":" Address size 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/ctn700/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/ASH-Lab/Dimitris/Research Data/SERT/240606 - SERT
> model building/SERT-IBL-NA-CL-cholesterols-waters_final_model_-
> _prepared.mae"
Chain information for SERT-IBL-NA-CL-cholesterols-waters_final_model_-
_prepared.mae #1
---
Chain | Description
A | No description available
Opened SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae
containing 1 structures (8650 atoms, 8779 bonds)
> set bgColor white
> lighting soft
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> rainbow
> color byhetero
> combine #1/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169
> select #1:IBL
36 atoms, 38 bonds, 1 residue, 1 model selected
> view sel
> select clear
> select #1/A:701@C08
1 atom, 1 residue, 1 model selected
> select up
36 atoms, 38 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hbonds sel color #fffb00 showDist true interModel false distSlop 1.0
> angleSlop 40.0 twoColors true slopColor #fffb00 intraMol false select true
> reveal true
1 hydrogen bonds found
0 strict hydrogen bonds found
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
36 atoms, 38 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> contacts sel overlapCutoff -0.3 interModel false intraMol false
> ignoreHiddenModels true select true color #00fdff reveal true log true
Allowed overlap: -0.3
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
38 contacts
atom1 atom2 overlap distance
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 HN07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CD1 0.392 2.308
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 HN07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CG 0.176 2.524
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 N07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CD1 0.118 3.207
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C03 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A GLY 442 HA3 0.067 2.633
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H013 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 169 O -0.062 2.542
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H141 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 335 O -0.063 2.543
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C12 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A SER 336 O -0.072 3.252
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 HN07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CE1 -0.091 2.791
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C17 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ILE 172 CG2 -0.092 3.492
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C03 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ILE 172 CG2 -0.110 3.510
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C01 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 173 HB2 -0.113 2.813
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C04 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A GLY 442 CA -0.122 3.522
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C08 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 HE1 -0.128 2.828
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C12 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 O -0.130 3.310
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C04 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A GLY 442 HA3 -0.145 2.845
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H151 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 OH -0.160 2.660
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 N07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CE1 -0.164 3.489
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H121 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A SER 336 O -0.173 2.653
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C17 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ILE 172 HG21 -0.175 2.875
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H152 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CE2 -0.181 2.881
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H123 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 O -0.188 2.668
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H102 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A SER 438 HB3 -0.197 2.197
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H123 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 96 O -0.199 2.679
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H012 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A GLY 442 C -0.208 2.908
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 N07 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CG -0.210 3.535
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H151 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 CZ -0.211 2.911
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C03 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A GLY 442 CA -0.212 3.612
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C16 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ILE 172 HG21 -0.226 2.926
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H152 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A PHE 341 CZ -0.237 2.937
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C12 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 96 O -0.241 3.421
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C01 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A LEU 443 HD23 -0.246 2.946
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C15 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 OH -0.256 3.456
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C03 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ILE 172 HG22 -0.256 2.956
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C08 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 CE1 -0.259 3.659
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 HC04 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 169 CB -0.264 2.964
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 C01 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A LEU 443 HG -0.265 2.965
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H151 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A TYR 95 CE1 -0.276 2.976
SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A IBL 701 H013 SERT-IBL-NA-CL-cholesterols-waters_final_model_-_prepared.mae #1/A ALA 173 HB2 -0.283 2.283
38 contacts
> ~display HC
> select clear
> select #1/A:701@C08
1 atom, 1 residue, 1 model selected
> select up
36 atoms, 38 bonds, 1 residue, 1 model selected
> color sel cyan
> color sel byhetero
> color sel cyan
> hide #!1 models
> hide #2 models
> show #!1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!1 models
> select #2/A:701@C09
1 atom, 1 residue, 1 model selected
> select up
36 atoms, 38 bonds, 1 residue, 1 model selected
> color sel cyan
> color sel byhetero
> show #!1 models
> select clear
> transparency #1 90 cartoons
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #2 models
> select #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169
214 atoms, 207 bonds, 14 residues, 1 model selected
> show #2 models
> hide #!1 models
> hide #2 cartoons
> show #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 cartoons
> rainbow sel
> color sel byhetero
> show #!1 models
> hide #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 cartoons
> hide #!1 models
> select add #2
8650 atoms, 8779 bonds, 549 residues, 1 model selected
> rainbow sel
> undo
> show sel atoms
> undo
> show sel cartoons
> rainbow sel
> color sel byhetero
> hide #2 cartoons
> show #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 cartoons
> show #!1 models
> label #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 height 0.5
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #2.1 models
> show #2.1 models
> close #2.1
> label #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 height 0.5
> show :NA,CL,HOH
> select clear
> select add #1/B:1@CL
1 atom, 1 residue, 1 model selected
> select add #1/C:1@NA
2 atoms, 2 residues, 1 model selected
> select add #1/C:2@NA
3 atoms, 3 residues, 1 model selected
> label sel height 0.5
> select clear
> select add #2.1
1 model selected
> hide #!1 models
> hide #!1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #!2 models
> show #!2 models
> select add #2
8650 atoms, 8779 bonds, 549 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2.1
1 model selected
No visible residues selected
> select add #2
8650 atoms, 8779 bonds, 549 residues, 2 models selected
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> show #1.3 models
> hide #1.3 models
> close #2.1
> label #2/A:101,335,95,98,176,438,437,172,341,443,439,177,338,169 height 0.5
> select add #1/B:1@CL
1 atom, 1 residue, 1 model selected
> select add #1/C:1@NA
2 atoms, 2 residues, 1 model selected
> select add #1/C:2@NA
3 atoms, 3 residues, 1 model selected
> label sel height 0.5
> select clear
> select add #1/B:1@CL
1 atom, 1 residue, 1 model selected
> select add #1/C:1@NA
2 atoms, 2 residues, 1 model selected
> select add #1/C:2@NA
3 atoms, 3 residues, 1 model selected
> label sel height 0.5
> hide #!2 models
> label sel height 0.5
> ui mousemode right label
> label #1/B:1
> select clear
> show #!2 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> label sel height 0.5
> label height 0.5
> select clear
> show #!1.1 models
> show #1.2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
36 atoms, 38 bonds, 1 residue, 1 model selected
> view sel
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ctn700/Desktop/movie1.mp4
Movie saved to /Users/ctn700/Desktop/movie1.mp4
> ui tool show "Side View"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> graphics silhouettes false
> graphics silhouettes true
> save IBL_BS.png supersample 4 height 2000 width 2000
> save IBL_BS.png supersample 4
> select clear
> save IBL_BS.png supersample 4
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide labels
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~label #1-2 residues
> save IBL_BS.png supersample 4
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/AtCAT4_Arg_MD_model.pdb"
AtCAT4_Arg_MD_model.pdb title:
Alphafold monomer V2.0 prediction for cationic amino acid transporter 4,
vacuolar (Q8W4K3) [more info...]
Chain information for AtCAT4_Arg_MD_model.pdb #3
---
Chain | Description
A | No description available
Non-standard residues in AtCAT4_Arg_MD_model.pdb #3
---
CLR — (CLR)
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!1 models
> hide #!1.1 models
> hide #1.2 models
> hide #2 models
> view
> rainbow #!3
> color #!3 byhetero
> label #3/A:108
> select clear
> select #3:ZR
Nothing selected
> select #3:602
27 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> close #3
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/AtCAT4_Arg_MD_model.pdb"
AtCAT4_Arg_MD_model.pdb title:
Alphafold monomer V2.0 prediction for cationic amino acid transporter 4,
vacuolar (Q8W4K3) [more info...]
Chain information for AtCAT4_Arg_MD_model.pdb #3
---
Chain | Description
A | No description available
Non-standard residues in AtCAT4_Arg_MD_model.pdb #3
---
ARG — (ARG)
CLR — (CLR)
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> view sel
> select clear
> dssp
> rainbow #3
> color #3 byhetero
> select clear
> select #3:21-56
393 atoms, 393 bonds, 28 residues, 1 model selected
> select #4:21-56
Nothing selected
> select #3:21-56
393 atoms, 393 bonds, 28 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> ~display HC
> select #3:21-56
393 atoms, 393 bonds, 28 residues, 1 model selected
> hide sel cartoons
> select clear
> label #3:21-56 height 0.5
> ui tool show "Side View"
> label delete residues
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> hbonds sel color #fffb00 showDist true interModel false distSlop 1.0
> angleSlop 40.0 twoColors true slopColor #fffb00 intraMol false select true
> reveal true
14 hydrogen bonds found
4 strict hydrogen bonds found
> hbonds sel color #fffb00 showDist true interModel false distSlop 1.0
> angleSlop 40.0 twoColors true slopColor #ff9300 intraMol false select true
> reveal true
15 hydrogen bonds found
4 strict hydrogen bonds found
> select #3/A:602@CA
1 atom, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 1 residue, 1 model selected
> select up
8379 atoms, 8472 bonds, 554 residues, 1 model selected
> select down
27 atoms, 26 bonds, 1 residue, 1 model selected
> view sel
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb"
Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #4
---
Chain | Description
A | No description available
B | No description available
> ματψημακερ #4 το #3
Unknown command: ματψημακερ #4 το #3
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AtCAT4_Arg_MD_model.pdb, chain A (#3) with AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb, chain A (#4), sequence alignment score =
2438
RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs:
1.231)
> dssp
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/phenix-folder-leicester-
> dataset/eLBOW_7/elbow.ORN.8xj5_C_ORN_sdf.001.cif"
Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
Nexus365/Dimitris - Newstead Lab/Postdoc/phenix-folder-leicester-
dataset/eLBOW_7/elbow.ORN.8xj5_C_ORN_sdf.001.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 19
No mmCIF models found.
> select clear
> select #4/A:603@C07
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 20 bonds, 1 residue, 1 model selected
> select clear
> rainbow #!3-4
> color #!3-4 byhetero
> dssp
> tile
2 models tiled
> tile off
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AtCAT4_Arg_MD_model.pdb, chain A (#3) with AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb, chain A (#4), sequence alignment score =
2438
RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs:
1.231)
> tile columns 2 spacingFactor 0.7
2 models tiled
> hide #!3 models
> tile off
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AtCAT4_Arg_MD_model.pdb, chain A (#3) with AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb, chain A (#4), sequence alignment score =
2438
RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs:
1.231)
> show #!3 models
> ui tool show "Side View"
> view
> hide #!3 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb"
Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #5
---
Chain | Description
A | No description available
B | No description available
> matchmaker #5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AtCAT4_Arg_MD_model.pdb, chain A (#3) with AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb, chain A (#5), sequence alignment score =
2438
RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs:
1.231)
> rainbow #!4-5
> color #!4-5 byhetero
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 20 bonds, 1 residue, 1 model selected
> view sel
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb"
Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #6
---
Chain | Description
A | No description available
B | No description available
> matchmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AtCAT4_Arg_MD_model.pdb, chain A (#3) with AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb, chain A (#6), sequence alignment score =
2438
RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs:
1.231)
> hide #!5 models
> addh #6
Summary of feedback from adding hydrogens to AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6
---
notes | No usable SEQRES records for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb (#6) chain A; guessing termini instead
Termini for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb (#6) chain B
determined from SEQRES records
Chain-initial residues that are actual N termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/A PRO 21, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/B GLN 1, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/A PRO 21, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/A TYR 456
Chain-initial residues that are not actual N termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/A TYR 456
Chain-final residues that are actual C termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/B SER 114, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/A GLY 410, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/A ASN 582
Chain-final residues that are not actual C termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/A ASN 582, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/A GLY 410
Missing OXT added to C-terminal residue AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/A GLY 410
Missing OXT added to C-terminal residue AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #6/A ASN 582
507 hydrogen bonds
Adding 'H' to AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #6/A TYR 456
4865 hydrogens added
> select #6/A:603@H07
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 22 bonds, 1 residue, 1 model selected
> select clear
> addcharges
Unknown command: addcharges
> ui tool show "Add Charges"
Closest equivalent command: addcharge #6 standardizeResidues 5BU,CSL,MSE,UMS
Using Amber 20 recommended default charges and atom types for standard
residues
Populating font family aliases took 64 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
Assigning partial charges to residue CLR (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpfzgctahe/ante.in.mol2 -fi
mol2 -o
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpfzgctahe/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(CLR) ``
(CLR) `Welcome to antechamber 20.0: molecular input file processor.`
(CLR) ``
(CLR) `Info: Finished reading file
(/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpfzgctahe/ante.in.mol2);
atoms read (74), bonds read (77).`
(CLR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CLR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CLR) ``
(CLR) ``
(CLR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CLR) `Info: Total number of electrons: 216; net charge: 0`
(CLR) ``
(CLR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(CLR) ``
(CLR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(CLR) ``
(CLR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CLR) ``
Charges for residue CLR determined
Assigning partial charges to residue AV0 (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpf621mhux/ante.in.mol2 -fi
mol2 -o
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpf621mhux/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(AV0) ``
(AV0) `Welcome to antechamber 20.0: molecular input file processor.`
(AV0) ``
(AV0) `Info: Finished reading file
(/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpf621mhux/ante.in.mol2);
atoms read (157), bonds read (160).`
(AV0) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(AV0) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(AV0) ``
(AV0) ``
(AV0) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(AV0) `Info: Total number of electrons: 546; net charge: 0`
(AV0) ``
(AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(AV0) ``
(AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(AV0) ``
(AV0) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(AV0) ``
Charges for residue AV0 determined
Assigning partial charges to residue ORN (net charge +1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuktuqyo_/ante.in.mol2 -fi
mol2 -o
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuktuqyo_/ante.out.mol2 -fo
mol2 -c bcc -nc 1 -j 5 -s 2 -dr n
(ORN) ``
(ORN) `Welcome to antechamber 20.0: molecular input file processor.`
(ORN) ``
(ORN) `Info: Finished reading file
(/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuktuqyo_/ante.in.mol2);
atoms read (24), bonds read (22).`
(ORN) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(ORN) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(ORN) ``
(ORN) ``
(ORN) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(ORN) `Info: Total number of electrons: 74; net charge: 1`
(ORN) ``
(ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(ORN) ``
(ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(ORN) ``
(ORN) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(ORN) ``
Charges for residue ORN determined
> select #6/A:603@C02
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 22 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fffb00 showDist true interModel false distSlop 1.0
> angleSlop 40.0 twoColors true slopColor #ff9300 intraMol false select true
> reveal true
1 hydrogen bonds found
0 strict hydrogen bonds found
> dssp
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/cryosparc_P60_J191_006_volume_map_sharp.mrc"
Opened cryosparc_P60_J191_006_volume_map_sharp.mrc as #7, grid size
288,288,288, pixel 0.835, shown at level 0.0608, step 2, values float32
> label #6/A:402
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb"
Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #8
---
Chain | Description
A | No description available
B | No description available
> hide #!6 models
> select add #6
9795 atoms, 9911 bonds, 2 pseudobonds, 635 residues, 5 models selected
> select subtract #6
Nothing selected
> select add #7
4 models selected
> show #!7 target m
> view #7 clip false
> volume #7 step 1
> volume #7 level 0.055
> volume #7 level 0.55
> volume #7 level 0.055
> volume #7 level 0.065
> volume #7 level 0.075
> volume #7 level 0.085
> volume #7 level 0.105
> volume #7 level 0.45
> volume #7 level 0.155
> select #7:ORN
Nothing selected
> view
> select #8:ORN
22 atoms, 20 bonds, 1 residue, 1 model selected
> view sel
> transparency 50
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 26 residues in model #8 to IUPAC-IUB
standards.
Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb
---
Chain | Description
8.2/A | No description available
8.2/B | No description available
> isolde tutorial
> clipper associate #7 toModel #8
Opened cryosparc_P60_J191_006_volume_map_sharp.mrc as #8.1.1.1, grid size
288,288,288, pixel 0.835, shown at step 1, values float32
> volume #8.1.1.1 level 0.155
> addh #8.2
Summary of feedback from adding hydrogens to AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2
---
notes | No usable SEQRES records for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb (#8.2) chain A; guessing termini instead
Termini for AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb (#8.2) chain B
determined from SEQRES records
Chain-initial residues that are actual N termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/A PRO 21, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/B GLN 1, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/A PRO 21, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/A TYR 456
Chain-initial residues that are not actual N termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/A TYR 456
Chain-final residues that are actual C termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/B SER 114, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/A GLY 410, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/A ASN 582
Chain-final residues that are not actual C termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/A ASN 582, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/A GLY 410
Missing OXT added to C-terminal residue AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/A GLY 410
Missing OXT added to C-terminal residue AtCAT4_final-
coot-9_saved_ongrid_J185-ORN.pdb #8.2/A ASN 582
507 hydrogen bonds
Adding 'H' to AtCAT4_final-coot-9_saved_ongrid_J185-ORN.pdb #8.2/A TYR 456
4865 hydrogens added
Loading residue template for CLR from internal database
> isolde parameterise sel override false
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmplkns969s/ante.in.mol2 -fi
mol2 -o
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmplkns969s/ante.out.mol2 -fo
mol2 -c bcc -nc 1 -j 5 -s 2 -dr n
(ORN) ``
(ORN) `Welcome to antechamber 20.0: molecular input file processor.`
(ORN) ``
(ORN) `Info: Finished reading file
(/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmplkns969s/ante.in.mol2);
atoms read (24), bonds read (22).`
(ORN) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(ORN) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(ORN) ``
(ORN) ``
(ORN) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(ORN) `Info: Total number of electrons: 74; net charge: 1`
(ORN) ``
(ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(ORN) ``
(ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(ORN) ``
(ORN) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(ORN) ``
Charges for residue ORN determined
OpenMM ffXML file ORN written to the current working directory.
New template added to forcefield as USER_ORN. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.
> isolde parameterise sel override false
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsafcl9ai/ante.in.mol2 -fi
mol2 -o
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsafcl9ai/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(AV0) ``
(AV0) `Welcome to antechamber 20.0: molecular input file processor.`
(AV0) ``
(AV0) `Info: Finished reading file
(/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpsafcl9ai/ante.in.mol2);
atoms read (157), bonds read (160).`
(AV0) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(AV0) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(AV0) ``
(AV0) ``
(AV0) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(AV0) `Info: Total number of electrons: 546; net charge: 0`
(AV0) ``
(AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(AV0) ``
(AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(AV0) ``
(AV0) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(AV0) ``
Charges for residue AV0 determined
OpenMM ffXML file AV0 written to the current working directory.
New template added to forcefield as USER_AV0. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.
> select #8:ORN
24 atoms, 22 bonds, 1 residue, 1 model selected
> label delete residues
> view sel
> isolde sim start #8.2/A:603
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
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-
> fix.pdb"
AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb title:
AtCAT4_final-coot-9_saved_ongrid_J185-ORN [more info...]
Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-
fix.pdb #7
---
Chain | Description
A | No description available
B | No description available
Non-standard residues in AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-
fix.pdb #7
---
AV0 — (AV0)
CLR — (CLR)
ORN — (ORN)
> hide #!8 models
> close #8
> close #6
> close #5
> close #4
> matchmaker #3 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb, chain A
(#7) with AtCAT4_Arg_MD_model.pdb, chain A (#3), sequence alignment score =
2438
RMSD between 470 pruned atom pairs is 0.602 angstroms; (across all 506 pairs:
1.231)
> show #!3 models
> hide #!3.1 models
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/cryosparc_P60_J191_006_volume_map_sharp.mrc"
Opened cryosparc_P60_J191_006_volume_map_sharp.mrc as #4, grid size
288,288,288, pixel 0.835, shown at level 0.0608, step 2, values float32
> hide #!3 models
> clipper associate #4 toModel #7
Opened cryosparc_P60_J191_006_volume_map_sharp.mrc as #4.1.1.1, grid size
288,288,288, pixel 0.835, shown at level 0.233, step 1, values float32
AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb title:
AtCAT4_final-coot-9_saved_ongrid_J185-ORN [more info...]
Chain information for AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-
fix.pdb
---
Chain | Description
4.2/A | No description available
4.2/B | No description available
Non-standard residues in AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-
fix.pdb #4.2
---
AV0 — (AV0)
CLR — (CLR)
ORN — (ORN)
> addh #4
Summary of feedback from adding hydrogens to AtCAT4_final-
coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2
---
notes | No usable SEQRES records for AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb (#4.2) chain A; guessing termini instead
No usable SEQRES records for AtCAT4_final-
coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb (#4.2) chain B; guessing termini
instead
Chain-initial residues that are actual N termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A PRO 21, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/B GLN 1
Chain-initial residues that are not actual N termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A TYR 456
Chain-final residues that are actual C termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/B SER 114
Chain-final residues that are not actual C termini: AtCAT4_final-
coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A ASN 582, AtCAT4_final-
coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A GLY 410
507 hydrogen bonds
Adding 'H' to AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A
TYR 456
AtCAT4_final-coot-9_saved_ongrid_J185-ORN_maestro-fix.pdb #4.2/A ASN 582 is
not terminus, removing H atom from 'C'
4863 hydrogens added
> select clear
> hide #!4.1 models
> show #!4.1 models
> isolde start
> start isolde
Unknown command: start isolde
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 26 residues in model #4.2 to IUPAC-IUB
standards.
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
Loading residue template for CLR from internal database
> isolde parameterise sel override false
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpa8rasspx/ante.in.mol2 -fi
mol2 -o
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpa8rasspx/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(AV0) ``
(AV0) `Welcome to antechamber 20.0: molecular input file processor.`
(AV0) ``
(AV0) `Info: Finished reading file
(/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpa8rasspx/ante.in.mol2);
atoms read (157), bonds read (160).`
(AV0) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(AV0) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(AV0) ``
(AV0) ``
(AV0) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(AV0) `Info: Total number of electrons: 546; net charge: 0`
(AV0) ``
(AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(AV0) ``
(AV0) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(AV0) ``
(AV0) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(AV0) ``
Charges for residue AV0 determined
OpenMM ffXML file AV0 written to the current working directory.
New template added to forcefield as USER_AV0. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.
> isolde parameterise sel override false
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuzxihuxn/ante.in.mol2 -fi
mol2 -o
/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuzxihuxn/ante.out.mol2 -fo
mol2 -c bcc -nc 1 -j 5 -s 2 -dr n
(ORN) ``
(ORN) `Welcome to antechamber 20.0: molecular input file processor.`
(ORN) ``
(ORN) `Info: Finished reading file
(/var/folders/ln/gpwsspvj397dw7vtsm_4b8880000gn/T/tmpuzxihuxn/ante.in.mol2);
atoms read (22), bonds read (21).`
(ORN) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(ORN) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(ORN) ``
(ORN) ``
(ORN) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(ORN) `Info: Total number of electrons: 72; net charge: 1`
(ORN) ``
(ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(ORN) ``
(ORN) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(ORN) ``
(ORN) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(ORN) ``
Charges for residue ORN determined
OpenMM ffXML file ORN written to the current working directory.
New template added to forcefield as USER_ORN. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.
> isolde sim start #4.2/A:603
ISOLDE: started sim
> view sel
> volume #4.1.1.1 level 0.1873
> rainbow sel
> select clear
> volume #4.1.1.1 level 0.1553
> volume #4.1.1.1 level 0.1793
> select up
22 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> show #!3 models
> hide #!3 models
> 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 #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select up
8063 atoms, 8158 bonds, 520 residues, 1 model selected
> select up
9791 atoms, 9908 bonds, 635 residues, 2 models selected
> select down
8063 atoms, 8158 bonds, 520 residues, 2 models selected
> select up
9791 atoms, 9908 bonds, 635 residues, 2 models selected
> isolde sim start #4.2/B,A,C
ISOLDE: started sim
> select clear
> rainbow #!4.2
> color #!4.2 bychain
> show #!4.2 cartoons
> rainbow #!4.2
> color #!4.2 bychain
> color #!4.2 byhetero
> ui tool show "Ramachandran Plot"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> isolde pepflip #4.2/A:54
> isolde pepflip #4.2/A:134
> volume #4.1.1.1 level 0.07538
> volume #4.1.1.1 level 0.142
> isolde pepflip #4.2/A:134
> ui tool show "Build Structure"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
You must select exactly one atom to modify.
> ui tool show "Build Structure"
> build start atom #4.2 res HOH
> build modify #4.2/het:1@He O 2 geometry trigonal name O1 resName UNL
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 17 residues in model #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> select up
9794 atoms, 9910 bonds, 636 residues, 1 model selected
> select up
9794 atoms, 9910 bonds, 636 residues, 3 models selected
> select down
9794 atoms, 9910 bonds, 636 residues, 2 models selected
> select down
3 atoms, 2 bonds, 1 residue, 2 models selected
> select up
9794 atoms, 9910 bonds, 636 residues, 1 model selected
> isolde sim start #4.2/B,A,C-het
ISOLDE: started sim
> select clear
> volume #4.1.1.1 level 0.155
> select up
40 atoms, 38 bonds, 2 residues, 1 model selected
> select down
2 atoms, 2 residues, 2 models selected
> select clear
> select up
95 atoms, 96 bonds, 7 residues, 2 models selected
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 6 residues in model #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> combine #4
> hide #!4 models
> hide #!4.1 models
> hide #4.3 models
> hide #!5 models
> hide #!4.2 models
> show #!5 models
> hide #!5 atoms
> dssp
> select #5:ORN
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #5:ORN
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Side View"
> view sel
> select clear
> select #5:ORN
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fffb00 showDist true interModel false distSlop 1.0
> angleSlop 40.0 twoColors true slopColor #ff9300 intraMol false select true
> reveal true
7 hydrogen bonds found
4 strict hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel color #fffb00 showDist true interModel false distSlop 1.5
> angleSlop 40.0 twoColors true slopColor #ff9300 intraMol false select true
> reveal true
14 hydrogen bonds found
7 strict hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel color #fffb00 interModel false distSlop 1.5 angleSlop 40.0
> intraMol false select true reveal true
15 hydrogen bonds found
> select clear
> select #5:116,117
33 atoms, 33 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> ~display HC
> select clear
> select #5:237
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> ~display HC
> select clear
> select #5:116,117,237,274,HOH,ORN,389,323,45
155 atoms, 149 bonds, 6 pseudobonds, 10 residues, 2 models selected
> select #5:116,117,237,274,HOH,ORN,389,323,45,240
174 atoms, 167 bonds, 7 pseudobonds, 11 residues, 2 models selected
> select #5:116,117,237,274,HOH,ORN,389,323,45,240,243
186 atoms, 178 bonds, 9 pseudobonds, 12 residues, 2 models selected
> select #5:116,117,237,274,HOH,ORN,389,323,45,240,243,UNL
189 atoms, 180 bonds, 12 pseudobonds, 13 residues, 2 models selected
> select #5:116,117,237,274,HOH,ORN,389,323,45,240,243,UNL,40,41
241 atoms, 231 bonds, 14 pseudobonds, 17 residues, 2 models selected
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/cryosparc_P60_J191_006_volume_map_sharp.mrc"
Opened cryosparc_P60_J191_006_volume_map_sharp.mrc as #6, grid size
288,288,288, pixel 0.835, shown at level 0.0608, step 2, values float32
> volume #6 step 1
> mask #6 near sel range 3
Unknown command: mask #6 near sel range 3
> volume zone #6 nearAtoms sel range 3
> transparency #6.1 50
> volume #6 level 0.1389
> select clear
> hide #!5 cartoons
> show #!5 cartoons
> transparency #6 cartoon 50
Missing or invalid "percent" argument: Expected a number
> transparency #6 50 cartoons
> transparency #5 50 cartoons
> transparency #5 85 cartoons
> select clear
> select #5:116,117,237,274,HOH,ORN,389,323,45,240,243,UNL,40,41
241 atoms, 231 bonds, 14 pseudobonds, 17 residues, 2 models selected
> view sel
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ctn700/Desktop/movie2.mp4
Movie saved to /Users/ctn700/Desktop/movie2.mp4
> select #5:21-56
1097 atoms, 1111 bonds, 72 residues, 1 model selected
> transparency #5 0 sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #5:sel 0 cartoons
> select clear
> transparency #5:21-56 0 cartoons
> dssp
> volume zone #6 nearAtoms sel range 3 inPlace True
Expected a keyword
> volume zone #6 nearAtoms sel range 3.5 inPlace True
Expected a keyword
> select #5:116,117,237,274,HOH,ORN,389,323,45,240,243,UNL,40,41
241 atoms, 231 bonds, 14 pseudobonds, 17 residues, 2 models selected
> volume zone #6 nearAtoms sel range 3.5
> select clear
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting shadows false
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting shadows false
> hide #!6 models
> select clear
> select #5:ORN
22 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> select #5:ORN
22 atoms, 21 bonds, 1 residue, 1 model selected
> show #!6 models
> select clear
> volume zone #6 nearAtoms sel range 3.5
no atoms specified for zone
> select #5:ORN
22 atoms, 21 bonds, 1 residue, 1 model selected
> volume zone #6 nearAtoms sel range 3.5
> volume #6 style mesh
> volume #6 color black
> volume #6 color #929292
> volume #6 color #00f900
> volume #6 color #0433ff
> volume #6 color #7a81ff
> volume #6 color #0433ff
> volume zone #6 nearAtoms sel range 4
> select clear
> select #5:ORN
22 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 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 M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,6
Model Number: MNWA3DK/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 11881.61.3
OS Loader Version: 11881.61.3
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 9 days, 4 hours, 25 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
HP P34hc G4:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
ChimeraX-Clipper: 0.23.1
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 10 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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